Genetic tools for metabolic engineering of Pichia pastoris

The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineeri...

Full description

Saved in:
Bibliographic Details
Published inEngineering Microbiology Vol. 3; no. 4; p. 100094
Main Authors Wu, Xiaoyan, Cai, Peng, Yao, Lun, Zhou, Yongjin J
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 01.12.2023
Elsevier
Subjects
Online AccessGet full text

Cover

Loading…
Abstract The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris. [Display omitted]
AbstractList The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris.The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris.
The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris. [Display omitted]
The methylotrophic yeast (also known as ) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of . The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in .
The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii ) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris . The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris . Image, graphical abstract
The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris.
ArticleNumber 100094
Author Yao, Lun
Cai, Peng
Wu, Xiaoyan
Zhou, Yongjin J
Author_xml – sequence: 1
  givenname: Xiaoyan
  surname: Wu
  fullname: Wu, Xiaoyan
  organization: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
– sequence: 2
  givenname: Peng
  surname: Cai
  fullname: Cai, Peng
  organization: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
– sequence: 3
  givenname: Lun
  surname: Yao
  fullname: Yao, Lun
  organization: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
– sequence: 4
  givenname: Yongjin J
  orcidid: 0000-0002-2369-3079
  surname: Zhou
  fullname: Zhou, Yongjin J
  email: zhouyongjin@dicp.ac.cn
  organization: Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
BackLink https://www.ncbi.nlm.nih.gov/pubmed/39628915$$D View this record in MEDLINE/PubMed
BookMark eNqFUctu1DAUtVARLaV_gFCWbGbwO-MuQFUFpVIlWMDacpyb6R0l9mB7KvH3OKRULQtYOT45j-t7XpKjEAMQ8prRNaNMv9utIWwn9GtOuagQpUY-Iydc63YlWiqOHn0fk7Ocd5XCN4YJZl6QY2H0fFEn5PwKAhT0TYlxzM0QUzNBcV0cK1YzMAAkDNsmDs1X9Lfomr3LJSbMr8jzwY0Zzu7PU_L908dvl59XN1-uri8vblZeCVpWvtOSGdUD7ZQaeuiN8RtN1UYwEKBaw4bWcSk7brzQirVGGkE77UH7TlTslFwvvn10O7tPOLn000aH9jcQ09a6VJ8wgvWD4kY5BdxQKbnqGHVScV1H6Du6ger1YfHaH7oJeg-hJDc-MX36J-Ct3cY7y5hm8-arw9t7hxR_HCAXO2H2MI4uQDxkK5ikpg4hRKW-eRz2kPJn-5UgF4JPMecEwwOFUTun2Z1derZzz3bpucrO_5J5LK5gnEfG8X_i94sYamV3CMlmjxA89JjAl7pT_LfBL1HfxAE
CitedBy_id crossref_primary_10_1093_glycob_cwad089
crossref_primary_10_1016_j_synbio_2023_06_008
crossref_primary_10_1016_j_synbio_2024_06_009
crossref_primary_10_1186_s12934_024_02353_w
crossref_primary_10_1007_s00253_023_12835_3
crossref_primary_10_1016_j_engmic_2023_100126
crossref_primary_10_3390_bioengineering11010092
crossref_primary_10_3390_jof10120854
crossref_primary_10_1016_j_tibtech_2024_03_007
crossref_primary_10_1128_mbio_02430_24
crossref_primary_10_1016_j_synbio_2025_01_005
crossref_primary_10_1016_j_biortech_2025_132256
crossref_primary_10_1360_SSC_2024_0161
crossref_primary_10_3390_jof9101027
crossref_primary_10_1021_cbe_4c00104
crossref_primary_10_1021_acssuschemeng_4c08784
Cites_doi 10.1002/bit.26363
10.1007/s00253-022-11948-5
10.1093/jimb/kuac029
10.1002/adbi.201900172
10.1186/s12934-016-0540-5
10.1007/978-1-4939-9024-5_3
10.1016/j.jbiotec.2016.11.031
10.3389/fbioe.2020.589468
10.1016/j.cell.2013.06.044
10.1016/j.jbiotec.2016.04.023
10.1128/AEM.02913-08
10.1186/s13068-021-02005-w
10.7717/peerj.9010
10.1038/nature24644
10.1128/AEM.02882-17
10.1002/yea.3426
10.1016/j.jbiotec.2010.09.957
10.1002/bit.26529
10.1021/sb300116y
10.1016/j.cell.2015.09.038
10.1016/j.femsre.2003.10.002
10.1126/science.1176945
10.1021/acssynbio.9b00372
10.1038/srep41850
10.1002/biot.201700340
10.1111/1751-7915.14060
10.1021/acssynbio.1c00172
10.1016/j.bej.2018.07.012
10.1021/acssynbio.1c00366
10.1371/journal.pone.0039720
10.1128/AEM.02843-10
10.3389/fmolb.2019.00043
10.1016/j.bj.2019.10.005
10.1016/j.jbiotec.2020.06.012
10.1007/s10529-013-1265-8
10.1093/nar/gkn369
10.1111/1567-1364.12016
10.1002/9783527807796.ch19
10.1007/BF00261194
10.1016/S1046-5928(02)00003-1
10.1016/j.ymben.2018.04.017
10.1016/j.biotechadv.2017.07.009
10.1016/j.btre.2015.03.005
10.1038/s41467-018-05915-w
10.1016/j.pep.2016.01.017
10.1038/nature17946
10.1186/1475-2859-12-6
10.1038/nbt.1544
10.1016/j.enzmictec.2020.109556
10.1016/j.ymben.2013.07.001
10.2144/btn-2021-0083
10.1021/acssynbio.1c00307
10.1093/femsyr/foy074
10.1038/s41587-020-0592-2
10.1093/femsle/fnac081
10.1016/j.gene.2012.01.006
10.1111/febs.13019
10.1186/1475-2859-9-50
10.1126/science.1232033
10.1016/j.biortech.2022.127690
10.1111/j.1567-1364.2009.00571.x
10.1126/sciadv.abl5166
10.1186/s12896-018-0492-4
10.1186/1475-2859-7-23
10.1016/j.cell.2014.05.010
10.1016/j.jbiotec.2015.10.005
10.1186/s40643-022-00551-1
10.1093/femsyr/fow051
10.1126/science.1231143
10.1038/s44160-022-00205-2
10.1186/s12934-022-01908-z
10.1016/j.biotechadv.2017.11.002
10.1074/jbc.M115.692053
10.1016/j.synbio.2021.03.001
10.1186/s12934-019-1194-x
10.1038/s41467-020-14465-z
10.1016/j.ymben.2017.12.009
10.1186/s12915-015-0186-5
10.1021/acssynbio.6b00178
10.1186/s12934-019-1112-2
10.1021/acssynbio.5b00199
10.3389/fbioe.2020.613771
10.1002/btpr.3008
10.1186/1475-2859-12-5
10.1093/femsyr/foab027
10.1038/srep27352
10.1002/biot.201000078
10.1002/bit.26041
10.3389/fmicb.2017.00780
10.3389/fmicb.2017.01698
10.1186/1752-0509-6-24
10.1016/j.jbiotec.2016.03.027
10.1126/sciadv.abq2157
10.1007/s11274-019-2654-5
10.1016/j.cell.2013.02.022
10.1016/j.jbiotec.2011.04.014
10.1093/nar/gkac765
10.1007/s00253-021-11287-x
10.1002/yea.3301
10.1021/acssynbio.0c00214
10.1093/nar/gkab535
10.1038/nature19802
10.1242/dev.005629
10.1016/j.jmb.2018.06.037
10.1021/acssynbio.9b00378
10.1007/s00253-021-11688-y
10.1128/spectrum.03760-22
10.1038/nbt.3737
10.1021/acssynbio.2c00026
10.1002/jcb.26474
10.1186/2191-0855-2-24
10.1038/s41586-019-1711-4
10.1007/s11274-019-2610-4
10.1126/science.aaf5573
10.1002/yea.1049
10.1186/s12918-017-0492-3
10.1186/1475-2859-5-17
10.1111/j.1567-1364.2011.00716.x
10.1093/nar/gkw020
10.1016/j.synbio.2021.04.005
10.1126/science.aar2400
10.1016/j.ymben.2012.01.006
10.1021/sb400091p
10.1186/s12864-016-2876-y
10.1002/yea.1666
10.1002/yea.1705
10.1111/j.1567-1364.2009.00503.x
10.1073/pnas.2201711119
10.1038/srep36997
10.1093/nar/gkaa1066
10.1007/s10529-015-1972-4
10.1016/j.fgb.2016.02.004
ContentType Journal Article
Copyright 2023 The Authors
2023 The Authors.
2023 The Authors 2023
Copyright_xml – notice: 2023 The Authors
– notice: 2023 The Authors.
– notice: 2023 The Authors 2023
DBID 6I.
AAFTH
AAYXX
CITATION
NPM
7X8
5PM
DOA
DOI 10.1016/j.engmic.2023.100094
DatabaseName ScienceDirect Open Access Titles
Elsevier:ScienceDirect:Open Access
CrossRef
PubMed
MEDLINE - Academic
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle CrossRef
PubMed
MEDLINE - Academic
DatabaseTitleList MEDLINE - Academic

PubMed


Database_xml – sequence: 1
  dbid: DOA
  name: DOAJ Directory of Open Access Journals
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 2
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
EISSN 2667-3703
ExternalDocumentID oai_doaj_org_article_cf5295a5e2904425b10a4526b64db08e
PMC11611016
39628915
10_1016_j_engmic_2023_100094
S2667370323000267
Genre Journal Article
Review
GroupedDBID 6I.
AAFTH
AAXUO
ALMA_UNASSIGNED_HOLDINGS
AMRAJ
EBS
FDB
GROUPED_DOAJ
M41
M~E
ROL
0R~
AALRI
AAYWO
AAYXX
ADVLN
AITUG
CITATION
NPM
7X8
5PM
ID FETCH-LOGICAL-c530t-cb64195de0b55fded99c8605831e3e5791f7a244b29c3651794930b6ce6cb39c3
IEDL.DBID DOA
ISSN 2667-3703
2097-4280
IngestDate Wed Aug 27 01:15:27 EDT 2025
Thu Aug 21 18:35:41 EDT 2025
Fri Jul 11 14:36:31 EDT 2025
Thu Jan 02 22:24:09 EST 2025
Thu Apr 24 22:51:53 EDT 2025
Tue Jul 01 01:19:01 EDT 2025
Fri Feb 23 02:36:36 EST 2024
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 4
Keywords Metabolic engineering
Pichia pastoris
CRISPR/Cas9
Genetic tools
Language English
License This is an open access article under the CC BY-NC-ND license.
2023 The Authors.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c530t-cb64195de0b55fded99c8605831e3e5791f7a244b29c3651794930b6ce6cb39c3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
ObjectType-Review-3
content type line 23
ORCID 0000-0002-2369-3079
OpenAccessLink https://doaj.org/article/cf5295a5e2904425b10a4526b64db08e
PMID 39628915
PQID 3140929533
PQPubID 23479
ParticipantIDs doaj_primary_oai_doaj_org_article_cf5295a5e2904425b10a4526b64db08e
pubmedcentral_primary_oai_pubmedcentral_nih_gov_11611016
proquest_miscellaneous_3140929533
pubmed_primary_39628915
crossref_primary_10_1016_j_engmic_2023_100094
crossref_citationtrail_10_1016_j_engmic_2023_100094
elsevier_sciencedirect_doi_10_1016_j_engmic_2023_100094
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2023-12-01
PublicationDateYYYYMMDD 2023-12-01
PublicationDate_xml – month: 12
  year: 2023
  text: 2023-12-01
  day: 01
PublicationDecade 2020
PublicationPlace Netherlands
PublicationPlace_xml – name: Netherlands
PublicationTitle Engineering Microbiology
PublicationTitleAlternate Eng Microbiol
PublicationYear 2023
Publisher Elsevier B.V
Elsevier
Publisher_xml – name: Elsevier B.V
– name: Elsevier
References Cong, Ran, Cox, Lin, Barretto, Habib, Hsu, Wu, Jiang, Marraffini, Zhang (bib0093) 2013; 339
Tan, Zhang, Karcher, Bock (bib0132) 2020; 11
Vogl, Sturmberger, Kickenweiz, Wasmayer, Schmid, Hatzl, Gerstmann, Pitzer, Wagner, Thallinger, Geier, Glieder (bib0030) 2016; 5
Malcı, Walls, Rios-Solis (bib0063) 2020; 8
Wang, Wang, Wang, Bai, Shi, Shen, Zhou, Zhou, Zhang, Cai (bib0034) 2016; 291
Delic, Mattanovich, Gasser (bib0049) 2013; 12
Gaudelli, Komor, Rees, Packer, Badran, Bryson, Liu (bib0128) 2017; 551
Liu, Shi, Song, Liu, Zhou, Wang, Zhang, Cai (bib0081) 2019; 18
Qi, Larson, Gilbert, Doudna, Weissman, Arkin, Lim (bib0104) 2013; 152
Yoshimasu, Ahn, Tanaka, Yada (bib0060) 2002; 25
Xu, Qi (bib0103) 2019; 431
Gao, Zuo, Xiao, Wang, Li, Xu, Ye, Feng, Jiang, Liu, Gao, Ma, Huang, Xu, Lian (bib0012) 2023; 2
Paul, Montoya (bib0116) 2020; 43
Qian, Yu, Chen, Kang, Ren, Liu, Lu, Zhao, Cai (bib0011) 2022; 11
Komor, Kim, Packer, Zuris, Liu (bib0127) 2016; 533
Wen, Tian, Xu, Zhou, Zhang, Cai (bib0110) 2020; 9
Li, Zhang, Li, Zhou, Cao, Huang, Cui (bib0087) 2017; 8
Gilbert, Larson, Morsut, Liu, Brar, Torres, Stern-Ginossar, Brandman, Whitehead, Doudna, Lim, Weissman, Qi (bib0105) 2013; 154
Schwarzhans, Luttermann, Wibberg, Winkler, Hubner, Huser, Kalinowski, Friehs (bib0068) 2017; 8
Liao, Li, Jameel, Xing, Zhang (bib0108) 2021; 105
Yang, Jiang, Yang (bib0088) 2009; 9
Cregg, Barringer, Hessler, Madden (bib0065) 1985; 5
Liu, Liu, Tao, Zhang, Wang, Wei (bib0008) 2015; 216
Matsumura (bib0120) 2022; 72
Portela, Vogl, Kniely, Fischer, Oliveira, Glieder (bib0041) 2017; 6
Fatma, Schultz, Zhao (bib0071) 2020; 36
He, Zhang, Lu (bib0027) 2023; 50
Gu, Gao, Cao, Dong, Lian, Huang, Cai, Xu (bib0092) 2019; 35
Ito, Kitagawa, Yamanishi, Katahira, Izawa, Irie, Furutani-Seiki, Matsuyama (bib0057) 2016; 6
Chung, Selvarasu, Camattari, Ryu, Lee, Ahn, Lee, Lee (bib0022) 2010; 9
Cai, Li, Zhai, Yao, Ma, Jia, Zhou (bib0073) 2022; 9
Naatsaari, Mistlberger, Ruth, Hajek, Hartner, Glieder (bib0085) 2012; 7
Heo, Hwang, Kang, Bae, Woo (bib0134) 2022; 10
Yang, Zhang (bib0002) 2018; 36
Wang, Cai, Shi, Wang, Zhu, Wang, Zhou, Zhou, Zhang (bib0035) 2016; 38
Gao, Jiang, Lian (bib0029) 2021; 6
Qin, Qian, Yao, Zhuang, Zhang, Chu (bib0052) 2011; 77
Papakonstantinou, Harris, Hearn (bib0080) 2009; 26
Ata, Prielhofer, Gasser, Mattanovich, Calik (bib0053) 2017; 114
Prielhofer, Maurer, Klein, Wenger, Kiziak, Gasser, Mattanovich (bib0135) 2013; 12
Vogl, Ruth, Pitzer, Kickenweiz, Glieder (bib0040) 2014; 3
Zhang, Graham, Tello, Liu, White (bib0122) 2016; 44
Zhang, Duan, Cai, Gao, Wu, Yao, Zhou (bib0102) 2022; 21
Yu, Gao, Zhai, Zhou (bib0078) 2021; 6
Abudayyeh, Gootenberg, Konermann, Joung, Slaymaker, Cox, Shmakov, Makarova, Semenova, Minakhin, Severinov, Regev, Lander, Koonin, Zhang (bib0123) 2016; 353
Ergun, Demir, Ozdamar, Gasser, Mattanovich, Calik (bib0042) 2020; 4
L. Gao, P. Cai & Y.J. Zhou, Advances in metabolic engineering of methylotrophic yeasts, Sheng Wu Gong Cheng Xue Bao 37 (2021) 966–979.
Cos, Ramón, Montesinos, Valero (bib0028) 2006; 5
Xu, Zhu, Zhu, Xing, Cai, Jiang, Zhou, Zhang (bib0139) 2018; 35
Karaoglan, Karaoglan, Inan (bib0138) 2016; 121
Hartner, Ruth, Langenegger, Johnson, Hyka, Lin-Cereghino, Lin-Cereghino, Kovar, Cregg, Glieder (bib0039) 2008; 36
Yan, Yu, Yao, Guo, Zhou, Gao (bib0026) 2022; 106
Wen, Tian, Liu, Zhang, Cai (bib0111) 2020; 320
Xue, Kong, Shen, Bai, Ren, Zhou, Zhang, Cai (bib0009) 2017; 242
Staley, Huang, Nattestad, Oshiro, Ray, Mulye, Li, Le, Stephens, Gomez, Moy, Nguyen, Franz, Lin-Cereghino, Lin-Cereghino (bib0045) 2012; 496
Gao, Xu, Zuo, Ye, Jiang, Feng, Huang, Xu, Lian (bib0082) 2022; 11
Russmayer, Buchetics, Gruber, Valli, Grillitsch, Modarres, Guerrasio, Klavins, Neubauer, Drexler, Steiger, Troyer, Al Chalabi, Krebiehl, Sonntag, Zellnig, Daum, Graf, Altmann, Koellensperger, Hann, Sauer, Mattanovich, Gasser (bib0020) 2015; 13
Weninger, Hatzl, Schmid, Vogl, Glieder (bib0025) 2016; 235
Gao, Ye, Cheng, Jiang, Yuan, Lian (bib0100) 2022; 11
Love, Shah, Whittaker, Wu, Bartlett, Ma, Leeson, Priest, Borowsky, Young, Love (bib0019) 2016; 17
Liu, Song, Peng, Zhu, Shi, Xu, Wang, Zhang, Cai (bib0109) 2022; 8
Yang, Teymorian, Olivares, Murthy (bib0051) 2015; 6
Liu, Cui, Su, Lu, Hou, Qi (bib0079) 2022; 15
Pan, Zhang, Shen, Tao, Li, Yan (bib0024) 2011; 11
Ito, Watanabe, Aikawa, Nishi, Nishiyama, Nakamura, Hasunuma, Okubo, Ishii, Kondo (bib0099) 2018; 18
Zhu, Liu, Yao, Zhang, Cai (bib0043) 2022
Küberl, Schneider, Thallinger, Anderl, Wibberg, Hajek, Jaenicke, Brinkrolf, Goesmann, Szczepanowski, Pühler, Schwab, Glieder, Pichler (bib0016) 2011; 154
Nett, Gerngross (bib0083) 2003; 20
Hsu, Lander, Zhang (bib0090) 2014; 157
Nakamura, Nishi, Noguchi, Ito, Watanabe, Nishiyama, Aikawa, Hasunuma, Ishii, Okubo, Kondo, Stable (bib0066) 2018; 84
Babaei, Sartori, Karpukhin, Abashkin, Matrosova, Borodina (bib0076) 2021; 21
Drinnenberg, Weinberg, Xie, Mower, Wolfe, Fink, Bartel (bib0126) 2009; 326
Wang, Wang, Leng, Ma, Bagadi (bib0061) 2020; 8
Klinner, Schäfer (bib0098) 2004; 28
Zetsche, Gootenberg, Abudayyeh, Slaymaker, Makarova, Essletzbichler, Volz, Joung, van der Oost, Regev, Koonin, Zhang (bib0096) 2015; 163
Cregg, Madden (bib0084) 1989; 219
Portela, Vogl, Ebner, Oliveira, Glieder (bib0044) 2018; 13
Cai, Wu, Deng, Gao, Shen, Yao, Zhou (bib0013) 2022; 119
Ahn, Hong, Park, Lee, Lee, Kim, Lee, Choi, Jung, Lee (bib0046) 2009; 75
Vogl, Kickenweiz, Pitzer, Sturmberger, Weninger, Biggs, Kohler, Baumschlager, Fischer, Hyden, Wagner, Baumann, Borth, Geier, Ajikumar, Glieder (bib0048) 2018; 9
Sohn, Graf, Kim, Gasser, Maurer, Ferrer, Mattanovich, Lee (bib0021) 2010; 5
Yamanishi, Ito, Kintaka, Imamura, Katahira, Ikeuchi, Moriya, Matsuyama (bib0055) 2013; 2
Bai Flagfeldt, Siewers, Huang, Nielsen (bib0075) 2009; 26
Ito, Terai, Ishigami, Hashiba, Nakamura, Bamba, Kumokita, Hasunuma, Asai, Ishii, Kondo (bib0058) 2020
Fina, Heux, Albiol, Ferrer (bib0014) 2022; 10
Zhang, Gu, Zheng, Peng, Li, Lin, Liang (bib0097) 2021; 10
Farazi, Juranek, Tuschl (bib0125) 2008; 135
Vogl, Sturmberger, Fauland, Hyden, Fischer, Schmid, Thallinger, Geier, Glieder (bib0037) 2018; 115
D. Mattanovich, M. Sauer & B. Gasser. Industrial Microorganisms
Wang, Wang, Shi, Qi, Zhang, Zhang, Zhou, Song, Cai (bib0036) 2017; 7
Karim, Curran, Alper (bib0059) 2013; 13
Liu, Zhang, Zhang, Yan, Zhang, Xu, Zhang (bib0047) 2016; 6
Bernauer, Radkohl, Lehmayer, Emmerstorfer-Augustin (bib0064) 2020; 11
Cai, Gao, Zhou (bib0089) 2019; 18
Stadlmayr, Mecklenbräuker, Rothmüller, Maurer, Sauer, Mattanovich, Gasser (bib0136) 2010; 150
in: C. Wittmann and J.C. Liao (Eds.), Industrial Biotechnology, 2017, pp. 687–714.
Peña, Gasser, Zanghellini, Steiger, Mattanovich (bib0004) 2018; 50
Prielhofer, Barrero, Steuer, Gassler, Zahrl, Baumann, Sauer, Mattanovich, Gasser, Marx (bib0118) 2017; 11
Sturmberger, Chappell, Geier, Krainer, Day, Vide, Trstenjak, Schiefer, Richardson, Soriaga, Darnhofer, Birner-Gruenberger, Glick, Tolstorukov, Cregg, Madden, Glieder (bib0018) 2016; 235
Xuan, Zhou, Zhang, Zhang, Song, Zhang (bib0033) 2009; 9
Mikkelsen, Buron, Salomonsen, Olsen, Hansen, Mortensen, Halkier (bib0074) 2012; 14
De Schutter, Lin, Tiels, Van Hecke, Glinka, Weber-Lehmann, Rouzé, Van de Peer, Callewaert (bib0015) 2009; 27
Casari, Rinaldi, Marsella, Gnugnoli, Colombo, Bonetti, Longhese (bib0101) 2019; 6
East-Seletsky, O'Connell, Knight, Burstein, Cate, Tjian, Doudna (bib0124) 2016; 538
Turkanoglu Ozcelik, Yilmaz, Inan (bib0032) 2019; 1923
Baumschabl, Prielhofer, Mattanovich, Steiger (bib0107) 2020; 9
Dalvie, Leal, Whittaker, Yang, Brady, Love, Love (bib0095) 2020; 9
Cai, Duan, Wu, Gao, Ye, Zhou (bib0031) 2021; 49
Landes, Gasser, Vorauer-Uhl, Lhota, Mattanovich, Maurer (bib0050) 2016; 113
Utomo, Hodgins, Ro (bib0115) 2021; 12
Schwarzhans, Luttermann, Geier, Kalinowski, Friehs (bib0001) 2017; 35
Liang, Zou, Lin, Zhang, Ye (bib0054) 2013; 35
Camattari, Goh, Yip, Tan, Ng, Tran, Liu, Liachko, Dunham, Rancati (bib0067) 2016; 15
Kong, Yu, Gao, Zhai, Zhou (bib0077) 2022; 369
Caspeta, Shoaie, Agren, Nookaew, Nielsen (bib0023) 2012; 6
Curran, Karim, Gupta, Alper (bib0056) 2013; 19
Wriessnegger, Moser, Emmerstorfer-Augustin, Leitner, Müller, Kaluzna, Schürmann, Mink, Pichler (bib0007) 2016; 89
Knight (bib0119) 2003
Massahi, Çalık (bib0137) 2018; 138
Mali, Yang, Esvelt, Aach, Guell, DiCarlo, Norville, Church (bib0094) 2013; 339
Wijsman, Świat, Marques, Hettinga, van den Broek, d. l. Torre Cortés, Mans, Pronk, Daran, Daran-Lapujade (bib0114) 2018; 19
Yang, Liu, Chen, Liu, Zhan, Liu, Bai (bib0106) 2020; 138
Zhang, Wang, Xu, Jiang, Shi, Sun, Huang (bib0112) 2021; 105
Liu, Lin, Guo, Wu, Zhang, Qi, Wang, Wang (bib0131) 2021; 14
Zhao, Li, Li, Xin, Hu, Price, Rosser, Bi, Zhang (bib0129) 2021; 39
Valli, Tatto, Peymann, Gruber, Landes, Ekker, Thallinger, Mattanovich, Gasser, Graf (bib0017) 2016; 16
Chang, Hsiung, Hong, Huang (bib0038) 2018; 18
Ahmad, Winkler, Kolmbauer, Pichler, Schwab, Emmerstorfer-Augustin (bib0070) 2019
Marx, Mattanovich, Sauer (bib0086) 2008; 7
Yang, Chen (bib0121) 2017; 358
Liu, Tu, Xu, Bai, Kong, Liu, Yu, Peng, Zhou, Zhang, Cai (bib0010) 2018; 45
Yamada, Ogura, Kimoto, Ogino (bib0062) 2019; 35
Anzalone, Randolph, Davis, Sousa, Koblan, Levy, Chen, Wilson, Newby, Raguram, Liu (bib0130) 2019; 576
Weninger, Fischer, Raschmanova, Kniely, Vogl, Glieder (bib0091) 2018; 119
Liu, Wang, Liu, Lu, Li, Wang, Ni, Li, Guo, Ma, Liao, Wang (bib0133) 2022; 8
Hagman, Säll, Piškur (bib0003) 2014; 281
Araya-Garay, Ageitos, Vallejo, Veiga-Crespo, Sánchez-Pérez, Villa (bib0006) 2012; 2
Yu, Cao, Gao, Zhou (bib0072) 2022; 361
Qi, Zhang, Jiang, Xu, Dong, Du, Zhou, Huang, Xu, Lian (bib0113) 2021; 8
Zetsche, Heidenreich, Mohanraju, Fedorova, Kneppers, DeGennaro, Winblad, Choudhury, Abudayyeh, Gootenberg, Wu, Scott, Severinov, van der Oost, Zhang (bib0117) 2017; 35
Gao (10.1016/j.engmic.2023.100094_bib0100) 2022; 11
Ata (10.1016/j.engmic.2023.100094_bib0053) 2017; 114
Malcı (10.1016/j.engmic.2023.100094_bib0063) 2020; 8
Karim (10.1016/j.engmic.2023.100094_bib0059) 2013; 13
Liu (10.1016/j.engmic.2023.100094_bib0008) 2015; 216
Portela (10.1016/j.engmic.2023.100094_bib0044) 2018; 13
Cregg (10.1016/j.engmic.2023.100094_bib0065) 1985; 5
Qi (10.1016/j.engmic.2023.100094_bib0113) 2021; 8
Drinnenberg (10.1016/j.engmic.2023.100094_bib0126) 2009; 326
Bernauer (10.1016/j.engmic.2023.100094_bib0064) 2020; 11
Nett (10.1016/j.engmic.2023.100094_bib0083) 2003; 20
Yamanishi (10.1016/j.engmic.2023.100094_bib0055) 2013; 2
De Schutter (10.1016/j.engmic.2023.100094_bib0015) 2009; 27
Zhang (10.1016/j.engmic.2023.100094_bib0112) 2021; 105
Pan (10.1016/j.engmic.2023.100094_bib0024) 2011; 11
Wang (10.1016/j.engmic.2023.100094_bib0035) 2016; 38
Karaoglan (10.1016/j.engmic.2023.100094_bib0138) 2016; 121
Zhang (10.1016/j.engmic.2023.100094_bib0102) 2022; 21
Zhao (10.1016/j.engmic.2023.100094_bib0129) 2021; 39
Yang (10.1016/j.engmic.2023.100094_bib0121) 2017; 358
Liu (10.1016/j.engmic.2023.100094_bib0133) 2022; 8
Stadlmayr (10.1016/j.engmic.2023.100094_bib0136) 2010; 150
Bai Flagfeldt (10.1016/j.engmic.2023.100094_bib0075) 2009; 26
Babaei (10.1016/j.engmic.2023.100094_bib0076) 2021; 21
Cong (10.1016/j.engmic.2023.100094_bib0093) 2013; 339
Valli (10.1016/j.engmic.2023.100094_bib0017) 2016; 16
Portela (10.1016/j.engmic.2023.100094_bib0041) 2017; 6
Li (10.1016/j.engmic.2023.100094_bib0087) 2017; 8
Klinner (10.1016/j.engmic.2023.100094_bib0098) 2004; 28
Ito (10.1016/j.engmic.2023.100094_bib0057) 2016; 6
Curran (10.1016/j.engmic.2023.100094_bib0056) 2013; 19
Gao (10.1016/j.engmic.2023.100094_bib0029) 2021; 6
Yang (10.1016/j.engmic.2023.100094_bib0051) 2015; 6
Xu (10.1016/j.engmic.2023.100094_bib0103) 2019; 431
Yang (10.1016/j.engmic.2023.100094_bib0106) 2020; 138
Sohn (10.1016/j.engmic.2023.100094_bib0021) 2010; 5
Camattari (10.1016/j.engmic.2023.100094_bib0067) 2016; 15
Gu (10.1016/j.engmic.2023.100094_bib0092) 2019; 35
Yoshimasu (10.1016/j.engmic.2023.100094_bib0060) 2002; 25
Vogl (10.1016/j.engmic.2023.100094_bib0048) 2018; 9
Cai (10.1016/j.engmic.2023.100094_bib0089) 2019; 18
Nakamura (10.1016/j.engmic.2023.100094_bib0066) 2018; 84
Liao (10.1016/j.engmic.2023.100094_bib0108) 2021; 105
Gao (10.1016/j.engmic.2023.100094_bib0012) 2023; 2
Zhu (10.1016/j.engmic.2023.100094_bib0043) 2022
Küberl (10.1016/j.engmic.2023.100094_bib0016) 2011; 154
Wijsman (10.1016/j.engmic.2023.100094_bib0114) 2018; 19
Yang (10.1016/j.engmic.2023.100094_bib0002) 2018; 36
Wang (10.1016/j.engmic.2023.100094_bib0061) 2020; 8
Qin (10.1016/j.engmic.2023.100094_bib0052) 2011; 77
Mali (10.1016/j.engmic.2023.100094_bib0094) 2013; 339
Xue (10.1016/j.engmic.2023.100094_bib0009) 2017; 242
Cai (10.1016/j.engmic.2023.100094_bib0031) 2021; 49
Kong (10.1016/j.engmic.2023.100094_bib0077) 2022; 369
Abudayyeh (10.1016/j.engmic.2023.100094_bib0123) 2016; 353
10.1016/j.engmic.2023.100094_bib0005
Yang (10.1016/j.engmic.2023.100094_bib0088) 2009; 9
Russmayer (10.1016/j.engmic.2023.100094_bib0020) 2015; 13
Knight (10.1016/j.engmic.2023.100094_bib0119) 2003
Cai (10.1016/j.engmic.2023.100094_bib0073) 2022; 9
Caspeta (10.1016/j.engmic.2023.100094_bib0023) 2012; 6
Love (10.1016/j.engmic.2023.100094_bib0019) 2016; 17
Dalvie (10.1016/j.engmic.2023.100094_bib0095) 2020; 9
Hagman (10.1016/j.engmic.2023.100094_bib0003) 2014; 281
Paul (10.1016/j.engmic.2023.100094_bib0116) 2020; 43
Weninger (10.1016/j.engmic.2023.100094_bib0091) 2018; 119
Liu (10.1016/j.engmic.2023.100094_bib0047) 2016; 6
Liu (10.1016/j.engmic.2023.100094_bib0079) 2022; 15
Liu (10.1016/j.engmic.2023.100094_bib0131) 2021; 14
Ahn (10.1016/j.engmic.2023.100094_bib0046) 2009; 75
Peña (10.1016/j.engmic.2023.100094_bib0004) 2018; 50
Farazi (10.1016/j.engmic.2023.100094_bib0125) 2008; 135
Vogl (10.1016/j.engmic.2023.100094_bib0030) 2016; 5
Heo (10.1016/j.engmic.2023.100094_bib0134) 2022; 10
Wang (10.1016/j.engmic.2023.100094_bib0036) 2017; 7
Xu (10.1016/j.engmic.2023.100094_bib0139) 2018; 35
Delic (10.1016/j.engmic.2023.100094_bib0049) 2013; 12
Papakonstantinou (10.1016/j.engmic.2023.100094_bib0080) 2009; 26
Liu (10.1016/j.engmic.2023.100094_bib0109) 2022; 8
Chang (10.1016/j.engmic.2023.100094_bib0038) 2018; 18
Cregg (10.1016/j.engmic.2023.100094_bib0084) 1989; 219
Ahmad (10.1016/j.engmic.2023.100094_bib0070) 2019
Qi (10.1016/j.engmic.2023.100094_bib0104) 2013; 152
Yu (10.1016/j.engmic.2023.100094_bib0072) 2022; 361
Baumschabl (10.1016/j.engmic.2023.100094_bib0107) 2020; 9
10.1016/j.engmic.2023.100094_bib0069
Casari (10.1016/j.engmic.2023.100094_bib0101) 2019; 6
Prielhofer (10.1016/j.engmic.2023.100094_bib0135) 2013; 12
Ergun (10.1016/j.engmic.2023.100094_bib0042) 2020; 4
Wriessnegger (10.1016/j.engmic.2023.100094_bib0007) 2016; 89
Liu (10.1016/j.engmic.2023.100094_bib0010) 2018; 45
Prielhofer (10.1016/j.engmic.2023.100094_bib0118) 2017; 11
Gilbert (10.1016/j.engmic.2023.100094_bib0105) 2013; 154
Matsumura (10.1016/j.engmic.2023.100094_bib0120) 2022; 72
Massahi (10.1016/j.engmic.2023.100094_bib0137) 2018; 138
Wang (10.1016/j.engmic.2023.100094_bib0034) 2016; 291
Staley (10.1016/j.engmic.2023.100094_bib0045) 2012; 496
Komor (10.1016/j.engmic.2023.100094_bib0127) 2016; 533
Gaudelli (10.1016/j.engmic.2023.100094_bib0128) 2017; 551
Vogl (10.1016/j.engmic.2023.100094_bib0040) 2014; 3
Liang (10.1016/j.engmic.2023.100094_bib0054) 2013; 35
Schwarzhans (10.1016/j.engmic.2023.100094_bib0068) 2017; 8
Turkanoglu Ozcelik (10.1016/j.engmic.2023.100094_bib0032) 2019; 1923
Cai (10.1016/j.engmic.2023.100094_bib0013) 2022; 119
Anzalone (10.1016/j.engmic.2023.100094_bib0130) 2019; 576
Yu (10.1016/j.engmic.2023.100094_bib0078) 2021; 6
Naatsaari (10.1016/j.engmic.2023.100094_bib0085) 2012; 7
Utomo (10.1016/j.engmic.2023.100094_bib0115) 2021; 12
Fina (10.1016/j.engmic.2023.100094_bib0014) 2022; 10
He (10.1016/j.engmic.2023.100094_bib0027) 2023; 50
Qian (10.1016/j.engmic.2023.100094_bib0011) 2022; 11
Zetsche (10.1016/j.engmic.2023.100094_bib0096) 2015; 163
Araya-Garay (10.1016/j.engmic.2023.100094_bib0006) 2012; 2
East-Seletsky (10.1016/j.engmic.2023.100094_bib0124) 2016; 538
Yan (10.1016/j.engmic.2023.100094_bib0026) 2022; 106
Landes (10.1016/j.engmic.2023.100094_bib0050) 2016; 113
Zhang (10.1016/j.engmic.2023.100094_bib0097) 2021; 10
Wen (10.1016/j.engmic.2023.100094_bib0110) 2020; 9
Xuan (10.1016/j.engmic.2023.100094_bib0033) 2009; 9
Yamada (10.1016/j.engmic.2023.100094_bib0062) 2019; 35
Ito (10.1016/j.engmic.2023.100094_bib0099) 2018; 18
Vogl (10.1016/j.engmic.2023.100094_bib0037) 2018; 115
Tan (10.1016/j.engmic.2023.100094_bib0132) 2020; 11
Cos (10.1016/j.engmic.2023.100094_bib0028) 2006; 5
Marx (10.1016/j.engmic.2023.100094_bib0086) 2008; 7
Wen (10.1016/j.engmic.2023.100094_bib0111) 2020; 320
Ito (10.1016/j.engmic.2023.100094_bib0058) 2020
Chung (10.1016/j.engmic.2023.100094_bib0022) 2010; 9
Zhang (10.1016/j.engmic.2023.100094_bib0122) 2016; 44
Fatma (10.1016/j.engmic.2023.100094_bib0071) 2020; 36
Liu (10.1016/j.engmic.2023.100094_bib0081) 2019; 18
Hsu (10.1016/j.engmic.2023.100094_bib0090) 2014; 157
Schwarzhans (10.1016/j.engmic.2023.100094_bib0001) 2017; 35
Hartner (10.1016/j.engmic.2023.100094_bib0039) 2008; 36
Sturmberger (10.1016/j.engmic.2023.100094_bib0018) 2016; 235
Mikkelsen (10.1016/j.engmic.2023.100094_bib0074) 2012; 14
Zetsche (10.1016/j.engmic.2023.100094_bib0117) 2017; 35
Gao (10.1016/j.engmic.2023.100094_bib0082) 2022; 11
Weninger (10.1016/j.engmic.2023.100094_bib0025) 2016; 235
References_xml – volume: 216
  start-page: 47
  year: 2015
  end-page: 55
  ident: bib0008
  article-title: Metabolic engineering of
  publication-title: J. Biotechnol.
– volume: 50
  year: 2023
  ident: bib0027
  article-title: Natural promoters and promoter engineering strategies for metabolic regulation in
  publication-title: J. Ind. Microbiol. Biotechnol.
– start-page: 557
  year: 2019
  end-page: 570
  ident: bib0070
  article-title: protease-deficient and auxotrophic strains generated by a novel, user-friendly vector toolbox for gene deletion
  publication-title: Yeast
– volume: 15
  start-page: 139
  year: 2016
  ident: bib0067
  article-title: Characterization of a panARS-based episomal vector in the methylotrophic yeast
  publication-title: Cell. Fact.
– volume: 10
  start-page: 2927
  year: 2021
  end-page: 2937
  ident: bib0097
  article-title: A novel and efficient genome editing tool assisted by CRISPR-Cas12a/Cpf1 for
  publication-title: ACS Synth. Biol.
– volume: 18
  start-page: 63
  year: 2019
  ident: bib0089
  article-title: CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications
  publication-title: Microb. Cell. Fact.
– volume: 154
  start-page: 312
  year: 2011
  end-page: 320
  ident: bib0016
  article-title: High-quality genome sequence of
  publication-title: J. Biotechnol.
– volume: 353
  start-page: aaf5573
  year: 2016
  ident: bib0123
  article-title: C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
  publication-title: Science
– volume: 533
  start-page: 420
  year: 2016
  end-page: 424
  ident: bib0127
  article-title: Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
  publication-title: Nature
– volume: 35
  start-page: 379
  year: 2018
  end-page: 385
  ident: bib0139
  article-title: Identification and characterization of novel promoters for recombinant protein production in yeast
  publication-title: Yeast
– volume: 6
  start-page: 110
  year: 2021
  end-page: 119
  ident: bib0029
  article-title: Development of synthetic biology tools to engineer
  publication-title: Synth. Syst. Biotechnol.
– volume: 326
  start-page: 544
  year: 2009
  end-page: 550
  ident: bib0126
  article-title: RNAi in Budding Yeast
  publication-title: Science
– volume: 9
  start-page: 26
  year: 2020
  end-page: 35
  ident: bib0095
  article-title: Host-informed expression of CRISPR guide RNA for genomic engineering in
  publication-title: ACS Synth. Biol.
– volume: 38
  start-page: 291
  year: 2016
  end-page: 298
  ident: bib0035
  article-title: PpNrg1 is a transcriptional repressor for glucose and glycerol repression of
  publication-title: Biotechnol. Lett.
– volume: 21
  start-page: foab027
  year: 2021
  ident: bib0076
  article-title: Expansion of EasyClone-MarkerFree toolkit for
  publication-title: FEMS Yeast Res.
– volume: 75
  start-page: 3528
  year: 2009
  end-page: 3534
  ident: bib0046
  article-title: Phosphate-responsive promoter of a
  publication-title: Appl. Environ. Microbiol.
– volume: 36
  start-page: e76
  year: 2008
  ident: bib0039
  article-title: Promoter library designed for fine-tuned gene expression in
  publication-title: Nucleic Acids Res.
– volume: 119
  year: 2022
  ident: bib0013
  article-title: Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast
  publication-title: Proc. Natl. Acad. Sci. U. S. A.
– volume: 291
  start-page: 6245
  year: 2016
  end-page: 6261
  ident: bib0034
  article-title: Mit1 transcription factor mediates methanol signaling and regulates the Alcohol Oxidase 1 (
  publication-title: J. Biol. Chem.
– volume: 77
  start-page: 3600
  year: 2011
  end-page: 3608
  ident: bib0052
  article-title: promoter library for fine-tuning of gene expression in
  publication-title: Appl. Environ. Microbiol.
– volume: 2
  start-page: 337
  year: 2013
  end-page: 347
  ident: bib0055
  article-title: A genome-wide activity assessment of terminator regions in
  publication-title: ACS Synth. Biol.
– volume: 10
  start-page: e03760
  year: 2022
  ident: bib0134
  article-title: High-fidelity cytosine base editing in a GC-Rich
  publication-title: Microbiol. Spectr.
– volume: 44
  start-page: 1789
  year: 2016
  end-page: 1799
  ident: bib0122
  article-title: Multiple nucleic acid cleavage modes in divergent type III CRISPR systems
  publication-title: Nucleic Acids Res.
– volume: 154
  start-page: 442
  year: 2013
  end-page: 451
  ident: bib0105
  article-title: CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
  publication-title: Cell
– volume: 5
  start-page: 17
  year: 2006
  ident: bib0028
  article-title: Operational strategies, monitoring and control of heterologous protein production in the methylotrophic yeast
  publication-title: Microb. Cell Fact.
– volume: 138
  start-page: 111
  year: 2018
  end-page: 120
  ident: bib0137
  article-title: Naturally occurring novel promoters around pyruvate branch-point for recombinant protein production in
  publication-title: Biochem. Eng. J.
– volume: 551
  start-page: 464
  year: 2017
  end-page: 471
  ident: bib0128
  article-title: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
  publication-title: Nature
– volume: 3
  start-page: 188
  year: 2014
  end-page: 191
  ident: bib0040
  article-title: Synthetic core promoters for
  publication-title: ACS Synth. Biol.
– volume: 121
  start-page: 112
  year: 2016
  end-page: 117
  ident: bib0138
  article-title: Comparison of
  publication-title: Protein Expression Purif.
– volume: 106
  start-page: 3449
  year: 2022
  end-page: 3464
  ident: bib0026
  article-title: Expanding the promoter toolbox for metabolic engineering of methylotrophic yeasts
  publication-title: Appl. Microbiol. Biotechnol.
– volume: 9
  start-page: 58
  year: 2022
  ident: bib0073
  article-title: Microbial synthesis of long-chain α-alkenes from methanol by engineering
  publication-title: Bioresour. Bioprocess.
– volume: 369
  start-page: fnac081
  year: 2022
  ident: bib0077
  article-title: Expanding the neutral sites for integrated gene expression in
  publication-title: FEMS Microbiol. Lett.
– volume: 13
  start-page: 80
  year: 2015
  ident: bib0020
  article-title: Systems-level organization of yeast methylotrophic lifestyle
  publication-title: BMC Biol.
– volume: 9
  start-page: 50
  year: 2010
  ident: bib0022
  article-title: Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast
  publication-title: Microb. Cell Fact.
– volume: 8
  start-page: e9010
  year: 2020
  ident: bib0061
  article-title: Expression of
  publication-title: PeerJ
– volume: 6
  start-page: 27352
  year: 2016
  ident: bib0047
  article-title: Discovery of a rhamnose utilization pathway and rhamnose-inducible promoters in
  publication-title: Sci. Rep.
– volume: 163
  start-page: 759
  year: 2015
  end-page: 771
  ident: bib0096
  article-title: Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system
  publication-title: Cell
– volume: 7
  start-page: e39720
  year: 2012
  ident: bib0085
  article-title: Deletion of the
  publication-title: PLoS ONE
– volume: 5
  start-page: 172
  year: 2016
  end-page: 186
  ident: bib0030
  article-title: A toolbox of diverse promoters related to methanol utilization: functionally verified parts for heterologous pathway expression in
  publication-title: ACS Synth. Biol.
– volume: 105
  start-page: 3873
  year: 2021
  end-page: 3882
  ident: bib0112
  article-title: Recent advances in the application of multiplex genome editing in
  publication-title: Appl. Microbiol. Biotechnol.
– volume: 11
  start-page: 547
  year: 2022
  end-page: 553
  ident: bib0100
  article-title: Enhancing homologous recombination efficiency in
  publication-title: ACS Synth. Biol.
– volume: 576
  start-page: 149
  year: 2019
  end-page: 157
  ident: bib0130
  article-title: Search-and-replace genome editing without double-strand breaks or donor DNA
  publication-title: Nature
– volume: 11
  start-page: 123
  year: 2017
  ident: bib0118
  article-title: GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast
  publication-title: BMC Syst. Biol.
– volume: 235
  start-page: 139
  year: 2016
  end-page: 149
  ident: bib0025
  article-title: Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast
  publication-title: J. Biotechnol.
– volume: 358
  start-page: 996
  year: 2017
  end-page: 997
  ident: bib0121
  article-title: Enhancing the RNA engineering toolkit
  publication-title: Science
– volume: 9
  start-page: 600
  year: 2009
  end-page: 609
  ident: bib0088
  article-title: as a counter-selectable marker for unmarked genetic modification of
  publication-title: FEMS Yeast Res.
– volume: 11
  start-page: 292
  year: 2011
  end-page: 298
  ident: bib0024
  article-title: Sequential deletion of
  publication-title: FEMS Yeast Res.
– volume: 115
  start-page: 1037
  year: 2018
  end-page: 1050
  ident: bib0037
  article-title: Methanol independent induction in
  publication-title: Biotechnol. Bioeng.
– volume: 6
  start-page: 63
  year: 2021
  end-page: 68
  ident: bib0078
  article-title: Screening neutral sites for metabolic engineering of methylotrophic yeast
  publication-title: Synth. Syst. Biotechnol.
– volume: 496
  start-page: 118
  year: 2012
  end-page: 127
  ident: bib0045
  article-title: Analysis of the 5′ untranslated region (5′UTR) of the alcohol oxidase 1 (
  publication-title: Gene
– volume: 14
  start-page: 104
  year: 2012
  end-page: 111
  ident: bib0074
  article-title: Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform
  publication-title: Metab. Eng.
– volume: 152
  start-page: 1173
  year: 2013
  end-page: 1183
  ident: bib0104
  article-title: Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
  publication-title: Cell
– year: 2003
  ident: bib0119
  article-title: Idempotent Vector Design For Standard Assembly of Biobricks
– volume: 1923
  start-page: 97
  year: 2019
  end-page: 112
  ident: bib0032
  article-title: Promoters
  publication-title: Methods Mol. Biol.
– volume: 12
  start-page: 6
  year: 2013
  ident: bib0049
  article-title: Repressible promoters – A novel tool to generate conditional mutants in
  publication-title: Microb. Cell Fact.
– volume: 35
  start-page: 37
  year: 2019
  ident: bib0062
  article-title: Toward the construction of a technology platform for chemicals production from methanol:
  publication-title: World J. Microbiol. Biotechnol.
– volume: 36
  start-page: e3008
  year: 2020
  ident: bib0071
  article-title: Recent advances in domesticating non-model microorganisms
  publication-title: Biotechnol. Prog.
– volume: 150
  start-page: 519
  year: 2010
  end-page: 529
  ident: bib0136
  article-title: Identification and characterisation of novel
  publication-title: J. Biotechnol.
– volume: 2
  start-page: 231
  year: 2023
  end-page: 242
  ident: bib0012
  article-title: Biosynthesis of catharanthine in engineered
  publication-title: Nat. Synth.
– volume: 26
  start-page: 545
  year: 2009
  end-page: 551
  ident: bib0075
  article-title: Characterization of chromosomal integration sites for heterologous gene expression in
  publication-title: Yeast
– volume: 157
  start-page: 1262
  year: 2014
  end-page: 1278
  ident: bib0090
  article-title: Development and applications of CRISPR-Cas9 for genome engineering
  publication-title: Cell
– volume: 361
  year: 2022
  ident: bib0072
  article-title: Overproduction of 3-hydroxypropionate in a super yeast chassis
  publication-title: Bioresour. Technol.
– volume: 12
  start-page: 5
  year: 2013
  ident: bib0135
  article-title: Induction without methanol: novel regulated promoters enable high-level expression in
  publication-title: Microb. Cell Fact.
– volume: 8
  start-page: 780
  year: 2017
  ident: bib0068
  article-title: A mitochondrial autonomously replicating sequence from
  publication-title: Front. Microbiol.
– volume: 16
  start-page: fow051
  year: 2016
  ident: bib0017
  article-title: Curation of the genome annotation of
  publication-title: FEMS Yeast Res.
– volume: 4
  year: 2020
  ident: bib0042
  article-title: Engineered deregulation of expression in yeast with designed hybrid-promoter architectures in coordination with discovered master regulator transcription factor
  publication-title: Adv. Biosyst.
– volume: 113
  start-page: 2633
  year: 2016
  end-page: 2643
  ident: bib0050
  article-title: The vitamin-sensitive promoter P
  publication-title: Biotechnol. Bioeng.
– volume: 11
  start-page: 623
  year: 2022
  end-page: 633
  ident: bib0082
  article-title: Synthetic biology toolkit for marker-less integration of multigene pathways into
  publication-title: ACS Synth. Biol.
– volume: 27
  start-page: 561
  year: 2009
  end-page: 566
  ident: bib0015
  article-title: Genome sequence of the recombinant protein production host
  publication-title: Nat. Biotechnol.
– volume: 235
  start-page: 121
  year: 2016
  end-page: 131
  ident: bib0018
  article-title: Refined
  publication-title: J. Biotechnol.
– start-page: 10187
  year: 2022
  end-page: 10199
  ident: bib0043
  article-title: Yeast transcriptional device libraries enable precise synthesis of value-added chemicals from methanol
  publication-title: Nucleic Acids Res.
– volume: 538
  start-page: 270
  year: 2016
  end-page: 273
  ident: bib0124
  article-title: Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
  publication-title: Nature
– volume: 25
  start-page: 229
  year: 2002
  end-page: 236
  ident: bib0060
  article-title: Soluble expression and purification of porcine pepsinogen from
  publication-title: Protein Expression Purif.
– volume: 8
  year: 2020
  ident: bib0063
  article-title: Multiplex genome engineering methods for yeast cell factory development
  publication-title: Front. Bioeng. Biotechnol.
– volume: 8
  start-page: eabl5166
  year: 2022
  ident: bib0109
  article-title: A programmable high-expression yeast platform responsive to user-defined signals
  publication-title: Sci. Adv.
– volume: 11
  year: 2020
  ident: bib0064
  article-title: as emerging model organism in fundamental research
  publication-title: Front. Microbiol.
– volume: 45
  start-page: 189
  year: 2018
  end-page: 199
  ident: bib0010
  article-title: Engineered monoculture and co-culture of methylotrophic yeast for de novo production of monacolin J and lovastatin from methanol
  publication-title: Metab. Eng.
– volume: 10
  year: 2022
  ident: bib0014
  article-title: Combining metabolic engineering and multiplexed screening methods for 3-hydroxyprionic acid production in
  publication-title: Front. Bioeng. Biotechnol.
– volume: 20
  start-page: 1279
  year: 2003
  end-page: 1290
  ident: bib0083
  article-title: Cloning and disruption of the
  publication-title: Yeast
– volume: 21
  start-page: 182
  year: 2022
  ident: bib0102
  article-title: Fusing an exonuclease with Cas9 enhances homologous recombination in
  publication-title: Microb. Cell Fact.
– volume: 5
  start-page: 3376
  year: 1985
  end-page: 3385
  ident: bib0065
  article-title: as a host system for transformations
  publication-title: Mol. Cell. Biol.
– volume: 119
  start-page: 3183
  year: 2018
  end-page: 3198
  ident: bib0091
  article-title: Expanding the CRISPR/Cas9 toolkit for
  publication-title: J. Cell. Biochem.
– volume: 26
  start-page: 311
  year: 2009
  end-page: 321
  ident: bib0080
  article-title: Expression of GFP using
  publication-title: Yeast
– volume: 9
  start-page: 1271
  year: 2009
  end-page: 1282
  ident: bib0033
  article-title: An upstream activation sequence controls the expression of
  publication-title: FEMS Yeast Res.
– volume: 84
  start-page: e02882
  year: 2018
  ident: bib0066
  article-title: Autonomously replicating plasmid vector containing
  publication-title: Appl. Environ. Microbiol.
– volume: 281
  start-page: 4805
  year: 2014
  end-page: 4814
  ident: bib0003
  article-title: Analysis of the yeast short-term Crabtree effect and its origin
  publication-title: FEBS J.
– volume: 18
  start-page: 144
  year: 2019
  ident: bib0081
  article-title: CRISPR-Cas9-mediated genomic multiloci integration in
  publication-title: Microb. Cell. Fact.
– reference: , in: C. Wittmann and J.C. Liao (Eds.), Industrial Biotechnology, 2017, pp. 687–714.
– volume: 320
  start-page: 80
  year: 2020
  end-page: 85
  ident: bib0111
  article-title: Engineered dynamic distribution of malonyl-CoA flux for improving polyketide biosynthesis in
  publication-title: J. Biotechnol.
– volume: 11
  start-page: 629
  year: 2020
  ident: bib0132
  article-title: Expanding the genome-targeting scope and the site selectivity of high-precision base editors
  publication-title: Nat. Commun.
– volume: 9
  start-page: 3202
  year: 2020
  end-page: 3209
  ident: bib0107
  article-title: Fine-tuning of transcription in
  publication-title: ACS Synth. Biol.
– volume: 13
  year: 2018
  ident: bib0044
  article-title: Alcohol Oxidase 1 (
  publication-title: Biotechnol. J.
– volume: 15
  start-page: 2223
  year: 2022
  end-page: 2234
  ident: bib0079
  article-title: Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in
  publication-title: Microb. Biotechnol.
– volume: 6
  start-page: 24
  year: 2012
  ident: bib0023
  article-title: Genome-scale metabolic reconstructions of
  publication-title: BMC Syst. Biol.
– volume: 36
  start-page: 182
  year: 2018
  end-page: 195
  ident: bib0002
  article-title: Engineering strategies for enhanced production of protein and bio-products in
  publication-title: Biotechnol. Adv.
– volume: 50
  start-page: 2
  year: 2018
  end-page: 15
  ident: bib0004
  article-title: Metabolic engineering of
  publication-title: Metab. Eng.
– reference: L. Gao, P. Cai & Y.J. Zhou, Advances in metabolic engineering of methylotrophic yeasts, Sheng Wu Gong Cheng Xue Bao 37 (2021) 966–979.
– volume: 6
  start-page: 471
  year: 2017
  end-page: 484
  ident: bib0041
  article-title: Synthetic core promoters as universal parts for fine-tuning expression in different yeast species
  publication-title: ACS Synth. Biol.
– volume: 35
  start-page: 79
  year: 2019
  ident: bib0092
  article-title: Construction of a series of episomal plasmids and their application in the development of an efficient CRISPR/Cas9 system in
  publication-title: World J. Microbiol. Biotechnol.
– volume: 19
  start-page: foy107
  year: 2018
  ident: bib0114
  article-title: A toolkit for rapid CRISPR-SpCas9 assisted construction of hexose-transport-deficient
  publication-title: FEMS Yeast Res.
– volume: 13
  start-page: 107
  year: 2013
  end-page: 116
  ident: bib0059
  article-title: Characterization of plasmid burden and copy number in
  publication-title: FEMS Yeast Res.
– volume: 138
  year: 2020
  ident: bib0106
  article-title: High efficiency CRISPR/Cas9 genome editing system with an eliminable episomal sgRNA plasmid in
  publication-title: Enzyme Microb. Technol.
– volume: 7
  start-page: 23
  year: 2008
  ident: bib0086
  article-title: Overexpression of the riboflavin biosynthetic pathway in
  publication-title: Microb. Cell Fact.
– volume: 6
  start-page: 43
  year: 2019
  ident: bib0101
  article-title: Processing of DNA double-strand breaks by the MRX complex in a chromatin context
  publication-title: Front. Mol. Biosci.
– volume: 18
  start-page: foy074
  year: 2018
  ident: bib0099
  article-title: Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in
  publication-title: FEMS Yeast Res.
– volume: 35
  start-page: 1865
  year: 2013
  end-page: 1871
  ident: bib0054
  article-title: Identification and characterization of P
  publication-title: Biotechnol. Lett.
– volume: 105
  start-page: 9211
  year: 2021
  end-page: 9218
  ident: bib0108
  article-title: A versatile toolbox for CRISPR-based genome engineering in
  publication-title: Appl. Microbiol. Biotechnol.
– volume: 39
  start-page: 35
  year: 2021
  end-page: 40
  ident: bib0129
  article-title: Glycosylase base editors enable C-to-A and C-to-G base changes
  publication-title: Nat. Biotechnol.
– volume: 35
  start-page: 31
  year: 2017
  end-page: 34
  ident: bib0117
  article-title: Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array
  publication-title: Nat. Biotechnol.
– volume: 8
  start-page: 1698
  year: 2017
  ident: bib0087
  article-title: A novel vector for construction of markerless multicopy overexpression Transformants in
  publication-title: Front. Microbiol.
– volume: 339
  start-page: 823
  year: 2013
  end-page: 826
  ident: bib0094
  article-title: RNA-guided human genome engineering via Cas9
  publication-title: Science
– volume: 8
  start-page: eabq2157
  year: 2022
  ident: bib0133
  article-title: Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in
  publication-title: Sci. Adv.
– volume: 72
  start-page: 185
  year: 2022
  end-page: 193
  ident: bib0120
  article-title: Golden Gate assembly of BioBrick-compliant parts using Type II restriction endonucleases
  publication-title: BioTechniques
– volume: 89
  start-page: 114
  year: 2016
  end-page: 125
  ident: bib0007
  article-title: Enhancing cytochrome P450-mediated conversions in
  publication-title: Fungal Genet. Biol.
– volume: 12
  year: 2021
  ident: bib0115
  article-title: Multiplex genome editing in yeast by CRISPR/Cas9 – a potent and agile tool to reconstruct complex metabolic pathways, Front
  publication-title: Plant Sci
– volume: 49
  start-page: 7791
  year: 2021
  end-page: 7805
  ident: bib0031
  article-title: Recombination machinery engineering facilitates metabolic engineering of the industrial yeast
  publication-title: Nucleic Acids Res
– volume: 18
  start-page: 81
  year: 2018
  ident: bib0038
  article-title: Enhancing the efficiency of the
  publication-title: BMC Biotechnol.
– start-page: 13000
  year: 2020
  end-page: 13012
  ident: bib0058
  article-title: Exchange of endogenous and heterogeneous yeast terminators in
  publication-title: Nucleic Acids Res.
– volume: 135
  start-page: 1201
  year: 2008
  end-page: 1214
  ident: bib0125
  article-title: The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members
  publication-title: Development
– volume: 9
  start-page: 3589
  year: 2018
  ident: bib0048
  article-title: Engineered bidirectional promoters enable rapid multi-gene co-expression optimization
  publication-title: Nat. Commun.
– volume: 6
  start-page: 36997
  year: 2016
  ident: bib0057
  article-title: Enhancement of protein production via the strong
  publication-title: Sci. Rep.
– volume: 9
  start-page: 1059
  year: 2020
  end-page: 1068
  ident: bib0110
  article-title: A synthetic malonyl-CoA metabolic oscillator in
  publication-title: ACS Synth. Biol.
– volume: 8
  year: 2021
  ident: bib0113
  article-title: PCR & Go: a pre-installed expression chassis for facile integration of multi-gene biosynthetic pathways
  publication-title: Front. Bioeng. Biotechnol.
– volume: 43
  start-page: 8
  year: 2020
  end-page: 17
  ident: bib0116
  article-title: CRISPR-Cas12a: functional overview and applications
  publication-title: Biomed. J.
– volume: 11
  start-page: 1600
  year: 2022
  end-page: 1612
  ident: bib0011
  article-title: De novo production of plant 4′-deoxyflavones baicalein and oroxylin a from ethanol in crabtree-negative yeast
  publication-title: ACS Synth. Biol.
– volume: 14
  start-page: 155
  year: 2021
  ident: bib0131
  article-title: Stress tolerance enhancement via
  publication-title: Biotechnol. Biofuels
– volume: 6
  start-page: 112
  year: 2015
  end-page: 118
  ident: bib0051
  article-title: Extracellular expression of alkaline phytase in
  publication-title: Biotechnol. Rep.
– volume: 431
  start-page: 34
  year: 2019
  end-page: 47
  ident: bib0103
  article-title: A CRISPR–dCas toolbox for genetic engineering and synthetic biology
  publication-title: J. Mol. Biol.
– volume: 339
  start-page: 819
  year: 2013
  end-page: 823
  ident: bib0093
  article-title: Multiplex genome engineering using CRISPR/Cas systems
  publication-title: Science
– volume: 17
  start-page: 550
  year: 2016
  ident: bib0019
  article-title: Comparative genomics and transcriptomics of
  publication-title: BMC Genomics
– volume: 19
  start-page: 88
  year: 2013
  end-page: 97
  ident: bib0056
  article-title: Use of expression-enhancing terminators in
  publication-title: Metab. Eng.
– volume: 114
  start-page: 2319
  year: 2017
  end-page: 2327
  ident: bib0053
  article-title: Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in
  publication-title: Biotechnol. Bioeng.
– volume: 242
  start-page: 64
  year: 2017
  end-page: 72
  ident: bib0009
  article-title: Methylotrophic yeast
  publication-title: J. Biotechnol.
– volume: 35
  start-page: 681
  year: 2017
  end-page: 710
  ident: bib0001
  article-title: Towards systems metabolic engineering in
  publication-title: Biotechnol. Adv.
– volume: 28
  start-page: 201
  year: 2004
  end-page: 223
  ident: bib0098
  article-title: Genetic aspects of targeted insertion mutagenesis in yeasts
  publication-title: FEMS Microbiol. Rev.
– reference: D. Mattanovich, M. Sauer & B. Gasser. Industrial Microorganisms:
– volume: 219
  start-page: 320
  year: 1989
  end-page: 323
  ident: bib0084
  article-title: Use of site-specific recombination to regenerate selectable markers
  publication-title: Mol. Gen. Genet.
– volume: 2
  start-page: 24
  year: 2012
  ident: bib0006
  article-title: Construction of a novel
  publication-title: AMB Express
– volume: 5
  start-page: 705
  year: 2010
  end-page: 715
  ident: bib0021
  article-title: Genome-scale metabolic model of methylotrophic yeast
  publication-title: Biotechnol. J.
– volume: 7
  start-page: 41850
  year: 2017
  ident: bib0036
  article-title: Methanol-independent protein expression by
  publication-title: Sci. Rep.
– volume: 114
  start-page: 2319
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0053
  article-title: Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris
  publication-title: Biotechnol. Bioeng.
  doi: 10.1002/bit.26363
– volume: 106
  start-page: 3449
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0026
  article-title: Expanding the promoter toolbox for metabolic engineering of methylotrophic yeasts
  publication-title: Appl. Microbiol. Biotechnol.
  doi: 10.1007/s00253-022-11948-5
– volume: 50
  year: 2023
  ident: 10.1016/j.engmic.2023.100094_bib0027
  article-title: Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae
  publication-title: J. Ind. Microbiol. Biotechnol.
  doi: 10.1093/jimb/kuac029
– volume: 4
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0042
  article-title: Engineered deregulation of expression in yeast with designed hybrid-promoter architectures in coordination with discovered master regulator transcription factor
  publication-title: Adv. Biosyst.
  doi: 10.1002/adbi.201900172
– volume: 15
  start-page: 139
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0067
  article-title: Characterization of a panARS-based episomal vector in the methylotrophic yeast Pichia pastoris for recombinant protein production and synthetic biology applications, Microb
  publication-title: Cell. Fact.
  doi: 10.1186/s12934-016-0540-5
– volume: 1923
  start-page: 97
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0032
  article-title: Pichia pastoris Promoters
  publication-title: Methods Mol. Biol.
  doi: 10.1007/978-1-4939-9024-5_3
– volume: 242
  start-page: 64
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0009
  article-title: Methylotrophic yeast Pichia pastoris as a chassis organism for polyketide synthesis via the full citrinin biosynthetic pathway
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2016.11.031
– volume: 12
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0115
  article-title: Multiplex genome editing in yeast by CRISPR/Cas9 – a potent and agile tool to reconstruct complex metabolic pathways, Front
  publication-title: Plant Sci
– volume: 8
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0063
  article-title: Multiplex genome engineering methods for yeast cell factory development
  publication-title: Front. Bioeng. Biotechnol.
  doi: 10.3389/fbioe.2020.589468
– volume: 154
  start-page: 442
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0105
  article-title: CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
  publication-title: Cell
  doi: 10.1016/j.cell.2013.06.044
– volume: 235
  start-page: 121
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0018
  article-title: Refined Pichia pastoris reference genome sequence
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2016.04.023
– volume: 75
  start-page: 3528
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0046
  article-title: Phosphate-responsive promoter of a Pichia pastoris sodium phosphate symporter
  publication-title: Appl. Environ. Microbiol.
  doi: 10.1128/AEM.02913-08
– volume: 14
  start-page: 155
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0131
  article-title: Stress tolerance enhancement via SPT15 base editing in Saccharomyces cerevisiae
  publication-title: Biotechnol. Biofuels
  doi: 10.1186/s13068-021-02005-w
– volume: 8
  start-page: e9010
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0061
  article-title: Expression of Aspergillus niger glucose oxidase in Pichia pastoris and its antimicrobial activity against Agrobacterium and Escherichia coli
  publication-title: PeerJ
  doi: 10.7717/peerj.9010
– volume: 551
  start-page: 464
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0128
  article-title: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
  publication-title: Nature
  doi: 10.1038/nature24644
– volume: 84
  start-page: e02882
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0066
  article-title: Autonomously replicating plasmid vector containing Pichia pastoris centromeric DNA
  publication-title: Appl. Environ. Microbiol.
  doi: 10.1128/AEM.02882-17
– start-page: 557
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0070
  article-title: Pichia pastoris protease-deficient and auxotrophic strains generated by a novel, user-friendly vector toolbox for gene deletion
  publication-title: Yeast
  doi: 10.1002/yea.3426
– volume: 150
  start-page: 519
  year: 2010
  ident: 10.1016/j.engmic.2023.100094_bib0136
  article-title: Identification and characterisation of novel Pichia pastoris promoters for heterologous protein production
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2010.09.957
– volume: 10
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0014
  article-title: Combining metabolic engineering and multiplexed screening methods for 3-hydroxyprionic acid production in Pichia pastoris
  publication-title: Front. Bioeng. Biotechnol.
– volume: 115
  start-page: 1037
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0037
  article-title: Methanol independent induction in Pichia pastoris by simple derepressed overexpression of single transcription factors
  publication-title: Biotechnol. Bioeng.
  doi: 10.1002/bit.26529
– volume: 2
  start-page: 337
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0055
  article-title: A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a ″Terminatome″ toolbox
  publication-title: ACS Synth. Biol.
  doi: 10.1021/sb300116y
– volume: 163
  start-page: 759
  year: 2015
  ident: 10.1016/j.engmic.2023.100094_bib0096
  article-title: Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system
  publication-title: Cell
  doi: 10.1016/j.cell.2015.09.038
– volume: 28
  start-page: 201
  year: 2004
  ident: 10.1016/j.engmic.2023.100094_bib0098
  article-title: Genetic aspects of targeted insertion mutagenesis in yeasts
  publication-title: FEMS Microbiol. Rev.
  doi: 10.1016/j.femsre.2003.10.002
– volume: 326
  start-page: 544
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0126
  article-title: RNAi in Budding Yeast
  publication-title: Science
  doi: 10.1126/science.1176945
– volume: 9
  start-page: 26
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0095
  article-title: Host-informed expression of CRISPR guide RNA for genomic engineering in Komagataella phaffii
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.9b00372
– volume: 7
  start-page: 41850
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0036
  article-title: Methanol-independent protein expression by AOX1 promoter with trans-acting elements engineering and glucose-glycerol-shift induction in Pichia pastoris
  publication-title: Sci. Rep.
  doi: 10.1038/srep41850
– volume: 13
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0044
  article-title: Pichia pastoris Alcohol Oxidase 1 (AOX1) core promoter engineering by high resolution systematic mutagenesis
  publication-title: Biotechnol. J.
  doi: 10.1002/biot.201700340
– volume: 15
  start-page: 2223
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0079
  article-title: Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica
  publication-title: Microb. Biotechnol.
  doi: 10.1111/1751-7915.14060
– volume: 10
  start-page: 2927
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0097
  article-title: A novel and efficient genome editing tool assisted by CRISPR-Cas12a/Cpf1 for Pichia pastoris
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.1c00172
– volume: 138
  start-page: 111
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0137
  article-title: Naturally occurring novel promoters around pyruvate branch-point for recombinant protein production in Pichia pastoris (Komagataella phaffii): pyruvate decarboxylase- and pyruvate kinase- promoters
  publication-title: Biochem. Eng. J.
  doi: 10.1016/j.bej.2018.07.012
– volume: 11
  start-page: 547
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0100
  article-title: Enhancing homologous recombination efficiency in Pichia pastoris for multiplex genome integration using short homology arms
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.1c00366
– volume: 7
  start-page: e39720
  year: 2012
  ident: 10.1016/j.engmic.2023.100094_bib0085
  article-title: Deletion of the Pichia pastoris KU70 homologue facilitates platform strain generation for gene expression and synthetic biology
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0039720
– volume: 77
  start-page: 3600
  year: 2011
  ident: 10.1016/j.engmic.2023.100094_bib0052
  article-title: GAP promoter library for fine-tuning of gene expression in Pichia pastoris
  publication-title: Appl. Environ. Microbiol.
  doi: 10.1128/AEM.02843-10
– volume: 6
  start-page: 43
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0101
  article-title: Processing of DNA double-strand breaks by the MRX complex in a chromatin context
  publication-title: Front. Mol. Biosci.
  doi: 10.3389/fmolb.2019.00043
– volume: 43
  start-page: 8
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0116
  article-title: CRISPR-Cas12a: functional overview and applications
  publication-title: Biomed. J.
  doi: 10.1016/j.bj.2019.10.005
– volume: 320
  start-page: 80
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0111
  article-title: Engineered dynamic distribution of malonyl-CoA flux for improving polyketide biosynthesis in Komagataella phaffii
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2020.06.012
– volume: 35
  start-page: 1865
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0054
  article-title: Identification and characterization of PGCW14: a novel, strong constitutive promoter of Pichia pastoris
  publication-title: Biotechnol. Lett.
  doi: 10.1007/s10529-013-1265-8
– volume: 36
  start-page: e76
  year: 2008
  ident: 10.1016/j.engmic.2023.100094_bib0039
  article-title: Promoter library designed for fine-tuned gene expression in Pichia pastoris
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkn369
– volume: 13
  start-page: 107
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0059
  article-title: Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications
  publication-title: FEMS Yeast Res.
  doi: 10.1111/1567-1364.12016
– ident: 10.1016/j.engmic.2023.100094_bib0069
  doi: 10.1002/9783527807796.ch19
– volume: 219
  start-page: 320
  year: 1989
  ident: 10.1016/j.engmic.2023.100094_bib0084
  article-title: Use of site-specific recombination to regenerate selectable markers
  publication-title: Mol. Gen. Genet.
  doi: 10.1007/BF00261194
– volume: 25
  start-page: 229
  year: 2002
  ident: 10.1016/j.engmic.2023.100094_bib0060
  article-title: Soluble expression and purification of porcine pepsinogen from Pichia pastoris
  publication-title: Protein Expression Purif.
  doi: 10.1016/S1046-5928(02)00003-1
– volume: 50
  start-page: 2
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0004
  article-title: Metabolic engineering of Pichia pastoris
  publication-title: Metab. Eng.
  doi: 10.1016/j.ymben.2018.04.017
– volume: 35
  start-page: 681
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0001
  article-title: Towards systems metabolic engineering in Pichia pastoris
  publication-title: Biotechnol. Adv.
  doi: 10.1016/j.biotechadv.2017.07.009
– volume: 6
  start-page: 112
  year: 2015
  ident: 10.1016/j.engmic.2023.100094_bib0051
  article-title: Extracellular expression of alkaline phytase in Pichia pastoris: influence of signal peptides, promoters and growth medium
  publication-title: Biotechnol. Rep.
  doi: 10.1016/j.btre.2015.03.005
– volume: 9
  start-page: 3589
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0048
  article-title: Engineered bidirectional promoters enable rapid multi-gene co-expression optimization
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-018-05915-w
– volume: 121
  start-page: 112
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0138
  article-title: Comparison of ADH3 promoter with commonly used promoters for recombinant protein production in Pichia pastoris
  publication-title: Protein Expression Purif.
  doi: 10.1016/j.pep.2016.01.017
– volume: 533
  start-page: 420
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0127
  article-title: Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
  publication-title: Nature
  doi: 10.1038/nature17946
– volume: 12
  start-page: 6
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0049
  article-title: Repressible promoters – A novel tool to generate conditional mutants in Pichia pastoris
  publication-title: Microb. Cell Fact.
  doi: 10.1186/1475-2859-12-6
– volume: 27
  start-page: 561
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0015
  article-title: Genome sequence of the recombinant protein production host Pichia pastoris
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.1544
– volume: 138
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0106
  article-title: High efficiency CRISPR/Cas9 genome editing system with an eliminable episomal sgRNA plasmid in Pichia pastoris
  publication-title: Enzyme Microb. Technol.
  doi: 10.1016/j.enzmictec.2020.109556
– volume: 19
  start-page: 88
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0056
  article-title: Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications
  publication-title: Metab. Eng.
  doi: 10.1016/j.ymben.2013.07.001
– volume: 72
  start-page: 185
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0120
  article-title: Golden Gate assembly of BioBrick-compliant parts using Type II restriction endonucleases
  publication-title: BioTechniques
  doi: 10.2144/btn-2021-0083
– volume: 11
  start-page: 623
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0082
  article-title: Synthetic biology toolkit for marker-less integration of multigene pathways into Pichia pastoris via CRISPR/Cas9
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.1c00307
– volume: 18
  start-page: foy074
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0099
  article-title: Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii
  publication-title: FEMS Yeast Res.
  doi: 10.1093/femsyr/foy074
– volume: 39
  start-page: 35
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0129
  article-title: Glycosylase base editors enable C-to-A and C-to-G base changes
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-020-0592-2
– volume: 369
  start-page: fnac081
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0077
  article-title: Expanding the neutral sites for integrated gene expression in Saccharomyces cerevisiae
  publication-title: FEMS Microbiol. Lett.
  doi: 10.1093/femsle/fnac081
– volume: 496
  start-page: 118
  year: 2012
  ident: 10.1016/j.engmic.2023.100094_bib0045
  article-title: Analysis of the 5′ untranslated region (5′UTR) of the alcohol oxidase 1 (AOX1) gene in recombinant protein expression in Pichia pastoris
  publication-title: Gene
  doi: 10.1016/j.gene.2012.01.006
– volume: 281
  start-page: 4805
  year: 2014
  ident: 10.1016/j.engmic.2023.100094_bib0003
  article-title: Analysis of the yeast short-term Crabtree effect and its origin
  publication-title: FEBS J.
  doi: 10.1111/febs.13019
– volume: 9
  start-page: 50
  year: 2010
  ident: 10.1016/j.engmic.2023.100094_bib0022
  article-title: Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement
  publication-title: Microb. Cell Fact.
  doi: 10.1186/1475-2859-9-50
– volume: 339
  start-page: 823
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0094
  article-title: RNA-guided human genome engineering via Cas9
  publication-title: Science
  doi: 10.1126/science.1232033
– volume: 361
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0072
  article-title: Overproduction of 3-hydroxypropionate in a super yeast chassis
  publication-title: Bioresour. Technol.
  doi: 10.1016/j.biortech.2022.127690
– volume: 9
  start-page: 1271
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0033
  article-title: An upstream activation sequence controls the expression of AOX1 gene in Pichia pastoris
  publication-title: FEMS Yeast Res.
  doi: 10.1111/j.1567-1364.2009.00571.x
– volume: 8
  start-page: eabl5166
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0109
  article-title: A programmable high-expression yeast platform responsive to user-defined signals
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abl5166
– volume: 18
  start-page: 81
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0038
  article-title: Enhancing the efficiency of the Pichia pastoris AOX1 promoter via the synthetic positive feedback circuit of transcription factor Mxr1
  publication-title: BMC Biotechnol.
  doi: 10.1186/s12896-018-0492-4
– volume: 7
  start-page: 23
  year: 2008
  ident: 10.1016/j.engmic.2023.100094_bib0086
  article-title: Overexpression of the riboflavin biosynthetic pathway in Pichia pastoris
  publication-title: Microb. Cell Fact.
  doi: 10.1186/1475-2859-7-23
– year: 2003
  ident: 10.1016/j.engmic.2023.100094_bib0119
– volume: 157
  start-page: 1262
  year: 2014
  ident: 10.1016/j.engmic.2023.100094_bib0090
  article-title: Development and applications of CRISPR-Cas9 for genome engineering
  publication-title: Cell
  doi: 10.1016/j.cell.2014.05.010
– volume: 216
  start-page: 47
  year: 2015
  ident: 10.1016/j.engmic.2023.100094_bib0008
  article-title: Metabolic engineering of Pichia pastoris for the production of dammarenediol-II
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2015.10.005
– volume: 9
  start-page: 58
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0073
  article-title: Microbial synthesis of long-chain α-alkenes from methanol by engineering Pichia pastoris
  publication-title: Bioresour. Bioprocess.
  doi: 10.1186/s40643-022-00551-1
– volume: 16
  start-page: fow051
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0017
  article-title: Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function
  publication-title: FEMS Yeast Res.
  doi: 10.1093/femsyr/fow051
– volume: 339
  start-page: 819
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0093
  article-title: Multiplex genome engineering using CRISPR/Cas systems
  publication-title: Science
  doi: 10.1126/science.1231143
– volume: 2
  start-page: 231
  year: 2023
  ident: 10.1016/j.engmic.2023.100094_bib0012
  article-title: Biosynthesis of catharanthine in engineered Pichia pastoris
  publication-title: Nat. Synth.
  doi: 10.1038/s44160-022-00205-2
– volume: 21
  start-page: 182
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0102
  article-title: Fusing an exonuclease with Cas9 enhances homologous recombination in Pichia pastoris
  publication-title: Microb. Cell Fact.
  doi: 10.1186/s12934-022-01908-z
– volume: 36
  start-page: 182
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0002
  article-title: Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: a review
  publication-title: Biotechnol. Adv.
  doi: 10.1016/j.biotechadv.2017.11.002
– volume: 291
  start-page: 6245
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0034
  article-title: Mit1 transcription factor mediates methanol signaling and regulates the Alcohol Oxidase 1 (AOX1) Promoter in Pichia pastoris
  publication-title: J. Biol. Chem.
  doi: 10.1074/jbc.M115.692053
– volume: 6
  start-page: 63
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0078
  article-title: Screening neutral sites for metabolic engineering of methylotrophic yeast Ogataea polymorpha
  publication-title: Synth. Syst. Biotechnol.
  doi: 10.1016/j.synbio.2021.03.001
– volume: 19
  start-page: foy107
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0114
  article-title: A toolkit for rapid CRISPR-SpCas9 assisted construction of hexose-transport-deficient Saccharomyces cerevisiae strains
  publication-title: FEMS Yeast Res.
– volume: 18
  start-page: 144
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0081
  article-title: CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris
  publication-title: Microb. Cell. Fact.
  doi: 10.1186/s12934-019-1194-x
– volume: 11
  start-page: 629
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0132
  article-title: Expanding the genome-targeting scope and the site selectivity of high-precision base editors
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-020-14465-z
– ident: 10.1016/j.engmic.2023.100094_bib0005
– volume: 45
  start-page: 189
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0010
  article-title: Engineered monoculture and co-culture of methylotrophic yeast for de novo production of monacolin J and lovastatin from methanol
  publication-title: Metab. Eng.
  doi: 10.1016/j.ymben.2017.12.009
– volume: 13
  start-page: 80
  year: 2015
  ident: 10.1016/j.engmic.2023.100094_bib0020
  article-title: Systems-level organization of yeast methylotrophic lifestyle
  publication-title: BMC Biol.
  doi: 10.1186/s12915-015-0186-5
– volume: 6
  start-page: 471
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0041
  article-title: Synthetic core promoters as universal parts for fine-tuning expression in different yeast species
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.6b00178
– volume: 18
  start-page: 63
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0089
  article-title: CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications
  publication-title: Microb. Cell. Fact.
  doi: 10.1186/s12934-019-1112-2
– volume: 5
  start-page: 172
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0030
  article-title: A toolbox of diverse promoters related to methanol utilization: functionally verified parts for heterologous pathway expression in Pichia pastoris
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.5b00199
– volume: 8
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0113
  article-title: PCR & Go: a pre-installed expression chassis for facile integration of multi-gene biosynthetic pathways
  publication-title: Front. Bioeng. Biotechnol.
  doi: 10.3389/fbioe.2020.613771
– volume: 36
  start-page: e3008
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0071
  article-title: Recent advances in domesticating non-model microorganisms
  publication-title: Biotechnol. Prog.
  doi: 10.1002/btpr.3008
– volume: 12
  start-page: 5
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0135
  article-title: Induction without methanol: novel regulated promoters enable high-level expression in Pichia pastoris
  publication-title: Microb. Cell Fact.
  doi: 10.1186/1475-2859-12-5
– volume: 21
  start-page: foab027
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0076
  article-title: Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites
  publication-title: FEMS Yeast Res.
  doi: 10.1093/femsyr/foab027
– volume: 6
  start-page: 27352
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0047
  article-title: Discovery of a rhamnose utilization pathway and rhamnose-inducible promoters in Pichia pastoris
  publication-title: Sci. Rep.
  doi: 10.1038/srep27352
– volume: 5
  start-page: 705
  year: 2010
  ident: 10.1016/j.engmic.2023.100094_bib0021
  article-title: Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production
  publication-title: Biotechnol. J.
  doi: 10.1002/biot.201000078
– volume: 113
  start-page: 2633
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0050
  article-title: The vitamin-sensitive promoter PTHI11 enables pre-defined autonomous induction of recombinant protein production in Pichia pastoris
  publication-title: Biotechnol. Bioeng.
  doi: 10.1002/bit.26041
– volume: 8
  start-page: 780
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0068
  article-title: A mitochondrial autonomously replicating sequence from Pichia pastoris for uniform high level recombinant protein production
  publication-title: Front. Microbiol.
  doi: 10.3389/fmicb.2017.00780
– volume: 8
  start-page: 1698
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0087
  article-title: A novel vector for construction of markerless multicopy overexpression Transformants in Pichia pastoris
  publication-title: Front. Microbiol.
  doi: 10.3389/fmicb.2017.01698
– volume: 6
  start-page: 24
  year: 2012
  ident: 10.1016/j.engmic.2023.100094_bib0023
  article-title: Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
  publication-title: BMC Syst. Biol.
  doi: 10.1186/1752-0509-6-24
– volume: 235
  start-page: 139
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0025
  article-title: Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2016.03.027
– volume: 11
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0064
  article-title: Komagataella phaffii as emerging model organism in fundamental research
  publication-title: Front. Microbiol.
– volume: 8
  start-page: eabq2157
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0133
  article-title: Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abq2157
– volume: 35
  start-page: 79
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0092
  article-title: Construction of a series of episomal plasmids and their application in the development of an efficient CRISPR/Cas9 system in Pichia pastoris
  publication-title: World J. Microbiol. Biotechnol.
  doi: 10.1007/s11274-019-2654-5
– volume: 152
  start-page: 1173
  year: 2013
  ident: 10.1016/j.engmic.2023.100094_bib0104
  article-title: Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
  publication-title: Cell
  doi: 10.1016/j.cell.2013.02.022
– volume: 154
  start-page: 312
  year: 2011
  ident: 10.1016/j.engmic.2023.100094_bib0016
  article-title: High-quality genome sequence of Pichia pastoris CBS7435
  publication-title: J. Biotechnol.
  doi: 10.1016/j.jbiotec.2011.04.014
– start-page: 10187
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0043
  article-title: Yeast transcriptional device libraries enable precise synthesis of value-added chemicals from methanol
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkac765
– volume: 105
  start-page: 3873
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0112
  article-title: Recent advances in the application of multiplex genome editing in Saccharomyces cerevisiae
  publication-title: Appl. Microbiol. Biotechnol.
  doi: 10.1007/s00253-021-11287-x
– volume: 35
  start-page: 379
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0139
  article-title: Identification and characterization of novel promoters for recombinant protein production in yeast Pichia pastoris
  publication-title: Yeast
  doi: 10.1002/yea.3301
– volume: 9
  start-page: 3202
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0107
  article-title: Fine-tuning of transcription in Pichia pastoris using dCas9 and RNA Scaffolds
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.0c00214
– volume: 49
  start-page: 7791
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0031
  article-title: Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkab535
– volume: 538
  start-page: 270
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0124
  article-title: Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
  publication-title: Nature
  doi: 10.1038/nature19802
– volume: 135
  start-page: 1201
  year: 2008
  ident: 10.1016/j.engmic.2023.100094_bib0125
  article-title: The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members
  publication-title: Development
  doi: 10.1242/dev.005629
– volume: 431
  start-page: 34
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0103
  article-title: A CRISPR–dCas toolbox for genetic engineering and synthetic biology
  publication-title: J. Mol. Biol.
  doi: 10.1016/j.jmb.2018.06.037
– volume: 9
  start-page: 1059
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0110
  article-title: A synthetic malonyl-CoA metabolic oscillator in Komagataella phaffii
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.9b00378
– volume: 105
  start-page: 9211
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0108
  article-title: A versatile toolbox for CRISPR-based genome engineering in Pichia pastoris
  publication-title: Appl. Microbiol. Biotechnol.
  doi: 10.1007/s00253-021-11688-y
– volume: 10
  start-page: e03760
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0134
  article-title: High-fidelity cytosine base editing in a GC-Rich Corynebacterium glutamicum with reduced DNA off-target editing effects
  publication-title: Microbiol. Spectr.
  doi: 10.1128/spectrum.03760-22
– volume: 35
  start-page: 31
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0117
  article-title: Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.3737
– volume: 11
  start-page: 1600
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0011
  article-title: De novo production of plant 4′-deoxyflavones baicalein and oroxylin a from ethanol in crabtree-negative yeast
  publication-title: ACS Synth. Biol.
  doi: 10.1021/acssynbio.2c00026
– volume: 119
  start-page: 3183
  year: 2018
  ident: 10.1016/j.engmic.2023.100094_bib0091
  article-title: Expanding the CRISPR/Cas9 toolkit for Pichia pastoris with efficient donor integration and alternative resistance markers
  publication-title: J. Cell. Biochem.
  doi: 10.1002/jcb.26474
– volume: 2
  start-page: 24
  year: 2012
  ident: 10.1016/j.engmic.2023.100094_bib0006
  article-title: Construction of a novel Pichia pastoris strain for production of xanthophylls
  publication-title: AMB Express
  doi: 10.1186/2191-0855-2-24
– volume: 576
  start-page: 149
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0130
  article-title: Search-and-replace genome editing without double-strand breaks or donor DNA
  publication-title: Nature
  doi: 10.1038/s41586-019-1711-4
– volume: 35
  start-page: 37
  year: 2019
  ident: 10.1016/j.engmic.2023.100094_bib0062
  article-title: Toward the construction of a technology platform for chemicals production from methanol: d-lactic acid production from methanol by an engineered yeast Pichia pastoris
  publication-title: World J. Microbiol. Biotechnol.
  doi: 10.1007/s11274-019-2610-4
– volume: 353
  start-page: aaf5573
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0123
  article-title: C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
  publication-title: Science
  doi: 10.1126/science.aaf5573
– volume: 20
  start-page: 1279
  year: 2003
  ident: 10.1016/j.engmic.2023.100094_bib0083
  article-title: Cloning and disruption of the PpURA5 gene and construction of a set of integration vectors for the stable genetic modification of Pichia pastoris
  publication-title: Yeast
  doi: 10.1002/yea.1049
– volume: 11
  start-page: 123
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0118
  article-title: GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris
  publication-title: BMC Syst. Biol.
  doi: 10.1186/s12918-017-0492-3
– volume: 5
  start-page: 17
  year: 2006
  ident: 10.1016/j.engmic.2023.100094_bib0028
  article-title: Operational strategies, monitoring and control of heterologous protein production in the methylotrophic yeast Pichia pastoris under different promoters: a review
  publication-title: Microb. Cell Fact.
  doi: 10.1186/1475-2859-5-17
– volume: 11
  start-page: 292
  year: 2011
  ident: 10.1016/j.engmic.2023.100094_bib0024
  article-title: Sequential deletion of Pichia pastoris genes by a self-excisable cassette
  publication-title: FEMS Yeast Res.
  doi: 10.1111/j.1567-1364.2011.00716.x
– volume: 44
  start-page: 1789
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0122
  article-title: Multiple nucleic acid cleavage modes in divergent type III CRISPR systems
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkw020
– volume: 6
  start-page: 110
  year: 2021
  ident: 10.1016/j.engmic.2023.100094_bib0029
  article-title: Development of synthetic biology tools to engineer Pichia pastoris as a chassis for the production of natural products
  publication-title: Synth. Syst. Biotechnol.
  doi: 10.1016/j.synbio.2021.04.005
– volume: 358
  start-page: 996
  year: 2017
  ident: 10.1016/j.engmic.2023.100094_bib0121
  article-title: Enhancing the RNA engineering toolkit
  publication-title: Science
  doi: 10.1126/science.aar2400
– volume: 14
  start-page: 104
  year: 2012
  ident: 10.1016/j.engmic.2023.100094_bib0074
  article-title: Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform
  publication-title: Metab. Eng.
  doi: 10.1016/j.ymben.2012.01.006
– volume: 3
  start-page: 188
  year: 2014
  ident: 10.1016/j.engmic.2023.100094_bib0040
  article-title: Synthetic core promoters for Pichia pastoris
  publication-title: ACS Synth. Biol.
  doi: 10.1021/sb400091p
– volume: 17
  start-page: 550
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0019
  article-title: Comparative genomics and transcriptomics of Pichia pastoris
  publication-title: BMC Genomics
  doi: 10.1186/s12864-016-2876-y
– volume: 26
  start-page: 311
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0080
  article-title: Expression of GFP using Pichia pastoris vectors with zeocin or G-418 sulphate as the primary selectable marker
  publication-title: Yeast
  doi: 10.1002/yea.1666
– volume: 5
  start-page: 3376
  year: 1985
  ident: 10.1016/j.engmic.2023.100094_bib0065
  article-title: Pichia pastoris as a host system for transformations
  publication-title: Mol. Cell. Biol.
– volume: 26
  start-page: 545
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0075
  article-title: Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae
  publication-title: Yeast
  doi: 10.1002/yea.1705
– volume: 9
  start-page: 600
  year: 2009
  ident: 10.1016/j.engmic.2023.100094_bib0088
  article-title: mazF as a counter-selectable marker for unmarked genetic modification of Pichia pastoris
  publication-title: FEMS Yeast Res.
  doi: 10.1111/j.1567-1364.2009.00503.x
– volume: 119
  year: 2022
  ident: 10.1016/j.engmic.2023.100094_bib0013
  article-title: Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast Pichia pastoris
  publication-title: Proc. Natl. Acad. Sci. U. S. A.
  doi: 10.1073/pnas.2201711119
– volume: 6
  start-page: 36997
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0057
  article-title: Enhancement of protein production via the strong DIT1 terminator and two RNA-binding proteins in Saccharomyces cerevisiae
  publication-title: Sci. Rep.
  doi: 10.1038/srep36997
– start-page: 13000
  year: 2020
  ident: 10.1016/j.engmic.2023.100094_bib0058
  article-title: Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkaa1066
– volume: 38
  start-page: 291
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0035
  article-title: PpNrg1 is a transcriptional repressor for glucose and glycerol repression of AOX1 promoter in methylotrophic yeast Pichia pastoris
  publication-title: Biotechnol. Lett.
  doi: 10.1007/s10529-015-1972-4
– volume: 89
  start-page: 114
  year: 2016
  ident: 10.1016/j.engmic.2023.100094_bib0007
  article-title: Enhancing cytochrome P450-mediated conversions in P. pastoris through RAD52 over-expression and optimizing the cultivation conditions
  publication-title: Fungal Genet. Biol.
  doi: 10.1016/j.fgb.2016.02.004
SSID ssj0002891319
ssib056474779
Score 2.3363538
SecondaryResourceType review_article
Snippet The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins....
The methylotrophic yeast (also known as ) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its...
The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii ) is widely used as a yeast cell factory for producing heterologous proteins....
SourceID doaj
pubmedcentral
proquest
pubmed
crossref
elsevier
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 100094
SubjectTerms CRISPR/Cas9
Genetic tools
Metabolic engineering
Pichia pastoris
Review
Title Genetic tools for metabolic engineering of Pichia pastoris
URI https://dx.doi.org/10.1016/j.engmic.2023.100094
https://www.ncbi.nlm.nih.gov/pubmed/39628915
https://www.proquest.com/docview/3140929533
https://pubmed.ncbi.nlm.nih.gov/PMC11611016
https://doaj.org/article/cf5295a5e2904425b10a4526b64db08e
Volume 3
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV07T8MwELZQJxYE4lVeChJrhBPHScwGiKpCAjFQqZsVPwKt2qSi6f_nLk5KA0MXVsdxfJ_PuS-6y2dCblQmmNHU-MB2Ix8Tc77ijPrWpElieZIltZbey2s8HEXPYz7eOOoLa8KcPLAD7lbnmIrKuA0FjcDBVEAzPBZbxZFRNLX49oWYt_ExNXXpswCcq_1Xri7ossXHfIKqhSHD2gAqok4sqiX7OyHpL-X8XTm5EYoG-2Sv4ZDevZv7AdmxxSG5QwFpaPCqspwtPeCi3txWsMQzaLM_qoNemXtvE6xw9hZZLRGyPCKjwdP749BvDkbwNeBY-RqMDwQ3lirOc2ONEDrF_CYLLAOARZAnGcRtFQrNYhThigSjKtY21opB2zHpFWVhT4mnooAaLVSeGxalJhMxDMuBYyRJnOcB7xPWQiR1oxqOh1fMZFseNpUOWInASgdsn_jruxZONWNL_wdEf90XNa_rBvAE2XiC3OYJfZK0aycb-uBoAQw12fL463apJewuTJlkhS1XS8lQDyzEEtw-OXFLv54kEzG6GUCUdpyiY0X3SjH5rBW8A-DZOJuz_7D7nOyiLa7G5oL0qq-VvQSmVKmrelN8AzrSD6U
linkProvider Directory of Open Access Journals
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Genetic+tools+for+metabolic+engineering+of+Pichia+pastoris&rft.jtitle=Engineering+Microbiology&rft.au=Wu%2C+Xiaoyan&rft.au=Cai%2C+Peng&rft.au=Yao%2C+Lun&rft.au=Zhou%2C+Yongjin+J&rft.date=2023-12-01&rft.issn=2667-3703&rft.eissn=2667-3703&rft.volume=3&rft.issue=4&rft.spage=100094&rft_id=info:doi/10.1016%2Fj.engmic.2023.100094&rft.externalDBID=NO_FULL_TEXT
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2667-3703&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2667-3703&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2667-3703&client=summon