Comparative Genomics and Transcriptional Analysis of Prophages Identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei
Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 propha...
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| Published in | Applied and Environmental Microbiology Vol. 72; no. 5; pp. 3130 - 3146 |
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| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Washington, DC
American Society for Microbiology
01.05.2006
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| Abstract | Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 prophages belong to the group of Sfi11-like pac site and cos site Siphoviridae, respectively. Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species. The attachment sites were determined for all these prophage elements; LgaI as well as Sal1 integrates in tRNA genes, while prophage Sal2 integrates in a predicted arginino-succinate lyase-encoding gene. In contrast, Lca1 and the Sal3 and Sal4 prophage remnants are integrated in noncoding regions in the L. casei ATCC 334 and L. salivarius UCC 118 genomes. Northern analysis showed that large parts of the prophage genomes are transcriptionally silent and that transcription is limited to genome segments located near the attachment site. Finally, pulsed-field gel electrophoresis followed by Southern blot hybridization with specific prophage probes indicates that these prophage sequences are narrowly distributed within lactobacilli. |
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| AbstractList | Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 prophages belong to the group of Sfi11-like pac site and cos site Siphoviridae, respectively. Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species. The attachment sites were determined for all these prophage elements; LgaI as well as Sal1 integrates in tRNA genes, while prophage Sal2 integrates in a predicted arginino-succinate lyase-encoding gene. In contrast, Lca1 and the Sal3 and Sal4 prophage remnants are integrated in noncoding regions in the L. casei ATCC 334 and L. salivarius UCC 118 genomes. Northern analysis showed that large parts of the prophage genomes are transcriptionally silent and that transcription is limited to genome segments located near the attachment site. Finally, pulsed-field gel electrophoresis followed by Southern blot hybridization with specific prophage probes indicates that these prophage sequences are narrowly distributed within lactobacilli. Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue Spotlights in the Current Issue AEM About AEM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AEM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0099-2240 Online ISSN: 1098-5336 Copyright © 2014 by the American Society for Microbiology. For an alternate route to AEM .asm.org, visit: AEM Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 prophages belong to the group of Sfi11-like pac site and cos site Siphoviridae, respectively. Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species. The attachment sites were determined for all these prophage elements; LgaI as well as Sal1 integrates in tRNA genes, while prophage Sal2 integrates in a predicted arginino-succinate lyase-encoding gene. In contrast, Lca1 and the Sal3 and Sal4 prophage remnants are integrated in noncoding regions in the L. casei ATCC 334 and L. salivarius UCC 118 genomes. Northern analysis showed that large parts of the prophage genomes are transcriptionally silent and that transcription is limited to genome segments located near the attachment site. Finally, pulsed-field gel electrophoresis followed by Southern blot hybridization with specific prophage probes indicates that these prophage sequences are narrowly distributed within lactobacilli. [PUBLICATION ABSTRACT] Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 prophages belong to the group of Sfi11-like pac site and cos site Siphoviridae , respectively. Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species. The attachment sites were determined for all these prophage elements; LgaI as well as Sal1 integrates in tRNA genes, while prophage Sal2 integrates in a predicted arginino-succinate lyase-encoding gene. In contrast, Lca1 and the Sal3 and Sal4 prophage remnants are integrated in noncoding regions in the L. casei ATCC 334 and L. salivarius UCC 118 genomes. Northern analysis showed that large parts of the prophage genomes are transcriptionally silent and that transcription is limited to genome segments located near the attachment site. Finally, pulsed-field gel electrophoresis followed by Southern blot hybridization with specific prophage probes indicates that these prophage sequences are narrowly distributed within lactobacilli. |
| Author | Claesson, Marcus J van Sinderen, Douwe Fitzgerald, Gerald F Barrangou, Rodolphe Altermann, Eric Klaenhammer, Todd R Broadbent, Jeff Li, Yin Bernini, Valentina Walker, Carey D Neviani, Erasmo Leahy, Sinead Zink, Ralf Canchaya, Carlos Steele, Jim Ventura, Marco McGrath, Stephen O'Toole, Paul W |
| AuthorAffiliation | Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland, 1 Department of Genetics, Anthropology and Evolution, University of Parma, Parma, Italy, 2 Genomic Sciences Program and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, North Carolina, 3 Chr. Hansen, Milwaukee, Wisconsin, 4 Department of Nutrition and Health, Cognis, Dusseldorf, Germany, 5 Department of Food Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 6 Department of Nutrition and Food Sciences, Utah State University, Logan, Utah 7 |
| AuthorAffiliation_xml | – name: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland, 1 Department of Genetics, Anthropology and Evolution, University of Parma, Parma, Italy, 2 Genomic Sciences Program and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, North Carolina, 3 Chr. Hansen, Milwaukee, Wisconsin, 4 Department of Nutrition and Health, Cognis, Dusseldorf, Germany, 5 Department of Food Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 6 Department of Nutrition and Food Sciences, Utah State University, Logan, Utah 7 |
| Author_xml | – sequence: 1 fullname: Ventura, Marco – sequence: 2 fullname: Canchaya, Carlos – sequence: 3 fullname: Bernini, Valentina – sequence: 4 fullname: Altermann, Eric – sequence: 5 fullname: Barrangou, Rodolphe – sequence: 6 fullname: McGrath, Stephen – sequence: 7 fullname: Claesson, Marcus J – sequence: 8 fullname: Li, Yin – sequence: 9 fullname: Leahy, Sinead – sequence: 10 fullname: Walker, Carey D – sequence: 11 fullname: Zink, Ralf – sequence: 12 fullname: Neviani, Erasmo – sequence: 13 fullname: Steele, Jim – sequence: 14 fullname: Broadbent, Jeff – sequence: 15 fullname: Klaenhammer, Todd R – sequence: 16 fullname: Fitzgerald, Gerald F – sequence: 17 fullname: O'Toole, Paul W – sequence: 18 fullname: van Sinderen, Douwe |
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| Keywords | Lactic acid bacteria Lactobacillus casei Transcription Genomics Bacteria Lactobacillaceae Genome Comparative study Lactobacillus salivarius Provirus Lactobacillus gasseri |
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| Notes | http://aem.asm.org/contents-by-date.0.shtml ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Corresponding author. Mailing address: Department of Genetics, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11/a, 43100 Parma, Italy. Phone: 39 521 906236. Fax: 39 521 905604. E-mail: marco.ventura@unipr.it. |
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| Snippet | Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2,... Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit... Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2,... |
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| SubjectTerms | Animals Bacteria bacteriophages Base Sequence Biological and medical sciences cheese starters DNA Evolutionary and Genomic Microbiology Fundamental and applied biological sciences. Psychology genes genetic recombination Genetics Genome, Bacterial Genome, Viral Genomics Humans Hybridization intestinal microorganisms Lactobacillus - genetics Lactobacillus - virology Lactobacillus casei Lactobacillus casei - virology Lactobacillus gasseri Lactobacillus salivarius Lactobacillus salivarius subsp. salivarius messenger RNA Microbiology Molecular Sequence Data nucleotide sequences Phylogeny prophage integration sites prophage sequences prophages Prophages - classification Prophages - genetics Prophages - isolation & purification Prophages - metabolism Ribonucleic acid RNA Sequence Analysis, DNA Siphoviridae Siphoviridae - classification Siphoviridae - genetics Siphoviridae - isolation & purification Siphoviridae - metabolism transcription (genetics) Transcription, Genetic Viral Proteins - genetics Viral Proteins - metabolism |
| Title | Comparative Genomics and Transcriptional Analysis of Prophages Identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei |
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