The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics
Summary We analysed the cold‐responsive gene repertoire for a psychrophilic methanogen, Methanolobus psychrophilus R15 through genomic and RNA‐seq assayed transcriptomic comparisons for cultures at 18°C (optimal temperature) versus 4°C. The differences found by RNA‐seq analysis were verified using q...
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Published in | Environmental microbiology reports Vol. 4; no. 6; pp. 633 - 641 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Blackwell Publishing Ltd
01.12.2012
John Wiley & Sons, Inc |
Subjects | |
Online Access | Get full text |
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Summary: | Summary
We analysed the cold‐responsive gene repertoire for a psychrophilic methanogen, Methanolobus psychrophilus R15 through genomic and RNA‐seq assayed transcriptomic comparisons for cultures at 18°C (optimal temperature) versus 4°C. The differences found by RNA‐seq analysis were verified using quantitative real time‐PCR assay. The results showed that as in the Antarctic methanogen, Methanococcoides burtonii, genes for methanogenesis, biosynthesis and protein synthesis were all downregulated by the cold in R15. However, the RNA polymerase complex was upregulated at cold, as well as a gene cluster for a putative exosome complex, suggesting that exosome‐mediated RNA decay may be cold‐accelerated. Unexpectedly, the chaperonin genes for both thermosome and GroES/EL were all upregulated at 4°C. Strain R15 possessed eight protein families for oxygen detoxification, including both anaerobe‐specific superoxide reductase (SOR) and the aerobe‐typical superoxide dismutase (SOD)‐catalase oxidant‐removing system, implying the higher oxidative tolerance. Compared with a mesophilic methanogen, R15 survived in higher paraquat, a redox‐cycling drug. Moreover, 71 one‐component systems and 50 two‐component systems for signal transduction ranked strain R15, together with M. burtonii, as being highly adaptive among archaea. Most of them exhibited cold‐enhanced expression, indicating their involvement in cold adaptation. This study has added new perspectives on the cold adaptation of methanogenic archaea. |
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Bibliography: | National Natural Science foundation of China - No. 30621005, 30830007 and 31000011 ark:/67375/WNG-2FT7HZ8R-Q Fig. S1. Correlation analysis of RNA-seq and qRT-PCR. A. correlation coefficient of fold changes between RNA-seq and qRT-PCR. B. correlation coefficient of fold changes between two batches of qRT-PCR.Table S1. Overview of the genome of R15 and the expression profiles of the genes.Table S2. Operon map of Methanolobus psychrophilus R15.Table S3. Verification of the transcriptomic data of 16 genes using qRT-PCR.Table S4. Differential transcript abundance of the genes for methanogenesis and biosynthesis from the cultures growing at 4°C versus 18°C.Table S5. Differential transcript abundance of genes for protein translation and processing from the cultures growing at 4°C versus 18°C.Table S6. Differential transcript abundance of genes for transcription and RNA processing from the cultures growing at 4°C versus 18°C.Table S7. Distribution of the oxygen detoxification genes in the available methanogen genomes.Table S8. Differential transcript abundance of the genes for antioxidation from the cultures growing at 4°C versus 18°C.Table S9. Signal transduction systems distributed in the genomes of the archaea growing at various temperatures.Table S10. Signal transduction systems in the genome of strain R15 and their temperature-responsive expression. ArticleID:EMI4389 istex:C4755E61691DC464E27534B5F73DA48B34545EF5 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1758-2229 1758-2229 |
DOI: | 10.1111/j.1758-2229.2012.00389.x |