Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW

Molecular Omics
Yunhai ShaoWeihong Zhong

Abstract

A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively. XJLW has a chromosome DNA and a mega-plasmid DNA. Ten percent of genes on chromosome DNA are strain-specific in genus Methylobacterium. Transcriptome analysis results showed that 623 genes were significantly up-regulated and that 207 genes were significantly down-regulated for growth in methanol. Among the up-regulated genes, 90 genes belong to strain-specific regions and are densely distributed in three areas. A specific gene (A3862_27225) annotated as methyltransferase was found ranking in the top 4 of up-regulated genes. This methyltransferase may play a role in the spec...Continue Reading

References

May 1, 1990·Applied Microbiology and Biotechnology·N AdroerC Solà
Nov 1, 1970·Journal of General Microbiology·A J Lawrence, J R Quayle
Jan 22, 2005·PLoS Biology·Christopher J MarxMary E Lidstrom
Mar 3, 2007·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Christoph MeierRobert M Esnouf
Mar 24, 2007·Science·Rodolphe BarrangouPhilippe Horvath
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Mar 6, 2009·Proceedings of the National Academy of Sciences of the United States of America·Rémi PeyraudJulia A Vorholt
Aug 27, 2016·Nature Microbiology·Madeline C WeissWilliam F Martin
May 5, 2017·Nucleic Acids Research·Claire BertelliFiona Sl Brinkman

❮ Previous
Next ❯

Citations

Mar 17, 2020·Applied Microbiology and Biotechnology·Yunhai ShaoWeihong Zhong
Apr 12, 2019·Applied Biochemistry and Biotechnology·Yunhai ShaoWeihong Zhong

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX5008686
SRX5008655

Methods Mentioned

BETA
electrophoresis
RNA Assay
RNA-Seq
dissection

Software Mentioned

Tophat2
IslandViewer
HGAP Assembly
VRprofile
ISsaga
IslandViewer4
BLAST
- Finder
CRISPR
KEGG

Related Concepts

Related Feeds

Bioremediation (ASM)

Bioremediation is the treatment and removal of harmful pollutants or contaminants through the use of microorganisms. Discover the latest research here.