The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9

Standards in Genomic Sciences
William J KellyEric Altermann

Abstract

Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan cow grazing a ryegrass/clover pasture, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. The 2.45 Mb BRM9 chromosome has an average G + C content of 41%, and encodes 2,352 protein-coding genes. The genes involved in methanogenesis are comparable to those found in other members of the Methanobacteriaceae with the exception that there is no [Fe]-hydrogenase dehydrogenase (Hmd) which links the methenyl-H4MPT reduction directly with the oxidation of H2. Compared to the rumen Methanobrevibacter strains, BRM9 has a much larger complement of genes involved in determining oxidative stress response, signal transduction and nitrogen fixation. BRM9 also has genes for the biosynthesis of the compatible solute ectoine that has not been reported to be produced by methanogens. The BRM9 genome has a prophage and two CRISPR repeat regions. Comparison to the genomes of other Methanobacterium strains shows a core genome of ~1,350 coding sequences and 190 strain-specific genes in BRM9, most of which are hypothetical proteins or prophage related.

References

Jun 1, 1979·Microbiological Reviews·W E BalchR S Wolfe
Feb 1, 1975·Canadian Journal of Microbiology·J G Zeikus, V G Bowen
Jan 1, 1992·Canadian Journal of Microbiology·K F JarrellM L Kalmokoff
Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·C R WoeseM L Wheelis
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 1, 1968·Journal of Bacteriology·K F LangenbergR S Wolfe
Mar 1, 1993·Nature Genetics·W Gish, D J States
Jan 27, 1999·Bioinformatics·S R Eddy
Jun 5, 1999·Microbiology and Molecular Biology Reviews : MMBR·B L Taylor, I B Zhulin
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Mar 8, 2000·Current Microbiology·G N JarvisK N Joblin
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Sep 26, 2003·Omics : a Journal of Integrative Biology·Eric Altermann, Todd R Klaenhammer
Aug 1, 1990·Applied and Environmental Microbiology·K N JoblinA G Williams
Oct 31, 2006·Journal of Bacteriology·Sunna HelgadóttirDavid E Graham
Apr 22, 2008·Applied and Environmental Microbiology·Peter H Janssen, Marek Kirs
May 10, 2008·Nature Biotechnology·Dawn FieldAnil Wipat
Jul 25, 2009·International Journal of Systematic and Evolutionary Microbiology·William M MoeFred A Rainey
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Dec 1, 2011·Nucleic Acids Research·Marco PuntaRobert D Finn
Jul 1, 2010·Animal : an International Journal of Animal Bioscience·M ClaussJ Hummel
Nov 6, 2012·Nucleic Acids Research·Sarah W BurgeAlex Bateman
Nov 30, 2012·Nucleic Acids Research·UNKNOWN NCBI Resource Coordinators
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Dec 1, 2012·Nucleic Acids Research·Daniel H HaftErin Beck
Jun 14, 2013·Animal : an International Journal of Animal Bioscience·S C LeahyG T Attwood
Jun 14, 2013·Animal : an International Journal of Animal Bioscience·D N WedlockB M Buddle
Aug 31, 2013·Standards in Genomic Sciences·S C LeahyG T Attwood
Jan 23, 2014·International Journal of Systematic and Evolutionary Microbiology·Hinsby Cadillo-QuirozStephen H Zinder

❮ Previous
Next ❯

Citations

Sep 30, 2020·Critical Reviews in Microbiology·Satish KumarYogesh Shouche
Sep 29, 2015·Standards in Genomic Sciences·Suzanne C LambieEric Altermann
Jun 28, 2019·The ISME Journal·Chris GreeningRoderick I Mackie
Mar 17, 2016·Standards in Genomic Sciences·William J KellySinead C Leahy
Dec 14, 2018·Archives of Virology·Sandro WolfMichael Rother
Aug 19, 2016·Standards in Genomic Sciences·William J KellySinead C Leahy
Apr 11, 2020·Frontiers in Microbiology·Rosalind A GilbertEleanor Jameson
May 14, 2021·Nature Reviews. Microbiology·Itzhak MizrahiSarah Moraïs
Oct 15, 2020·Microorganisms·Gonzalo Martinez-FernandezChristopher S McSweeney

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP006933

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

MIGS
Glimmer
SignalP
BLASTN
ARTEMIS
TMHMM
INFERNAL
BLASTP
BLAST
HMMER

Related Concepts

Related Feeds

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.