The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

[1]  S. Jonjić,et al.  Modulation of natural killer cell activity by viruses. , 2010, Current opinion in microbiology.

[2]  S. Spring,et al.  Complete genome sequence of Thermosphaera aggregans type strain (M11TLT) , 2010, Standards in genomic sciences.

[3]  H. Klenk,et al.  En route to a genome-based classification of Archaea and Bacteria? , 2010, Systematic and applied microbiology.

[4]  Natalia N. Ivanova,et al.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.

[5]  Lynne A. Goodwin,et al.  Complete genome sequence of Haloterrigena turkmenica type strain (4kT) , 2010, Standards in genomic sciences.

[6]  H. Hemmi,et al.  Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. , 2010, Biochemical and biophysical research communications.

[7]  Nicole R. Buan,et al.  Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase , 2010, Molecular microbiology.

[8]  S. Ragsdale,et al.  Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in Methanosarcina mazei , 2009, Journal of bacteriology.

[9]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[10]  L. Rohlin,et al.  Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A , 2010, BMC Microbiology.

[11]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[12]  A. Guss,et al.  Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri , 2009, Proceedings of the National Academy of Sciences.

[13]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[14]  Sean D. Hooper,et al.  Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens , 2009, PloS one.

[15]  Karen Willcox,et al.  Kinetics and kinematics for translational motions in microgravity during parabolic flight. , 2009, Aviation, space, and environmental medicine.

[16]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[17]  A. Guss,et al.  Differences in Hydrogenase Gene Expression between Methanosarcina acetivorans and Methanosarcina barkeri , 2009, Journal of bacteriology.

[18]  G. Gottschalk,et al.  RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea* , 2009, Journal of Biological Chemistry.

[19]  N. Pace,et al.  Diversity and Stratification of Archaea in a Hypersaline Microbial Mat , 2008, Applied and Environmental Microbiology.

[20]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[21]  K. Schleifer,et al.  The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. , 2008, Systematic and applied microbiology.

[22]  Y. Koga,et al.  A dendrogram of archaea based on lipid component parts composition and its relationship to rRNA phylogeny. , 2008, Systematic and applied microbiology.

[23]  Anne-Kristin Kaster,et al.  Methanogenic archaea: ecologically relevant differences in energy conservation , 2008, Nature Reviews Microbiology.

[24]  O. Gascuel,et al.  An improved general amino acid replacement matrix. , 2008, Molecular biology and evolution.

[25]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[26]  W. Whitman,et al.  Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea , 2008, Annals of the New York Academy of Sciences.

[27]  V. Müller,et al.  The coupling ion in the methanoarchaeal ATP synthases: H(+) vs. Na(+) in the A(1)A(o) ATP synthase from the archaeon Methanosarcina mazei Gö1. , 2007, FEMS microbiology letters.

[28]  J. Chun,et al.  EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. , 2007, International journal of systematic and evolutionary microbiology.

[29]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[30]  D. Maeder,et al.  The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes , 2006, Journal of bacteriology.

[31]  Qingbo Li,et al.  Electron Transport in the Pathway of Acetate Conversion to Methane in the Marine Archaeon Methanosarcina acetivorans , 2006, Journal of bacteriology.

[32]  W. F. Fricke,et al.  The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis , 2006, Journal of bacteriology.

[33]  J. Krzycki.  The direct genetic encoding of pyrrolysine. , 2005, Current opinion in microbiology.

[34]  D. Canfield,et al.  Community Composition of a Hypersaline Endoevaporitic Microbial Mat , 2005, Applied and Environmental Microbiology.

[35]  T. Swartz,et al.  The Mrp system: a giant among monovalent cation/proton antiporters? , 2005, Extremophiles.

[36]  T. Hansen.  Bergey's Manual of Systematic Bacteriology , 2005 .

[37]  I. Booth,et al.  Gating the bacterial mechanosensitive channels: MscS a new paradigm? , 2004, Current opinion in microbiology.

[38]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[39]  U. Deppenmeier.  The Membrane-Bound Electron Transport System of Methanosarcina Species , 2004, Journal of bioenergetics and biomembranes.

[40]  H. Harmsen,et al.  Taxonomic description of Methanococcoides euhalobius and its transfer to the Methanohalophilus genus , 1997, Antonie van Leeuwenhoek.

[41]  H. Cypionka,et al.  Influence of oxygen on sulfate reduction and growth of sulfate-reducing bacteria , 1993, Archives of Microbiology.

[42]  D. B. Nedwell,et al.  Inhibition of methanogenesis by sulphate reducing bacteria competing for transferred hydrogen , 1978, Archives of Microbiology.

[43]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[44]  Paramvir S. Dehal,et al.  Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. , 2003, Genome research.

[45]  Olivier Poch,et al.  RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments , 2003, Bioinform..

[46]  R. Overbeek,et al.  The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. , 2002, Journal of molecular microbiology and biotechnology.

[47]  Robert H. White,et al.  Identification of Coenzyme M Biosynthetic Phosphosulfolactate Synthase , 2002, The Journal of Biological Chemistry.

[48]  Robert H. White,et al.  The genome of M. acetivorans reveals extensive metabolic and physiological diversity. , 2002, Genome research.

[49]  Robert H. White,et al.  Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. , 2002, Natural product reports.

[50]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[51]  G. Gottschalk,et al.  The Na(+)-translocating methyltransferase complex from methanogenic archaea. , 2001, Biochimica et biophysica acta.

[52]  G. Gottschalk,et al.  The F420H2 Dehydrogenase fromMethanosarcina mazei Is a Redox-driven Proton Pump Closely Related to NADH Dehydrogenases* , 2000, The Journal of Biological Chemistry.

[53]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[54]  H. Kumagai,et al.  The rnf gene products in Rhodobacter capsulatus play an essential role in nitrogen fixation during anaerobic DMSO-dependent growth in the dark , 1998, Archives of Microbiology.

[55]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[56]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[57]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[58]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[59]  R. Gunsalus,et al.  Halotolerance in Methanosarcina spp.: Role of N(sup(epsilon))-Acetyl-(beta)-Lysine, (alpha)-Glutamate, Glycine Betaine, and K(sup+) as Compatible Solutes for Osmotic Adaptation , 1995, Applied and environmental microbiology.

[60]  C. Woese,et al.  Transfer of Methanolobus siciliae to the genus Methanosarcina, naming it Methanosarcina siciliae, and emendation of the genus Methanosarcina. , 1994, International journal of systematic bacteriology.

[61]  Y. Koga,et al.  Taxonomic Significance of the Distribution of Component Parts of Polar Ether Lipids in Methanogens , 1993 .

[62]  Z. Yang,et al.  Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. , 1993, Molecular biology and evolution.

[63]  D. Boone,et al.  Isolation and Characterization of Methanohalophilus portucalensis sp. nov. and DNA Reassociation Study of the Genus Methanohalophilus , 1993 .

[64]  R. Gunsalus,et al.  Biosynthetic pathways of the osmolytes N epsilon-acetyl-beta-lysine, beta-glutamine, and betaine in Methanohalophilus strain FDF1 suggested by nuclear magnetic resonance analyses , 1992, Journal of bacteriology.

[65]  D. E. Robertson,et al.  Composition, Variation, and Dynamics of Major Osmotic Solutes in Methanohalophilus Strain FDF1 , 1992, Applied and environmental microbiology.

[66]  D. Boone,et al.  Isolation and characterization of a dimethyl sulfide-degrading methanogen, Methanolobus siciliae HI350, from an oil well, characterization of M. siciliae T4/MT, and emendation of M. siciliae. , 1991, International journal of systematic bacteriology.

[67]  J. Paterek,et al.  Methanohalophilus mahii gen. nov., sp. nov., a Methylotrophic Halophilic Methanogen† , 1988 .

[68]  J. Paterek,et al.  Isolation and Characterization of a Halophilic Methanogen from Great Salt Lake , 1985, Applied and environmental microbiology.

[69]  R. Oremland,et al.  Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. , 1982, Applied and environmental microbiology.

[70]  M. Lai,et al.  Biosynthetic Pathways of the Osmolytes N-Acetyl-p-Lysine, 13-Glutamine, and Betaine in Methanohalophilus Strain FDF1 Suggested by Nuclear Magnetic Resonance Analyses , 2022 .