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DNA microarray analysis of Methanosarcina mazei Gö1 reveals adaptation to different methanogenic substrates

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Abstract

Methansarcina mazei Gö1 DNA arrays were constructed and used to evaluate the genomic expression patterns of cells grown on either of two alternative methanogenic substrates, acetate or methanol, as sole carbon and energy source. Analysis of differential transcription across the genome revealed two functionally grouped sets of genes that parallel the central biochemical pathways in, and reflect many known features of, acetate and methanol metabolism. These include the acetate-induced genes encoding acetate activating enzymes, acetyl-CoA synthase/CO dehydrogenase, and carbonic anhydrase. Interestingly, additional genes expressed at significantly higher levels during growth on acetate included two energy-conserving complexes (the Ech hydrogenase, and the A1A0-type ATP synthase). Many previously unknown features included the induction by acetate of genes coding for ferredoxins and flavoproteins, an aldehyde:ferredoxin oxidoreductase, enzymes for the synthesis of aromatic amino acids, and components of iron, cobalt and oligopeptide uptake systems. In contrast, methanol-grown cells exhibited elevated expression of genes assigned to the methylotrophic pathway of methanogenesis. Expression of genes for components of the translation apparatus was also elevated in cells grown in the methanol medium relative to acetate, and was correlated with the faster growth rate observed on the former substrate. These experiments provide the first comprehensive insight into substrate-dependent gene expression in a methanogenic archaeon. This genome-wide approach, coupled with the complementary molecular and biochemical tools, should greatly accelerate the exploration of Methanosarcina cell physiology, given the present modest level of our knowledge of these large archaeal genomes.

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References

  • Abbanat DR, Ferry JG (1991) Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA. Proc Natl Acad Sci USA 88:3272–3276

    Google Scholar 

  • Aceti DJ, Ferry JG (1988) Purification and characterization of acetate kinase from acetate-grown Methanosarcina thermophila: evidence for regulation of synthesis. J Biol Chem 263:15444–15448

    Google Scholar 

  • Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P, Guest JR (1997) A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system. Microbiology 143:3633–3647

    Google Scholar 

  • Augstein A, Barth K, Gentsch M, Kohlwein SD, Barth G (2003) Characterization, localization and functional analysis of Gpr1p, a protein affecting sensitivity to acetic acid in the yeast Yarrowia lipolytica. Microbiology 149:589–600

    Google Scholar 

  • Bäumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier U (2000) The F420H2 dehydrogenase from Methanosarcina mazei Gö1 is a redox-driven proton pump closely related to NADH dehydrogenases. J Biol Chem 275:17968–17973

    Google Scholar 

  • Böhm R, Sauter M, Böck A (1990) Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Mol Microbiol 4:231–243

    Google Scholar 

  • Brown NL, Stoyanov JV, Kidd SP, Hobman JL (2003) The MerR family of transcriptional regulators. FEMS Microbiol Rev 27:145–163

    Google Scholar 

  • Brüggemann H, Falinski F, Deppenmeier U (2000) The F420H2:quinone oxidoreductase of Archaeoglobus fulgidus: identification and overproduction of the F420H2-oxidizing subunit. Eur J Biochem 267:5810–5814

    Google Scholar 

  • Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609–640

    CAS  PubMed  Google Scholar 

  • Crouzet J, Levy-Schil S, Cameron B, Cauchois L, Rigault S, Rouyez MC, Blanche F, Debussche L, Thibaut D (1991) Nucleotide sequence and genetic analysis of a 131-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyl-transferase, cobyric acid synthase, and bifunctional cobinamide kinase-cobinamide phosphate guanylyltransferase. J Bacteriol 173:6074–6087

    Google Scholar 

  • Debussche L, Couder M, Thibaut D, Cameron B, Crouzet J, Blanche F (1992) Assay, purification and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans. J Bacteriol 174:7445–7451

    Google Scholar 

  • Demeyer D, Fievez V (2000) Ruminants and environment: methanogenesis. Ann Zootechnie 49:95–112

    Google Scholar 

  • Deppenmeier U (2002a) The unique biochemistry of methanogenesis. Prog Nucleic Acids Res 71:223–283

    Google Scholar 

  • Deppenmeier U (2002b) Redox-driven proton translocation in methanogenic Archaea. Cell Mol Life Sci 59:1–21

    Google Scholar 

  • Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R et al (2002) The genome of Methanosarcina mazei : evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461

    CAS  PubMed  Google Scholar 

  • Ding YH, Zhang SP, Tomb JF, Ferry JG (2002) Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila. FEMS Microbiol Lett 215:127–132

    Google Scholar 

  • Eggen RIL, VanKranenburg R, Vriesema AJM, Geerling ACM, Verhagen MFJM, Hagen WR, de Vos WM (1996) Carbon monoxide dehydrogenase from Methanosarcina frisia Gö1. Characterization of the enzyme and the regulated expression of two operon-like cdh gene clusters. J Biol Chem 271:14256–14263

    Google Scholar 

  • Ferry RG (1997) Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila. Biofactors 6:25–35

    CAS  PubMed  Google Scholar 

  • Ferry RG (1999) Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol Rev 23:13–38

    Google Scholar 

  • Fox JD, Kerby RL, Roberts GP, Ludden PW (1996) Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme. J Bacteriol 178:1515–1521

    Google Scholar 

  • Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh WS et al (2002) The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532–542

    Article  CAS  PubMed  Google Scholar 

  • Galperin MY, Nikolskaya AN, Koonin EV (2001) Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett 203:11–21

    Google Scholar 

  • Grahame DA (2003) Acetate C–C bond formation and decomposition in the anaerobic world: the structure of a central enzyme and its key active-site metal cluster. Trends Biochem Sci 28:221–224

    Google Scholar 

  • Hedderich R, Klimmek O, Kröger A, Dirmeier R, Keller M, Stetter KO (1998) Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiol Rev 22:353–381

    Google Scholar 

  • Hedge P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29:548–550

    Google Scholar 

  • Hippe H, Caspari D, Fiebig K, Gottschalk G (1979) Utilization of trimethylamine and other N-methyl compounds for growth and methane formation by Methanosarcina barkeri . Proc Natl Acad Sci USA 76:494–498

    CAS  PubMed  Google Scholar 

  • Hüser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Pühler A, Wiegräbe I, Tauch A (2003) Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. J Biotechnol 106:269–286

    Google Scholar 

  • Ide T, Bäumer S, Deppenmeier U (1999) Energy conservation by the H2:heterodisulfide oxidoreductase from Methanosarcina mazei Gö1: identification of two proton-translocating segments. J Bacteriol 181:4076–4080

    Google Scholar 

  • Jablonski PE, Dimarco AA, Bobik TA, Cabell MC, Ferry JG (1990) Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila. J Bacteriol 172:1271–1275

    Google Scholar 

  • Keltjens JT, Vogels GD (1993) Conversion of methanol and methylamines to methane and carbon dioxide. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman and Hall, New York, pp 253–303

    Google Scholar 

  • Lange C, Rittmann D, Wendisch VF, Bott M, Sahm H (2003) Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl Environ Microbiol 69:2521–2532

    Google Scholar 

  • Lee MLT, Kuo FC, Whitmore GA, Sklar J (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Nat Soc Sci USA 97:9834–9839

    Google Scholar 

  • Lindahl PA (2002) The Ni-containing carbon monoxide dehydrogenase family: light at the end of the tunnel? Biochemistry 41:2097–2105

    Article  CAS  PubMed  Google Scholar 

  • Lundie LL, Ferry JG (1989) Activation of acetate by Methanosarcina thermophila—purification and characterization of phosphotransacetylase. J Biol Chem 264:18392–18396

    Google Scholar 

  • Maupin-Furlow J, Ferry JG (1996) Characterization of the cdhD and cdhE genes encoding subunits of the corrinoid/iron-sulfur enzyme of the CO dehydrogenase complex from Methanosarcina thermophila. J Bacteriol 178:340–346

    Google Scholar 

  • Mayer F, Jussofie A, Salzmann M, Lübben M, Rohde M, Gottschalk G (1987) Immunoelectron microscopic demonstration of ATPase on the cytoplasmic membrane of the methanogenic bacterium strain Gö1. J Bacteriol 169:2307–2309

    Google Scholar 

  • Meuer J, Bartoschek S, Koch J, Künkel A, Hedderich R (1999) Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri. Eur J Biochem 265:325–335

    Google Scholar 

  • Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc Natl Acad Sci USA 99:5632–5637

    Google Scholar 

  • Michel R, Massanz C, Kostka S, Richter M, Fiebig K (1995) Biochemical characterization of the 8-hydroxy-5-deazaflavin-reactive hydrogenase from Methanosarcina barkeri Fusaro. Eur J Biochem 233:727–735

    Google Scholar 

  • Müller V, Gruber G (2003) ATP synthases: structure, function and evolution of unique energy converters. Cell Mol Life Sci 60:474–494

    Google Scholar 

  • Müller V, Blaut M, Gottschalk G (1993) Bioenergetics of methanogenesis. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman and Hall, New York, pp 361–406

    Google Scholar 

  • Musfeldt M, Selig M, Schönheit P (1999) Acetyl coenzyme A synthetase (ADP forming) from the hyperthermophilic archaeon Pyrococcus furiosus: identification, cloning, separate expression of the encoding genes, acdAI and acdBI, in Escherichia coli, and in vitro reconstitution of the active heterotetrameric enzyme from its recombinant subunits. J Bacteriol 181:5885–5888

    CAS  PubMed  Google Scholar 

  • Paul L, Ferguson DJ, Krzycki JA (2000) The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. J Bacteriol 182:2520–2529

    Google Scholar 

  • Rajeevan MS, Vernon SD, Taysavang N, Unger ER (2001) Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J Mol Diagnostics 1:26–31

    Google Scholar 

  • Raux E, Schubert HL, Warren MJ (2000) Biosynthesis of cobalamin (vitamin B-12): a bacterial conundrum. Cell Mol Life Sci 57:1880–1893

    Google Scholar 

  • Saier MH, Ramseier TM, Reizer J (1996) Regulation of carbon utilization. In: Neidhardt FC, Curtiss R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, pp 1325–1343

    Google Scholar 

  • Sauter M, Böhm R, Böck A (1992) Mutational analysis of the operon (hyc) determining hydrogenase-3 formation in Escherichia coli. Mol Microbiol 6:1523–1532

    Google Scholar 

  • Singh-Wissmann K, Ferry JG (1995) Transcriptional regulation of the phosphotransacetylase-encoding and acetate kinase-encoding genes (pta and ack) from Methanosarcina thermophila. J Bacteriol 177:1699–1702

    Google Scholar 

  • Smith MW, Neidhardt FC (1983a) Proteins induced by aerobiosis in Escherichia coli. J Bacteriol 154:344–350

    Google Scholar 

  • Smith MW, Neidhardt FC (1983b) Proteins induced by anaerobiosis in Escherichia coli. J Bacteriol 154:336–343

    CAS  PubMed  Google Scholar 

  • Sowers KR, Thai TT, Gunsalus RP (1993) Transcriptional regulation of the carbon monoxide dehydrogenase gene (cdhA) in Methanosarcina thermophila. J Biol Chem 268:23172–23178

    Google Scholar 

  • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440–9445

    Google Scholar 

  • Tallant TC, Krzycki JA (1997) Methylthiol:coenzyme M methyltransferase from Methanosarcina barkeri, an enzyme of methanogenesis from dimethylsulfide and methylmercaptopropionate. J Bacteriol 179:6902–6911

    Google Scholar 

  • Tao H, Bausch C, Richmond C, Blattner FR, Conway T (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181:6425–6440

    CAS  PubMed  Google Scholar 

  • Taylor BL, Zhulin IB, Johnson MS (1999) Aerotaxis and other energy-sensing behavior in bacteria. Annu Rev Microbiol 53:103–128

    Article  CAS  PubMed  Google Scholar 

  • Terlesky K, Nelson MJK, Ferry JG (1986) Isolation of an enzyme complex with carbon monoxide dehydrogenase activity containing corrinoid and nickel from acetate-grown Methanosarcina thermophila. J Bacteriol 168:1053–1058

    Google Scholar 

  • Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144:2377–2406

    CAS  PubMed  Google Scholar 

  • Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29:2549–2557

    Google Scholar 

  • Tusher V, Tibshirani R, Chu C (2001) Significance analysis of microarrays applied to ionizingradiation response. Proc Natl Acad Sci USA 98:5116–5121

    Article  Google Scholar 

  • Vorholt JA, Thauer RK (1997) The active species of ’CO2’ utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. Eur J Biochem 248:919–924

    Google Scholar 

  • Vorholt JA, Vaupel M, Thauer RK (1996) A polyferredoxin with eight [4Fe-4S] clusters as a subunit of molybdenum formylmethanofuran dehydrogenase from Methanosarcina barkeri. Eur J Biochem 236:309–317

    Google Scholar 

  • Westenberg DJ, Braune A, Ruppert C, Müller V, Herzberg C, Gottschalk G, Blaut M (1999) The F420H2-dehydrogenase from Methanolobus tindarius: cloning of the ffd operon and expression of the genes in Escherichia coli. FEMS Microbiol Lett 170:389–398

    Google Scholar 

  • Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL (2001) Model-based clustering and data transformations for gene expression data. Bioinformatics 17:977–987

    Google Scholar 

  • Zhulin IB, Taylor BL, Dixon R (1997) PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Trends Biochem Sci 22:331–333

    Google Scholar 

  • Zinder SH (1993) Physiological ecology of methanogens. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman and Hall, New York, pp 128–206

    Google Scholar 

  • Zinder SH, Elias AF (1985) Growth substrate effects on acetate and methanol catabolism in Methanosarcina sp. strain TM-1. J Bacteriol 163:317–323

    Google Scholar 

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Acknowledgements

The authors thank Arnim Wiezer, Dr. Anke Henne, Dr. Heiko Liesegang (Göttingen Genomics Laboratory), and Dr. Ruth Schmitz (Dept. of General Microbiology, University of Göttingen) for support in producing the DNA arrays and for stimulating discussions. The work was supported by grants from the Deutsche Forschungsgemeinschaft (Grant No. De488/7-2) to U. Deppenmeier), the U.S. Department of Energy (DOE; Grant No. DE-FG03-86ER13498) to R. P. Gunsalus, and the Ministry for Science and Culture of the State of Lower Saxony to the Göttingen Genomics Laboratory, and by funds provided to the Competence Network Göttingen “Genome Research on Bacteria” by the German Federal Ministry of Education and Research (BMBF) (to G. Gottschalk)

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Authors and Affiliations

  1. Department of Biological Sciences, University of Wisconsin-Milwaukee, N. Maryland Ave, 3209, Milwaukee, WI, 53211, USA

    Raymond Hovey & Uwe Deppenmeier

  2. Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Gottingen, Germany

    Sabine Lentes

  3. Göttingen Genomics Laboratory and Competence Centre for Genome Research on Bacteria, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, 37077, Gottingen, Germany

    Armin Ehrenreich & Gerhard Gottschalk

  4. Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095-1489, USA

    Kirsty Salmon, Karla Saba & Robert P. Gunsalus

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  1. Raymond Hovey
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  2. Sabine Lentes
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  3. Armin Ehrenreich
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Correspondence to Uwe Deppenmeier.

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Hovey, R., Lentes, S., Ehrenreich, A. et al. DNA microarray analysis of Methanosarcina mazei Gö1 reveals adaptation to different methanogenic substrates. Mol Genet Genomics 273, 225–239 (2005). https://doi.org/10.1007/s00438-005-1126-9

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