Summary
DNA fragments cloned from the methanogenic archaebacterium Methanobrevibacter smithii which complement mutations in the purE and proC genes of E. coli have been sequenced. Sequence analyses, transposon mutagenesis and expression in E. coli minicells indicate that purE and proC complementations result from the synthesis of M. smithii polypeptides with molecular weights of 36,697 and 27,836 respectively. The encoding genes appear to be located in operons. The M. smithii genome contains 69% A/T basepairs (bp) which is reflected in unusual codon usages and intergenic regions containing approximately 85% A/T bp. An insertion element, designated ISM1, was found within the cloned M. smithii DNA located adjacent to the proC complementing region. ISM1 is 1381 bp in length, has 29 bp terminal inverted repeat sequences and contains one major ORF encoded in 87% of the ISM1 sequence. ISM1 is mobile, present in approximately 10 copies per genome and integration duplicates 8 bp at the site of insertion. The duplicated sequences show homology with sequences within the 29bp terminal repeat sequence of ISM1. Comparison of our data with sequences from halophilic archaebacteria suggests that 5′GAANTTTCA and 5′TTTTAATATAAA may be consensus promoter sequences for archaebacteria. These sequences closely resemble the consensus sequences which precede Drosophila heatshock genes (Pelham 1982; Davidson et al. 1983). Methanogens appear to employ the eubacterial system of mRNA: 16SrRNA hybridization to ensure initiation of translation; the consensus ribosome binding sequence is 5′AGGTGA.
References
Balch WE, Wolfe RS (1979) Specificity and biological distribution of coenzyme M (2-mercaptoethanesulfonic acid). J Bacteriol 137:256–263
Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS (1979) Methanogens: Reevaluation of a unique biological group. Microbiol Rev 43:260–296
Bedouelle H, Schmeissner U, Hoenung M, Rosenberg M (1982) Promoters of the malEFG and malK-lamB operons in Escheriachia coli K12. J Mol Biol 161:519–531
Berman ML, Enquist LW, Silhavy TJ (1982) Advanced bacterial genetics 1982. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Betlach M, Pfeifer F, Friedman J, Boyer HW (1983) Bacterio-opsin mutants of Halobacterium halobium. Proc Natl Acad Sci USA 80:1416–1420
Betlach M, Friedman J, Boyer HB, Pfeifer F (1984) Characterization of a halobacterial gene affecting bacterio-opsin gene expression. Nucl Acids Res 12:7949–7959
Cue D, Beckler GS, Reeve JN, Konisky J (1985) Structure and sequence divergence of two archaebacterial genes. Proc Natl Acad Sci USA (in press)
Daniels CJ, Gupta R, Doolittle WF (1985a) Transcription and excision of a large intron in the tRNAtrp gene of an archaebacterium, Halobacterium volcanii. J Biol Chem 260:3132–3134
Daniels CJ, Hofman JD, MacWilliam JG, Doolittle WF, Woese CR, Leuhrsen KR, Fox GE (1985b) Sequence of 5S ribosomal RNA gene regions and their products in the archaebacterium Halobacterium volcanii. Mol Gen Genet 198:270–274
DasSarma S, RajBhandary UL, Khorana HG (1983) High-frequency spontaneous mutation in the bacterio-opsin gene in halobacterium halobium is mediated by transposable elements. Proc Natl Acad Sci USA 80:2201–2205
Davidson EH, Jacobs HT, Britten RJ (1983) Very short repeats and coordinate induction of genes. Nature 301:468–470
Davis RW, Botstein D, Roth JR (1980) Advanced bacterial genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
deBruijn FJ, Lupski JR (1984) The use of transposon Tn5 mutagenesis in the rapid generation of correlated physical and genetic maps of DNA segments cloned into multicopy plasmids — a review. Gene 27:131–149
Deutch AH, Smith CJ, Rushlow KE, Kretschmer PJ (1982) Escherichia coli 1-pyrroline-5-carboxylate reductase: gene sequence, protein overproduction and purification. Nucl Acids Res 10:7701–7714
Dunn R, McCoy J, Simsek M, Majumdar A, Chang SJ, RajBhandary UL, Khorana HG (1981) The bacteriorhodopsin gene. Proc Natl Acad Sci USA 78:6744–6748
Eirich LD, Vogels GD, Wolfe RS (1979) Distribution of coenzyme F420 and properties of its hydrolytic fragments. J Bacteriol 140:20–27
Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci USA 74:4537–4541
Gots JS, Benson CE, Jochimsen B, Koduri KR (1977) Microbial models and regulatory elements in the control of purine metabolism. In: Purine and pyrimidine metabolism, Ciba Foundation Symposium 48. North Holland, Elsevier, Amsterdam, pp 23–41
Hamilton PT, Reeve JN (1984) Cloning and expression of archaebacterial DNA from methanogens in Escherichia coli. In: Strohl WR, Tuovinen OH (eds) Microbial chemoautotrophy. The Ohio State University Press, Columbus, pp 291–307
Holzer G, Oro J, Tornabene TG (1979) Gas chromatographic-mass spectrometric analysis of neutral lipids from methanogenic and thermoacidophilic bacteria. J Chromatogr 186:795–809
Hook LA, Corder RE, Hamilton PT, Frea JI, Reeve JN (1984) Development of a plating system for genetic exchange studies in methanogens using a modified ultra-low oxygen chamber. In: Strohl WR, Touvinen OH (eds) Microbial chemoautotrophy. The Ohio State University Press, Columbus, pp 275–289
Huet J, Schnabel R, Sentenac A, Zillig W (1983) Archaebacteria and eukaryotes possess DNA-dependent RNA polymerase of a common type. EMBO J 2:1291–1294
Hui I, Dennis PP (1985) Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum. J Biol Chem 260:899–906
Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146:1–21
Jarsch M, Altenbuchner J, Böck A (1983) Physical organization of the genes for ribosomal RNA in Methanococcus vannielii. Mol Gen Genet 189:41–47
Kaine BP, Gupta R, Woese CR (1983) Putative introns in the tRNA genes of prokaryotes. Proc Natl Acad Sci USA 80:3309–3312
Kandler O, König H (1978) Chemical composition of the peptidoglycan free cell walls of methanogenic bacteria. Arch Microbiol 118:141–152
Kessel M, Klink F (1980) Archaebacterial elongation factor is ADP-ribosylated by diphtheria toxin. Nature 287:250–251
Klein A, Schnorr M (1984) Genome complexity of methanogenic bacteria. J Bacteriol 158:628–631
Klipp W, Pühler A (1984) Determination of coding regions on multicopy plasmids: Analysis of the chloramphenicol acetyltransferase gene of plasmid pACYC184. In: Pühler A, Timmis KN (eds) Advanced molecular genetics. Springer-Verlag, pp 224–235
Kushner DJ, Onishi H (1968) Absence of normal cell wall constituents from the outer layers of Halobacterium cutirubrum. Can J Biochem 46:997–998
Makula RA, Singer ME (1978) Ether-containing lipids of methanogenic bacteria. Biochem Biophys Res Commun 82:716–722
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Mankin AS, Teterina NL, Rubtsov PM, Baratova LA, Kagramanova VK (1984) Putative promoter region of the rRNA operon from the archaebacterium Halobacterium halobium. Nucl Acids Res 12:6537–6546
Maxam AM, Gilbert W (1980) Sequencing end-labeled DNA with base specific chemical cleavage. Methods Enzymol 65:499–580
Morris CJ, Reeve JN (1984) Functional expression of an archaebacterial gene from the methanogen Methanosarcina barkeri in Escherichia coli and Bacillus subtilis. In: Crawford RL, Hansen RS (eds) Microbial growth on Cl compounds. American Society for Microbiology, Washington DC, pp 205–209
Neumann H, Gierl A, Tu J, Leibrock J, Staiger D, Zillig W (1983) Organization of the genes for ribosomal RNA in archaebacteria. Mol Gen Genet 192:66–72
Pelham HR (1982) A regulatory upstream promoter element in the Drosophila Hsp 70 heat-shock gene. Cell 30:517–528
Reeve JN (1979) Use of minicells for bacteriophage directed polypeptide biosynthesis. Methods Enzymol 68:493–503
Reeve JN, Trun NJ, Hamilton PT (1982) Beginning genetics with methanogens. In: Hollaender A, DeMoss RD, Kaplan S, Konisky J, Savage D, Wolfe RS (eds) Genetic engineering of microorganisms for chemicals. Plenum Publishing, New York, pp 233–244
Rimm DL, Horness D, Kucera J, Blattner FR (1980) Construction of coliphage lambda charon vectors with BamHI cloning sites. Gene 12:301–309
Sapienza C, Doolittle WF (1982) Unusual physical organization of the Halobacterium genome. Nature 295:384–389
Sapienza C, Rose MR, Doolittle WF (1982) High-frequency genomic rearrangements involving archaebacterial repeat sequence elements. Nature 299:182–185
Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342–1346
Simsek M, Das Sarma S, RajBhandary UL, Khorana HG (1982) A transposable element from Halobacterium halobium which inactivates the bacteriorhodopsin gene. Proc Natl Acad Sci USA 79:7268–7272
Steitz JA (1978) Methanogenic bacteria. Nature 273:100–101
Tornabene TG, Langworthy TA (1978) Diphytanyl and dibiphytanyl glycerol ether lipids of methanogenic archaebacteria. Science 203:51–53
Vieira J, Messing J (1982) The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259–268
Weiss RL (1974) Subunit cell wall of Sulfolobus acidocaldarius. J Bacteriol 118:275–284
White A, Handler P, Smith EL, Hill RL, Lehman IR (1978) Principles of biochemistry. McGraw-Hill. Inc New York, pp 861–866
Wich G, Jarsch M, Böck A (1984) Apparent operon for a 5S ribosomal RNA gene and for tRNA genes in the archaebacterium Methanococcus vannielii. Mol Gen Genet 196:146–151
Woese CR, Fox GF (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090
Woese CR, Magrum LJ, Fox GE (1978) Archaebacteria. J Mol Evol 11:245–252
Xu W, Doolittle WF (1983) Structure of the archaebacterial transposable element ISH50. Nucl Acids Res 11:4195–4199
Author information
Authors and Affiliations
Additional information
Communicated by A. Böck
Rights and permissions
About this article
Cite this article
Hamilton, P.T., Reeve, J.N. Structure of genes and an insertion element in the methane producing archaebacterium Methanobrevibacter smithii . Molec. Gen. Genet. 200, 47–59 (1985). https://doi.org/10.1007/BF00383311
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF00383311