1887

Abstract

SUMMARY: Soil bacteria, such as Sinorhizobium meliloti, are subject to variation in environmental conditions, including carbon- and nitrogen-deprivation. The ability of bacteria to sense changes in their environment and respond accordingly is of vital importance to their survival and persistence in the soil and rhizosphere. A derivative of Tn5 which creates transcriptional fusions to the promoterless luxAB genes was used to mutagenize 5. meliloti 1021 and 5000 insertion mutants were subsequently screened for gene fusions induced by selected environmental stresses. The isolation of 21 gene fusions induced by nitrogen-deprivation and 12 induced by carbon-deprivation is described. Cloning and partial DNA sequence analysis of the transposon-tagged loci revealed a variety of novel genes, as well as S. meliloti genes with significant similarity to known bacterial loci. In addition, nodule occupancy studies were carried out with selected TnSluxAB insertion mutants to examine the role of the tagged genes in competition.

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1998-11-01
2024-04-16
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References

  1. Aidoo K.A., Wong A., Alexander D.C., Rittammer R.A., Jensen S.E. 1994; Cloning, sequencing and disruption of a gene from Streptomyces clavuligerus involved in clavulanic acid biosynthesis.. Gene 41:41–46
    [Google Scholar]
  2. Alexander D.M., St John A.C. 1994; Characterization of the carbon starvation-inducible and stationary phase-inducible gene sip encoding an outer membrane lipoprotein in Escherichia coli. . Mol Microbiol 11:1059–1071
    [Google Scholar]
  3. Alexander D.M., Damerau K., St John A.C. 1993; Carbo-hydrate uptake genes in Escherichia coli induced by carbon starvation.. Curr Microbiol 27:335–340
    [Google Scholar]
  4. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. 1990; Basic local alignment search tool.. J Mol Biol 403:403–410
    [Google Scholar]
  5. Baur H., Luethi E., Stalon V., Mercenier A., Haas D. 1989; Sequence analysis and expression of the arginine-deiminase and carbamate-kinase genes of Pseudomonas aeruginosa. . Eur J Biochem 179:53–60
    [Google Scholar]
  6. Beauchamp C.J., Kloepper J.W., Lemke P.A. 1993; Lumino- metric analyses of plant root colonization by bioluminescent pseudomonads.. Can J Microbiol 39:434–441
    [Google Scholar]
  7. Bell A.W., Bucket S.D., Groarke J.M., Hope J.N., Kingsley D.H., Hermodson M.A. 1986; The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12.. J Biol Chem 261:7652–7658
    [Google Scholar]
  8. Berg B.L., Li J., Heider J., Stewart V. 1991; Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHl operon and evidence that opal (UGA) encodes selenocysteine.. J Biol Chem 266:22380–22385
    [Google Scholar]
  9. Beringer J.E. 1974; R factor transfer in Rhizobium legumino- sarum. . J Gen Microbiol 84:188–198
    [Google Scholar]
  10. Black T.A., Cai Y., Wolk P.C. 1993; Spatial expression and autoregulation of hetR, a gene involved in the control of heterocyst development in Anabaena. . Mol Microbiol 9:77–84
    [Google Scholar]
  11. Blattner F.R., Plunkett G. III Bloch C.A. 14 other authors 1997; The complete genome sequence of Escherichia coli K-12.. Science 277:1453–1474
    [Google Scholar]
  12. Boelens J., Zoutman D., Campbell J., Verstraete W., Paranchych W. 1993; The use of bioluminescence as a reporter to study the adherence of the plant growth promoting rhizo- pseudomonads 7NSK2 and ANP15 to canola roots.. Can J Microbiol 39:329–334
    [Google Scholar]
  13. Boyer H.W., Roulland-Dussoix D. 1969; A complementation analysis of the restriction and modification of DNA in Escherichia coli. . J Mol Biol 459:459–472
    [Google Scholar]
  14. Breton J., Berks B.C., Reilly A., Thomson A.J., Ferguson S.J., Richardson D.J. 1994; Characterization of the paramagnetic iron-containing redox centres of Thiosphaera pantotropha peri- plasmic nitrate reductase.. FEBS Lett 345:76–80
    [Google Scholar]
  15. Broughton W.J., Dilworth M.J. 1971; Control of leghaemo- globin synthesis in snake beans.. Biochem J 125:1075–1080
    [Google Scholar]
  16. de Bruijn F.J., Rossbach S. 1994; Transposon mutagenesis.. In Methods for General and Molecular Biology pp. 387–405 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  17. de Bruijn F.J., Rossbach S., Schneider M., Ratet P., Messmer S., Szeto W.W., Ausubel F.M., Schell J. 1989; Rhizobium meliloti 1021 has three differentially regulated loci involved in glutamine biosynthesis, none of which is essential for symbiotic nitrogen fixation.. J Bacteriol 171:1673–1682
    [Google Scholar]
  18. Carmi O.A., Stewart G.S., Ulitzur S., Kuhn J. 1987; Use of bacterial luciferase to establish a promoter probe vehicle capable of nondestructive real-time analysis of gene expression in Bacillus spp.. J Bacteriol 169:2165–2170
    [Google Scholar]
  19. D’Hooghe I., vander Wauwe C., Michiels J., Tricot C., de Wilde P., Vanderleyden J., Stalon V. 1997; The arginine deiminase pathway in Rhizobium etli: DNA sequence analysis and functional study of the arcABC genes.. J Bacteriol 179:7403–7409
    [Google Scholar]
  20. Ditta G., Stanfield S., Corbin D., Helinski D.R. 1980; Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. . Proc Natl Acad Sci USA 777347–7351
    [Google Scholar]
  21. Downie J.A., Johnston A.W.B. 1988; Nodulation of legumes by Rhizobium. . Plant Cell Environ 11:403–412
    [Google Scholar]
  22. Eggink G., Engel H., Vriend G., Terpstra P., Witholt B. 1990; Rubredoxin reductase of Pseudomonas oleovorans: structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints.. J Mol Biol 212:135–142
    [Google Scholar]
  23. Fernandez-Pinas F., Leganes F., Wolk C.P. 1994; A third genetic locus required for the formation of heterocysts in Anabaena sp strain PCC 7120.. J Bacteriol 176:5277–5283
    [Google Scholar]
  24. Fleischmann R.D., Adams M.D., White O. 37 other authors 1995; Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.. Science 269:496–512
    [Google Scholar]
  25. Freiberg C., Fellay R., Bairoch A., Broughton W.J., Rosenthal A., Perret X. 1997; Molecular basis of symbiosis between Rhizobium and legumes.. Nature 394:394–401
    [Google Scholar]
  26. Givskov M., Eberl L., Molin S. 1994; Responses to nutrient starvation in Pseudomonas putida KT2442: two-dimensional electrophoretic analysis of starvation- and stress-induced proteins.. J Bacteriol 4816:4816–4824
    [Google Scholar]
  27. Glucksmann M.A., Reuber T.L., Walker G.C. 1993; Family of glycosyl transferases needed for the synthesis of succinoglycan by Rhizobium meliloti. . J Bacteriol 175:7033–7044
    [Google Scholar]
  28. Goldman B.S., Lin J.T., Stewart V. 1994; Identification and structure of the nasR gene encoding a nitrate- and nitrite- responsive positive regulator of nasFEDCBA (nitrate assimilation) operon expression in Klebsiella pneumoniae M5al.. J Bacteriol 176:5077–5085
    [Google Scholar]
  29. Gray J.X., Djordjevic M.A., Rolfe B.G. 1990; Two genes that regulate exopolysaccharide production in Rhizobium sp. strain NGR234: DNA sequences and resultant phenotypes.. J Bacteriol 172:193–203
    [Google Scholar]
  30. Gray T.R.G. 1976; Survival of vegetative microbes in soil.. In The Survival of Vegetative Microbes (Society for General Microbiology Symposium 26) pp. 327–364 Edited by Gray T. R. G., Postgate J. R. Cambridge: Cambridge University Press;
    [Google Scholar]
  31. Groat R.G., Schultz J.E., Zychlinsky E., Bockman A., Matin A. 1986; Starvation proteins in Escherichia coli: kinetics of synthesis and role in starvation survival.. J Bacteriol 486:486–493
    [Google Scholar]
  32. Hanahan D. 1983; Studies on transformation of Escherichia coli with plasmids.. J Mol Biol 166:557–580
    [Google Scholar]
  33. Harms N., de Vries G.E., Maurer K., Hoogendijk J., Stouthamer A.H. 1987; Isolation and nucleotide sequence of the methanol dehydrogenase structural gene from Paracoccus denitrificans. . J Bacteriol 169:3969–3975
    [Google Scholar]
  34. Heitzer A., Malachowsky K., Thonnard J.E., Bienkowski P.R., White D.C., Sayler G.S. 1994; Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium.. Appl Environ Microbiol 60:1487–1494
    [Google Scholar]
  35. Honeycutt R.J., McClelland M., Sobral B.W. 1993; Physical map of the genome of Rhizobium meliloti 1021.. J Bacteriol 175:6945–6952
    [Google Scholar]
  36. Hoshino T., Kose K. 1990; Cloning, nucleotide sequences and identification of products of the Pseudomonas aeruginosa PAO bra genes, which encode the high-affinity branched-chain amino acid transport system.. J Bacteriol 172:5531–5539
    [Google Scholar]
  37. Jansson J. 1995; Tracking genetically engineered micro-organisms in nature.. Curr Opin Biotechnol 6:275–283
    [Google Scholar]
  38. Jimenez-Zurdo J.L., van Dillewijn P., Soto M.J., de Felipe M.R., Olivares J., Toro N. 1995; Characterization of a Rhizobium meliloti proline dehydrogenase mutant altered in nodulation efficiency and competitiveness on alfalfa roots.. Mol Plant-Microbe Interact 492:492–498
    [Google Scholar]
  39. Kaiser D. 1986; Control of multicellular development: Dictyo- stelium and Myxococcus. . Annu Rev Genet 539:539–566
    [Google Scholar]
  40. Kaneko T., Sato S., Kotani H. 21 other authors 1996; Sequence analysis of the genome of the unicellular cyano-bacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions.. DNA Res 3:109–136
    [Google Scholar]
  41. Kim Y., Watrud L.S., Matin A. 1995; A carbon starvation survival gene of Pseudomonas putida is regulated by sigma 54.. J Bacteriol 177:1850–1859
    [Google Scholar]
  42. Kiss G.B., Vincze É., Kálmán Z., Forrai T., Kondorosi Á. 1979; Genetic and biochemical analysis of mutants affected in nitrate reduction in Rhizobium meliloti.. J Gen Microbiol 113:105–118
    [Google Scholar]
  43. Kjelleberg S. 1993 Starvation in Bacteria. New York & London: Plenum;
    [Google Scholar]
  44. Kragelund L., Christoffersen B., Nybroe O., de Bruijn F.J. 1995; Isolation of lux reporter gene fusions in Pseudomonas fluorescens DF57 inducible by nitrogen or phosphorus starvation.. FEMS Microbiol Ecol 17:95–106
    [Google Scholar]
  45. Kragelund L., Hosbond C., Nybroe O. 1997; Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere.. Appl Environ Microbiol 63:4920–4928
    [Google Scholar]
  46. Lange L.N., Hengge-Aronis R. 1991; Identification of a central regulator of stationary-phase gene expression in Escherichia coli.. Mol Microbiol 5:49–59
    [Google Scholar]
  47. Leigh J.A., Walker G.C. 1994; Exopolysaccharides of Rhizobium: synthesis, regulation and symbiotic function.. Trends Genet 10:63–67
    [Google Scholar]
  48. Leigh J.A., Signer E.R., Walker G.C. 1985; Exopolysac-charide-deficient mutants of Rhizobium meliloti that form ineffective nodules.. Proc Natl Acad Sci USA 826231–6235
    [Google Scholar]
  49. Lin J.T., Goldman B.S., Stewart V. 1993; Structures of genes nasA and nasB, encoding assimilatory nitrate and nitrite reductases in Klebsiella pneumoniae M5al.. J Bacteriol 175:2370–2378
    [Google Scholar]
  50. Long S., Reed J.W., Himawan J., Walker G.C. 1988; Genetic analysis of a cluster of genes required for synthesis of the calcofluor-binding exopolysaccharide of Rhizobium meliloti.. J Bacteriol 170:4239–4248
    [Google Scholar]
  51. Losick R., Youngman P., Piggot P.J. 1986; Genetics of endospore formation in Bacillus subtilis.. Annu Rev Genet 20:625–669
    [Google Scholar]
  52. Lynch J.M. 1988; The terrestrial environment.. In Microorganisms in Action: Concepts and Applications pp. 224–248 Edited by Lynch J.M., Hobbes J.E. Oxford: Blackwell Scientific;
    [Google Scholar]
  53. Machlin S.M., Hanson R.S. 1988; Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum methanol dehydrogenase structural gene.. J Bacteriol 170:4739–4747
    [Google Scholar]
  54. Magasanik B., Neidhardt F.C. 1987; Regulation of carbon and nitrogen utilization.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp. 807–876 Edited by Niedhardt F.C. others Washington, DC: American Society for Microbiology;
    [Google Scholar]
  55. Matin A. 1991; The molecular basis of carbon-starvation-induced general resistance in Escherichia coli.. Mol Microbiol 5:3–10
    [Google Scholar]
  56. Matin A., Auger E.A., Blum P.H., Schultz J.E. 1989; Genetic basis of starvation survival in nondifferentiating bacteria.. Annu Rev Microbiol 43:293–316
    [Google Scholar]
  57. Meade H.M., Long S.R., Ruvkun G.B., Brown S.E., Ausubel F.M. 1982; Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis.. J Bacteriol 149:114–122
    [Google Scholar]
  58. Meighen E.A. 1991; Molecular biology of bacterial biolumin-escence.. Microbiol Rev 55:123–142
    [Google Scholar]
  59. Meighen E.A., Dunlap P.V. 1993; Physiological, biochemical and genetic control of bacterial bioluminescence.. Adv Microb Physiol 34:1–67
    [Google Scholar]
  60. Metting B. 1985; Soil microbiology and biotechnology.. In Biotechnology: Applications and Research pp. 196–214 Edited by Ovellette R.P., Cheremisinoff P.A. Lancanster, PA: Technomic Publishers;
    [Google Scholar]
  61. Mills i., Wyborn N.R., Greenwood J.A., Williams S.G., Jones C.W. 1998; Characterization of a binding protein dependent active transport system for short-chain amides and urea in the methylotrophic bacterium Methylophilus methylotrophus.. Eur J Biochem 251:45–53
    [Google Scholar]
  62. Möller A., Gustafsson K., Jansson J.K. 1994; Specific monitoring by PCR amplification and bioluminescence of firefly luciferase gene-tagged bacteria added to environmental samples.. FEMS Microbiol Ecol 15:193–206
    [Google Scholar]
  63. Müller P., Keller M., Weng W.M., Quandt J., Arnold W., Puhler A. 1993; Genetic analysis of the Rhizobium meliloti exoYFQ operon: ExoY is homologous to sugar transferases and ExoQ represents a transmembrane protein.. Mol Plant-Microbe Interact 6:55–65
    [Google Scholar]
  64. Nagy I., Schoofs G., Compernolle F., Proost P., Vanderleyden J., de Mot R. 1995; Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothiate) and biosafening by Rhodo- coccus sp. strain N186/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase.. J Bacteriol 177:676–687
    [Google Scholar]
  65. NystrÖm T., Flardh K., Kjelleberg S. 1990; Responses to multiple-nutrient starvation in marine Vibrio sp. strain CCUG15956.. J Bacteriol 172:7085–7097
    [Google Scholar]
  66. Ogawa K., Akagawa E., Yamane K., Sun Z.W., LaCelle M., Zuber P., Nakano M.M. 1995; The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.. J Bacteriol 177:1409–1413
    [Google Scholar]
  67. Omata T., Andriesse X., Hirano A. 1993; Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synecbococcus sp. PCC7942.. Mol Gen Genet 236:193–202
    [Google Scholar]
  68. Onichshuk O.P., Sharypova L.S., Simarov B.B. 1994; Isolation and characterization of the Rhizobium meliloti Tn5-mutants with impaired nodulation competitiveness.. Plant Soil 167:267–274
    [Google Scholar]
  69. Ozga D.A., Lara J.C., Leig J.A. 1994; The regulation of exopolysaccharide production is important at two levels of nodule development in Rhizobium meliloti.. Mol Plant-Microbe Interact 7:758–765
    [Google Scholar]
  70. Peakman T., Crouzet J., Mayaux J.F., Busby S., Mohan S., Harborne N., Wootton J., Nicolson R., Cole J. 1990; Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome.. Eur J Biochem 191:315–323
    [Google Scholar]
  71. Philipp W.J., Poulet S., Eiglmeier K., Pascopella L., Bala-subramanian V., Heym B., Bergh S., Bloom B.R., Jacobs W.R., Cole S.T. 1996; An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae.. Proc Natl Acad Sci USA 933132–3137
    [Google Scholar]
  72. Plunkett G., Burland V., Daniels D.L., Blattner F.R. 1993; Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87-2 to 89-2 minutes.. Nucleic Acids Res 21:3391–3398
    [Google Scholar]
  73. Ras J., Reijnders W.N., Van Spanning R.J., Harms N., Oltmann L.F., Stouthamer A.H. 1991; Isolation, sequencing, and mutagenesis of the gene encoding cytochrome c553i of Paracoccus denitrificans and characterization of the mutant strain.. J Bacteriol 173:6971–6979
    [Google Scholar]
  74. Saint C.P., Romas P. 1996; 4-Methylphthalate catabolism in Burkholderia (Pseudomonas) cepacia Pc701: a gene encoding a phthalate specific permease forms part of a novel gene cluster.. Microbiology 142:2407–2418
    [Google Scholar]
  75. Sambrook J., Fritsch E.F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  76. Sanger F., Nicklen S., Coulson A.R. 1977; DNA sequencing with chain-terminating inhibitors.. Proc Natl Acad Sci USA 745463–5467
    [Google Scholar]
  77. Sanjuan J., Olivares J. 1991; NifA-NtrA regulatory system activates transcription of nfe, a gene locus involved in nodulation competitiveness of Rhizobium meliloti.. Arch Microbiol 155:543–548
    [Google Scholar]
  78. Scripture J.B., Voelker C., Miller S., O´Donnel R.T., Polgar L., Rade J., Horazdovsky B.F., Hogg R.W. 1987; High-affinity l-arabinose transport operon: nucleotide sequence and analysis of gene products.. J Mol Biol 197:37–46
    [Google Scholar]
  79. Shields J.A., Paul E.A., Lowe W.E. 1973; Turnover of microbial tissue in soil under field conditions.. Soil Biol Biochem 5:753–764
    [Google Scholar]
  80. Silhavy T.J., Berman M.L., Enquist L.W. 1984 Experiments with Gene Fusions. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  81. Sloam A., Ally A., Ally D., Pero J. 1988; Gene encoding a minor extracellular protease in Bacillus subtilis.. J Bacteriol 170:5557–5563
    [Google Scholar]
  82. Smith D.R., Doucette-Stamm L.A., Deloughery G. 33 other authors 1997; Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics.. J Bacteriol 179:7135–7155
    [Google Scholar]
  83. Spector M.P., Aliabadi Z., Gonzalez T., Foster J.W. 1986; Global control in Salmonella typhimurium: two-dimensional electrophoretic analysis of starvation: anaerobiosis: and heat shock-inducible proteins.. J Bacteriol 168:420–424
    [Google Scholar]
  84. Spector M.P., Park Y.K., Tirgari S., Gonzalez T., Foster J.W. 1988; Identification and characterization of starvation-regulated genetic loci in Salmonella typhimurium by using Mud-directed lacZ operon fusions.. J Bacteriol 170:345–351
    [Google Scholar]
  85. Sutherland I.W. 1979; Microbial exopolysaccharides: control of synthesis and acylation.. In Microbial Polysaccharides and Polysaccharases pp. 1–28 Edited by Berkeley R. C. W., Gooday G.W., Ellwood D.C. New York: Academic Press;
    [Google Scholar]
  86. Uhde G, Jording D., Selbitschka W., Puhler A. 1997; Stationary-phase mutants of Sinorhizobium meliloti are impaired in stationary-phase survival or in recovery to logaritmic growth.. J Bacteriol 179:6432–6440
    [Google Scholar]
  87. Unthan M., Klipp W., Schmid G.H. 1996; Nucleotide sequence of the nar beta gene encoding assimilatory nitrate reductase from the cyanobacterium Oscillatoria chalybea.. Biochim Biophys Acta1 1305:19–24
    [Google Scholar]
  88. de Weger L.A., Dunbar P., Mahafee W.F., Lugtenberg B.J.J., Sayler G.S. 1991; Use of bioluminescence markers to detect Pseudomonas bacteria in the rhizosphere.. Appl Environ Microbiol 57:3641–3644
    [Google Scholar]
  89. Weichart D., Lange R., Henneberg N., Hengge-Aronis R. 1993; Identification and characterization of stationary phase-inducible genes in Escherichia coli.. Mol Microbiol 10:407–420
    [Google Scholar]
  90. Wolk P.G, Cai Y., Panoff J.M. 1991; Use of a transposon with luciferase as a reporter to identify environmentally responsive genes in a cyanobacterium.. Proc Natl Acad Sci USA 885355–5359
    [Google Scholar]
  91. Woodson K., Devine K.M. 1994; Analysis of a ribose transport operon from Bacillus subtilis.. Microbiology 140:1829–1838
    [Google Scholar]
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