1887

Abstract

Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified by proteome analysis. A total of 770 proteins were identified: 73.8 and 21.3 % of these occurred only in the periplasm and OMVs, respectively, and only 4.9 % were found in both locations. The majority of proteins found in either location were present only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively, were present at both sampling times, indicating a time-dependent differential sorting of proteins into the two compartments. The OMVs contained proteins with physiologically varied roles, including Rhizobium adhering proteins (Rap), polysaccharidases, polysaccharide export proteins, auto-aggregation and adherence proteins, glycosyl transferases, peptidoglycan binding and cross-linking enzymes, potential cell wall-modifying enzymes, porins, multidrug efflux RND family proteins, ABC transporter proteins and heat shock proteins. As expected, proteins with known periplasmic localizations (phosphatases, phosphodiesterases, pyrophosphatases) were found only in the periplasm, along with numerous proteins involved in amino acid and carbohydrate metabolism and transport. Nearly one-quarter of the proteins present in the OMVs were also found in our previous analysis of the R. etli total exproteome of MM-grown cells, indicating that these nanoparticles are an important mechanism for protein excretion in this species.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000720
2018-10-25
2019-12-08
Loading full text...

Full text loading...

/deliver/fulltext/micro/165/6/638.html?itemId=/content/journal/micro/10.1099/mic.0.000720&mimeType=html&fmt=ahah

References

  1. Green ER, Mecsas J. Bacterial secretion systems: an overview. Microbiol Spectr 2016;4:1–19 [CrossRef][PubMed]
    [Google Scholar]
  2. Tsirigotaki A, de Geyter J, Šoštaric N, Economou A, Karamanou S. Protein export through the bacterial Sec pathway. Nat Rev Microbiol 2017;15:21–36 [CrossRef][PubMed]
    [Google Scholar]
  3. Chatterjee SN, Chaudhuri K. Outer Membrane Vesicles of Bacteria Berlin, Heidelberg: Springer Berlin Heidelberg; 2012
    [Google Scholar]
  4. Weiner JH, Li L. Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. Biochim Biophys Acta 2008;1778:1698–1713 [CrossRef][PubMed]
    [Google Scholar]
  5. Goemans C, Denoncin K, Collet JF. Folding mechanisms of periplasmic proteins. Biochim Biophys Acta 2014;1843:1517–1528 [CrossRef][PubMed]
    [Google Scholar]
  6. Roier S, Zingl FG, Cakar F, Durakovic S, Kohl P et al. A novel mechanism for the biogenesis of outer membrane vesicles in Gram-negative bacteria. Nat Commun 2016;7:10515 [CrossRef][PubMed]
    [Google Scholar]
  7. Orench-Rivera N, Kuehn MJ. Environmentally controlled bacterial vesicle-mediated export. Cell Microbiol 2016;18:1525–1536 [CrossRef][PubMed]
    [Google Scholar]
  8. Beveridge TJ. Structures of gram-negative cell walls and their derived membrane vesicles. J Bacteriol 1999;181:4725–4733[PubMed]
    [Google Scholar]
  9. Bonnington KE, Kuehn MJ. Protein selection and export via outer membrane vesicles. Biochim Biophys Acta 2014;1843:1612–1619 [CrossRef][PubMed]
    [Google Scholar]
  10. Mashburn-Warren LM, Whiteley M. Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 2006;61:839–846 [CrossRef][PubMed]
    [Google Scholar]
  11. Toyofuku M, Morinaga K, Hashimoto Y, Uhl J, Shimamura H et al. Membrane vesicle-mediated bacterial communication. ISME J 2017;11:1504–1509 [CrossRef][PubMed]
    [Google Scholar]
  12. Jan AT. Outer membrane vesicles (OMVs) of Gram-negative bacteria: a perspective update. Front Microbiol 2017;8:1053 [CrossRef][PubMed]
    [Google Scholar]
  13. Deakin WJ, Broughton WJ. Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol 2009;7:312–320 [CrossRef][PubMed]
    [Google Scholar]
  14. Meneses N, Mendoza-Hernández G, Encarnación S. The extracellular proteome of Rhizobium etli CE3 in exponential and stationary growth phase. Proteome Sci 2010;8:51 [CrossRef][PubMed]
    [Google Scholar]
  15. Meneses N, Taboada H, Dunn MF, Vargas M, Buchs N et al. The naringenin-induced exoproteome of Rhizobium etli CE3. Arch Microbiol 2017;199:737–755 [CrossRef][PubMed]
    [Google Scholar]
  16. Lynch JB, Alegado RA. Spheres of hope, packets of doom: the good and bad of outer membrane vesicles in interspecies and ecological dynamics. J Bacteriol 2017;199:1–10 [CrossRef][PubMed]
    [Google Scholar]
  17. Katsir L, Bahar O. Bacterial outer membrane vesicles at the plant-pathogen interface. PLoS Pathog 2017;13:e1006306 [CrossRef][PubMed]
    [Google Scholar]
  18. Krehenbrink M, Edwards A, Downie JA. The superoxide dismutase SodA is targeted to the periplasm in a SecA-dependent manner by a novel mechanism. Mol Microbiol 2011;82:164–179 [CrossRef][PubMed]
    [Google Scholar]
  19. Encarnación S, Dunn M, Willms K, Mora J, Dunn M. Fermentative and aerobic metabolism in Rhizobium etli. J Bacteriol 1995;177:3058–3066 [CrossRef][PubMed]
    [Google Scholar]
  20. McBroom AJ, Kuehn MJ. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. Mol Microbiol 2007;63:545–558 [CrossRef][PubMed]
    [Google Scholar]
  21. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976;72:248–254 [CrossRef][PubMed]
    [Google Scholar]
  22. Bhasin M, Garg A, Raghava GP. PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics 2005;21:2522–2524 [CrossRef][PubMed]
    [Google Scholar]
  23. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO et al. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 2004;5:R35–R35.13 [CrossRef][PubMed]
    [Google Scholar]
  24. Glenn AR, Dilworth MJ. An examination of Rhizobium leguminosarum for the production of extracellular and periplasmic proteins. J Gen Microbiol 1979;112:405–409 [CrossRef]
    [Google Scholar]
  25. Imperi F, Ciccosanti F, Perdomo AB, Tiburzi F, Mancone C et al. Analysis of the periplasmic proteome of Pseudomonas aeruginosa, a metabolically versatile opportunistic pathogen. Proteomics 2009;9:1901–1915 [CrossRef][PubMed]
    [Google Scholar]
  26. Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B et al. Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol 2011;77:1276–1283 [CrossRef][PubMed]
    [Google Scholar]
  27. Watt SA, Wilke A, Patschkowski T, Niehaus K. Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics 2005;5:153–167 [CrossRef][PubMed]
    [Google Scholar]
  28. Han MJ, Kim JY, Kim JA. Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains. J Biosci Bioeng 2014;117:437–442 [CrossRef][PubMed]
    [Google Scholar]
  29. Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G et al. LocTree3 prediction of localization. Nucleic Acids Res 2014;42:W350–W355 [CrossRef][PubMed]
    [Google Scholar]
  30. Encarnación S, Guzmán Y, Dunn MF, Hernández M, del Carmen Vargas M et al. Proteome analysis of aerobic and fermentative metabolism in Rhizobium etli CE3. Proteomics 2003;3:1077–1085 [CrossRef][PubMed]
    [Google Scholar]
  31. Streeter JG. Analysis of periplasmic enzymes in intact cultured bacteria and bacteroids of Bradyrhizobium japonicum and Rhizobium leguminosarum biovar phaseoli. Microbiology 1989;135:3477–3484 [CrossRef]
    [Google Scholar]
  32. Lee EY, Bang JY, Park GW, Choi DS, Kang JS et al. Global proteomic profiling of native outer membrane vesicles derived from Escherichia coli. Proteomics 2007;7:3143–3153 [CrossRef][PubMed]
    [Google Scholar]
  33. Dauros Singorenko P, Chang V, Whitcombe A, Simonov D, Hong J et al. Isolation of membrane vesicles from prokaryotes: a technical and biological comparison reveals heterogeneity. J Extracell Vesicles 2017;6:1324731–14 [CrossRef][PubMed]
    [Google Scholar]
  34. Kulp A, Kuehn MJ. Biological functions and biogenesis of secreted bacterial outer membrane vesicles. Annu Rev Microbiol 2010;64:163–184 [CrossRef][PubMed]
    [Google Scholar]
  35. Avila-Calderón ED, Lopez-Merino A, Jain N, Peralta H, López-Villegas EO et al. Characterization of outer membrane vesicles from Brucella melitensis and protection induced in mice. Clin Dev Immunol 2012;2012:1–13 [CrossRef][PubMed]
    [Google Scholar]
  36. Bai J, Kim SI, Ryu S, Yoon H. Identification and characterization of outer membrane vesicle-associated proteins in Salmonella enterica serovar Typhimurium. Infect Immun 2014;82:4001–4010 [CrossRef][PubMed]
    [Google Scholar]
  37. Choi CW, Park EC, Yun SH, Lee SY, Lee YG et al. Proteomic characterization of the outer membrane vesicle of Pseudomonas putida KT2440. J Proteome Res 2014;13:4298–4309 [CrossRef][PubMed]
    [Google Scholar]
  38. Schwechheimer C, Kuehn MJ. Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. Nat Rev Microbiol 2015;13:605–619 [CrossRef][PubMed]
    [Google Scholar]
  39. Schwechheimer C, Sullivan CJ, Kuehn MJ. Envelope control of outer membrane vesicle production in Gram-negative bacteria. Biochemistry 2013;52:3031–3040 [CrossRef][PubMed]
    [Google Scholar]
  40. Bittinger MA, Handelsman J. Identification of genes in the RosR regulon of Rhizobium etli. J Bacteriol 2000;182:1706–1713 [CrossRef][PubMed]
    [Google Scholar]
  41. Salazar E, Díaz-Mejía JJ, Moreno-Hagelsieb G, Martínez-Batallar G, Mora Y et al. Characterization of the NifA-RpoN regulon in Rhizobium etli in free life and in symbiosis with Phaseolus vulgaris. Appl Environ Microbiol 2010;76:4510–4520 [CrossRef][PubMed]
    [Google Scholar]
  42. Vercruysse M, Fauvart M, Jans A, Beullens S, Braeken K et al. Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli. Genome Biol 2011;12:R17–19 [CrossRef][PubMed]
    [Google Scholar]
  43. Reyes-Pérez A, Vargas MC, Hernández M, Aguirre-von-Wobeser E, Pérez-Rueda E et al. Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42. Arch Microbiol 2016;198:847–860 [CrossRef][PubMed]
    [Google Scholar]
  44. Lee EY, Choi DS, Kim KP, Gho YS. Proteomics in gram-negative bacterial outer membrane vesicles. Mass Spectrom Rev 2008;27:535–555 [CrossRef][PubMed]
    [Google Scholar]
  45. Delepelaire P. Type I secretion in gram-negative bacteria. Biochim Biophys Acta 2004;1694:149–161 [CrossRef][PubMed]
    [Google Scholar]
  46. Downie JA. The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol Rev 2010;34:150–170 [CrossRef][PubMed]
    [Google Scholar]
  47. Ausmees N, Jacobsson K, Lindberg M. A unipolarly located, cell-surface-associated agglutinin, RapA, belongs to a family of Rhizobium-adhering proteins (Rap) in Rhizobium leguminosarum bv. trifolii. Microbiology 2001;147:549–559 [CrossRef][PubMed]
    [Google Scholar]
  48. Mongiardini EJ, Ausmees N, Pérez-Giménez J, Julia Althabegoiti M, Ignacio Quelas J et al. The rhizobial adhesion protein RapA1 is involved in adsorption of rhizobia to plant roots but not in nodulation. FEMS Microbiol Ecol 2008;65:279–288 [CrossRef][PubMed]
    [Google Scholar]
  49. Pérez-Giménez J, Mongiardini EJ, Althabegoiti MJ, Covelli J, Quelas JI et al. Soybean lectin enhances biofilm formation by Bradyrhizobium japonicum in the absence of plants. Int J Microbiol 2009;2009:1–8 [CrossRef]
    [Google Scholar]
  50. Berne C, Ducret A, Hardy GG, Brun YV. Adhesins involved in attachment to abiotic surfaces by Gram-negative bacteria. Microbiol Spectr 2015;3:1–45 [CrossRef][PubMed]
    [Google Scholar]
  51. Finnie C, Zorreguieta A, Hartley NM, Downie JA. Characterization of Rhizobium leguminosarum exopolysaccharide glycanases that are secreted via a type I exporter and have a novel heptapeptide repeat motif. J Bacteriol 1998;180:1691–1699[PubMed]
    [Google Scholar]
  52. Russo DM, Williams A, Edwards A, Posadas DM, Finnie C et al. Proteins exported via the PrsD-PrsE type I secretion system and the acidic exopolysaccharide are involved in biofilm formation by Rhizobium leguminosarum. J Bacteriol 2006;188:4474–4486 [CrossRef][PubMed]
    [Google Scholar]
  53. Zorreguieta A, Finnie C, Downie JA. Extracellular glycanases of Rhizobium leguminosarum are activated on the cell surface by an exopolysaccharide-related component. J Bacteriol 2000;182:1304–1312 [CrossRef][PubMed]
    [Google Scholar]
  54. Balsalobre C, Silván JM, Berglund S, Mizunoe Y, Uhlin BE et al. Release of the type I secreted alpha-haemolysin via outer membrane vesicles from Escherichia coli. Mol Microbiol 2006;59:99–112 [CrossRef][PubMed]
    [Google Scholar]
  55. Economou A, Hamilton WD, Johnston AW, Downie JA. The Rhizobium nodulation gene nodO encodes a Ca2(+)-binding protein that is exported without N-terminal cleavage and is homologous to haemolysin and related proteins. Embo J 1990;9:349–354[PubMed]
    [Google Scholar]
  56. Braun M, Silhavy TJ. Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol Microbiol 2002;45:1289–1302 [CrossRef][PubMed]
    [Google Scholar]
  57. Magnet S, Dubost L, Marie A, Arthur M, Gutmann L. Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli. J Bacteriol 2008;190:4782–4785 [CrossRef][PubMed]
    [Google Scholar]
  58. Naamala J, Jaiswal SK, Dakora FD. Antibiotics Resistance in Rhizobium: Type, Process, Mechanism and Benefit for Agriculture. Curr Microbiol 2016;72:804–816 [CrossRef][PubMed]
    [Google Scholar]
  59. González-Sánchez A, Cubillas CA, Miranda F, Dávalos A, García-de Los Santos A. The ropAe gene encodes a porin-like protein involved in copper transit in Rhizobium etli CFN42. Microbiologyopen 2018;7:e00573 [CrossRef][PubMed]
    [Google Scholar]
  60. Roest HP, Bloemendaal CJ, Wijffelman CA, Lugtenberg BJ. Isolation and characterization of ropA homologous genes from Rhizobium leguminosarum biovars viciae and trifolii. J Bacteriol 1995;177:4985–4991 [CrossRef][PubMed]
    [Google Scholar]
  61. Crook MB, Draper AL, Guillory RJ, Griffitts JS. The Sinorhizobium meliloti essential porin RopA1 is a target for numerous bacteriophages. J Bacteriol 2013;195:3663–3671 [CrossRef][PubMed]
    [Google Scholar]
  62. Pérez-Montaño F, del Cerro P, Jiménez-Guerrero I, López-Baena FJ, Cubo MT et al. RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt. BMC Genomics 2016;17:1–11 [CrossRef]
    [Google Scholar]
  63. Guerrero-Mandujano A, Hernández-Cortez C, Ibarra JA, Castro-Escarpulli G. The outer membrane vesicles: Secretion system type zero. Traffic 2017;18:425–432 [CrossRef][PubMed]
    [Google Scholar]
  64. Eda S, Mitsui H, Minamisawa K. Involvement of the smeAB multidrug efflux pump in resistance to plant antimicrobials and contribution to nodulation competitiveness in Sinorhizobium meliloti. Appl Environ Microbiol 2011;77:2855–2862 [CrossRef][PubMed]
    [Google Scholar]
  65. Knowles TJ, Scott-Tucker A, Overduin M, Henderson IR. Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nat Rev Microbiol 2009;7:206–214 [CrossRef][PubMed]
    [Google Scholar]
  66. Hussain S, Bernstein HD. The Bam complex catalyzes efficient insertion of bacterial outer membrane proteins into membrane vesicles of variable lipid composition. J Biol Chem 2018;293:2959–2973 [CrossRef][PubMed]
    [Google Scholar]
  67. Hernández-Mendoza A, Nava N, Santana O, Abreu-Goodger C, Tovar A et al. Diminished redundancy of outer membrane factor proteins in rhizobiales: a nodT homolog is essential for free-living Rhizobium etli. J Mol Microbiol Biotechnol 2007;13:22–34 [CrossRef][PubMed]
    [Google Scholar]
  68. Yurgel SN, Kahn ML. Dicarboxylate transport by rhizobia. FEMS Microbiol Rev 2004;28:489–501 [CrossRef][PubMed]
    [Google Scholar]
  69. Meneses N, Taboada H, Dunn MF, Vargas MDC, Buchs N et al. The naringenin-induced exoproteome of Rhizobium etli CE3. Arch Microbiol 2017;199:737–755 [CrossRef]
    [Google Scholar]
  70. Mashburn LM, Whiteley M. Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature 2005;437:422–425 [CrossRef][PubMed]
    [Google Scholar]
  71. Krol E, Becker A. Rhizobial homologs of the fatty acid transporter FadL facilitate perception of long-chain acyl-homoserine lactone signals. Proc Natl Acad Sci USA 2014;111:10702–10707 [CrossRef][PubMed]
    [Google Scholar]
  72. Zhang Y, Smallbone LA, Dicenzo GC, Morton R, Finan TM. Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti. BMC Microbiol 2016;16:1–13 [CrossRef][PubMed]
    [Google Scholar]
  73. Aguilera L, Toloza L, Giménez R, Odena A, Oliveira E et al. Proteomic analysis of outer membrane vesicles from the probiotic strain Escherichia coli Nissle 1917. Proteomics 2014;14:222–229 [CrossRef][PubMed]
    [Google Scholar]
  74. Vipond C, Wheeler JX, Jones C, Feavers IM, Suker J. Characterization of the protein content of a meningococcal outer membrane vesicle vaccine by polyacrylamide gel electrophoresis and mass spectrometry. Hum Vaccin 2005;1:80–84 [CrossRef][PubMed]
    [Google Scholar]
  75. Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M et al. Riboregulation in plant-associated α-proteobacteria. RNA Biol 2014;11:550–562 [CrossRef][PubMed]
    [Google Scholar]
  76. Maougal RT, Bargaz A, Sahel C, Amenc L, Djekoun A et al. Localization of the Bacillus subtilis beta-propeller phytase transcripts in nodulated roots of Phaseolus vulgaris supplied with phytate. Planta 2014;239:901–908 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000720
Loading
/content/journal/micro/10.1099/mic.0.000720
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error