Skip to main content
SpringerLink
Log in

Computational and functional analysis of β-lactam resistance in Zymomonas mobilis

  • Section Cellular and Molecular Biology
  • Published:
Biologia Aims and scope Submit manuscript

Abstract

Zymomonas mobilis, a Gram-negative ethanologenic non-pathogenic bacterium, is reported to exhibit resistance to high concentrations of β-lactam antibiotics. In the present study, Z. mobilis was found to be resistant to I-IV generations of cephalosporins and carbapenems, i.e. narrow, broad and extended spectrum β-lactam antibiotics. We have analysed the genome of Z. mobilis (GenBank accession No.: NC 006526) harbouring multiple genes coding for β-lactamases (BLA), β-lactamase domain containing proteins (BDP) and penicillin binding proteins (PBP). The conserved domain database analysis of BDPs predicted them to be members of metallo β-lactamase superfamily. Further, class C specific multidomain AmpC (β-lactamase C) was found in the three β-lactamases. The β-lactam resistance determinants motifs, HXHXD, KXG, SXXK, SXN, and YXN are present in the BLAs, BDPs and PBPs of Z. mobilis. The predicted theoretical pI and aliphatic index values suggested their stability. One of the PBPs, PBP2, was predicted to share functional association with rod shape determining proteins (GenBank accession Nos. YP_162095 and YP_162091). Homology modelling of three dimensional structures of the β-lactam resistance determinants and further docking studies with penicillin and other β-lactam antibiotics indicated their substrate-specificity. Semi-quantitative PCR analysis indicated that the expression of all BLAs and one BDP are induced by penicillin. Disk diffusion assay, SDS-PAGE and zymogram analysis confirms the substrate specificity of the β-lactam resistance determinants. This study gives a broader picture of the β-lactam resistance determinants of a non-pathogenic ethanologenic Z. mobilis bacterium that could have implications in laboratories since it is routinely used in many research laboratories in the world for ethanol, fructooligosaccharides, levan production and has also been reported to be present in wine and beer as a spoilage organism.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

BLA:

β-lactamase

BDP:

β-lactamase domain containing protein

IS:

insertion sequence

NMPDR:

National Microbial Pathogen Database Resource

PBP:

penicillin binding protein

PDB:

Protein Data Bank

References

  • Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. & Lipman D.J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  • Ambler R.P. 1980. The structure of β-lactamases. Phil. Trans. R. Soc. Lond. B. Biol. Sci. 289: 321–331.

    Article  CAS  Google Scholar 

  • Arakawa Y., Ohta M., Kido N., Mori M., Ito H., Komatsu T., Fujii Y. & Kato N. 1989. Chromosomal β-lactamase of Klebsiella oxytoca, a new Class A enzyme that hydrolyzes broad spectrum β-lactam antibiotics. Antimicrob. Agents. Chemother. 33: 63–70.

    Article  PubMed  CAS  Google Scholar 

  • Audic S., Robert C., Campagna B., Parinello H., Claverie J.M., Raoult D. & Drancourt M. 2007. Genome analysis of Minibacterium massilliensis highlights the convergent evolution of water-living bacteria. Plos Genetics 3: 1454–1463.

    Article  CAS  Google Scholar 

  • Basta T., Keck A., Klein J. & Stolz A. 2004. Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J. Bacteriol. 186: 3862–3872.

    Article  PubMed  CAS  Google Scholar 

  • Bekers M., Laukevics J., Upite D., Kaminska E., Vigants A., Viesturs U., Pankova L. & Danilevics A. 2002. Fructooligosaccharide and levan producing activity of Zymomonas mobilis extracellular levansucrase. Process Biochem. 38: 701–706.

    Article  CAS  Google Scholar 

  • Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. & Bourne P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235–242.

    Article  PubMed  CAS  Google Scholar 

  • Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T. & Tasumi M. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535–542.

    Article  PubMed  CAS  Google Scholar 

  • Bikadi Z. & Hazai E. 2009. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J. Cheminf. 1: 15.

    Article  Google Scholar 

  • Binkowski T.A., Naghibzadeh S. & Liang J. 2003. CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res. 31: 3352–3355.

    Article  PubMed  CAS  Google Scholar 

  • Callebaut I., Moshous D. & Mornon J.P. 2002. Metallo-β-lactamase fold within nucleic acids processing enzymes: the β-CASP family. Nucleic Acids Res. 30: 3592–3601.

    Article  PubMed  CAS  Google Scholar 

  • Castrignano T., De Meo P.D. Cozzetto D., Talamo I.G. & Tramontano A. 2006. The PMDB protein model database. Nucleic Acids Res. 34: D306–D309.

    Article  PubMed  CAS  Google Scholar 

  • Crittenden R.G. & Playne M.J. 2002. Puri?cation of food-grade oligosaccharides using immobilised cells of Zymomonas mobilis. Appl. Microbiol. Biotechnol. 58: 297–302.

    Article  PubMed  CAS  Google Scholar 

  • Conway T., Fliege R., Jones-Kilpatrick D., Liu J., Barnell W.O. & Egan S.E. 1991. Cloning, characterization and expression of the Zymomonas mobilis eda gene that encodes 2-keto-3-deoxy-6-phosphogluconate aldolase of the Entner-Doudoroff pathway. Mol. Microbiol. 5: 2901–2911.

    Article  PubMed  CAS  Google Scholar 

  • Couture F., Lachapelle J. & Levesque R.C. 1992. Phylogeny of LCR-1 and OXA-5 and other class A and D β-lactamases. Mol. Microbiol. 6: 1695–1705.

    Article  Google Scholar 

  • Di Gulmi A.M., Dessen A., Dideberg, O. & Vemet T. 2003. The glycosyltransferase domain of penicillin binding protein 2a from Streptococcus pneumoniae catalyses the polymerization of murein glycan chains. J. Bacteriol. 185: 4418–4423.

    Article  Google Scholar 

  • Dogra C., Raina V., Pal R., Suar M., Lal S., Gartemann K.H., Holliger C., Meer J.R.V.D. & Lal R. 2004. Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. J. Bacteriol. 186: 2225–2235.

    Article  PubMed  CAS  Google Scholar 

  • Donald H.M., Scaife W., Amyes S.G.B. & Young H.K. 2000. Sequence analysis of ARI-1, a novel OXA β-lactamase, responsible for imipenem resistance in Acinetobacter baumannii 6B92. Antimicrob. Agents Chemother. 44: 196–199.

    Article  PubMed  CAS  Google Scholar 

  • DeLano WL. The PyMOL Molecular Graphics System. http://www.pymol.org (accessed 03.04.2011).

  • Feller J., Sonnet P. & Gerday C. 1995. The β-lactamase secreted by the Antartic psychrophile Psychrobacter immobilis A8. Appl. Microbiol. Biotechnol. 61: 4474–4476.

    CAS  Google Scholar 

  • Fisher J.F., Meroueh S.O. & Mobashery S. 2005. Bacterial resistance to β-lactam antibiotics: compelling opportunism, compelling opportunity. Chem. Rev. 105: 395–424.

    Article  PubMed  CAS  Google Scholar 

  • Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D. & Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server, pp. 571–607. In: Walker J.M. (ed.), The Proteomics Protocols Handbook, Humana Press, New York.

    Chapter  Google Scholar 

  • Ghuysen J. 1991. Serine β-lactamases and penicillin-binding proteins. Annu. Rev. Microbiol. 45: 37–67.

    Article  PubMed  CAS  Google Scholar 

  • Guex N. & Peitsch M.C. 1997. SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 18: 2714–2723.

    Article  PubMed  CAS  Google Scholar 

  • Gunasekaran P. & Raj K.C. 1999. Ethanol fermentation technology — Zymomonas mobilis. Curr. Sci. 77: 56–68.

    CAS  Google Scholar 

  • Harris A.G., Hazell S.L. & Netting A.G. 2000. Use of digoxigenin labeled ampicillin in the identification of penicillin-binding proteins in Helicobacter pylori. J. Antimicrob. Chemother. 45: 591–598.

    Article  PubMed  CAS  Google Scholar 

  • Hooft R.W., Vriend G., Sander C. & Abola E.E. 1996. Errors in protein structures. Nature 381: 272–272.

    Article  PubMed  CAS  Google Scholar 

  • Karibian D. & Starka G. 1987. The penicillin-binding proteins of Zymomonas mobilis ZM4. FEMS. Microbiol. Lett. 41: 121–125.

    Article  CAS  Google Scholar 

  • Lambert C., Léonard N., De Bolle X. & Depiereux E. 2002. ESyPred3D: prediction of proteins 3D structures. Bioinformatics 18: 1250–1256.

    Article  PubMed  CAS  Google Scholar 

  • Laskowski R.A., MacArthur M.W., Moss D.S. & Thornton J.M. 1993. PROCHECK — a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26: 283–291.

    Article  CAS  Google Scholar 

  • Lauro F.M., McDougald D., Thomas T., Williams T.J., Egan S., Rice S., DeMaere M.Z., Ting L., Ertan H., Johnson J., Ferriera S., Lapidus A., Anderson I., Kyrpides N., Munk A.C., Detter C., Han C.S., Brown M.V., Robb F.T., Kjelleberg S. & Cavicchiolia R. 2009. The genomic basis of trophic strategy in marine bacteria. Proc. Natl. Acad. Sci. USA 106: 15527–15533.

    Article  PubMed  CAS  Google Scholar 

  • Liang W.L., Huang H.M., Lin R.D. & Hou W.C. 2003. Screening for natural inhibitors of penicillinase by copolymerization of hydrolyzed starch or glycogen in sodium dodecylsulfate polyacrylamide gels for detecting penicillinase activity. Bot. Bull. Acad. Sin. 44: 187–191.

    CAS  Google Scholar 

  • Lindberg F., Westman L. & Normark S. 1987. Regulatory components in Citrobacter freudenii ampC β-lactamase induction. Proc. Natl. Acad. Sci. USA 82: 4620–4624.

    Article  Google Scholar 

  • Mahillon J. & Chandler M. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62: 725–774.

    PubMed  CAS  Google Scholar 

  • Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Marchler G.H., Mullokandov M., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Yamashita R.A., Yin J.J., Zhang D. & Bryant S.H. 2005. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33: 192–196.

    Article  Google Scholar 

  • Massova I. & Mobashery S. 1998. Kinship and diversification of bacterial penicillin-binding proteins and β-lactamases. Antimicrob. Agents Chemother. 42: 1–17.

    Article  PubMed  CAS  Google Scholar 

  • Matsuzawa H., Asoh S., Kuna K., Muraiso K., Takasuga A. & Ohta T. 1989. Nucleotide sequence of the rodA gene responsible for the rod shape of Escherichia coli: rodA and pbpA gene, encoding penicillin-binding protein 2 constitute the rodA operon. J. Bacteriol. 171: 558–560.

    PubMed  CAS  Google Scholar 

  • McNeil L.K., Reich C., Aziz R.K., Bartels D., Cohoon M., Disz T., Edwards R.A., Gerdes S., Hwang K., Kubal M., Margaryan G.R., Meyer F., Mihalo W., Olsen G.J., Olson R., Osterman A., Paarmann D., Paczian T., Parrello B., Pusch G.D., Rodionov D.A., Shi X., Vassieva O., Vonstein V., Zagnitko O., Xia F., Zinner J., Overbeek R. & Stevens R. 2007. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35: 347–353.

    Article  Google Scholar 

  • Mottl H., Terpstra P. & Keck W. 1991. Penicillin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicillin-interacting proteins. FEMS Microbiol. Lett. 78: 213–220

    CAS  Google Scholar 

  • Mukundan A.G., Kannan T.R. & Gunasekaran P. 1994. Cloning and expression of the Zymomonas mobilis β-lactamase gene in Escherichia coli. Indian Microbiol. 34: 187–192.

    Google Scholar 

  • Nampoothiri K.M., Rubex R., Patel A.K., Narayanan S.S., Krishna S., Das S.M. & Pandey A. 2008. Molecular cloning, overexpression and biochemical characterization of hypothetical β-lactamases of Mycobacterium tuberculosis H37Rv. J. Appl. Microbiol. 105: 59–67.

    Article  PubMed  CAS  Google Scholar 

  • Ninane G., Joly J. & Kraytman M. 1978. Bronchopulmonary infection due to Branhamella catarrhalis: 11 cases assessed by transtracheal puncture. Br. Med. J. 1: 276–278.

    Article  PubMed  CAS  Google Scholar 

  • Pal R., Bala S., Dadhwal M., Kumar M., Dhingra G., Prakash O., Prabagaran S.R., Shivaji S., Cullum J., Holliger C. & Lal R. 2005. Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of Sphingomonas chungbukensis as Sphingobium chungbukense comb. nov. Int. J. Syst. Evol. Microbiol. 55: 1965–1972.

    Article  PubMed  CAS  Google Scholar 

  • Poirel L., Guibert M. & Girlich D. 1999. Cloning, sequence analyses, expression and distribution of ampC-ampR from Morganella morganii clinical isolates. Antimicrob. Agents Chemother. 43: 769–776.

    PubMed  CAS  Google Scholar 

  • Poirel L., Naas T., Nicholas D., Collet L., Bellais S., Ca Vallo J.D. & Nordmann P. 2000. Characterization of VIM-2, a carbapenem-hydrolyzing metallo-β-lactamase and its plasmid and integron borne gene from a Pseudomonas aeruginosa clinical isolate in France. Antimicrob. Agents Chemother. 44: 891–897.

    Article  PubMed  CAS  Google Scholar 

  • Rajnish K.N., Kishore Choudhary G.M. & Gunasekaran P. 2008. Functional characterization of a putative endoglucanase gene in the genome of Zymomonas mobilis. Biotechnol. Lett. 30: 1461–1467.

    Article  PubMed  CAS  Google Scholar 

  • Rajnish K.N., Sheik Asraf S., Manju N. & Gunasekaran P. 2011. Functional characterization of a putative β-lactamase gene in the genome of Zymomonas mobilis. Biotechnol. Lett. 33: 2425–2430.

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J. & Russell D. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

    Google Scholar 

  • Schwede T., Kopp J., Guex N. & Peitsch M.C. 2003. SWISSMODEL: an automated protein homology-modelling server. Nucleic Acids Res. 31: 3381–3385.

    Article  PubMed  CAS  Google Scholar 

  • Seo J.S., Chong H., Park H.S., Yoon K.O., Jung C., Kim J.J., Hong J.H., Kim H., Kim J.H., Kil J.I., Park C.J., Oh H.M., Lee J.S., Jin S.J., Um H.W., Lee H.J., Oh S.J., Kim J.Y., Kang H.L., Lee S.Y., Lee K.J. & Kang HS. 2005. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol. 23: 63–68.

    Article  PubMed  CAS  Google Scholar 

  • Sheik Asraf S., Rajnish K.N. & Gunasekaran P. 2012. Computational analysis of the tertiary structures of the β-lactam resistance determinants of Zymomonas mobilis. Proceedings of International Conference on Advances in Electrical and Electronics, Information, Communication and Bioinformatics (AEEICB 12), pp. 380–383.

    Google Scholar 

  • Sibold C., Henrichsen J. Konig A., Martin C., Chalkley L. & Hakenbeck R. 1994. Mosaic pbpX genes of major clones of penicillin-resistant Streptococcus pneumoniae have evolved from pbpX genes of a penicillin-sensitive Streptococcus oralis. Mol. Microbiol. 12: 1013–1023.

    Article  PubMed  CAS  Google Scholar 

  • Takeuchi M., Hamana K. & Hiraishi A. 2001. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51: 1405–1417.

    PubMed  CAS  Google Scholar 

  • Tajima M., Takenouchi Y., Sugawara S., Inoue M. & Mitsuhashi S. 1980. Purification and properties of chromosomally mediated β-lactamase from Citrobacter freundii GN7391. J. Gen. Microbiol. 121: 449–456.

    PubMed  CAS  Google Scholar 

  • Thompson J.D., Higgins D.G. & Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.

    Article  PubMed  CAS  Google Scholar 

  • Tigerstrom R.G. & Boras G.J. 1990. β-Lactamase of Lysobacter enzymogenes: induction, purification and Characterization. J. Gen. Microbiol. 136: 521–527.

    Article  Google Scholar 

  • von Mering C.V., Huynen M., Jaeggi D., Schmidt S., Bork P. & Snel B. 2003. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258–261.

    Article  Google Scholar 

  • Wang Y., Geer L.Y. Chappey C., Kans J.A. & Bryant S.H. 2000. Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci. 25: 300–302.

    Article  PubMed  CAS  Google Scholar 

  • Wright G.D. 2007. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5: 175–186.

    Article  PubMed  CAS  Google Scholar 

  • Yabuuchi E., Yamamoto H., Terakubo S., Okamura N., Naka T., Fujiwara N., Kobayashi K., Kosako Y. & Hiraishi A. 2001. Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer. Int. J. Syst. Evol. Microbiol. 51: 281–292.

    PubMed  CAS  Google Scholar 

  • Zheng B., Tan S., Gao J., Han H., Liu J., Lu G., Liu D., Yi Y., Zhu B. & Gao G.F. 2011. An unexpected similarity between antibiotic-resistant NDM-1 and β-lactamase II from Erythrobacter litoralis. Protein Cell 2: 250–258.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India

    Sheik Asraf Sheik Abdul Kader & Gunasekaran Paramasamy

  2. UGC-Networking Resource Centre in Biological Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India

    Mahalakshmi Ayyasamy & Sridhar Jayavel

  3. Department of Genetic Engineering, School of Bioengineering, SRM University, SRM Nagar, Kattankulathur, 603203, India

    Rajnish K. Narayanan

Authors
  1. Sheik Asraf Sheik Abdul Kader
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mahalakshmi Ayyasamy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajnish K. Narayanan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sridhar Jayavel
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gunasekaran Paramasamy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gunasekaran Paramasamy.

Additional information

Based on a contribution presented at the International Conference on Industrial Biotechnology (ICIB-2012), November 21–23, 2012, Punjabi University, Patiala (Pb.), India

all authors contributed equally to this work

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sheik Abdul Kader, S.A., Ayyasamy, M., Narayanan, R.K. et al. Computational and functional analysis of β-lactam resistance in Zymomonas mobilis . Biologia 68, 1054–1067 (2013). https://doi.org/10.2478/s11756-013-0274-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.2478/s11756-013-0274-3

Key k]words

Search

Navigation