Abstract
Most bacterial cells are surrounded by a peptidoglycan cell wall that is essential for their integrity. The major synthases of this exoskeleton are called penicillin-binding proteins (PBPs)1,2. Surprisingly little is known about how cells control these enzymes, given their importance as drug targets. In the model Gram-negative bacterium Escherichia coli, outer membrane lipoproteins are critical activators of the class A PBPs (aPBPs)3,4, bifunctional synthases capable of polymerizing and crosslinking peptidoglycan to build the exoskeletal matrix1. Regulators of PBP activity in Gram-positive bacteria have yet to be discovered but are likely to be distinct due to the absence of an outer membrane. To uncover Gram-positive PBP regulatory factors, we used transposon-sequencing (Tn-Seq)5 to screen for mutations affecting the growth of Streptococcus pneumoniae cells when the aPBP synthase PBP1a was inactivated. Our analysis revealed a set of genes that were essential for growth in wild-type cells yet dispensable when pbp1a was deleted. The proteins encoded by these genes include the conserved cell wall elongation factors MreC and MreD2,6,7, as well as a membrane protein of unknown function (SPD_0768) that we have named CozE (coordinator of zonal elongation). Our results indicate that CozE is a member of the MreCD complex of S. pneumoniae that directs the activity of PBP1a to the midcell plane where it promotes zonal cell elongation and normal morphology. CozE homologues are broadly distributed among bacteria, suggesting that they represent a widespread family of morphogenic proteins controlling cell wall biogenesis by the PBPs.
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Change history
14 July 2017
In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.
References
Lovering, A. L., Safadi, S. S. & Strynadka, N. C. J. Structural perspective of peptidoglycan biosynthesis and assembly. Annu. Rev. Biochem. 81, 451–478 (2012).
Typas, A., Banzhaf, M., Gross, C. A. & Vollmer, W. From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat. Rev. Microbiol. 10, 123–136 (2011).
Typas, A. et al. Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143, 1097–1109 (2010).
Paradis-bleau, C. et al. Lipoprotein cofactors located in the outer membrane activate bacterial cell wall polymerases. Cell 143, 1110–1120 (2011).
van Opijnen, T., Bodi, K. L. & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 6, 767–772 (2009).
Pinho, M. G., Kjos, M. & Veening, J.-W. How to get (a)round: mechanisms controlling growth and division of coccoid bacteria. Nat. Rev. Microbiol. 11, 601–614 (2013).
Land, A. D. & Winkler, M. E. The requirement for pneumococcal MreC and MreD is relieved by inactivation of the gene encoding PBP1a. J. Bacteriol. 193, 4166–4179 (2011).
Hakenbeck, R. Discovery of β-lactam-resistant variants in diverse pneumococcal populations. Genome Med. 6, 72 (2014).
Paik, J., Kern, I., Lurz, R. & Hakenbeck, R. Mutational analysis of the Streptococcus pneumoniae bimodular class A penicillin-binding proteins. J. Bacteriol. 181, 3852–3856 (1999).
Gawronski, J. D., Wong, S. M. S., Giannoukos, G., Ward, D. V. & Akerley, B. J. Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc. Natl Acad. Sci. USA 106, 16422–16427 (2009).
Langridge, G. C. et al. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 19, 2308–2316 (2009).
Job, V., Carapito, R., Vernet, T., Dessen, A. & Zapun, A. Common alterations in PBP1a from resistant Streptococcus pneumoniae decrease its reactivity toward β-lactams: structural insights. J. Biol. Chem. 283, 4886–4894 (2008).
van Opijnen, T. & Camilli, A. A fine scale phenotype–genotype virulence map of a bacterial pathogen. Genome Res. 22, 2541–2551 (2012).
Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44, D279–D285 (2015).
Tsui, H. C. T. et al. Suppression of a deletion mutation in the gene encoding essential PBP2b reveals a new lytic transglycosylase involved in peripheral peptidoglycan synthesis in Streptococcus pneumoniae D39. Mol. Microbiol. 100, 1039–1065 (2016).
Kloosterman, T. G., van der Kooi-Pol, M. M., Bijlsma, J. J. E. & Kuipers, O. P. The novel transcriptional regulator SczA mediates protection against Zn2+ stress by activation of the Zn2+-resistance gene czcD in Streptococcus pneumoniae. Mol. Microbiol. 65, 1049–1063 (2007).
Lanie, J. A. et al. Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J. Bacteriol. 189, 38–51 (2007).
Rice, K. C. & Bayles, K. W. Molecular control of bacterial death and lysis. Microbiol. Mol. Biol. Rev. 72, 85–109 (2008).
Guiral, S., Mitchell, T. J., Martin, B. & Claverys, J.-P. Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. Proc. Natl Acad. Sci. USA 102, 8710–8715 (2005).
Boersma, M. J. et al. Minimal peptidoglycan (PG) turnover in wild-type and PG hydrolase and cell division mutants of Streptococcus pneumoniae D39 growing planktonically and in host-relevant biofilm. J. Bacteriol. 197, 3472–3485 (2015).
Kuru, E. et al. In situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent d-amino acids. Angew. Chem. Int. Ed. 51, 12519–12523 (2012).
Karimova, G., Pidoux, J., Ullmann, A. & Ladant, D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc. Natl Acad. Sci. USA 95, 5752–5756 (1998).
Kruse, T., Bork-Jensen, J. & Gerdes, K. The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex. Mol. Microbiol. 55, 78–89 (2005).
Jones, L. J. F., Carballido-López, R. & Errington, J. Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis. Cell 104, 913–922 (2001).
Tsui, H.-C. T. et al. Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39. Mol. Microbiol. 94, 21–40 (2014).
Meeske, A. J. et al. SEDS proteins are a widespread family of bacterial cell wall polymerases. Nature 537, 634–638 (2016).
Cho, H. et al. Bacterial cell wall biogenesis is mediated by SEDS and PBP polymerase families functioning semi-autonomously. Nat. Microbiol. 1, 16172 (2016).
Varma, A., de Pedro, M. A. & Young, K. D. FtsZ directs a second mode of peptidoglycan synthesis in Escherichia coli. J. Bacteriol. 189, 5692–5704 (2007).
de Pedro, M. A., Quintela, J. C., Höltje, J. V. & Schwarz, H. Murein segregation in Escherichia coli. J. Bacteriol. 179, 2823–2834 (1997).
Aaron, M. et al. The tubulin homologue FtsZ contributes to cell elongation by guiding cell wall precursor synthesis in Caulobacter crescentus. Mol. Microbiol. 64, 938–952 (2007).
Hoskins, J. et al. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183, 5709–5717 (2001).
Avery, O. T., MacLeod, C. M. & McCarty, M. Studies on the chemical nature of the substance inducing of transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III. J. Exp. Med. 79, 137–158 (1944).
Robertson, G. T., Ng, W. L., Foley, J., Gilmour, R. & Winkler, M. E. Global transcriptional analysis of clpP mutations of type 2 Streptococcus pneumoniae and their effects on physiology and virulence. J. Bacteriol. 184, 3508–3520 (2002).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Hava, D. L., Hemsley, C. J. & Camilli, A. Transcriptional regulation in the Streptococcus pneumoniae rlrA pathogenicity islet by RlrA. J. Bacteriol. 185, 413–421 (2003).
Sung, C. K., Li, H., Claverys, J. P. & Morrison, D. A. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl. Environ. Microbiol. 67, 5190–5196 (2001).
Eberhardt, A., Wu, L. J., Errington, J., Vollmer, W. & Veening, J. W. Cellular localization of choline-utilization proteins in Streptococcus pneumoniae using novel fluorescent reporter systems. Mol. Microbiol. 74, 395–408 (2009).
Lemon, K. P. & Grossman, A. D. Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science 282, 1516–1519 (1998).
Sung, M.-T. et al. Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli. Proc. Natl Acad. Sci. USA 106, 8824–8829 (2009).
Chan, P. F. et al. Characterization of a novel fucose-regulated promoter (PfcsK) suitable for gene essentiality and antibacterial mode-of-action studies in Streptococcus pneumoniae. J. Bacteriol. 185, 2051–2058 (2003).
Bendezú, F. O., Hale, C. A., Bernhardt, T. G. & de Boer, P. A. J. Rodz (YfgA) is required for proper assembly of the MreB actin cytoskeleton and cell shape in E. coli. EMBO J. 28, 193–204 (2009).
Lampe, D. J., Akerley, B. J., Rubin, E. J., Mekalanos, J. J. & Robertson, H. M. Hyperactive transposase mutants of the Himar1 mariner transposon. Proc. Natl Acad. Sci. USA 96, 11428–11433 (1999).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Carver, T., Harris, S. R., Berriman, M., Parkhill, J. & McQuillan, J. A. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464–469 (2012).
Letunic, I. & Bork, P. Interactive Tree of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).
Meisner, J. et al. FtsEX is required for CwlO peptidoglycan hydrolase activity during cell wall elongation in Bacillus subtilis. Mol. Microbiol. 89, 1069–1083 (2013).
Acknowledgements
The authors thank all members of the Bernhardt and Rudner laboratories for support and comments. A. Fenton was a jointly mentored postdoctoral fellow bridging work in both laboratories. The authors thank R. Yunck, H. Kimsey, M. Winkler, T. van Opijnen, A. Camilli, N. Campo, J.-W. Veening, T. Vernet and D. Morrison for strains, reagents and technical assistance. This work was supported by the National Institutes of Health (R01AI083365 to T.G.B., CETR U19 AI109764 to T.G.B. and D.Z.R., GM073831 to D.Z.R. and RC2 GM092616 to D.Z.R.).
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A.K.F. performed all experiments, designed part of the experimental programme and co-authored the manuscript. L.E.M. carried out essential pilot experiments for the project. D.T.C.L. helped adopt the Tn-seq data analysis pipeline and proofread the manuscript. D.Z.R. and T.G.B. co-supervised the project and co-authored the manuscript.
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Supplementary Figures 1-17; Supplementary Tables 1-4; Supplementary References (PDF 18554 kb)
Supplementary Table 5
Raw Tn-seq analysis data for wt vs pbp1a (XLSX 120 kb)
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Fenton, A., El Mortaji, L., Lau, D. et al. CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae. Nat Microbiol 2, 16237 (2017). https://doi.org/10.1038/nmicrobiol.2016.237
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DOI: https://doi.org/10.1038/nmicrobiol.2016.237
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