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Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

Nguyen, Lam T. and Gumbart, James C. and Beeby, Morgan and Jensen, Grant J. (2015) Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape. Proceedings of the National Academy of Sciences of the United States of America, 112 (28). E3689-E3698. ISSN 0027-8424. PMCID PMC4507204. https://resolver.caltech.edu/CaltechAUTHORS:20150702-111849094

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Abstract

Bacteria are surrounded by a peptidoglycan (PG) cell wall that must be remodeled to allow cell growth. While many structural details and properties of PG and the individual enzymes involved are known, how the process is coordinated to maintain cell integrity and rod shape is not understood. We have developed a coarse-grained method to simulate how individual transglycosylases, transpeptidases, and endopeptidases could introduce new material into an existing unilayer PG network. We find that a simple model with no enzyme coordination fails to maintain cell wall integrity and rod shape. We then iteratively analyze failure modes and explore different mechanistic hypotheses about how each problem might be overcome by the macromolecules involved. In contrast to a current theory, which posits that long MreB filaments are needed to coordinate PG insertion sites, we find that local coordination of enzyme activities in individual complexes can be sufficient to maintain cell integrity and rod shape. We also present possible molecular explanations for the existence of monofunctional transpeptidases and glycosidases (glycoside hydrolases), trimeric peptide crosslinks, cell twisting during growth, and synthesis of new strands in pairs.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1073/pnas.1504281112DOIArticle
http://www.pnas.org/content/112/28/E3689PublisherArticle
http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1504281112/-/DCSupplementalPublisherSupporting Information
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507204/PubMed CentralArticle
ORCID:
AuthorORCID
Beeby, Morgan0000-0001-6413-9835
Jensen, Grant J.0000-0003-1556-4864
Additional Information:© 2015 National Academy of Sciences. Edited by Joe Lutkenhaus, University of Kansas Medical Center, Kansas City, KS, and approved June 15, 2015 (received for review March 3, 2015). Published ahead of print June 30, 2015. The authors thank Catherine Oikonomou for revising the manuscript for clarity. Author contributions: L.T.N., M.B., and G.J.J. designed research; L.T.N. performed research; L.T.N. and J.C.G. contributed new reagents/analytic tools; L.T.N., J.C.G., M.B., and G.J.J. analyzed data; and L.T.N., J.C.G., M.B., and G.J.J. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1504281112/-/DCSupplemental.
Subject Keywords:coarse-grained modeling; cell wall synthesis; morphogenesis
Issue or Number:28
PubMed Central ID:PMC4507204
Record Number:CaltechAUTHORS:20150702-111849094
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150702-111849094
Official Citation:Lam T. Nguyen, James C. Gumbart, Morgan Beeby, and Grant J. Jensen Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape PNAS 2015 112 (28) E3689-E3698; published ahead of print June 30, 2015, doi:10.1073/pnas.1504281112
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:58751
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Jul 2015 19:46
Last Modified:03 Oct 2019 08:39

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