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      A Cell Cycle and Nutritional Checkpoint Controlling Bacterial Surface Adhesion

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          Abstract

          In natural environments, bacteria often adhere to surfaces where they form complex multicellular communities. Surface adherence is determined by the biochemical composition of the cell envelope. We describe a novel regulatory mechanism by which the bacterium, Caulobacter crescentus, integrates cell cycle and nutritional signals to control development of an adhesive envelope structure known as the holdfast. Specifically, we have discovered a 68-residue protein inhibitor of holdfast development (HfiA) that directly targets a conserved glycolipid glycosyltransferase required for holdfast production (HfsJ). Multiple cell cycle regulators associate with the hfiA and hfsJ promoters and control their expression, temporally constraining holdfast development to the late stages of G1. HfiA further functions as part of a ‘nutritional override’ system that decouples holdfast development from the cell cycle in response to nutritional cues. This control mechanism can limit surface adhesion in nutritionally sub-optimal environments without affecting cell cycle progression. We conclude that post-translational regulation of cell envelope enzymes by small proteins like HfiA may provide a general means to modulate the surface properties of bacterial cells.

          Author Summary

          Bacteria predominantly exist within surface-attached communities that facilitate metabolic cooperation, sharing of genetic information, and protect cells against stress. The freshwater bacterium, Caulobacter crescentus elaborates an adhesive structure known as the holdfast, which enables surface attachment. We have discovered a novel mechanism that controls holdfast development in response to cell cycle and environmental cues. This regulatory mechanism involves a small protein inhibitor, HfiA, which targets a conserved holdfast synthesis enzyme and ensures that the holdfast is produced at the appropriate stage of cell development and under the appropriate environmental conditions. To our knowledge, the regulatory system we report here is unprecedented, and provides a mechanism for integrative control of bacterial cell adhesion in response to cell cycle and environmental signals.

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          Most cited references43

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          Microbial biofilms.

          Direct observations have clearly shown that biofilm bacteria predominate, numerically and metabolically, in virtually all nutrient-sufficient ecosystems. Therefore, these sessile organisms predominate in most of the environmental, industrial, and medical problems and processes of interest to microbiologists. If biofilm bacteria were simply planktonic cells that had adhered to a surface, this revelation would be unimportant, but they are demonstrably and profoundly different. We first noted that biofilm cells are at least 500 times more resistant to antibacterial agents. Now we have discovered that adhesion triggers the expression of a sigma factor that derepresses a large number of genes so that biofilm cells are clearly phenotypically distinct from their planktonic counterparts. Each biofilm bacterium lives in a customized microniche in a complex microbial community that has primitive homeostasis, a primitive circulatory system, and metabolic cooperativity, and each of these sessile cells reacts to its special environment so that it differs fundamentally from a planktonic cell of the same species.
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            CDD: conserved domains and protein three-dimensional structure

            CDD, the Conserved Domain Database, is part of NCBI’s Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.
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              Quantification of protein half-lives in the budding yeast proteome.

              A complete description of protein metabolism requires knowledge of the rates of protein production and destruction within cells. Using an epitope-tagged strain collection, we measured the half-life of >3,750 proteins in the yeast proteome after inhibition of translation. By integrating our data with previous measurements of protein and mRNA abundance and translation rate, we provide evidence that many proteins partition into one of two regimes for protein metabolism: one optimized for efficient production or a second optimized for regulatory efficiency. Incorporation of protein half-life information into a simple quantitative model for protein production improves our ability to predict steady-state protein abundance values. Analysis of a simple dynamic protein production model reveals a remarkable correlation between transcriptional regulation and protein half-life within some groups of coregulated genes, suggesting that cells coordinate these two processes to achieve uniform effects on protein abundances. Our experimental data and theoretical analysis underscore the importance of an integrative approach to the complex interplay between protein degradation, transcriptional regulation, and other determinants of protein metabolism.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                January 2014
                January 2014
                23 January 2014
                : 10
                : 1
                : e1004101
                Affiliations
                [1 ]Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
                [2 ]Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva, Switzerland
                [3 ]Committee on Microbiology, University of Chicago, Chicago, Illinois, United States of America
                Universidad de Sevilla, Spain
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: AF JH CF SKR PHV SC. Performed the experiments: AF JH CF SKR. Analyzed the data: AF JH CF PHV SC. Wrote the paper: AF PHV SC.

                [¤]

                Current address: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India.

                Article
                PGENETICS-D-13-02114
                10.1371/journal.pgen.1004101
                3900383
                24465221
                36efc25d-f217-4de6-810a-313adda923ae
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 5 August 2013
                : 19 November 2013
                Page count
                Pages: 14
                Funding
                SC acknowledges support for this project from National Institutes of Health Grant R01GM087353. The Center for Research Informatics is funded by the Biological Sciences Division at the University of Chicago with additional funding provided by the Institute for Translational Medicine, CTSA grant number UL1 RR024999 from the National Institutes of Health. PHV is supported by grant SNF # 31003A_143660. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Genetics
                Molecular Genetics
                Gene Identification and Analysis
                Gene Regulation
                Gene Function
                Genetic Screens
                Microbiology
                Bacteriology
                Bacterial Biochemistry
                Bacterial Biofilms
                Bacterial Physiology
                Microbial Growth and Development
                Microbial Physiology
                Model Organisms
                Prokaryotic Models
                Caulobacter Crescentus
                Molecular Cell Biology
                Cell Adhesion

                Genetics
                Genetics

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