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Jiang M, Sullivan SM, Walker AK, Strahler JR, Andrews PC, Maddock JR. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J Bacteriol 2007; 189:3434-44. [PMID: 17337586 PMCID: PMC1855874 DOI: 10.1128/jb.00090-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16 degrees C and 37 degrees C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.
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Affiliation(s)
- M Jiang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
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Thiem S, Kentner D, Sourjik V. Positioning of chemosensory clusters in E. coli and its relation to cell division. EMBO J 2007; 26:1615-23. [PMID: 17332753 PMCID: PMC1829377 DOI: 10.1038/sj.emboj.7601610] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 01/25/2007] [Indexed: 11/09/2022] Open
Abstract
Chemotaxis receptors and associated signalling proteins in Escherichia coli form clusters that consist of thousands of molecules and are the largest native protein complexes described to date in bacteria. Clusters are located at the cell poles and laterally along the cell body, and play an important role in signal transduction. Much work has been done to study the structure and function of receptor clusters, but the significance of their positioning and the underlying mechanisms are not understood. Here, we used fluorescence imaging to study cluster distribution and follow cluster dynamics during cell growth. Our data show that lateral clusters localise to specific periodic positions along the cell body, which mark future division sites and are involved in the localisation of the replication machinery. The chemoreceptor cluster positioning is thus intricately related to the overall structure and division of an E. coli cell.
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Affiliation(s)
- Sebastian Thiem
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - David Kentner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg 69120, Germany. Tel.: +49 6221 546858; Fax: +49 6221 545894; E-mail:
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53
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Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD. Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes. Nucleic Acids Res 2007; 35:e37. [PMID: 17272300 PMCID: PMC1874593 DOI: 10.1093/nar/gkl1158] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for chromosomal tagging with one or more fluorescent protein genes (EGFP, EYFP, mRFP1, DsRed2). We used λ-Red recombination to precisely and efficiently position PCR-generated DNA targeting cassettes containing a fluorescent protein gene and an antibiotic resistance marker, at the C-termini of the CDSs of interest, creating in-frame fusions under the control of their native promoters. We incorporated cre/loxP and flpe/frt technology to enable multiple rounds of chromosomal tagging events to be performed sequentially with minimal disruption to the target locus, thus allowing sets of proteins to be co-localized within the cell. The visualization of labeled proteins in live E. coli cells using fluorescence microscopy revealed a striking variety of distributions including: membrane and nucleoid association, polar foci and diffuse cytoplasmic localization. Fifty of the fifty-two independent targeting experiments performed were successful, and 21 of the 23 selected CDSs could be fluorescently visualized. Our results show that E. coli has an organized and dynamic proteome, and demonstrate that this approach is applicable for tagging and (co-) localizing CDSs on a genome-wide scale.
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Affiliation(s)
- Rory M. Watt
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Jing Wang
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Meikid Leong
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Hsiang-fu Kung
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Kathryn S.E. Cheah
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Depei Liu
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Antoine Danchin
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Jian-Dong Huang
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China, The Center for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, P.R. China, Unité GGB, CNRS URA 2171, Institut Pasteur, 28 rue Dr. Roux, 75015 Paris, France and HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong SAR, China
- *To whom correspondence should be addressed. (+852) 2819 2810(+852) 2855 1254
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Abstract
The recent development of specific probes for lipid molecules has led to the discovery of lipid domains in bacterial membranes, that is, of membrane areas differing in lipid composition. A view of the membrane as a patchwork is replacing the assumption of lipid homogeneity inherent in the fluid mosaic model of Singer and Nicolson (Science 1972, 175: 720-731). If thus membranes have complex lipid structure, questions arise about how it is generated and maintained, and what its function might be. How do lipid domains relate to the functionally distinct regions in bacterial cells as they are identified by protein localization techniques? This review assesses the current knowledge on the existence of cardiolipin (CL) and phosphatidylethanolamine (PE) domains in bacterial cell membranes and on the specific cellular localization of certain membrane proteins, which include phospholipid synthases, and discusses possible mechanisms, both chemical and physiological, for the formation of the lipid domains. We propose that bacterial membranes contain a mosaic of microdomains of CL and PE, which are to a significant extent self-assembled according to their respective intrinsic chemical characteristics. We extend the discussion to the possible relevance of the domains to specific cellular processes, including cell division and sporulation.
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Affiliation(s)
- Kouji Matsumoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Technology, Saitama University, 255 Shimo-ohkubo, Saitama 338-8570, Japan.
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55
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Abstract
Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.
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Affiliation(s)
- Kevin D Young
- Department of Microbiology and Immunology, University of North Dakota School of Medicine, Grand Forks, ND 58202-9037, USA.
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56
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Orme R, Douglas CWI, Rimmer S, Webb M. Proteomic analysis of Escherichia coli biofilms reveals the overexpression of the outer membrane protein OmpA. Proteomics 2006; 6:4269-77. [PMID: 16888722 DOI: 10.1002/pmic.200600193] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacterial colonisation and biofilm formation on the surface of urinary catheters is a common cause of nosocomial infection, and as such is a major impediment to their long-term use. Understanding the mechanisms of biofilm formation on urinary catheters is critical to their control and will aid the future development of materials used in their manufacture. In this report we have used proteomic analysis coupled with immunoassays to show that the major outer membrane protein (OmpA) of Escherichia coli is overexpressed during biofilm formation. A series of synthetic hydrogels being developed for potential use as catheter coatings were used as the substrata and OmpA expression was increased in biofilms on all these surfaces, as well as being a feature of both a laboratory and a clinical strain of E. coli. Up-regulation of OmpA may, therefore, be a common feature of E. coli biofilms. These findings present OmpA as a potential target for biofilm inhibition and may contribute to the rational design of biofilm inhibiting hydrogel coatings for urinary catheters.
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Affiliation(s)
- Rowan Orme
- University of Manchester, Faculty of Medicine and Human Health, Centre for Molecular Medicine, Department of Medical Genetics, Manchester, UK
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57
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Rice JJ, Schohn A, Bessette PH, Boulware KT, Daugherty PS. Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci 2006; 15:825-36. [PMID: 16600968 PMCID: PMC2242469 DOI: 10.1110/ps.051897806] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A bacterial display methodology was developed for N- and C-terminal display and demonstrated to enable rapid screening of very large peptide libraries with high precision and efficiency. To overcome limitations of insertional fusion display libraries, a new scaffold was developed through circular permutation of the Escherichia coli outer membrane protein OmpX that presents both N and C termini on the external cell surface. Circularly permuted OmpX (CPX) display was directly compared to insertional fusion display by screening comparable peptide libraries in each format using magnetic and fluorescence activated cell sorting. CPX display enabled in situ measurement of dissociation rate constants with improved accuracy and, consequently, improved affinity discrimination during screening and ranking of isolated clones. Using streptavidin as a model target, bacterial display yielded the well-characterized HP(Q)/(M) motif obtained previously using several alternative peptide display systems, as well as three additional motifs (L(I)/(V) CQNVCY, CGWMY(F)/(Y)xEC, ERCWYVMHWPCNA). Using CPX display, a very high affinity streptavidin-binding peptide was isolated having a dissociation rate constant k(off) = 0.002sec(-1) even after grafting to the C terminus of an unrelated protein. Comparison of individual clones obtained from insertional fusion and terminal fusion libraries suggests that the N-terminal display yields sequences with greater diversity, affinity, and modularity. CPX bacterial display thus provides a highly effective method for screening peptide libraries to rapidly generate ligands with high affinity and specificity.
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Affiliation(s)
- Jeffrey J Rice
- Department of Chemical Engineering, University of California, Santa Brabara, 93106, USA
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58
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Lai EM, Shih HW, Wen SR, Cheng MW, Hwang HH, Chiu SH. Proteomic analysis ofAgrobacterium tumefaciens response to thevir gene inducer acetosyringone. Proteomics 2006; 6:4130-6. [PMID: 16791832 DOI: 10.1002/pmic.200600254] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Agrobacterium tumefaciens causes crown gall disease in a wide range of plants by transforming plants through the transfer and integration of its transferred DNA (T-DNA) into the host genome. In the present study, we used two-dimensional gel electrophoresis to examine the protein expression profiles of A. tumefaciens in response to the phenolic compound acetosyringone (AS), a known plant-released virulence (vir) gene inducer. Using mass spectrometry, we identified 11 proteins consisting of 9 known AS-induced Vir proteins and 2 newly discovered AS-induced proteins, an unknown protein Y4mC (Atu6162) and a small heat shock protein HspL (Atu3887). Further expression analysis revealed that the AS-induced expression of Y4mC and HspL is regulated by the VirA/VirG two-component system. This report presents the first proteomics study successfully identifying both known and new AS-induced proteins that are implicated in Agrobacterium virulence.
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Affiliation(s)
- Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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59
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Papa R, Glagla S, Danchin A, Schweder T, Marino G, Duilio A. Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125. Extremophiles 2006; 10:483-91. [PMID: 16791470 DOI: 10.1007/s00792-006-0525-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
The capability of microorganisms to utilize different carbohydrates as energy source reflects the availability of these substrates in their habitat. Investigation of the proteins involved in carbohydrate usage, in parallel with analysis of their expression, is then likely to provide information on the interaction between microorganisms and their ecosystem. We analysed the growth behaviour of the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in the presence and in the absence of different carbon source. A marked increase in the optical density was detected when L: -malate was added to the growth medium. Bacterial proteins differently expressed in the presence of L: -malate were identified by proteomic profiling experiments. On the basis of their relative increase, six proteins were selected for further analyses. Among these, the expression of a putative outer membrane porin was demonstrated to be heavily induced by L: -malate. The presence of a functionally active two-component regulatory system very likely controlled by L: -malate was found in the upstream region of the porin gene. A non functional genomic porin mutant was then constructed showing a direct involvement of the protein in the uptake of L: -malate. To the best of our knowledge, the occurrence of such a regulatory system has never been reported in Pseudoalteromonads so far and might constitute a key step in the development of an effective inducible cold expression system.
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Affiliation(s)
- Rosanna Papa
- Department of Organic Chemistry and Biochemistry, Federico II University of Naples, Napoli, Italy
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60
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Han MJ, Lee SY. The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 2006; 70:362-439. [PMID: 16760308 PMCID: PMC1489533 DOI: 10.1128/mmbr.00036-05] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.
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Affiliation(s)
- Mee-Jung Han
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
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61
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Cordwell SJ. Technologies for bacterial surface proteomics. Curr Opin Microbiol 2006; 9:320-9. [PMID: 16679049 DOI: 10.1016/j.mib.2006.04.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/27/2006] [Indexed: 01/11/2023]
Abstract
Proteins from bacterial membranes are notoriously difficult to analyze using the traditional technologies encompassed under the term 'proteomics'. This is because of several factors, including the comparatively low abundance of most membrane proteins within a complex mixture containing cytoplasmic metabolic enzymes, the poor solubility of membrane components such as phospholipids, lipopolysaccharides and peptidoglycans, and the inherent hydrophobicity of many integral membrane proteins that contain up to 15 transmembrane-spanning regions. Recent advances in gel-based and chromatographic separations, coupled with protein and peptide labelling and the exquisite sensitivity of mass spectrometry, are finally beginning to overcome these problems. New technologies in membrane proteomics enable comparative analysis of these recalcitrant proteins from bacteria under a variety of biological conditions.
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Affiliation(s)
- Stuart J Cordwell
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.
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62
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Everberg H, Clough J, Henderson P, Jergil B, Tjerneld F, Ramírez IBR. Isolation of Escherichia coli inner membranes by metal affinity two-phase partitioning. J Chromatogr A 2006; 1118:244-52. [PMID: 16647072 DOI: 10.1016/j.chroma.2006.03.123] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 03/29/2006] [Accepted: 03/31/2006] [Indexed: 10/24/2022]
Abstract
As reduction of sample complexity is a central issue in membrane proteomic research, the need for new pre-fractionation methods is significant. Here we present a method for fast and efficient enrichment of Escherichia coli inner membranes expressing a His-tagged integral membrane L-fucose-proton symporter (FucP). An enriched inner membrane fraction was obtained from a crude membrane mixture using affinity two-phase partitioning in combination with nickel-nitrilotriacetic acid (Ni-NTA) immobilized on agarose beads. Due to interaction between the beads and FucP, inner membranes were selectively partitioned to the bottom phase of a polymer/polymer aqueous two-phase system consisting of poly(ethylene glycol) (PEG) and dextran. The partitioning of membranes was monitored by assaying the activity of an inner membrane marker protein and measuring the total protein content in both phases. The enrichment of inner membrane proteins in the dextran phase was also investigated by proteomic methodology, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), trypsin digestion and liquid chromatography in combination with tandem mass spectrometry (LC-MS/MS). Using a high level of significance (99.95%) in the subsequent database search, 36 proteins assigned to the inner membrane were identified in the bottom phase, compared to 29 when using the standard sucrose gradient centrifugation method for inner membrane isolation. Furthermore, metal affinity two-phase partitioning was up to 10 times faster than sucrose gradient centrifugation. The separation conditions in these model experiments provide a basis for the selective isolation of E. coli membranes expressing His-tagged proteins and can therefore facilitate research on such membrane proteomes.
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Affiliation(s)
- Henrik Everberg
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-22100 Lund, Sweden
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63
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Albrecht R, Zeth K, Söding J, Lupas A, Linke D. Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:415-8. [PMID: 16582500 PMCID: PMC2222561 DOI: 10.1107/s1744309106010190] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 03/20/2006] [Indexed: 11/10/2022]
Abstract
OmpW is an eight-stranded 21 kDa molecular-weight beta-barrel protein from the outer membrane of Gram-negative bacteria. It is a major antigen in bacterial infections and has implications in antibiotic resistance and in the oxidative degradation of organic compounds. OmpW from Escherichia coli was cloned and the protein was expressed in inclusion bodies. A method for refolding and purification was developed which yields properly folded protein according to circular-dichroism measurements. The protein has been crystallized and crystals were obtained that diffracted to a resolution limit of 3.5 angstroms. The crystals belong to space group P422, with unit-cell parameters a = 122.5, c = 105.7 angstroms. A homology model of OmpW is presented based on known structures of eight-stranded beta-barrels, intended for use in molecular-replacement trials.
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Affiliation(s)
- Reinhard Albrecht
- Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Kornelius Zeth
- Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
- Correspondence e-mail:
| | - Johannes Söding
- Max Planck Institute of Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Andrei Lupas
- Max Planck Institute of Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Dirk Linke
- Max Planck Institute of Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, D-72076 Tübingen, Germany
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64
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Ying T, Wang H, Li M, Wang J, Wang J, Shi Z, Feng E, Liu X, Su G, Wei K, Zhang X, Huang P, Huang L. Immunoproteomics of outer membrane proteins and extracellular proteins of Shigella flexneri 2a 2457T. Proteomics 2006; 5:4777-93. [PMID: 16281178 DOI: 10.1002/pmic.200401326] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Shigella flexneri 2a is an important pathogen causing bacillary dysentery in humans. In order to investigate any potential vaccine candidate proteins present in outer membrane proteins (OMPs) and extracellular proteins of S. flexneri 2a 2457T, we use the proteome mapping and database analyzing techniques. A subproteome map and database of OMPs were established first. One hundred and nine of the total 126 marked spots were cut out and processed to MALDI-TOF-MS and PMF. Eighty-seven spots were identified and they represented 55 OMP entries. Furthermore, immunoproteomics analysis of OMPs and extracellular proteins were performed. Total of 34 immunoreactive spots were identified, in which 22 and 12 were from OMPs and extracellular proteins, respectively. Eight novel antigens were found and some of these antigens may be potential vaccine candidate proteins. These results are useful for future studying of pathogenicity, vaccine, and novel antibacterial drugs. Maps and tables of all identified proteins are available on the Internet at www.proteomics.com.cn.
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Affiliation(s)
- Tianyi Ying
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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65
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Xu C, Lin X, Ren H, Zhang Y, Wang S, Peng X. Analysis of outer membrane proteome ofEscherichia coli related to resistance to ampicillin and tetracycline. Proteomics 2006; 6:462-73. [PMID: 16372265 DOI: 10.1002/pmic.200500219] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The elucidation of the molecular details of antibiotic resistance will lead to improvements in extending the efficacy of current antimicrobials. In the current study, proteomic methodologies were applied to characterize functional outer membrane proteins (Omps) of E. coli K-12 responded to tetracycline and ampicillin resistance for understanding of universal pathways that form barriers for antimicrobial agents. For this purpose, E. coli K-12 expressional outer membrane proteome was characterized and identified with the use of 2-DE and MALDI-TOF/MS methods. Then, differential Omps due to tetracycline or ampcilin resistance were determined by comparison between tetracycline minimum inhibitory concentration (MIC)10, ampicillin MIC10, control0 and control10, showing 9 proteins with 11 spots for tetracycline and 8 protein with 9 spots for ampicillin, showing a difference in only 1 protein (decreased LamB in tetracyclin) between the two antibiotics. Among the proteins, 3 were known as antibiotic-resistant proteins, including TolC, OmpC and YhiU, while FimD precursor, LamB, Tsx, YfiO, OmpW, NlpB were first reported here to be antibiotic-resistance-related proteins. Our findings will be helpful for further understanding of antibiotic-resistant mechanism(s). This study also shows that the combination of Omp purification methods certainly contributes the sensitivity of Omp detection.
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Affiliation(s)
- Changxin Xu
- Center for Proteomics, Department of Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, PR China
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66
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Bucarey SA, Villagra NA, Martinic MP, Trombert AN, Santiviago CA, Maulén NP, Youderian P, Mora GC. The Salmonella enterica serovar Typhi tsx gene, encoding a nucleoside-specific porin, is essential for prototrophic growth in the absence of nucleosides. Infect Immun 2005; 73:6210-9. [PMID: 16177292 PMCID: PMC1230887 DOI: 10.1128/iai.73.10.6210-6219.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Salmonella enterica serovar Typhi tsx gene encodes a porin that facilitates the import of nucleosides. When serovar Typhi is grown under anaerobic conditions, Tsx is among the outer membrane proteins whose expression increases dramatically. This increase in expression is due, at least in part, to increased transcription and is dependent on Fnr but not on ArcA. A mutant derivative of serovar Typhi strain STH2370 with a deletion of the tsx gene is an auxotroph that requires either adenosine or thymidine for growth on minimal medium. In contrast, an otherwise isogenic nupG nupC double mutant, defective in the inner membrane nucleoside permeases, is a prototroph. Because anaerobic growth enhances the virulence of serovar Typhi in vitro, we assessed the role that the tsx gene plays in pathogenicity and found that the serovar Typhi STH2370 Deltatsx mutant is defective in survival within human macrophage-like U937 cells. To understand why the Deltatsx mutant is an auxotroph, we selected for insertions of minitransposon T-POP in the Deltatsx genetic background that restored prototrophy. One T-POP insertion that suppressed the Deltatsx mutation in the presence of the inducer tetracycline was located upstream of the pyrD gene. The results of reverse transcription-PCR analysis showed that addition of the inducer decreased the rate of pyrD transcription. These results suggest that the Tsx porin and the balance of products of the tsx and pyrD genes play critical roles in membrane assembly and integrity and thus in the virulence of serovar Typhi.
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Affiliation(s)
- Sergio A Bucarey
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile
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67
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Park SJ, Lee SY, Cho J, Kim TY, Lee JW, Park JH, Han MJ. Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl Microbiol Biotechnol 2005; 68:567-79. [PMID: 16041571 DOI: 10.1007/s00253-005-0081-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2005] [Revised: 06/23/2005] [Accepted: 06/24/2005] [Indexed: 10/25/2022]
Abstract
Through metabolic engineering, scientists seek to modify the metabolic pathways of living organisms to facilitate optimized, efficient production of target biomolecules. During the past decade, we have seen notable improvements in biotechnology, many of which have been based on metabolically engineered microorganisms. Recent developments in the fields of functional genomics, transcriptomics, proteomics, and metabolomics have changed metabolic engineering strategies from the local pathway level to the whole system level. This article focuses on recent advances in the field of metabolic engineering, which have been powered by the combined approaches of the various "omics" that allow us to understand the microbial metabolism at a global scale and to develop more effectively redesigned metabolic pathways for the enhanced production of target bioproducts.
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Affiliation(s)
- S J Park
- Corporate R&D, LG Chem, Ltd./Research Park, Yuseong-gu, Daejeon, Republic of Korea.
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68
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Abstract
The products of the hexacistronic spoVA operon of Bacillus subtilis may be involved in the transport of dipicolinic acid into the forespore during sporulation and its release during spore germination. The major hydrophilic coding region of B. subtilis spoVAD was cloned, the protein was expressed in Escherichia coli as a His tag fusion protein, and a rabbit antiserum was raised against the purified protein. Western blot analyses of fractions from B. subtilis spores showed that SpoVAD is an integral inner membrane protein present at levels >50-fold higher than those of the spore's nutrient germinant receptors that are also present in the inner membrane. SpoVAD also persisted in outgrowing spores.
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Affiliation(s)
- Venkata Ramana Vepachedu
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
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69
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Wehmhöner D, Dieterich G, Fischer E, Baumgärtner M, Wehland J, Jänsch L. “LANESPECTOR”, a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography - tandem mass spectrometry analysis: Application toListeria monocytogenes membrane proteins. Electrophoresis 2005; 26:2450-60. [PMID: 15966022 DOI: 10.1002/elps.200410348] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteomics is required to provide insight into any type of subproteome. While the workflow based on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) can be applied for many subproteomes and comprises well-established strategies for data presentation and data analysis, the comprehensive investigation of membrane proteomes remains a challenging task. We present a number of procedures that provide an insight into such systems. We have established a novel protocol for the efficient preparation of membrane fractions, which is used here for the human pathogen Listeria monocytogenes that overcomes difficulties associated with ribosomes. Subsequently, we have used the combination of sodium dodecyl sulfate (SDS)-PAGE and liquid chromatography-tandem mass spectrometry for the characterization of the membrane proteome. Three hundred and one different membrane proteins could be identified, including 70 proteins that exhibited 2-15 transmembrane domains. However, a remarkably high ratio of proteins was detected in gel sections that were not in accordance with their expected migration behavior during SDS-PAGE. Protein identifications based on MASCOT significance criteria could be shown to be of high quality and therefore could not be the explanation of this observation. Consequently we have developed LaneSpector, a general visualization tool that allows the systematic comparison between apparent and calculated protein masses, which is routinely applicable to any high-throughput approach using a mass-dependent separation dimension prior to LC-MS/MS. The detailed presentation of the LaneSpector plot promotes the validation of the analytical process and might help to reveal relevant biological processes such as proteolysis or other post-translational modifications.
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Affiliation(s)
- Dirk Wehmhöner
- Department of Cell Biology, GBF-German Research Centre for Biotechnology, Braunschweig, Germany
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70
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Nishibori A, Kusaka J, Hara H, Umeda M, Matsumoto K. Phosphatidylethanolamine domains and localization of phospholipid synthases in Bacillus subtilis membranes. J Bacteriol 2005; 187:2163-74. [PMID: 15743965 PMCID: PMC1064036 DOI: 10.1128/jb.187.6.2163-2174.2005] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Application of the cardiolipin (CL)-specific fluorescent dye 10-N-nonyl-acridine orange has recently revealed CL-rich domains in the septal regions and at the poles of the Bacillus subtilis membrane (F. Kawai, M. Shoda, R. Harashima, Y. Sadaie, H. Hara, and K. Matsumoto, J. Bacteriol. 186:1475-1483, 2004). This finding prompted us to examine the localization of another phospholipid, phosphatidylethanolamine (PE), with the cyclic peptide probe, Ro09-0198 (Ro), that binds specifically to PE. Treatment with biotinylated Ro followed by tetramethyl rhodamine-conjugated streptavidin revealed that PE is localized in the septal membranes of vegetative cells and in the membranes of the polar septum and the engulfment membranes of sporulating cells. When the mutant cells of the strains SDB01 (psd1::neo) and SDB02 (pssA10::spc), which both lack PE, were examined under the same conditions, no fluorescence was observed. The localization of the fluorescence thus evidently reflected the localization of PE-rich domains in the septal membranes. Similar PE-rich domains were observed in the septal regions of the cells of many Bacillus species. In Escherichia coli cells, however, no PE-rich domains were found. Green fluorescent protein fusions to the enzymes that catalyze the committed steps in PE synthesis, phosphatidylserine synthase, and in CL synthesis, CL synthase and phosphatidylglycerophosphate synthase, were localized mainly in the septal membranes in B. subtilis cells. The majority of the lipid synthases were also localized in the septal membranes; this includes 1-acyl-glycerol-3-phosphate acyltransferase, CDP-diacylglycerol synthase, phosphatidylserine decarboxylase, diacylglycerol kinase, glucolipid synthase, and lysylphosphatidylglycerol synthase. These results suggest that phospholipids are produced mostly in the septal membranes and that CL and PE are kept from diffusing out to lateral ones.
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Affiliation(s)
- Ayako Nishibori
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Sakura, Saitama, Saitama 338-8570, Japan
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71
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Abstract
In rod-shaped bacteria, a surprisingly large number of proteins are localized to the cell poles. Polar positioning of proteins is crucial to many fundamental cellular processes. Formation of the pole occurs at the time of a prior cell division event and involves coordination of the cell division machinery with septal placement of newly-synthesized peptidoglycan. Development of polar peptidoglycan and outer membrane depends on the formation of the cytokinetic FtsZ ring at midcell. By contrast, positioning of at least two polar proteins depends on signals independent of both the assembly of the FtsZ ring and the synthesis of septal and polar peptidoglycan. We propose a model for distinct but interrelated developmental pathways for polar cell envelope synthesis and positional information recognized by polar proteins.
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Affiliation(s)
- Anuradha Janakiraman
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital/Harvard Medical School, 65 Landsdowne St., Cambridge, MA 02139, USA
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72
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Wissel MC, Wendt JL, Mitchell CJ, Weiss DS. The transmembrane helix of the Escherichia coli division protein FtsI localizes to the septal ring. J Bacteriol 2005; 187:320-8. [PMID: 15601716 PMCID: PMC538840 DOI: 10.1128/jb.187.1.320-328.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FtsI (also called PBP3) of Escherichia coli is a transpeptidase required for synthesis of peptidoglycan in the division septum and is one of about a dozen division proteins that localize to the septal ring. FtsI comprises a short amino-terminal cytoplasmic domain, a single transmembrane helix (TMH), and a large periplasmic domain that encodes the catalytic (transpeptidase) activity. We show here that a 26-amino-acid fragment of FtsI is sufficient to direct green fluorescent protein to the septal ring in cells depleted of wild-type FtsI. This fragment extends from W22 to V47 and corresponds to the TMH. This is a remarkable finding because it is unusual [corrected] for a TMH to target a protein to a site more specific than the membrane. Alanine-scanning mutagenesis of the TMH identified several residues important for septal localization. These residues cluster on one side of an alpha-helix, which we propose interacts directly with another division protein to recruit FtsI to the septal ring.
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Affiliation(s)
- Mark C Wissel
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
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73
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Abstract
Finding out where specific functions are carried out within a bacterial cell has now become technically feasible. Here we consider recent experiments aimed at determining where bacteria translocate proteins across the cytoplasmic membrane using the Sec machinery.
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Affiliation(s)
- Anthony P Pugsley
- Molecular Genetics Unit, CNRS URA 2172 Institut Pasteur, 25 rue du Dr Roux, 75724 Paris CEDEX 15, France.
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74
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447475 DOI: 10.1002/cfg.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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