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Girardin RC, Bai G, He J, Sui H, McDonough KA. AbmR (Rv1265) is a novel transcription factor of Mycobacterium tuberculosis that regulates host cell association and expression of the non-coding small RNA Mcr11. Mol Microbiol 2018; 110:811-830. [PMID: 30207611 PMCID: PMC6282994 DOI: 10.1111/mmi.14126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022]
Abstract
Gene regulatory networks used by Mycobacterium tuberculosis (Mtb) during infection include many genes of unknown function, confounding efforts to determine their roles in Mtb biology. Rv1265 encodes a conserved hypothetical protein that is expressed during infection and in response to elevated levels of cyclic AMP. Here, we report that Rv1265 is a novel auto‐inhibitory ATP‐binding transcription factor that upregulates expression of the small non‐coding RNA Mcr11, and propose that Rv1265 be named ATP‐binding mcr11regulator (AbmR). AbmR directly and specifically bound DNA, as determined by electrophoretic mobility shift assays, and this DNA‐binding activity was enhanced by AbmR’s interaction with ATP. Genetic knockout of abmR in Mtb increased abmR promoter activity and eliminated growth phase‐dependent increases in mcr11 expression during hypoxia. Mutagenesis identified arginine residues in the carboxy terminus that are critical for AbmR’s DNA‐binding activity and gene regulatory function. Limited similarity to other DNA‐ or ATP‐binding domains suggests that AbmR belongs to a novel class of DNA‐ and ATP‐binding proteins. AbmR was also found to form large organized structures in solution and facilitate the serum‐dependent association of Mtb with human lung epithelial cells. These results indicate a potentially complex role for AbmR in Mtb biology.
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Affiliation(s)
- Roxie C Girardin
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Haixin Sui
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
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2
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Stuart MK, Hudman DA, Nachtrab SN, Hiatt JL, Seo J, Pullen SJ, Sargentini NJ. Fine Epitope Mapping of Monoclonal Antibodies to the DNA Repair Protein, RadA. Monoclon Antib Immunodiagn Immunother 2017; 36:83-94. [PMID: 28581365 DOI: 10.1089/mab.2017.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repair of DNA damage is vital to the health and survival of all organisms. In Escherichia coli, a protein known as RadA (or Sms) participates in recombinational repair, a process that uses an undamaged DNA strand in one DNA duplex to fill a gap in a homologous DNA strand in a sister DNA duplex. In a prior report, we described the production of monoclonal antibodies (MAbs) specific for RadA. Here, we investigated the epitopes recognized by two of the antibodies, MAbs 6F5 and 2A2. Premature stop codons (ochre mutations) were introduced into the radA gene at selected sites, and the truncated RadA proteins were probed by western blotting. Deletion of as few as four amino acids (457-460) from the C-terminus of RadA significantly increased the sensitivity of E. coli to ultraviolet (UV) radiation and abolished recognition of RadA by MAb 6F5. Single alanine substitutions made between positions 443-460 also adversely affected the ability of MAb 6F5 to bind to RadA, further supporting the idea that MAb 6F5 is specific for the RadA C-terminus. An ochre mutation at position 258 abolished the recognition of RadA by MAb 2A2, whereas an ochre mutation at position 279 did not, suggesting that MAb 2A2 binds to an epitope between residues 258 and 279. MAb 2A2 recognition of RadA was destroyed by endoproteinase glu-C cleavage of RadA at position 266, and by a single alanine substitution at position 265. In a competitive enzyme-linked immunosorbent assay (ELISA), a synthetic peptide comprising residues 263-273 of RadA blocked MAb 2A2 recognition of immobilized full-length RadA by more than 97%. We infer from our results that MAb 6F5 binds to the extreme C-terminus of RadA and that MAb 2A2 is specific for an epitope within positions 263-273.
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Affiliation(s)
- Melissa K Stuart
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Deborah A Hudman
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Stephanie N Nachtrab
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Jacob L Hiatt
- 2 Lakeland Regional Medical Center , Saint Joseph, Michigan
| | - Jin Seo
- 3 Truman State University , Kirksville, Missouri
| | | | - Neil J Sargentini
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
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Maheshwari S, Brylinski M. Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 2017; 18:257. [PMID: 28499419 PMCID: PMC5427563 DOI: 10.1186/s12859-017-1675-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved. RESULTS In this study, we developed a new method to discover and model protein interactions employing an exhaustive all-to-all docking strategy. This approach integrates molecular modeling, structural bioinformatics, machine learning, and functional annotation filters in order to provide interaction data for the bottom-up assembly of protein interaction networks. Encouragingly, the success rates for dimer modeling is 57.5 and 48.7% when experimental and computer-generated monomer structures are employed, respectively. Further, our protocol correctly identifies 81% of protein-protein interactions at the expense of only 19% false positive rate. As a proof of concept, 61,913 protein-protein interactions were confidently predicted and modeled for the proteome of E. coli. Finally, we validated our method against the human immune disease pathway. CONCLUSIONS Protein docking supported by evolutionary restraints and machine learning can be used to reliably identify and model biologically relevant protein assemblies at the proteome scale. Moreover, the accuracy of the identification of protein-protein interactions is improved by considering only those protein pairs co-localized in the same cellular compartment and involved in the same biological process. The modeling protocol described in this communication can be applied to detect protein-protein interactions in other organisms and pathways as well as to construct dimer structures and estimate the confidence of protein interactions experimentally identified with high-throughput techniques.
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Affiliation(s)
- Surabhi Maheshwari
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA. .,Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, USA.
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4
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Cooper DL, Lovett ST. Recombinational branch migration by the RadA/Sms paralog of RecA in Escherichia coli. eLife 2016; 5. [PMID: 26845522 PMCID: PMC4786428 DOI: 10.7554/elife.10807] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/03/2016] [Indexed: 12/31/2022] Open
Abstract
RadA (also known as 'Sms') is a highly conserved protein, found in almost all eubacteria and plants, with sequence similarity to the RecA strand exchange protein and a role in homologous recombination. We investigate here the biochemical properties of the E. coli RadA protein and several mutant forms. RadA is a DNA-dependent ATPase, a DNA-binding protein and can stimulate the branch migration phase of RecA-mediated strand transfer reactions. RadA cannot mediate synaptic pairing between homologous DNA molecules but can drive branch migration to extend the region of heteroduplex DNA, even without RecA. Unlike other branch migration factors RecG and RuvAB, RadA stimulates branch migration within the context of the RecA filament, in the direction of RecA-mediated strand exchange. We propose that RadA-mediated branch migration aids recombination by allowing the 3’ invading strand to be incorporated into heteroduplex DNA and to be extended by DNA polymerases. DOI:http://dx.doi.org/10.7554/eLife.10807.001 Damage to the DNA of a cell can cause serious harm, and so cells have several ways in which they can repair DNA. Most of these processes rely on the fact that each of the two strands that make up a DNA molecule can be used as a template to build the other strand. However, this is not possible if both strands of the DNA break in the same place. This form of damage can be repaired in a process called homologous recombination, which uses an identical copy of the broken DNA molecule to repair the broken strands. As a result, this process can only occur during cell division shortly after a cell has duplicated its DNA. One important step of homologous recombination is called strand exchange. This involves one of the broken strands swapping places with part of the equivalent strand in the intact DNA molecule. To do so, the strands of the intact DNA molecule separate in the region that will be used for the repair, and the broken strand can then use the other non-broken DNA strand as a template to replace any missing sections of DNA. The region of the intact DNA molecule where the strands need to separate often grows during this process: this is known as branch migration. In bacteria, a protein called RecA plays a fundamental role in controlling strand exchange, but there are other, similar proteins whose roles in homologous recombination are less well known. Cooper and Lovett have now purified one of these proteins, called RadA, from the Escherichia coli species of bacteriato study how it affects homologous recombination. This revealed that RadA can bind to single-stranded DNA and stimulate branch migration to increase the rate of homologous recombination. Further investigation revealed that RadA allows branch migration to occur even when RecA is missing, but that RadA is unable to begin strand exchange if RecA is not present. The process of branch migration stabilizes the DNA molecules during homologous recombination and may also allow the repaired DNA strand to engage the machinery that copies DNA. Cooper and Lovett also used genetic techniques to alter the structure of specific regions of RadA and found out which parts of the protein affect the ability of RadA to stimulate branch migration. Future challenges are to find out what effect RadA has on the structure of RecA and how RadA promotes branch migration. DOI:http://dx.doi.org/10.7554/eLife.10807.002
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Affiliation(s)
- Deani L Cooper
- Department of Biology, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Susan T Lovett
- Department of Biology, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
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5
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Specificity of the E. coli LysR-type transcriptional regulators. PLoS One 2010; 5:e15189. [PMID: 21187915 PMCID: PMC3004787 DOI: 10.1371/journal.pone.0015189] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 10/29/2010] [Indexed: 12/12/2022] Open
Abstract
Background Families of paralogous oligomeric proteins are common in biology. How the specificity of assembly evolves is a fundamental question of biology. The LysR-Type Transcriptional Regulators (LTTR) form perhaps the largest family of transcriptional regulators in bacteria. Because genomes often encode many LTTR family members, it is assumed that many distinct homooligomers are formed simultaneously in the same cell without interfering with each other's activities, suggesting specificity in the interactions. However, this assumption has not been systematically tested. Methodology/Principal Findings A negative-dominant assay with λcI repressor fusions was used to evaluate the assembly of the LTTRs in E. coli K-12. Thioredoxin (Trx)-LTTR fusions were used to challenge the homooligomeric interactions of λcI-LTTR fusions. Eight cI-LTTR fusions were challenged with twenty-eight Trx fusions. LTTRs could be divided into three classes based on their interactions with other LTTRs. Conclusions/Significance Multimerization of LTTRs in E. coli K-12 is mostly specific. However, under the conditions of the assay, many LTTRs interact with more than one noncognate partner. The physiological significance and physical basis for these interactions are not known.
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Sucaet Y, Wurtele ES. MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. BMC Res Notes 2010; 3:312. [PMID: 21083943 PMCID: PMC2998519 DOI: 10.1186/1756-0500-3-312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/18/2010] [Indexed: 11/26/2022] Open
Abstract
Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api.
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Affiliation(s)
- Yves Sucaet
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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7
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Abstract
Deletion analysis and alanine-scanning based on a homology-based interaction model were used to identify determinants of oligomerization in the transcriptional regulator CynR, a member of the LysR-type transcriptional regulator (LTTR) family. Deletion analysis confirmed that the putative regulatory domain of CynR was essential for driving the oligomerization of lambda repressor-CynR fusion proteins. The interaction surface of a different LTTR and OxyR was mapped onto a multiple sequence alignment of the LTTR family. This mapping identified putative contacts in the CynR regulatory domain dimer interface, which were targeted for alanine-scanning mutagenesis. Oligomerization was assayed by the ability of mutant lambda repressor-CynR fusions to assemble in E. coli revealing interesting similarities and differences between OxyR and CynR.
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Affiliation(s)
- Gwendowlyn S Knapp
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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8
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Abstract
We examine the contribution of residues at the dimer interface of the transcriptional regulator OxyR to oligomerization. Residues in contact across the dimer interface of OxyR were identified using the program Quaternary Contacts (QContacts). Site-directed mutagenesis was performed on the non-alanine or glycine residues identified in the resultant contact profile and the oligomerization ability of the mutant proteins was tested using the lambdacI repressor system to identify residues that are hot spots in OxyR. We compared the properties of these hot spots to those described in the literature from other systems. The hot spots identified in this study are not especially conserved amongst a set of OxyR orthologs.
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Affiliation(s)
- Gwendowlyn S Knapp
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
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9
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Novel Structure of the Conserved Gram-Negative Lipopolysaccharide Transport Protein A and Mutagenesis Analysis. J Mol Biol 2008; 380:476-88. [DOI: 10.1016/j.jmb.2008.04.045] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 04/15/2008] [Accepted: 04/16/2008] [Indexed: 11/19/2022]
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Xu Q, Canutescu AA, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL. Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol 2008; 381:487-507. [PMID: 18599072 DOI: 10.1016/j.jmb.2008.06.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 05/30/2008] [Accepted: 06/02/2008] [Indexed: 11/27/2022]
Abstract
Many proteins function as homo-oligomers and are regulated via their oligomeric state. For some proteins, the stoichiometry of homo-oligomeric states under various conditions has been studied using gel filtration or analytical ultracentrifugation experiments. The interfaces involved in these assemblies may be identified using cross-linking and mass spectrometry, solution-state NMR, and other experiments. However, for most proteins, the actual interfaces that are involved in oligomerization are inferred from X-ray crystallographic structures using assumptions about interface surface areas and physical properties. Examination of interfaces across different Protein Data Bank (PDB) entries in a protein family reveals several important features. First, similarities in space group, asymmetric unit size, and cell dimensions and angles (within 1%) do not guarantee that two crystals are actually the same crystal form, containing similar relative orientations and interactions within the crystal. Conversely, two crystals in different space groups may be quite similar in terms of all the interfaces within each crystal. Second, NMR structures and an existing benchmark of PDB crystallographic entries consisting of 126 dimers as well as larger structures and 132 monomers were used to determine whether the existence or lack of common interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. Monomeric proteins tend to have common interfaces across only a minority of crystal forms, whereas higher-order structures exhibit common interfaces across a majority of available crystal forms. The data can be used to estimate the probability that an interface is biological if two or more crystal forms are available. Finally, the Protein Interfaces, Surfaces, and Assemblies (PISA) database available from the European Bioinformatics Institute is more consistent in identifying interfaces observed in many crystal forms compared with the PDB and the European Bioinformatics Institute's Protein Quaternary Server (PQS). The PDB, in particular, is missing highly likely biological interfaces in its biological unit files for about 10% of PDB entries.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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Jin H, Hayes GL, Darbha NS, Meyer E, LiWang PJ. Investigation of CC and CXC chemokine quaternary state mutants. Biochem Biophys Res Commun 2005; 338:987-99. [PMID: 16256937 DOI: 10.1016/j.bbrc.2005.10.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Accepted: 10/07/2005] [Indexed: 11/29/2022]
Abstract
The chemokine family forms two different types of homodimer despite members sharing nearly identical folds. To study the formation of quaternary structure in this family, rational mutagenesis was employed on a representative member of each subfamily (MIP-1beta and IL-8). The variants were studied by analytical ultracentrifugation and NMR, and it was determined that formation of a folded monomer from a natural chemokine dimer is reasonably facile, while conversion between dimer types is not. Monomeric variants of MIP-1beta and IL-8 were randomly mutated and a lambda phage-based selection system was employed in a novel way to screen for dimerization. A total of 6,000,000 random mutants were screened, but no dimers were formed, suggesting again that the chemokine fold is robust and amenable to sequence variation, while the chemokine dimer is much more difficult to attain. This work represents a biophysical analysis of an array of chemokine quaternary state variants.
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Affiliation(s)
- Hongjun Jin
- Department of Biochemistry and Biophysics, Texas A&M University, TAMU 2128, College Station, TX 77843-2128, USA
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Abstract
The complement of expressed cellular proteins - the proteome - is organized into functional, structured networks of protein interactions that mediate assembly of molecular machines and dynamic cellular pathways. Recent studies reveal the biological roles of protein interactions in bacteriophage T7 and Helicobacter pylori, and new methods allow to compare and to predict interaction networks in other species. Smaller scale networks provide biological insights into DNA replication and chromosome dynamics in Bacillus subtilis and Archeoglobus fulgidus, and into the assembly of multiprotein complexes such as the type IV secretion system of Agrobacterium tumefaciens, and the cell division machinery of Escherichia coli. Genome-wide interaction networks in several species are needed to obtain a biologically meaningful view of the higher order organization of the proteome in bacteria.
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Affiliation(s)
- Philippe Noirot
- Laboratoire de Génétique Microbienne, INRA, domaine de Vilvert, 78352 Jouy en Josas cedex, France.
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