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Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis. Environ Microbiol 2016; 18:3403-3424. [DOI: 10.1111/1462-2920.13230] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Eugeni Belda
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology; 28, rue du Dr. Roux, Paris, Cedex 15 75724 France
| | - Ruben G. A. van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Maria José Lopez-Sanchez
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Valérie Barbe
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center; 2 rue Gaston Crémieux 91057 Evry France
| | - Claire Fraser
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore MD USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
- School of Biology, Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Anne Morgat
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics; Geneva CH-1206 Switzerland
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - David Vallenet
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Zoé Rouy
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Claudine Médigue
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
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Structural analysis of hypothetical proteins from Helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins. Int J Mol Sci 2012; 13:7109-7137. [PMID: 22837682 PMCID: PMC3397514 DOI: 10.3390/ijms13067109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/29/2012] [Accepted: 06/01/2012] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.
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Abstract
Genomic sequences have been determined for a number of strains of Helicobacter pylori (H pylori) and related bacteria. With the development of microarray analysis and the wide use of subtractive hybridization techniques, comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria. It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties. A great pool of auxillary genes are mainly from the categories of cag pathogenicity islands, outer membrane proteins, restriction-modification system and hypothetical proteins of unknown function. Persistence of H pylori in the human stomach leads to the diversification of the genome. Comparative genomics suggest that a host jump has occurs from humans to felines. Candidate genes specific for the development of the gastric diseases were identified. With the aid of proteomics, population genetics and other molecular methods, future comparative genomic studies would dramatically promote our understanding of the evolution, pathogenesis and microbiology of H pylori.
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Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. BMC Bioinformatics 2007; 8:47. [PMID: 17286872 PMCID: PMC1805508 DOI: 10.1186/1471-2105-8-47] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 02/08/2007] [Indexed: 11/15/2022] Open
Abstract
Background Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs) are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy. Results Based on a biological representation of the translation process, we applied Bayesian statistics to create a score function for predicting translation initiation sites. In contrast to existing programs, our combination of methods uses supervised learning to optimally use the set of known translation initiation sites. We combined the Ribosome Binding Site (RBS) sequence, the distance between the translation initiation site and the RBS sequence, the base composition of the start codon, the nucleotide composition (A-rich sequences) following start codons, and the expected distribution of the protein length in a Bayesian scoring function. To further increase the prediction accuracy, we also took into account the operon orientation. The outcome of the procedure achieved a prediction accuracy of 93.2% in 858 E. coli genes from the EcoGene data set and 92.7% accuracy in a data set of 1243 Bacillus subtilis 'non-y' genes. We confirmed the performance in the GC-rich Gamma-Proteobacteria Herminiimonas arsenicoxydans, Pseudomonas aeruginosa, and Burkholderia pseudomallei K96243. Conclusion Hon-yaku, being based on a careful choice of elements important in translation, improved the prediction accuracy in B. subtilis data sets and other bacteria except for E. coli. We believe that most remaining mispredictions are due to atypical ribosomal binding sequences used in specific translation control processes, or likely errors in the training data sets.
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Kakizawa S, Oshima K, Nishigawa H, Jung HY, Wei W, Suzuki S, Tanaka M, Miyata SI, Ugaki M, Namba S. Secretion of immunodominant membrane protein from onion yellows phytoplasma through the Sec protein-translocation system in Escherichia coli. MICROBIOLOGY-SGM 2004; 150:135-142. [PMID: 14702406 DOI: 10.1099/mic.0.26521-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A gene that encodes a putative SecE protein, which is a component of the Sec protein-translocation system, was cloned from the onion yellows phytoplasma (OY). The identification of this gene and the previously reported genes encoding SecA and SecY provides evidence that the Sec system exists in phytoplasma. In addition, a gene encoding an antigenic membrane protein (Amp) (a type of immunodominant membrane protein) of OY was cloned and sequenced. The OY amp gene consisted of 702 nt encoding a protein of 233 aa which was highly similar to Amp of aster yellows phytoplasma (AY). Part of OY Amp was overexpressed in Escherichia coli, purified, and used to raise an anti-Amp polyclonal antibody. The anti-Amp antibody reacted specifically with an OY-infected plant extract in Western blot analysis and was therefore useful for the detection of OY as well as Amp. Amp has a conserved protein motif that is known to be exported by the Sec system of E. coli. A partial OY Amp protein expressed in E. coli was localized in the periplasm as a shorter, putatively processed form of the protein. It had probably been exported from the cytoplasm to the periplasm through the Sec system. Moreover, OY Amp protein expressed in OY and detected in OY-infected plants was apparently also processed. Because phytoplasmas cannot be cultured or transformed, little information is available regarding their protein secretion systems. This study suggests that the Sec system operates in this phytoplasma to export OY Amp.
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Affiliation(s)
- Shigeyuki Kakizawa
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Kenro Oshima
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Hisashi Nishigawa
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Hee-Young Jung
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Wei Wei
- Division of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shiho Suzuki
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Minoru Tanaka
- National Agricultural Research Center, National Agricultural Research Organization, 3-1-1 Kannondai, Tsukuba-shi, Ibaraki 305-8666, Japan
| | - Shin-Ichi Miyata
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Masashi Ugaki
- Division of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
| | - Shigetou Namba
- Division of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Division of Integrated Biosciences, The University of Tokyo, 202 Bioscience Bldg, 5-1-5 Kashiwanoha, Chiba 277-8562, Japan
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Fitchen N, Williams P, Hardie KR. Functional complementation of E. coli secD and secG mutants by Helicobacter pylori homologues. FEMS Microbiol Lett 2004; 229:57-63. [PMID: 14659543 DOI: 10.1016/s0378-1097(03)00786-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Sec machinery is one mechanism used by bacteria to translocate proteins across their cytoplasmic membrane. Most of the Sec components have been identified within the important gastric pathogen, Helicobacter pylori, however their functionality has not yet been demonstrated. Here we report the existence of putative homologues to the Sec components yajC (HP1450) and yidC (HP1551), and demonstrate the ability of the H. pylori secD (HP1550) and secG (HP1255) homologues to facilitate inner membrane translocation of the maltose-binding protein MalE, by complementation of the respective secretion-deficient Escherichia coli mutants, thus providing evidence of their functionality.
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Affiliation(s)
- Nicola Fitchen
- Institute of Infection, Immunity, and Inflammation, University of Nottingham, Queen's Medical School, C-floor West block, Nottingham NG7 2UH, UK
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Bocs S, Cruveiller S, Vallenet D, Nuel G, Médigue C. AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res 2003; 31:3723-6. [PMID: 12824403 PMCID: PMC168996 DOI: 10.1093/nar/gkg590] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED AMIGene (Annotation of MIcrobial Genes) is an application for automatically identifying the most likely coding sequences (CDSs) in a large contig or a complete bacterial genome sequence. The first step in AMIGene is dedicated to the construction of Markov models that fit the input genomic data (i.e. the gene model), followed by the combination of well-known gene-finding methods and an heuristic approach for the selection of the most likely CDSs. The web interface allows the user to select one or several gene models applied to the analysis of the input sequence by the AMIGene program and to visualize the list of predicted CDSs graphically and in a downloadable text format. The AMIGene web site is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/amigene/index.html ( CONTACT sbocs@genoscope.cns.fr).
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Affiliation(s)
- Stéphanie Bocs
- Génoscope/UMR-CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Crémieux, F-91006 Evry, France
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Boneca IG, de Reuse H, Epinat JC, Pupin M, Labigne A, Moszer I. A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res 2003; 31:1704-14. [PMID: 12626712 PMCID: PMC152854 DOI: 10.1093/nar/gkg250] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Huge amounts of genomic information are currently being generated. Therefore, biologists require structured, exhaustive and comparative databases. The PyloriGene database (http://genolist.pasteur.fr/PyloriGene) was developed to respond to these needs, by integrating and connecting the information generated during the sequencing of two distinct strains of Helicobacter pylori. This led to the need for a general annotation consensus, as the physical and functional annotations of the two strains differed significantly in some cases. A revised functional classification system was created to accommodate the existing data and to make it possible to classify coding sequences (CDS) into several functional categories to harmonize CDS classification. The annotation of the two complete genomes was revised in the light of new data, allowing us to reduce the percentage of hypothetical proteins from approximately 40 to 33%. This resulted in the reassignment of functions for 108 CDS (approximately 7% of all CDS). Interestingly, the functions of only approximately 13% of CDS (222 out of 1658 CDS) were annotated as a result of work done directly on H.pylori genes. Finally, comparison of the two published genomes revealed a significant amount of size variation between corresponding (orthologous) CDS. Most of these size variations were due to natural polymorphisms, although other sources of variation were identified, such as pseudogenes, new genes potentially regulated by slipped-strand mispairing mechanism, or frame-shifts. 113 of these differences were due to different start codon assignments, a common problem when constructing physical annotations.
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Affiliation(s)
- Ivo G Boneca
- Unité de Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France.
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