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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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2
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Kozak K, Papierniak-Wygladala A, Palusińska M, Barabasz A, Antosiewicz DM. Regulation and Function of Metal Uptake Transporter NtNRAMP3 in Tobacco. FRONTIERS IN PLANT SCIENCE 2022; 13:867967. [PMID: 35712563 PMCID: PMC9195099 DOI: 10.3389/fpls.2022.867967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/29/2022] [Indexed: 05/06/2023]
Abstract
Natural resistance-associated macrophage protein (NRAMP) genes encode proteins with low substrate specificity, important for maintaining metal cross homeostasis in the cell. The role of these proteins in tobacco, an important crop plant with wide application in the tobacco industry as well as in phytoremediation of metal-contaminated soils, remains unknown. Here, we identified NtNRAMP3, the closest homologue to NRAMP3 proteins from other plant species, and functionally characterized it. A NtNRAMP3-GFP fusion protein was localized to the plasma membrane in tobacco epidermal cells. Expression of NtNRAMP3 in yeast was able to rescue the growth of Fe and Mn uptake defective Δfet3fet4 and Δsmf1 mutant yeast strains, respectively. Furthermore, NtNRAMP3 expression in wild-type Saccharomyces cerevisiae DY1457 yeast strain increased sensitivity to elevated concentrations of iron (Fe), manganese (Mn), copper (Cu), cobalt (Co), nickel (Ni), and cadmium (Cd). Taken together, these results point to a possible role in the uptake of metals. NtNRAMP3 was expressed in the leaves and to a lesser extent in the roots of tobacco plants. Its expression occurred mainly under control conditions and decreased very sharply in deficiency and excess of the tested metals. GUS-based analysis of the site-specific activity of the NtNRAMP3 promoter showed that it was primarily expressed in the xylem of leaf blades. Overall, our data indicate that the main function of NtNRAMP3 is to maintain cross homeostasis of Fe, Mn, Co, Cu, and Ni (also Cd) in leaves under control conditions by controlling xylem unloading.
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Affiliation(s)
| | | | | | | | - Danuta Maria Antosiewicz
- Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland
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3
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Lery LMS, Frangeul L, Tomas A, Passet V, Almeida AS, Bialek-Davenet S, Barbe V, Bengoechea JA, Sansonetti P, Brisse S, Tournebize R. Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor. BMC Biol 2014; 12:41. [PMID: 24885329 PMCID: PMC4068068 DOI: 10.1186/1741-7007-12-41] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 12/17/2022] Open
Abstract
Background Klebsiella pneumoniae strains are pathogenic to animals and humans, in which they are both a frequent cause of nosocomial infections and a re-emerging cause of severe community-acquired infections. K. pneumoniae isolates of the capsular serotype K2 are among the most virulent. In order to identify novel putative virulence factors that may account for the severity of K2 infections, the genome sequence of the K2 reference strain Kp52.145 was determined and compared to two K1 and K2 strains of low virulence and to the reference strains MGH 78578 and NTUH-K2044. Results In addition to diverse functions related to host colonization and virulence encoded in genomic regions common to the four strains, four genomic islands specific for Kp52.145 were identified. These regions encoded genes for the synthesis of colibactin toxin, a putative cytotoxin outer membrane protein, secretion systems, nucleases and eukaryotic-like proteins. In addition, an insertion within a type VI secretion system locus included sel1 domain containing proteins and a phospholipase D family protein (PLD1). The pld1 mutant was avirulent in a pneumonia model in mouse. The pld1 mRNA was expressed in vivo and the pld1 gene was associated with K. pneumoniae isolates from severe infections. Analysis of lipid composition of a defective E. coli strain complemented with pld1 suggests an involvement of PLD1 in cardiolipin metabolism. Conclusions Determination of the complete genome of the K2 reference strain identified several genomic islands comprising putative elements of pathogenicity. The role of PLD1 in pathogenesis was demonstrated for the first time and suggests that lipid metabolism is a novel virulence mechanism of K. pneumoniae.
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Affiliation(s)
- Letícia M S Lery
- Institut Pasteur - Pathogénie Microbienne Moléculaire, Paris, France.
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Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae. Antimicrob Agents Chemother 2014; 58:4207-10. [PMID: 24752259 DOI: 10.1128/aac.02773-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including β-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6'-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers.
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Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00280-13. [PMID: 23766401 PMCID: PMC3707572 DOI: 10.1128/genomea.00280-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two species commonly isolated from the external ear canal of Caprinae.
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Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00348-13. [PMID: 23766408 PMCID: PMC3707579 DOI: 10.1128/genomea.00348-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium. These three species are regularly isolated from bovine clinical specimens, although their role in disease is unclear.
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Complete nucleotide sequence of the first KPC-2- and SHV-12-encoding IncX plasmid, pKpS90, from Klebsiella pneumoniae. Antimicrob Agents Chemother 2012; 57:618-20. [PMID: 23089759 DOI: 10.1128/aac.01712-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete nucleotide sequence of the pKpS90 plasmid, carrying the bla(KPC-2) and bla(SHV-12) genes. This plasmid was isolated from a sequence type 258 (ST258) Klebsiella pneumoniae strain responsible for an outbreak in a French university hospital in 2009. pKpS90 is a 53,286-bp plasmid that belongs to the IncX incompatibility group. pKpS90 consists of a backbone from IncX plasmids, in which the KPC-2-encoding Tn4401 transposon and a bla(SHV-12)-encoding region have been inserted.
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Dupuy V, Manso-Silván L, Barbe V, Thebault P, Dordet-Frisoni E, Citti C, Poumarat F, Blanchard A, Breton M, Sirand-Pugnet P, Thiaucourt F. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides "Small Colony". PLoS One 2012; 7:e46821. [PMID: 23071648 PMCID: PMC3468273 DOI: 10.1371/journal.pone.0046821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/05/2012] [Indexed: 02/06/2023] Open
Abstract
Mycoplasma mycoides subsp. mycoides "Small Colony" (MmmSC) is responsible for contagious bovine pleuropneumonia (CBPP) in bovidae, a notifiable disease to the World Organization for Animal Health (OIE). Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th) century through the cattle trade and was eradicated from most continents by stamping-out policies. During the 20(th) century it persisted in Africa, and it reappeared sporadically in Southern Europe. Yet, classical epidemiology studies failed to explain the re-occurrence of the disease in Europe in the 1990s. The objectives of this study were to obtain a precise phylogeny of this pathogen, reconstruct its evolutionary history, estimate the date of its emergence, and determine the origin of the most recent European outbreaks. A large-scale genomic approach based on next-generation sequencing technologies was applied to construct a robust phylogeny of this extremely monomorphic pathogen by using 20 representative strains of various geographical origins. Sixty two polymorphic genes of the MmmSC core genome were selected, representing 83601 bp in total and resulting in 139 SNPs within the 20 strains. A robust phylogeny was obtained that identified a lineage specific to European strains; African strains were scattered in various branches. Bayesian analysis allowed dating the most recent common ancestor for MmmSC around 1700. The strains circulating in Sub-Saharan Africa today, however, were shown to descend from a strain that existed around 1810. MmmSC emerged recently, about 300 years ago, and was most probably exported from Europe to other continents, including Africa, during the 19(th) century. Its diversity is now greater in Africa, where CBPP is enzootic, than in Europe, where outbreaks occurred sporadically until 1999 and where CBPP may now be considered eradicated unless MmmSC remains undetected.
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Affiliation(s)
- Virginie Dupuy
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
| | - Lucía Manso-Silván
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
| | | | - Patricia Thebault
- Université de Bordeaux, Centre de bioinformatique et de génomique fonctionnelle, CBiB, Bordeaux, France
| | - Emilie Dordet-Frisoni
- Institut National de Recherche Agronomique, école vétérinaire de Toulouse UMR 1225, Toulouse, France
- Université de Toulouse, INP, ENVT, UMR1225, IHAP, Toulouse, France
| | - Christine Citti
- Institut National de Recherche Agronomique, école vétérinaire de Toulouse UMR 1225, Toulouse, France
- Université de Toulouse, INP, ENVT, UMR1225, IHAP, Toulouse, France
| | - François Poumarat
- Agence Nationale de Sécurité Sanitaire, Laboratoire de Lyon, UMR mycoplasmoses des ruminants, Lyon, France
| | - Alain Blanchard
- Université de Bordeaux, UMR1332, Villenave d'Ornon, France
- Institut National de Recherche Agronomique, UMR1332, Villenave d'Ornon, France
| | - Marc Breton
- Université de Bordeaux, UMR1332, Villenave d'Ornon, France
- Institut National de Recherche Agronomique, UMR1332, Villenave d'Ornon, France
| | - Pascal Sirand-Pugnet
- Université de Bordeaux, UMR1332, Villenave d'Ornon, France
- Institut National de Recherche Agronomique, UMR1332, Villenave d'Ornon, France
| | - François Thiaucourt
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
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Drieux L, Decre D, Frangeul L, Arlet G, Jarlier V, Sougakoff W. Complete nucleotide sequence of the large conjugative pTC2 multireplicon plasmid encoding the VIM-1 metallo- -lactamase. J Antimicrob Chemother 2012; 68:97-100. [DOI: 10.1093/jac/dks367] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, Izar B, Mohamed W, Mraheil MA, Domann E, Schaffrath S, Kärst U, Goesmann A, Oehm S, Pühler A, Merkl R, Vorwerk S, Glaser P, Garrido P, Rusniok C, Buchrieser C, Goebel W, Chakraborty T. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics 2012; 13:144. [PMID: 22530965 PMCID: PMC3464598 DOI: 10.1186/1471-2164-13-144] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 04/12/2012] [Indexed: 12/13/2022] Open
Abstract
Background Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. Results The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. Conclusion Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
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Affiliation(s)
- Torsten Hain
- Institute of Medical Microbiology, Justus-Liebig-University, Schubertstrasse 81, Giessen, D-35392, Germany
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Emergence of atypical Mycoplasma agalactiae strains harboring a new prophage and associated with an alpine wild ungulate mortality episode. Appl Environ Microbiol 2012; 78:4659-68. [PMID: 22522685 DOI: 10.1128/aem.00332-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterium Mycoplasma agalactiae is responsible for contagious agalactia (CA) in small domestic ruminants, a syndrome listed by the World Organization for Animal Health and responsible for severe damage to the dairy industry. Recently, we frequently isolated this pathogen from lung lesions of ibexes during a mortality episode in the French Alps. This situation was unusual in terms of host specificity and tissue tropism, raising the question of M. agalactiae emergence in wildlife. To address this issue, the ibex isolates were characterized using a combination of approaches that included antigenic profiles, molecular typing, optical mapping, and whole-genome sequencing. Genome analyses showed the presence of a new, large prophage containing 35 coding sequences (CDS) that was detected in most but not all ibex strains and has a homolog in Mycoplasma conjunctivae, a species causing keratoconjunctivitis in wild ungulates. This and the presence in all strains of large integrated conjugative elements suggested highly dynamic genomes. Nevertheless, M. agalactiae strains circulating in the ibex population were shown to be highly related, most likely originating from a single parental clone that has also spread to another wild ungulate species of the same geographical area, the chamois. These strains clearly differ from strains described in Europe so far, including those found nearby, before CA eradication a few years ago. While M. agalactiae pathogenicity in ibexes remains unclear, our data showed the emergence of atypical strains in Alpine wild ungulates, raising the question of a role for the wild fauna as a potential reservoir of pathogenic mycoplasmas.
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Complete genome sequence of the animal pathogen Listeria ivanovii, which provides insights into host specificities and evolution of the genus Listeria. J Bacteriol 2012; 193:6787-8. [PMID: 22072644 DOI: 10.1128/jb.06120-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete and annotated genome sequence of the animal pathogen Listeria ivanovii subsp. ivanovii strain PAM 55 (serotype 5), isolated in 1997 in Spain from an outbreak of abortion in sheep. The sequence and its analysis are available at an interactive genome browser at the Institut Pasteur (http://genolist.pasteur.fr/LivaList/).
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Fevre C, Passet V, Deletoile A, Barbe V, Frangeul L, Almeida AS, Sansonetti P, Tournebize R, Brisse S. PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma. PLoS Negl Trop Dis 2011; 5:e1052. [PMID: 21629720 PMCID: PMC3101168 DOI: 10.1371/journal.pntd.0001052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 04/26/2011] [Indexed: 11/21/2022] Open
Abstract
Rhinoscleroma is a chronic granulomatous infection of the upper airways caused by the bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. The disease is endemic in tropical and subtropical areas, but its diagnosis remains difficult. As a consequence, and despite available antibiotherapy, some patients evolve advanced stages that can lead to disfiguration, severe respiratory impairment and death by anoxia. Because identification of the etiologic agent is crucial for the definitive diagnosis of the disease, the aim of this study was to develop two simple PCR assays. We took advantage of the fact that all Klebsiella pneumoniae subsp. rhinoscleromatis isolates are (i) of capsular serotype K3; and (ii) belong to a single clone with diagnostic single nucleotide polymorphisms (SNP). The complete sequence of the genomic region comprising the capsular polysaccharide synthesis (cps) gene cluster was determined. Putative functions of the 21 genes identified were consistent with the structure of the K3 antigen. The K3-specific sequence of gene Kr11509 (wzy) was exploited to set up a PCR test, which was positive for 40 K3 strains but negative when assayed on the 76 other Klebsiella capsular types. Further, to discriminate Klebsiella pneumoniae subsp. rhinoscleromatis from other K3 Klebsiella strains, a specific PCR assay was developed based on diagnostic SNPs in the phosphate porin gene phoE. This work provides rapid and simple molecular tools to confirm the diagnostic of rhinoscleroma, which should improve patient care as well as knowledge on the prevalence and epidemiology of rhinoscleroma.
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Affiliation(s)
- Cindy Fevre
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Virginie Passet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Alexis Deletoile
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | - Lionel Frangeul
- Institut Pasteur, Intégration et Analyse Génomique, Paris, France
| | - Ana S. Almeida
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Régis Tournebize
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
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Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective. BMC Genomics 2011; 12:114. [PMID: 21324191 PMCID: PMC3053259 DOI: 10.1186/1471-2164-12-114] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 02/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagious bovine pleuropneumonia. Its very close relative, Mycoplasma mycoides subsp. capri (Mmc), is a more ubiquitous pathogen in small ruminants causing mastitis, arthritis, keratitis, pneumonia and septicaemia and is also found as saprophyte in the ear canal. To understand the genetics underlying these phenotypic differences, we compared the MmmSC PG1 type strain genome, which was already available, with the genome of an Mmc field strain (95010) that was sequenced in this study. We also compared the 95010 genome with the recently published genome of another Mmc strain (GM12) to evaluate Mmc strain diversity. RESULTS The MmmSC PG1 genome is 1,212 kbp and that of Mmc 95010 is ca. 58 kbp shorter. Most of the sequences present in PG1 but not 95010 are highly repeated Insertion Sequences (three types of IS) and large duplicated DNA fragments. The 95010 genome contains five types of IS, present in fewer copies than in PG1, and two copies of an integrative conjugative element. These mobile genetic elements have played a key role in genome plasticity, leading to inversions of large DNA fragments. Comparison of the two genomes suggested a marked decay of the PG1 genome that seems to be correlated with a greater number of IS. The repertoire of gene families encoding surface proteins is smaller in PG1. Several genes involved in polysaccharide metabolism and protein degradation are also absent from, or degraded in, PG1. CONCLUSIONS The genome of MmmSC PG1 is larger than that of Mmc 95010, its very close relative, but has less coding capacity. This is the result of large genetic rearrangements due to mobile elements that have also led to marked gene decay. This is consistent with a non-adaptative genomic complexity theory, allowing duplications or pseudogenes to be maintained in the absence of adaptive selection that would lead to purifying selection and genome streamlining over longer evolutionary times. These findings also suggest that MmmSC only recently adapted to its bovine host.
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Specific real-time PCR for simultaneous detection and identification of Legionella pneumophila serogroup 1 in water and clinical samples. Appl Environ Microbiol 2010; 77:1708-17. [PMID: 21193672 DOI: 10.1128/aem.02261-10] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Legionella pneumophila, a bacterium that replicates within aquatic amoebae and persists in the environment as a free-living microbe, is the causative agent of Legionnaires' disease. Among the many Legionella species described, L. pneumophila is associated with 90% of human disease, and within the 15 serogroups (Sg), L. pneumophila Sg1 causes more than 84% of Legionnaires' disease worldwide. Thus, rapid and specific identification of L. pneumophila Sg1 is of the utmost importance for evaluation of the contamination of collective water systems and the risk posed. Previously we had shown that about 20 kb of the 33-kb locus carrying the genes coding for the proteins involved in lipopolysaccharide biosynthesis (LPS gene cluster) by L. pneumophila was highly specific for Sg1 strains and that three genes (lpp0831, wzm, and wzt) may serve as genetic markers. Here we report the sequencing and comparative analyses of this specific region of the LPS gene cluster in L. pneumophila Sg6, -10, -12, -13, and -14. Indeed, the wzm and wzt genes were present only in the Sg1 LPS gene cluster, which showed a very specific gene content with respect to the other five serogroups investigated. Based on this observation, we designed primers and developed a classical and a real-time PCR method for the detection and simultaneous identification of L. pneumophila Sg1 in clinical and environmental isolates. Evaluation of the selected primers with 454 Legionella and 38 non-Legionella strains demonstrated 100% specificity. Sensitivity, specificity, and predictive values were further evaluated with 209 DNA extracts from water samples of hospital water supply systems and with 96 respiratory specimens. The results showed that the newly developed quantitative Sg1-specific PCR method is a highly specific and efficient tool for the surveillance and rapid detection of high-risk L. pneumophila Sg1 in water and clinical samples.
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Cazalet C, Gomez-Valero L, Rusniok C, Lomma M, Dervins-Ravault D, Newton HJ, Sansom FM, Jarraud S, Zidane N, Ma L, Bouchier C, Etienne J, Hartland EL, Buchrieser C. Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease. PLoS Genet 2010; 6:e1000851. [PMID: 20174605 PMCID: PMC2824747 DOI: 10.1371/journal.pgen.1000851] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 01/20/2010] [Indexed: 12/15/2022] Open
Abstract
Legionella pneumophila and L. longbeachae are two species of a large genus of bacteria that are ubiquitous in nature. L. pneumophila is mainly found in natural and artificial water circuits while L. longbeachae is mainly present in soil. Under the appropriate conditions both species are human pathogens, capable of causing a severe form of pneumonia termed Legionnaires' disease. Here we report the sequencing and analysis of four L. longbeachae genomes, one complete genome sequence of L. longbeachae strain NSW150 serogroup (Sg) 1, and three draft genome sequences another belonging to Sg1 and two to Sg2. The genome organization and gene content of the four L. longbeachae genomes are highly conserved, indicating strong pressure for niche adaptation. Analysis and comparison of L. longbeachae strain NSW150 with L. pneumophila revealed common but also unexpected features specific to this pathogen. The interaction with host cells shows distinct features from L. pneumophila, as L. longbeachae possesses a unique repertoire of putative Dot/Icm type IV secretion system substrates, eukaryotic-like and eukaryotic domain proteins, and encodes additional secretion systems. However, analysis of the ability of a dotA mutant of L. longbeachae NSW150 to replicate in the Acanthamoeba castellanii and in a mouse lung infection model showed that the Dot/Icm type IV secretion system is also essential for the virulence of L. longbeachae. In contrast to L. pneumophila, L. longbeachae does not encode flagella, thereby providing a possible explanation for differences in mouse susceptibility to infection between the two pathogens. Furthermore, transcriptome analysis revealed that L. longbeachae has a less pronounced biphasic life cycle as compared to L. pneumophila, and genome analysis and electron microscopy suggested that L. longbeachae is encapsulated. These species-specific differences may account for the different environmental niches and disease epidemiology of these two Legionella species.
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Affiliation(s)
- Christel Cazalet
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS URA 2171, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS URA 2171, Paris, France
| | - Christophe Rusniok
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS URA 2171, Paris, France
| | - Mariella Lomma
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS URA 2171, Paris, France
| | | | - Hayley J. Newton
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Fiona M. Sansom
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Sophie Jarraud
- Centre National de Référence des Legionella, Université de Lyon, INSERM U851, Faculté de Médecine, IFR 128, Lyon, France
| | - Nora Zidane
- Institut Pasteur, Plate-forme Génomique, Pasteur Génopole Ile de France, Paris, France
| | - Laurence Ma
- Institut Pasteur, Plate-forme Génomique, Pasteur Génopole Ile de France, Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Plate-forme Génomique, Pasteur Génopole Ile de France, Paris, France
| | - Jerôme Etienne
- Centre National de Référence des Legionella, Université de Lyon, INSERM U851, Faculté de Médecine, IFR 128, Lyon, France
| | - Elizabeth L. Hartland
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS URA 2171, Paris, France
- * E-mail:
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Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis. J Bacteriol 2010; 192:2266-76. [PMID: 20139183 DOI: 10.1128/jb.01659-09] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Streptococcus gallolyticus (formerly known as Streptococcus bovis biotype I) is an increasing cause of endocarditis among streptococci and frequently associated with colon cancer. S. gallolyticus is part of the rumen flora but also a cause of disease in ruminants as well as in birds. Here we report the complete nucleotide sequence of strain UCN34, responsible for endocarditis in a patient also suffering from colon cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome revealed unique features among streptococci, probably related to its adaptation to the rumen environment and its capacity to cause endocarditis. S. gallolyticus has the capacity to use a broad range of carbohydrates of plant origin, in particular to degrade polysaccharides derived from the plant cell wall. Its genome encodes a large repertoire of transporters and catalytic activities, like tannase, phenolic compounds decarboxylase, and bile salt hydrolase, that should contribute to the detoxification of the gut environment. Furthermore, S. gallolyticus synthesizes all 20 amino acids and more vitamins than any other sequenced Streptococcus species. Many of the genes encoding these specific functions were likely acquired by lateral gene transfer from other bacterial species present in the rumen. The surface properties of strain UCN34 may also contribute to its virulence. A polysaccharide capsule might be implicated in resistance to innate immunity defenses, and glucan mucopolysaccharides, three types of pili, and collagen binding proteins may play a role in adhesion to tissues in the course of endocarditis.
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Nouvel LX, Sirand-Pugnet P, Marenda MS, Sagné E, Barbe V, Mangenot S, Schenowitz C, Jacob D, Barré A, Claverol S, Blanchard A, Citti C. Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. BMC Genomics 2010; 11:86. [PMID: 20122262 PMCID: PMC2824730 DOI: 10.1186/1471-2164-11-86] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 02/02/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study. RESULTS The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms. CONCLUSION Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.
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Affiliation(s)
- Laurent X Nouvel
- Université de Toulouse, ENVT, UMR 1225 Interactions Hôtes - Agents Pathogènes, 31076 Toulouse, France
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Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, Barré A, Avenaud P, Jacob D, Couloux A, Barbe V, de Daruvar A, Blanchard A, Bébéar C. Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet 2009; 5:e1000677. [PMID: 19816563 PMCID: PMC2751442 DOI: 10.1371/journal.pgen.1000677] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 09/07/2009] [Indexed: 12/24/2022] Open
Abstract
Mycoplasma hominis is an opportunistic human mycoplasma. Two other pathogenic human species, M. genitalium and Ureaplasma parvum, reside within the same natural niche as M. hominis: the urogenital tract. These three species have overlapping, but distinct, pathogenic roles. They have minimal genomes and, thus, reduced metabolic capabilities characterized by distinct energy-generating pathways. Analysis of the M. hominis PG21 genome sequence revealed that it is the second smallest genome among self-replicating free living organisms (665,445 bp, 537 coding sequences (CDSs)). Five clusters of genes were predicted to have undergone horizontal gene transfer (HGT) between M. hominis and the phylogenetically distant U. parvum species. We reconstructed M. hominis metabolic pathways from the predicted genes, with particular emphasis on energy-generating pathways. The Embden–Meyerhoff–Parnas pathway was incomplete, with a single enzyme absent. We identified the three proteins constituting the arginine dihydrolase pathway. This pathway was found essential to promote growth in vivo. The predicted presence of dimethylarginine dimethylaminohydrolase suggested that arginine catabolism is more complex than initially described. This enzyme may have been acquired by HGT from non-mollicute bacteria. Comparison of the three minimal mollicute genomes showed that 247 CDSs were common to all three genomes, whereas 220 CDSs were specific to M. hominis, 172 CDSs were specific to M. genitalium, and 280 CDSs were specific to U. parvum. Within these species-specific genes, two major sets of genes could be identified: one including genes involved in various energy-generating pathways, depending on the energy source used (glucose, urea, or arginine) and another involved in cytadherence and virulence. Therefore, a minimal mycoplasma cell, not including cytadherence and virulence-related genes, could be envisaged containing a core genome (247 genes), plus a set of genes required for providing energy. For M. hominis, this set would include 247+9 genes, resulting in a theoretical minimal genome of 256 genes. Mycoplasma hominis, M. genitalium, and Ureaplasma parvum are human pathogenic bacteria that colonize the urogenital tract. They have minimal genomes, and thus have a minimal metabolic capacity. However, they have distinct energy-generating pathways and distinct pathogenic roles. We compared the genomes of these three human pathogen minimal species, providing further insight into the composition of hypothetical minimal gene sets needed for life. To this end, we sequenced the whole M. hominis genome and reconstructed its energy-generating pathways from gene predictions. Its unusual major energy-producing pathway through arginine hydrolysis was confirmed in both genome analyses and in vivo assays. Our findings suggest that M. hominis and U. parvum underwent genetic exchange, probably while sharing a common host. We proposed a set of genes likely to represent a minimal genome. For M. hominis, this minimal genome, not including cytadherence and virulence-related genes, can be defined comprising the 247 genes shared by the three minimal genital mollicutes, combined with a set of nine genes needed for energy production for cell metabolism. This study provides insight for the synthesis of artificial genomes.
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Affiliation(s)
- Sabine Pereyre
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Pascal Sirand-Pugnet
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Laure Beven
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Alain Charron
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Hélène Renaudin
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Aurélien Barré
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
| | - Philippe Avenaud
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Daniel Jacob
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
| | | | - Valérie Barbe
- Génoscope, Centre National de Séquençage, Evry, France
| | - Antoine de Daruvar
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
- CNRS UMR 5800, Laboratoire Bordelais de Recherche en Informatique, Talence, France
| | - Alain Blanchard
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Cécile Bébéar
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
- * E-mail:
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Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Médigue C, Polz MF, Mazel D. Genome sequence ofVibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environ Microbiol 2009; 11:1959-70. [DOI: 10.1111/j.1462-2920.2009.01918.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Occurrence, plasticity, and evolution of the vpma gene family, a genetic system devoted to high-frequency surface variation in Mycoplasma agalactiae. J Bacteriol 2009; 191:4111-21. [PMID: 19376859 DOI: 10.1128/jb.00251-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma agalactiae, an important pathogen of small ruminants, exhibits a very versatile surface architecture by switching multiple, related lipoproteins (Vpmas) on and off. In the type strain, PG2, Vpma phase variation is generated by a cluster of six vpma genes that undergo frequent DNA rearrangements via site-specific recombination. To further comprehend the degree of diversity that can be generated at the M. agalactiae surface, the vpma gene repertoire of a field strain, 5632, was analyzed and shown to contain an extended repertoire of 23 vpma genes distributed between two loci located 250 kbp apart. Loci I and II include 16 and 7 vpma genes, respectively, with all vpma genes of locus II being duplicated at locus I. Several Vpmas displayed a chimeric structure suggestive of homologous recombination, and a global proteomic analysis further indicated that at least 13 of the 16 Vpmas can be expressed by the 5632 strain. Because a single promoter is present in each vpma locus, concomitant Vpma expression can occur in a strain with duplicated loci. Consequently, the number of possible surface combinations is much higher for strain 5632 than for the type strain. Finally, our data suggested that insertion sequences are likely to be involved in 5632 vpma locus duplication at a remote chromosomal position. The role of such mobile genetic elements in chromosomal shuffling of genes encoding major surface components may have important evolutionary and epidemiological consequences for pathogens, such as mycoplasmas, that have a reduced genome and no cell wall.
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Rosso ML, Chauvaux S, Dessein R, Laurans C, Frangeul L, Lacroix C, Schiavo A, Dillies MA, Foulon J, Coppée JY, Médigue C, Carniel E, Simonet M, Marceau M. Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression. BMC Microbiol 2008; 8:211. [PMID: 19055764 PMCID: PMC2631605 DOI: 10.1186/1471-2180-8-211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 12/03/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In man, infection by the Gram-negative enteropathogen Yersinia pseudotuberculosis is usually limited to the terminal ileum. However, in immunocompromised patients, the microorganism may disseminate from the digestive tract and thus cause a systemic infection with septicemia. RESULTS To gain insight into the metabolic pathways and virulence factors expressed by the bacterium at the blood stage of pseudotuberculosis, we compared the overall gene transcription patterns (the transcriptome) of bacterial cells cultured in either human plasma or Luria-Bertani medium. The most marked plasma-triggered metabolic consequence in Y. pseudotuberculosis was the switch to high glucose consumption, which is reminiscent of the acetogenic pathway (known as "glucose overflow") in Escherichia coli. However, upregulation of the glyoxylate shunt enzymes suggests that (in contrast to E. coli) acetate may be further metabolized in Y. pseudotuberculosis. Our data also indicate that the bloodstream environment can regulate major virulence genes (positively or negatively); the yadA adhesin gene and most of the transcriptional units of the pYV-encoded type III secretion apparatus were found to be upregulated, whereas transcription of the pH6 antigen locus was strongly repressed. CONCLUSION Our results suggest that plasma growth of Y. pseudotuberculosis is responsible for major transcriptional regulatory events and prompts key metabolic reorientations within the bacterium, which may in turn have an impact on virulence.
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Affiliation(s)
- Marie-Laure Rosso
- Inserm U801, Lille, F-59019, Université Lille II, Faculté de Médecine Henri Warembourg), Lille, France.
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Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HCP, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, de Marsac NT. Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 2008; 9:274. [PMID: 18534010 PMCID: PMC2442094 DOI: 10.1186/1471-2164-9-274] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Accepted: 06/05/2008] [Indexed: 11/29/2022] Open
Abstract
Background The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There has been little investigation of the genomics of these cyanobacteria. Results Deciphering the 5,172,804 bp sequence of Microcystis aeruginosa PCC 7806 has revealed the high plasticity of its genome: 11.7% DNA repeats containing more than 1,000 bases, 6.8% putative transposases and 21 putative restriction enzymes. Compared to the genomes of other cyanobacterial lineages, strain PCC 7806 contains a large number of atypical genes that may have been acquired by lateral transfers. Metabolic pathways, such as fermentation and a methionine salvage pathway, have been identified, as have genes for programmed cell death that may be related to the rapid disappearance of Microcystis blooms in nature. Analysis of the PCC 7806 genome also reveals striking novel biosynthetic features that might help to elucidate the ecological impact of secondary metabolites and lead to the discovery of novel metabolites for new biotechnological applications. M. aeruginosa and other large cyanobacterial genomes exhibit a rapid loss of synteny in contrast to other microbial genomes. Conclusion Microcystis aeruginosa PCC 7806 appears to have adopted an evolutionary strategy relying on unusual genome plasticity to adapt to eutrophic freshwater ecosystems, a property shared by another strain of M. aeruginosa (NIES-843). Comparisons of the genomes of PCC 7806 and other cyanobacterial strains indicate that a similar strategy may have also been used by the marine strain Crocosphaera watsonii WH8501 to adapt to other ecological niches, such as oligotrophic open oceans.
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Sequence of conjugative plasmid pIP1206 mediating resistance to aminoglycosides by 16S rRNA methylation and to hydrophilic fluoroquinolones by efflux. Antimicrob Agents Chemother 2008; 52:2581-92. [PMID: 18458128 DOI: 10.1128/aac.01540-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Self-transferable IncFI plasmid pIP1206, isolated from an Escherichia coli clinical isolate, carries two new resistance determinants: qepA, which confers resistance to hydrophylic fluoroquinolones by efflux, and rmtB, which specifies a 16S rRNA methylase conferring high-level aminoglycoside resistance. Analysis of the 168,113-bp sequence (51% G+C) revealed that pIP1206 was composed of several subregions separated by copies of insertion sequences. Of 151 open reading frames, 56 (37%) were also present in pRSB107, isolated from a bacterium in a sewage treatment plant. pIP1206 contained four replication regions (RepFIA, RepFIB, and two partial RepFII regions) and a transfer region 91% identical with that of pAPEC-O1-ColBM, a plasmid isolated from an avian pathogenic E. coli. A putative oriT region was found upstream from the transfer region. The antibiotic resistance genes tet(A), catA1, bla(TEM-1), rmtB, and qepA were clustered in a 33.5-kb fragment delineated by two IS26 elements that also carried a class 1 integron, including the sulI, qacEDelta1, aad4, and dfrA17 genes and Tn10, Tn21, and Tn3-like transposons. The plasmid also possessed a raffinose operon, an arginine deiminase pathway, a putative iron acquisition gene cluster, an S-methylmethionine metabolism operon, two virulence-associated genes, and a type I DNA restriction-modification (R-M) system. Three toxin/antitoxin systems and the R-M system ensured stabilization of the plasmid in the host bacteria. These data suggest that the mosaic structure of pIP1206 could have resulted from recombination between pRSB107 and a pAPEC-O1-ColBM-like plasmid, combined with structural rearrangements associated with acquisition of additional DNA by recombination and of mobile genetic elements by transposition.
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Zhao F, Zhao F, Li T, Bryant DA. A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res 2008; 36:3455-62. [PMID: 18445633 PMCID: PMC2425481 DOI: 10.1093/nar/gkn168] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Gap closing is considered one of the most challenging and time-consuming tasks in bacterial genome sequencing projects, especially with the emergence of new sequencing technologies, such as pyrosequencing, which may result in large amounts of data without the benefit of large insert libraries for contig scaffolding. We propose a novel algorithm to align contigs with more than one reference genome at a time. This approach can successfully overcome the limitations of low degrees of conserved gene order for the reference and target genomes. A pheromone trail-based genetic algorithm (PGA) was used to search globally for the optimal placement for each contig. Extensive testing on simulated and real data sets shows that PGA significantly outperforms previous methods, especially when assembling genomes that are only moderately related. An extended version of PGA can predict additional candidate connections for each contig and can thus increase the likelihood of identifying the correct arrangement of each contig. The software and test data sets can be accessed at http://sourceforge.net/projects/pga4genomics/.
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Affiliation(s)
- Fangqing Zhao
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Cazalet C, Jarraud S, Ghavi-Helm Y, Kunst F, Glaser P, Etienne J, Buchrieser C. Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species. Genome Res 2008; 18:431-41. [PMID: 18256241 DOI: 10.1101/gr.7229808] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genomics can provide the basis for understanding the evolution of emerging, lethal human pathogens such as Legionella pneumophila, the causative agent of Legionnaires' disease. This bacterium replicates within amoebae and persists in the environment as a free-living microbe. Among the many Legionella species described, L. pneumophila is associated with 90% of human disease and within the 15 serogroups (Sg), L. pneumophila Sg1 causes over 84% of Legionnaires' disease worldwide. Why L. pneumophila Sg1 is so predominant is unknown. Here, we report the first comprehensive screen of the gene content of 217 L. pneumophila and 32 non-L. pneumophila strains isolated from humans and the environment using a Legionella DNA-array. Strikingly, we uncovered a high conservation of virulence- and eukaryotic-like genes, indicating strong environmental selection pressures for their preservation. No specific hybridization profile differentiated clinical and environmental strains or strains of different serogroups. Surprisingly, the gene cluster coding the determinants of the core and the O side-chain synthesis of the lipopolysaccaride (LPS cluster) determining Sg1 was present in diverse genomic backgrounds, strongly implicating the LPS of Sg1 itself as a principal cause of the high prevalence of Sg1 strains in human disease and suggesting that the LPS cluster can be transferred horizontally. Genomic analysis also revealed that L. pneumophila is a genetically diverse species, in part due to horizontal gene transfer of mobile genetic elements among L. pneumophila strains, but also between different Legionella species. However, the genomic background also plays a role in disease causation as demonstrated by the identification of a globally distributed epidemic strain exhibiting the genotype of the sequenced L. pneumophila strain Paris.
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Affiliation(s)
- Christel Cazalet
- Unité de Génomique des Microorganismes Pathogènes, Institut Pasteur, 75724 Paris Cedex 15, France
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Chauvaux S, Rosso ML, Frangeul L, Lacroix C, Labarre L, Schiavo A, Marceau M, Dillies MA, Foulon J, Coppée JY, Médigue C, Simonet M, Carniel E. Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague. MICROBIOLOGY-SGM 2007; 153:3112-3124. [PMID: 17768254 DOI: 10.1099/mic.0.2007/006213-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Yersinia pestis is the aetiologic agent of plague. Without appropriate treatment, the pathogen rapidly causes septicaemia, the terminal and fatal phase of the disease. In order to identify bacterial genes which are essential during septicaemic plague in humans, we performed a transcriptome analysis on the fully virulent Y. pestis CO92 strain grown in either decomplemented human plasma or Luria-Bertani medium, incubated at either 28 or 37 degrees C and harvested at either the mid-exponential or the stationary growth phase. Y. pestis genes involved in 12 iron-acquisition systems and one iron-storage system (bfr, bfd) were specifically induced in human plasma. Of these, the ybt and tonB genes (encoding the yersiniabactin siderophore virulence factor and the siderophore transporter, respectively) were induced at 37 degrees C, i.e. under conditions mimicking the mammalian environment. Growth in human plasma also upregulated genes involved in the synthesis of five fimbrial-like structures (including the Psa virulence factor), and in purine/pyrimidine metabolism (the nrd genes). Genes known to play a role in the virulence of several bacterial pathogens (such as those encoding the Lpp lipoprotein and non-iron metal-uptake proteins) were induced in human plasma, during either the exponential or the stationary phase. Finally, 120 genes encoding proteins of unknown function were upregulated in human plasma. Eleven of these genes were specifically transcribed at 37 degrees C and may thus represent new virulence factors that are important during the septicaemic phase of human plague.
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Affiliation(s)
- Sylvie Chauvaux
- Yersinia Research Unit, Institut Pasteur, 28 rue du Dr. Roux, F-75724 Paris cedex 15, France
| | | | | | | | | | | | | | | | - Jeannine Foulon
- Yersinia Research Unit, Institut Pasteur, 28 rue du Dr. Roux, F-75724 Paris cedex 15, France
| | | | | | | | - Elisabeth Carniel
- Yersinia Research Unit, Institut Pasteur, 28 rue du Dr. Roux, F-75724 Paris cedex 15, France
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Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barré A, Barbe V, Schenowitz C, Mangenot S, Couloux A, Segurens B, de Daruvar A, Blanchard A, Citti C. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 2007; 3:e75. [PMID: 17511520 PMCID: PMC1868952 DOI: 10.1371/journal.pgen.0030075] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 04/02/2007] [Indexed: 11/18/2022] Open
Abstract
Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that ∼18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma–host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts. Mycoplasmas are cell wall–lacking prokaryotes that evolved from ancestors common to Gram-positive bacteria by way of massive losses of genetic material. With their minimal genome, mycoplasmas are considered to be the simplest free-living organisms, yet several species are successful pathogens of man and animal. In this study, we challenged the commonly accepted view in which mycoplasma evolution is driven only by genome down-sizing. Indeed, we showed that a significant amount of genes underwent horizontal transfer among different mycoplasma species that share the same ruminant hosts. In these species, the occurrence of a genetic element that can promote DNA transfer via cell-to-cell contact suggests that some mycoplasmas may have retained or acquired sexual competence. Transferred genes were found to encode proteins that are likely to be associated with mycoplasma–host interactions. Sharing genetic resources via horizontal gene transfer may provide mycoplasmas with a means for adapting to new niches or to new hosts and for avoiding irreversible genome erosion.
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Affiliation(s)
- Pascal Sirand-Pugnet
- Université Bordeaux 2, UMR1090, Villenave d'Ornon, France
- INRA, UMR1090, Villenave d'Ornon, France
| | - Carole Lartigue
- Université Bordeaux 2, UMR1090, Villenave d'Ornon, France
- INRA, UMR1090, Villenave d'Ornon, France
| | | | - Daniel Jacob
- Centre de Bioinformatique de Bordeaux, Université Bordeaux 2, Bordeaux, France
| | - Aurélien Barré
- Centre de Bioinformatique de Bordeaux, Université Bordeaux 2, Bordeaux, France
| | - Valérie Barbe
- Genoscope, Centre National de Séquençage, Evry, France
| | | | | | | | | | - Antoine de Daruvar
- Centre de Bioinformatique de Bordeaux, Université Bordeaux 2, Bordeaux, France
| | - Alain Blanchard
- Université Bordeaux 2, UMR1090, Villenave d'Ornon, France
- INRA, UMR1090, Villenave d'Ornon, France
| | - Christine Citti
- INRA, ENVT, UMR1225, Toulouse, France
- * To whom correspondence should be addressed. E-mail:
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Abstract
UNLABELLED The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure. MOTIVATION To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly. AVAILABILITY OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay.
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Affiliation(s)
- Daniel C Richter
- Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany.
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30
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Krin E, Chakroun N, Turlin E, Givaudan A, Gaboriau F, Bonne I, Rousselle JC, Frangeul L, Lacroix C, Hullo MF, Marisa L, Danchin A, Derzelle S. Pleiotropic role of quorum-sensing autoinducer 2 in Photorhabdus luminescens. Appl Environ Microbiol 2006; 72:6439-51. [PMID: 17021191 PMCID: PMC1610301 DOI: 10.1128/aem.00398-06] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial virulence is an integrative process that may involve quorum sensing. In this work, we compared by global expression profiling the wild-type entomopathogenic Photorhabdus luminescens subsp. laumondii TT01 to a luxS-deficient mutant unable to synthesize the type 2 quorum-sensing inducer AI-2. AI-2 was shown to regulate more than 300 targets involved in most compartments and metabolic pathways of the cell. AI-2 is located high in the hierarchy, as it controls the expression of several transcriptional regulators. The regulatory effect of AI-2 appeared to be dose dependent. The luxS-deficient strain exhibited decreased biofilm formation and increased type IV/V pilus-dependent twitching motility. AI-2 activated its own synthesis and transport. It also modulated bioluminescence by regulating the synthesis of spermidine. AI-2 was further shown to increase oxidative stress resistance, which is necessary to overcome part of the innate immune response of the host insect involving reactive oxygen species. Finally, we showed that the luxS-deficient strain had attenuated virulence against the lepidopteran Spodoptera littoralis. We concluded that AI-2 is involved mainly in early steps of insect invasion in P. luminescens.
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Affiliation(s)
- Evelyne Krin
- Unité de Génétique des Génomes Bactériens (URA2171), Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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31
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Arner E, Tammi MT, Tran AN, Kindlund E, Andersson B. DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. BMC Bioinformatics 2006; 7:155. [PMID: 16549006 PMCID: PMC1459207 DOI: 10.1186/1471-2105-7-155] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 03/20/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem. RESULTS We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license. CONCLUSION With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.
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Affiliation(s)
- Erik Arner
- Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden
| | - Martti T Tammi
- Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden
| | - Anh-Nhi Tran
- Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden
| | - Ellen Kindlund
- Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden
| | - Bjorn Andersson
- Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden
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32
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Gaudriault S, Duchaud E, Lanois A, Canoy AS, Bourot S, Derose R, Kunst F, Boemare N, Givaudan A. Whole-genome comparison between Photorhabdus strains to identify genomic regions involved in the specificity of nematode interaction. J Bacteriol 2006; 188:809-14. [PMID: 16385072 PMCID: PMC1347316 DOI: 10.1128/jb.188.2.809-814.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterium Photorhabdus establishes a highly specific association with Heterorhabditis, its nematode host. Photorhabdus strains associated with Heterorhabditis bacteriophora or Heterorhabditis megidis were compared using a Photorhabdus DNA microarray. We describe 31 regions belonging to the Photorhabdus flexible gene pool. Distribution analysis of regions among the Photorhabdus genus identified loci possibly involved in nematode specificity.
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Affiliation(s)
- S Gaudriault
- Laboratoire EMIP Ecologie Microbienne des Insectes et Interaction Hôtes-Pathogène, Université Montpellier II, UMR1133 INRA-UMII, 34095 Montpellier Cedex 5, France.
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Chatterjee SS, Hossain H, Otten S, Kuenne C, Kuchmina K, Machata S, Domann E, Chakraborty T, Hain T. Intracellular gene expression profile of Listeria monocytogenes. Infect Immun 2006; 74:1323-38. [PMID: 16428782 PMCID: PMC1360297 DOI: 10.1128/iai.74.2.1323-1338.2006] [Citation(s) in RCA: 274] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Listeria monocytogenes is a gram-positive, food-borne microorganism responsible for invasive infections with a high overall mortality. L. monocytogenes is among the very few microorganisms that can induce uptake into the host cell and subsequently enter the host cell cytosol by breaching the vacuolar membrane. We infected the murine macrophage cell line P388D1 with L. monocytogenes strain EGD-e and examined the gene expression profile of L. monocytogenes inside the vacuolar and cytosolic environments of the host cell by using whole-genome microarray and mutant analyses. We found that approximately 17% of the total genome was mobilized to enable adaptation for intracellular growth. Intracellularly expressed genes showed responses typical of glucose limitation within bacteria, with a decrease in the amount of mRNA encoding enzymes in the central metabolism and a temporal induction of genes involved in alternative-carbon-source utilization pathways and their regulation. Adaptive intracellular gene expression involved genes that are associated with virulence, the general stress response, cell division, and changes in cell wall structure and included many genes with unknown functions. A total of 41 genes were species specific, being absent from the genome of the nonpathogenic Listeria innocua CLIP 11262 strain. We also detected 25 genes that were strain specific, i.e., absent from the genome of the previously sequenced L. monocytogenes F2365 serotype 4b strain, suggesting heterogeneity in the gene pool required for intracellular survival of L. monocytogenes in host cells. Overall, our study provides crucial insights into the strategy of intracellular survival and measures taken by L. monocytogenes to escape the host cell responses.
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Affiliation(s)
- Som Subhra Chatterjee
- Institute for Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, D-35392 Giessen, Germany
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34
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Brochet M, Couvé E, Zouine M, Vallaeys T, Rusniok C, Lamy MC, Buchrieser C, Trieu-Cuot P, Kunst F, Poyart C, Glaser P. Genomic diversity and evolution within the species Streptococcus agalactiae. Microbes Infect 2006; 8:1227-43. [PMID: 16529966 DOI: 10.1016/j.micinf.2005.11.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 11/21/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
Streptococcus agalactiae is a leading cause of invasive infections in neonates, and responsible for bovine mastitis. It is also a commensal bacterium adapted to asymptomatic colonization of the mammalian gut and of the genitourinary tract. Here, we report the analysis of a collection of 75 strains of human and animal origin by using serotyping, multilocus sequence typing, whole genome DNA-array hybridizations and sequence comparison of putatively virulence-associated loci. Although the most variable parts of the genome are the previously predicted genomic islands, significant genetic variations were present in the genome backbone. Evolution within genes encoding surface and secreted proteins and those involved in the biosynthesis of different capsular types is mainly due to recombination events leading to the replacement of a locus of several genes or to the allelic exchange of the internal part of a gene. These two processes, which led to a broad diversity of surface protein patterns, are probably involved in the diversity of interactions with the host and its immune system. According to gene content comparisons and phylogeny, recent gene replacements by horizontal gene transfer may occur but are rare events. Although specific gene patterns, with respect to the origin of the strains and the epidemiological characteristics, were not identified, we show that the recently described hypervirulent ST-17 lineage is a homogeneous group. The study highlights for the first time that this lineage contains a specific and conserved set of surface proteins, probably accounting for its high capacity to cause infections in newborns.
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Affiliation(s)
- Mathieu Brochet
- Unité de Génomique des Microorganismes Pathogènes-URA CNRS 2171, Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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35
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Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Médigue C. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 2006; 34:53-65. [PMID: 16407324 PMCID: PMC1326237 DOI: 10.1093/nar/gkj406] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at .
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Affiliation(s)
- David Vallenet
- Atelier de Génomique Comparative, CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry, Cedex, France.
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36
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37
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Bourhy P, Frangeul L, Couvé E, Glaser P, Saint Girons I, Picardeau M. Complete nucleotide sequence of the LE1 prophage from the spirochete Leptospira biflexa and characterization of its replication and partition functions. J Bacteriol 2005; 187:3931-40. [PMID: 15937155 PMCID: PMC1151745 DOI: 10.1128/jb.187.12.3931-3940.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first and, to date, only extrachromosomal circular replicon identified in the spirochete Leptospira is the LE1 prophage from Leptospira biflexa. The 74-kb LE1 genome has a GC content of 36%, which is similar to the GC content of Leptospira spp. Most of the 79 predicted open reading frames (ORFs) showed no similarities to known ORFs. However 21 ORFs appeared to be organized in clusters that could code for head and tail structural proteins and immunity repressor proteins. In addition, the pattern of gene expression showed that several LE1 genes are expressed specifically either in LE1 prophage or in L. biflexa late after infection. Since the LE1 prophage replicates autonomously as a circular replicon in L. biflexa, we were able to engineer an L. biflexa-Escherichia coli shuttle vector from a 5.3-kb DNA fragment of LE1 (Saint Girons et al., J. Bacteriol. 182:5700-5705, 2000), opening this genus to genetic manipulation. In this study, base compositional asymmetry confirms the location of the LE1 replication region and suggests that LE1 replicates via a bidirectional Theta-like replication mechanism from this unique origin. By subcloning experiments, the replication region can be narrowed down to a 1-kb region. This minimal replication region consists of a rep encoding a protein of 180 amino acids. Upstream from rep, putative partitioning genes, called parA and parB, were found to be similar to the par loci in Borrelia plasmids. A significant increase of plasmid stability in L. biflexa can be seen only when both parA and parB are present. These results enable the construction of new shuttle vectors for studying the genetics of Leptospira spp. This study will also contribute to a better knowledge of phages unrelated to lambdoid phages.
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Affiliation(s)
- Pascale Bourhy
- Laboratoire des Spirochètes, Institut Pasteur, 25 rue du docteur Roux, 75724 Paris Cedex 15, France
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38
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Braun BR, van het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Zito R, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Köhler G, Morschhäuser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A. A human-curated annotation of the Candida albicans genome. PLoS Genet 2005; 1:36-57. [PMID: 16103911 PMCID: PMC1183520 DOI: 10.1371/journal.pgen.0010001] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 03/14/2005] [Indexed: 11/24/2022] Open
Abstract
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.
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Affiliation(s)
- Burkhard R Braun
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Marco van het Hoog
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe d'Enfert
- Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, Paris, France
| | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Jan Dungan
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Alan Kuo
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Diane O Inglis
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - M. Andrew Uhl
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | | | - Michael Lorenz
- Department of Microbiology and Molecular Genetics, Utah-Houston Medical School, Houston, Texas, United States of America
| | - Anastasia Levitin
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Ursula Oberholzer
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Catherine Bachewich
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Doreen Harcus
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Anne Marcil
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Daniel Dignard
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Tatiana Iouk
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Rosa Zito
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Lionel Frangeul
- Plate-Forme Intégration et Analyse Génomique, Institut Pasteur, Paris, France
| | - Fredj Tekaia
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, Paris, France
| | | | - Edwin Wang
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Carol A Munro
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Steve Bates
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Neil A Gow
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Lois L Hoyer
- Department of Veterinary Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gerwald Köhler
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Wurzburg, Wurzburg, Germany
| | - George Newport
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Sadri Znaidi
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Martine Raymond
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Bernard Turcotte
- Department of Medicine, Royal Victoria Hospital, McGill University, Montreal, Quebec, Canada
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Maria Costanzo
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Jan Ihmels
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dominique Sanglard
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Nina Agabian
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Aaron P Mitchell
- Department of Microbiology and Institute of Cancer Research, Columbia University, New York, New York, United States of America
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - André Nantel
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
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39
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Hejnova J, Dobrindt U, Nemcova R, Rusniok C, Bomba A, Frangeul L, Hacker J, Glaser P, Sebo P, Buchrieser C. Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31). MICROBIOLOGY-SGM 2005; 151:385-398. [PMID: 15699189 DOI: 10.1099/mic.0.27469-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Colonization by the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31) has proved to be safe and efficient in the prophylaxis and treatment of nosocomial infections and diarrhoea of preterm and newborn infants in Czech paediatric clinics over the past three decades. In searching for traits contributing to this beneficial effect related to the gut colonization capacity of the strain, the authors have analysed its genome by DNA-DNA hybridization to E. coli K-12 (MG1655) genomic DNA arrays and to 'Pathoarrays', as well as by multiplex PCR, bacterial artificial chromosome (BAC) library cloning and shotgun sequencing. Four hundred and ten E. coli K-12 ORFs were absent from A0 34/86, while 72 out of 456 genes associated with pathogenicity islands of E. coli and Shigella were also detected in E. coli A0 34/86. Furthermore, extraintestinal pathogenic E. coli-related genes involved in iron uptake and adhesion were detected by multiplex PCR, and genes encoding the HlyA and cytotoxic necrotizing factor toxins, together with 21 genes of the uropathogenic E. coli 536 pathogenicity island II, were identified by analysis of 2304 shotgun and 1344 BAC clone sequences of A0 34/86 DNA. Multiple sequence comparisons identified 31 kb of DNA specific for E. coli A0 34/86; some of the genes carried by this DNA may prove to be implicated in the colonization capacity of the strain, enabling it to outcompete pathogens. Among 100 examined BAC clones roughly covering the A0 34/86 genome, one reproducibly conferred on the laboratory strain DH10B an enhanced capacity to persist in the intestine of newborn piglets. Sequencing revealed that this BAC clone carried gene clusters encoding gluconate and mannonate metabolism, adhesion (fim), invasion (ibe) and restriction/modification functions. Hence, the genome of this clinically safe and highly efficient colonizer strain appears to harbour many 'virulence-associated' genes. These results highlight the thin line between bacterial 'virulence' and 'fitness' or 'colonization' factors, and question the definition of enterobacterial virulence factors.
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Affiliation(s)
- Jana Hejnova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
- Unité de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Ulrich Dobrindt
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Radka Nemcova
- Research Institute of Veterinary Medicine, Hlinkova 1/A, 040 01 Kosice, Slovakia
| | - Christophe Rusniok
- Unité de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Alojz Bomba
- Research Institute of Veterinary Medicine, Hlinkova 1/A, 040 01 Kosice, Slovakia
| | - Lionel Frangeul
- Plate-Forme 4 - Intégration et Analyse Génomique, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Jörg Hacker
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Philippe Glaser
- Unité de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Peter Sebo
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Carmen Buchrieser
- Unité de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris, France
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40
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d'Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, Tekaia F, Bader O, Albrecht A, Castillo L, Dominguez A, Ernst JF, Fradin C, Gaillardin C, Garcia-Sanchez S, de Groot P, Hube B, Klis FM, Krishnamurthy S, Kunze D, Lopez MC, Mavor A, Martin N, Moszer I, Onésime D, Perez Martin J, Sentandreu R, Valentin E, Brown AJP. CandidaDB: a genome database for Candida albicans pathogenomics. Nucleic Acids Res 2005; 33:D353-7. [PMID: 15608215 PMCID: PMC540078 DOI: 10.1093/nar/gki124] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses that can assist the researcher in the evaluation of gene function for the purpose of specific or large-scale analysis. CandidaDB is based on GenoList, a generic relational data schema and a World Wide Web interface that has been adapted to the handling of eukaryotic genomes. The interface allows users to browse easily through genome data and retrieve information. CandidaDB also provides more elaborate tools, such as pattern searching, that are tightly connected to the overall browsing system. As the C.albicans genome is diploid and still incompletely assembled, CandidaDB provides tools to browse the genome by individual supercontigs and to examine information about allelic sequences obtained from complementary contigs. CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.
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Affiliation(s)
- C d'Enfert
- Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, Paris, France.
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41
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Lamy MC, Zouine M, Fert J, Vergassola M, Couve E, Pellegrini E, Glaser P, Kunst F, Msadek T, Trieu-Cuot P, Poyart C. CovS/CovR of group B streptococcus: a two-component global regulatory system involved in virulence. Mol Microbiol 2005; 54:1250-68. [PMID: 15554966 DOI: 10.1111/j.1365-2958.2004.04365.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this study, we carried out a detailed structural and functional analysis of a Streptococcus agalactiae (GBS) two-component system which is orthologous to the CovS/CovR (CsrS/CsrR) regulatory system of Streptococcus pyogenes. In GBS, covR and covS are part of a seven gene operon transcribed from two promoters that are not regulated by CovR. A DeltacovSR mutant was found to display dramatic phenotypic changes such as increased haemolytic activity and reduced CAMP activity on blood agar. Adherence of the DeltacovSR mutant to epithelial cells was greatly increased and analysis by transmission electron microscopy revealed the presence at its surface of a fibrous extracellular matrix that might be involved in these intercellular interactions. However, the DeltacovSR mutant was unable to initiate growth in RPMI and its viability in human normal serum was greatly impaired. A major finding of this phenotypic analysis was that the CovS/CovR system is important for GBS virulence, as a 3 log increase of the LD(50) of the mutant strain was observed in the neonate rat sepsis model. The pleiotropic phenotype of the DeltacovSR mutant is in full agreement with the large number of genes controlled by CovS/CovR as seen by expression profiling analysis, many of which encode potentially secreted or cell surface-associated proteins: 76 genes are repressed whereas 63 were positively regulated. CovR was shown to bind directly to the regulatory regions of several of these genes and a consensus CovR recognition sequence was proposed using both DNase I footprinting and computational analyses.
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Affiliation(s)
- Marie-Cécile Lamy
- INSERM U-570, Faculté de Médecine Necker-Enfants Malades, 75730 Paris Cedex 15, France
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42
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Cazalet C, Rusniok C, Brüggemann H, Zidane N, Magnier A, Ma L, Tichit M, Jarraud S, Bouchier C, Vandenesch F, Kunst F, Etienne J, Glaser P, Buchrieser C. Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat Genet 2004; 36:1165-73. [PMID: 15467720 DOI: 10.1038/ng1447] [Citation(s) in RCA: 485] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 09/09/2004] [Indexed: 11/09/2022]
Abstract
Legionella pneumophila, the causative agent of Legionnaires' disease, replicates as an intracellular parasite of amoebae and persists in the environment as a free-living microbe. Here we have analyzed the complete genome sequences of L. pneumophila Paris (3,503,610 bp, 3,077 genes), an endemic strain that is predominant in France, and Lens (3,345,687 bp, 2,932 genes), an epidemic strain responsible for a major outbreak of disease in France. The L. pneumophila genomes show marked plasticity, with three different plasmids and with about 13% of the sequence differing between the two strains. Only strain Paris contains a type V secretion system, and its Lvh type IV secretion system is encoded by a 36-kb region that is either carried on a multicopy plasmid or integrated into the chromosome. Genetic mobility may enhance the versatility of L. pneumophila. Numerous genes encode eukaryotic-like proteins or motifs that are predicted to modulate host cell functions to the pathogen's advantage. The genome thus reflects the history and lifestyle of L. pneumophila, a human pathogen of macrophages that coevolved with fresh-water amoebae.
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Affiliation(s)
- Christel Cazalet
- Laboratoire de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28, rue du Dr. Roux, 75724 Paris Cedex 15, France
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43
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Trad S, Allignet J, Frangeul L, Davi M, Vergassola M, Couve E, Morvan A, Kechrid A, Buchrieser C, Glaser P, El-Solh N. DNA macroarray for identification and typing of Staphylococcus aureus isolates. J Clin Microbiol 2004; 42:2054-64. [PMID: 15131170 PMCID: PMC404631 DOI: 10.1128/jcm.42.5.2054-2064.2004] [Citation(s) in RCA: 35] [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
A DNA macroarray containing 465 intragenic amplicons was designed to identify Staphylococcus aureus at the species level and to type S. aureus isolates. The genes selected included those encoding (i) S. aureus-specific proteins, (ii) staphylococcal and enterococcal proteins mediating antibiotic resistance and factors involved in their expression, (iii) putative virulence proteins and factors controlling their expression, and (iv) proteins produced by mobile elements. The macroarray was hybridized with the cellular DNAs of 80 S. aureus clinical isolates that were previously typed by analyses of their antibiograms and SmaI patterns. The set selected contained unrelated, endemic, and outbreak-related isolates belonging to 45 SmaI genotypes. In a gene content dendrogram, the 80 isolates were distributed into 52 clusters. The outbreak-related isolates were linked in the same or a closely related cluster(s). Clustering based on gene content provided a better discrimination than SmaI pattern analysis for the tested mecA(+) isolates that were endemic to Europe. All of the antibiotic resistance genes detected could be correlated with their corresponding phenotypes, except for one isolate which carried a mecA gene without being resistant. The 16 isolates responsible for bone infections were distinguishable from the 12 isolates from uninfected nasal carriers by a significantly higher prevalence of the sdrD gene coding for a putative SD (serine-aspartate) adhesin (in 15 and 7 isolates, respectively). In conclusion, the macroarray designed for this study offers an attractive and rapid typing method which has the advantage of providing additional information concerning the gene content of the isolate of interest.
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Affiliation(s)
- Salim Trad
- Département Ecosystèmes et Epidémiologie des Maladies Infectieuses, Institut Pasteur, Paris, France
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44
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Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature 2004; 430:35-44. [PMID: 15229592 DOI: 10.1038/nature02579] [Citation(s) in RCA: 1187] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/19/2004] [Indexed: 11/09/2022]
Abstract
Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
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Affiliation(s)
- Bernard Dujon
- Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie.
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45
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Doumith M, Cazalet C, Simoes N, Frangeul L, Jacquet C, Kunst F, Martin P, Cossart P, Glaser P, Buchrieser C. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect Immun 2004; 72:1072-83. [PMID: 14742555 PMCID: PMC321639 DOI: 10.1128/iai.72.2.1072-1083.2004] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a food-borne bacterial pathogen that causes a wide spectrum of diseases, such as meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13 L. monocytogenes serovars described, invasive disease is mostly associated with serovar 4b strains. To investigate the genetic diversity of L. monocytogenes strains with different virulence potentials, we partially sequenced an epidemic serovar 4b strain and compared it with the complete sequence of the nonepidemic L. monocytogenes EGDe serovar 1/2a strain. We identified an unexpected genetic divergence between the two strains, as about 8% of the sequences were serovar 4b specific. These sequences included seven genes coding for surface proteins, two of which belong to the internalin family, and three genes coding for transcriptional regulators, all of which might be important in different steps of the infectious process. Based on the sequence information, we then characterized the gene content of 113 Listeria strains by using a newly designed Listeria array containing the "flexible" part of the sequenced Listeria genomes. Hybridization results showed that all of the previously identified virulence factors of L. monocytogenes were present in the 93 L. monocytogenes strains tested. However, distinct patterns of the presence or absence of other genes were identified among the different L. monocytogenes serovars and Listeria species. These results allow new insights into the evolution of L. monocytogenes, suggesting that early divergence of the ancestral L. monocytogenes serovar 1/2c strains from the serovar 1/2b strains led to two major phylogenetic lineages, one of them including the serogroup 4 strains, which branched off the serovar 1/2b ancestral lineage, leading (mostly by gene loss) to the species Listeria innocua. The identification of 30 L. monocytogenes-specific and several serovar-specific marker genes, such as three L. monocytogenes serovar 4b-specific surface protein-coding genes, should prove powerful for the rapid tracing of listeriosis outbreaks, but it also represents a fundamental basis for the functional study of virulence differences between L. monocytogenes strains.
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Affiliation(s)
- Michel Doumith
- Laboratoire des Listeria, Centre National de Référence des Listeria, World Health Organization Collaborating Center for Foodborne Listeriosis, Institut Pasteur, 75724 Paris 15, France
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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47
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Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Médigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol 2003; 21:1307-13. [PMID: 14528314 DOI: 10.1038/nbt886] [Citation(s) in RCA: 410] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Accepted: 08/18/2003] [Indexed: 11/09/2022]
Abstract
Photorhabdus luminescens is a symbiont of nematodes and a broad-spectrum insect pathogen. The complete genome sequence of strain TT01 is 5,688,987 base pairs (bp) long and contains 4,839 predicted protein-coding genes. Strikingly, it encodes a large number of adhesins, toxins, hemolysins, proteases and lipases, and contains a wide array of antibiotic synthesizing genes. These proteins are likely to play a role in the elimination of competitors, host colonization, invasion and bioconversion of the insect cadaver, making P. luminescens a promising model for the study of symbiosis and host-pathogen interactions. Comparison with the genomes of related bacteria reveals the acquisition of virulence factors by extensive horizontal transfer and provides clues about the evolution of an insect pathogen. Moreover, newly identified insecticidal proteins may be effective alternatives for the control of insect pests.
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Affiliation(s)
- Eric Duchaud
- Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
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