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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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Leal-Morales A, Pulido-Sánchez M, López-Sánchez A, Govantes F. Transcriptional organization and regulation of the Pseudomonas putida flagellar system. Environ Microbiol 2021; 24:137-157. [PMID: 34859548 DOI: 10.1111/1462-2920.15857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 01/22/2023]
Abstract
A single region of the Pseudomonas putida genome, designated the flagellar cluster, includes 59 genes potentially involved in the biogenesis and function of the flagellar system. Here, we combine bioinformatics and in vivo gene expression analyses to clarify the transcriptional organization and regulation of the flagellar genes in the cluster. We have identified 11 flagellar operons and characterized 22 primary and internal promoter regions. Our results indicate that synthesis of the flagellar apparatus and core chemotaxis machinery is regulated by a three-tier cascade in which fleQ is a Class I gene, standing at the top of the transcriptional hierarchy. FleQ- and σ54 -dependent Class II genes encode most components of the flagellar structure, part of the chemotaxis machinery and multiple regulatory elements, including the flagellar σ factor FliA. FliA activation of Class III genes enables synthesis of the filament, one stator complex and completion of the chemotaxis apparatus. Accessory regulatory proteins and an intricate operon architecture add complexity to the regulation by providing feedback and feed-forward loops to the main circuit. Because of the high conservation of the gene arrangement and promoter motifs, we believe that the regulatory circuit presented here may also apply to other environmental pseudomonads.
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Affiliation(s)
- Antonio Leal-Morales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Marta Pulido-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Fernando Govantes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
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Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F, Moreno R. Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region. Nucleic Acids Res 2021; 49:9211-9228. [PMID: 34379788 PMCID: PMC8450116 DOI: 10.1093/nar/gkab672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Insertion sequences (ISs) are mobile genetic elements that only carry the information required for their own transposition. Pseudomonas putida KT2440, a model bacterium, has seven copies of an IS called ISPpu9 inserted into repetitive extragenic palindromic sequences. This work shows that the gene for ISPpu9 transposase, tnp, is regulated by two small RNAs (sRNAs) named Asr9 and Ssr9, which are encoded upstream and downstream of tnp, respectively. The tnp mRNA has a long 5′-untranslated region (5′-UTR) that can fold into a secondary structure that likely includes the ribosome-binding site (RBS). Mutations weakening this structure increased tnp mRNA translation. Asr9, an antisense sRNA complementary to the 5′-UTR, was shown to be very stable. Eliminating Asr9 considerably reduced tnp mRNA translation, suggesting that it helps to unfold this secondary structure, exposing the RBS. Ectopic overproduction of Asr9 increased the transposition frequency of a new ISPpu9 entering the cell by conjugation, suggesting improved tnp expression. Ssr9 has significant complementarity to Asr9 and annealed to it in vitro forming an RNA duplex; this would sequester it and possibly facilitate its degradation. Thus, the antisense Asr9 sRNA likely facilitates tnp expression, improving transposition, while Ssr9 might counteract Asr9, keeping tnp expression low.
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Affiliation(s)
- Guillermo Gómez-García
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Angel Ruiz-Enamorado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Luis Yuste
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
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Aranda-Olmedo I, Rubio LA. Dietary legumes, intestinal microbiota, inflammation and colorectal cancer. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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Quentin Y, Siguier P, Chandler M, Fichant G. Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. BMC Genomics 2018; 19:475. [PMID: 29914351 PMCID: PMC6006769 DOI: 10.1186/s12864-018-4836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
Background Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family. Results A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles. Conclusions We established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA editing, they may confer adaptive responses to host cell physiology and metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-018-4836-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
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Bertels F, Gokhale CS, Traulsen A. Discovering Complete Quasispecies in Bacterial Genomes. Genetics 2017; 206:2149-2157. [PMID: 28630115 PMCID: PMC5560812 DOI: 10.1534/genetics.117.201160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/08/2017] [Indexed: 01/15/2023] Open
Abstract
Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to 10 different REPIN populations from 10 different bacterial strains and estimate effective duplication rates. Our estimated duplication rates range from ∼5 × 10-9 to 15 × 10-9 duplications per bacterial generation per REPIN. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size, and we also see an example of competition between two REPIN populations.
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Affiliation(s)
- Frederic Bertels
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Chaitanya S Gokhale
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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DNA repeat sequences: diversity and versatility of functions. Curr Genet 2016; 63:411-416. [PMID: 27743028 DOI: 10.1007/s00294-016-0654-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 12/26/2022]
Abstract
Although discovered decades ago, the molecular identification, the diversity and versatility of functions, and the evolutionary origin of repeat DNA sequences (REPs) containing palindromic units in prokaryotes are now bringing attention to a wide range of biological scientists. A brief account of the current state of the repeat DNA sequences is presented here.
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Charnavets T, Nunvar J, Nečasová I, Völker J, Breslauer KJ, Schneider B. Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases. Biopolymers 2016; 103:585-96. [PMID: 25951997 PMCID: PMC4690160 DOI: 10.1002/bip.22666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 01/19/2023]
Abstract
Repetitive extragenic palindrome (REP)—associated tyrosine transposase enzymes (RAYTs) bind REP DNA domains and catalyze their cleavage. Genomic sequence analyses identify potential noncoding REP sequences associated with RAYT-encoding genes. To probe the conformational space of potential RAYT DNA binding domains, we report here spectroscopic and calorimetric measurements that detect and partially characterize the solution conformational heterogeneity of REP oligonucleotides from six bacterial species. Our data reveal most of these REP oligonucleotides adopt multiple conformations, suggesting that RAYTs confront a landscape of potential DNA substrates in dynamic equilibrium that could be selected, enriched, and/or induced via differential binding. Thus, the transposase-bound DNA motif may not be the predominant conformation of the isolated REP domain. Intriguingly, for several REPs, the circular dichroism spectra suggest guanine tetraplexes as potential alternative or additional RAYT recognition elements, an observation consistent with these REP domains being highly nonrandom, with tetraplex-favoring 5′-G and 3′-C-rich segments. In fact, the conformational heterogeneity of REP domains detected and reported here, including the formation of noncanonical DNA secondary structures, may reflect a general feature required for recognition by RAYT transposases. Based on our biophysical data, we propose guanine tetraplexes as an additional DNA recognition element for binding by RAYT transposase enzymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 585–596, 2015.
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Affiliation(s)
- Tatsiana Charnavets
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jaroslav Nunvar
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Iva Nečasová
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08903
| | - Bohdan Schneider
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
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Fernández M, Porcel M, de la Torre J, Molina-Henares MA, Daddaoua A, Llamas MA, Roca A, Carriel V, Garzón I, Ramos JL, Alaminos M, Duque E. Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains. Front Microbiol 2015; 6:871. [PMID: 26379646 PMCID: PMC4548156 DOI: 10.3389/fmicb.2015.00871] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/10/2015] [Indexed: 01/12/2023] Open
Abstract
Pseudomonas putida strains are ubiquitous in soil and water but have also been reported as opportunistic human pathogens capable of causing nosocomial infections. In this study we describe the multilocus sequence typing of four P. putida strains (HB13667, HB8234, HB4184, and HB3267) isolated from in-patients at the Besançon Hospital (France). The four isolates (in particular HB3267) were resistant to a number of antibiotics. The pathogenicity and virulence potential of the strains was tested ex vivo and in vivo using different biological models: human tissue culture, mammalian tissues, and insect larvae. Our results showed a significant variability in the ability of the four strains to damage the host; HB13667 did not exhibit any pathogenic traits, HB4184 caused damage only ex vivo in human tissue cultures, and HB8234 had a deleterious effect in tissue culture and in vivo on rat skin, but not in insect larvae. Interestingly, strain HB3267 caused damage in all the model systems studied. The putative evolution of these strains in medical environments is discussed.
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Affiliation(s)
- Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Bio-Iliberis R&D Granada, Spain
| | - Mario Porcel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Unit of Integrated Plant Protection, Department of Plant Protection Biology, Swedish University of Agricultural Sciences Alnarp, Sweden
| | - Jesús de la Torre
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - M A Molina-Henares
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Abengoa Research Sevilla, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | | | - Victor Carriel
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada and Instituto de Investigación Biosanitaria Ibs Granada, Spain
| | - Ingrid Garzón
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada and Instituto de Investigación Biosanitaria Ibs Granada, Spain
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Abengoa Research Sevilla, Spain
| | - Miguel Alaminos
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada and Instituto de Investigación Biosanitaria Ibs Granada, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Abengoa Research Sevilla, Spain
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Pizarro-Tobías P, Fernández M, Niqui JL, Solano J, Duque E, Ramos JL, Roca A. Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial. Microb Biotechnol 2015; 8:77-92. [PMID: 25079309 PMCID: PMC4321375 DOI: 10.1111/1751-7915.12138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 05/25/2014] [Indexed: 12/04/2022] Open
Abstract
Forest fires pose a serious threat to countries in the Mediterranean basin, often razing large areas of land each year. After fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. In this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected Mediterranean ecosystem after a controlled fire. Our bioremediation strategy combined the use of Pseudomonas putida strains, indigenous culturable microbes and annual grasses. After 8 months of monitoring soil quality parameters, including the removal of monoaromatic and polycyclic aromatic hydrocarbons as well as vegetation cover, we found that the site had returned to pre-fire status. Microbial population analysis revealed that fires induced changes in the indigenous microbiota and that rhizoremediation favours the recovery of soil microbiota in time. The results obtained in this study indicate that the rhizoremediation strategy could be presented as a viable and cost-effective alternative for the treatment of ecosystems affected by fires.
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Affiliation(s)
| | | | - José Luis Niqui
- Bio-Ilíberis R&DPolígono Industrial Juncaril, Peligros, Granada, 18210, Spain
| | - Jennifer Solano
- Bio-Ilíberis R&DPolígono Industrial Juncaril, Peligros, Granada, 18210, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín-CSICGranada, Granada, 18008, Spain
| | - Juan-Luis Ramos
- Estación Experimental del Zaidín-CSICGranada, Granada, 18008, Spain
| | - Amalia Roca
- Bio-Ilíberis R&DPolígono Industrial Juncaril, Peligros, Granada, 18210, Spain
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Abstract
Repetitive extragenic palindromic (REP) sequences are a ubiquitous feature of bacterial genomes. Recent work shows that REPs are remnants of a larger mobile genetic element termed a REPIN. REPINs consists of two REP sequences in inverted orientation separated by a spacer region and are thought to be non-autonomous mobile genetic elements that exploit the transposase encoded by REP-Associated tYrosine Transposases (RAYTs). Complimentarity between the two ends of the REPIN suggests that the element forms hairpin structures in single stranded DNA or RNA. In addition to REPINs, other more complex arrangements of REPs have been identified in bacterial genomes, including the genome of the model organism Pseudomonas fluorescens SBW25. Here, we summarize existing knowledge and present new data concerning REPIN diversity. We also consider factors affecting the evolution of REPIN diversity, the ease with which REPINs might be co-opted by host genomes and the consequences of REPIN activity for the structure of bacterial genomes.
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Sharma PK, Fu J, Zhang X, Fristensky B, Sparling R, Levin DB. Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains. AMB Express 2014; 4:37. [PMID: 25401060 PMCID: PMC4230813 DOI: 10.1186/s13568-014-0037-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 12/13/2022] Open
Abstract
A novel strain of Pseudomonas putida LS46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-PHAs). P.putida LS46 was differentiated from other P.putida strains on the basis of cpn60 (UT). The complete genome of P.putida LS46 was sequenced and annotated. Its chromosome is 5,86,2556 bp in size with GC ratio of 61.69. It is encoding 5316 genes, including 7 rRNA genes and 76 tRNA genes. Nucleotide sequence data of the complete P. putida LS46 genome was compared with nine other P. putida strains (KT2440, F1, BIRD-1, S16, ND6, DOT-T1E, UW4, W619 and GB-1) identified either as biocontrol agents or as bioremediation agents and isolated from different geographical region and different environment. BLASTn analysis of whole genome sequences of the ten P. putida strains revealed nucleotide sequence identities of 86.54 to 97.52%. P.putida genome arrangement was LS46 highly similar to P.putida BIRD1 and P.putida ND6 but was markedly different than P.putida DOT-T1E, P.putida UW4 and P.putida W619. Fatty acid biosynthesis (fab), fatty acid degradation (fad) and PHA synthesis genes were highly conserved among biocontrol and bioremediation P.putida strains. Six genes in pha operon of P. putida LS46 showed >98% homology at gene and proteins level. It appears that polyhydroxyalkanoate (PHA) synthesis is an intrinsic property of P. putida and was not affected by its geographic origin. However, all strains, including P. putida LS46, were different from one another on the basis of house keeping genes, and presence of plasmid, prophages, insertion sequence elements and genomic islands. While P. putida LS46 was not selected for plant growth promotion or bioremediation capacity, its genome also encoded genes for root colonization, pyoverdine synthesis, oxidative stress (present in other soil isolates), degradation of aromatic compounds, heavy metal resistance and nicotinic acid degradation, manganese (Mn II) oxidation. Genes for toluene or naphthalene degradation found in the genomes of P. putida F1, DOT-T1E, and ND6 were absent in the P. putida LS46 genome. Heavy metal resistant genes encoded by the P. putida W619 genome were also not present in the P. putida LS46 genome. Despite the overall similarity among genome of P.putida strains isolated for different applications and from different geographical location a number of differences were observed in genome arrangement, occurrence of transposon, genomic islands and prophage. It appears that P.putida strains had a common ancestor and by acquiring some specific genes by horizontal gene transfer it differed from other related strains.
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Molina L, Udaondo Z, Duque E, Fernández M, Molina-Santiago C, Roca A, Porcel M, de la Torre J, Segura A, Plesiat P, Jeannot K, Ramos JL. Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS One 2014; 9:e81604. [PMID: 24465371 PMCID: PMC3894933 DOI: 10.1371/journal.pone.0081604] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 10/15/2013] [Indexed: 12/31/2022] Open
Abstract
Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from in-patients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, ß-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts.
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Affiliation(s)
- Lázaro Molina
- Laboratorio de Investigación y Control Agroalimentario, Universidad de Huelva, Huelva, Spain
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Centro de Investigación en Química Sostenible, Universidad de Huelva, Huelva, Spain
| | - Zulema Udaondo
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Carlos Molina-Santiago
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Bio-Iliberis Research and Development, Peligros-Granada, Spain
| | - Mario Porcel
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús de la Torre
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Ana Segura
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patrick Plesiat
- Centre Hospitalier Régional Universitaire - Hôpital Jean Minjoz, Besançon, France
| | - Katy Jeannot
- Centre Hospitalier Régional Universitaire - Hôpital Jean Minjoz, Besançon, France
| | - Juan-Luis Ramos
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics 2013; 14:537. [PMID: 23924250 PMCID: PMC3751351 DOI: 10.1186/1471-2164-14-537] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads. RESULTS The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. CONCLUSIONS Application of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.
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Di Nocera PP, De Gregorio E, Rocco F. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes. BMC Genomics 2013; 14:522. [PMID: 23902135 PMCID: PMC3733652 DOI: 10.1186/1471-2164-14-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. RESULTS We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. CONCLUSIONS CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
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Affiliation(s)
- Pier Paolo Di Nocera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy.
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Nunvar J, Licha I, Schneider B. Evolution of REP diversity: a comparative study. BMC Genomics 2013; 14:385. [PMID: 23758774 PMCID: PMC3686654 DOI: 10.1186/1471-2164-14-385] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/03/2013] [Indexed: 12/05/2022] Open
Abstract
Background Repetitive extragenic palindromic elements (REPs) constitute a group of bacterial genomic repeats known for their high abundance and several roles in host cells´ physiology. We analyzed the phylogenetic distribution of particular REP classes in genomic sequences of sixty-three bacterial strains belonging to the Pseudomonas fluorescens species complex and ten strains of Stenotrophomonas sp., in order to assess intraspecific REP diversity and to gain insight into long-term REP evolution. Results Based on proximity to RAYT (REP-associated tyrosine transposase) genes, twenty-two and thirteen unique REP classes were determined in fluorescent pseudomonads and stenotrophomonads, respectively. In stenotrophomonads, REP elements were typically found in tens or a few hundred copies per genome. REPs of fluorescent pseudomonads were generally more numerous, occurring in hundreds or even over a thousand perfect copies of particular REP class per genome. REP sequences showed highly heterogeneous distribution. The abundances of REP classes roughly followed host strains´ phylogeny, differing markedly among individual clades. High abundances of particular REP classes appeared to depend on the presence of the cognate RAYT gene, and deviations from this state could be attributed to recent or ancient mutations of rayt-flanking REPs, or RAYT loss. RAYTs of both studied bacterial groups are monophyletic, and their cognate REPs show species-specific characteristics, suggesting shared evolutionary history of REPs, RAYTs and their hosts. Conclusions The results of our large-scale analysis show that REP elements constitute intriguingly dynamic components of genomes of fluorescent pseudomonads and stenotrophomonads, and indicate that REP diversification and proliferation are ongoing processes. High numbers of REPs have apparently been retained during the entire evolutionary time since the establishment of these two bacterial lineages, probably because of their beneficial effect on host long-term fitness. REP elements in these bacteria represent a suitable platform to study the interplay between repeated elements, their mobilizers and host bacterial cells.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 2, Czech Republic.
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Fernández M, Conde S, Duque E, Ramos JL. In vivo gene expression of Pseudomonas putida KT2440 in the rhizosphere of different plants. Microb Biotechnol 2013; 6:307-13. [PMID: 23433036 PMCID: PMC3815925 DOI: 10.1111/1751-7915.12037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/14/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida KT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 105–106 cfu g soil−1. Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacteria's successful establishment in this niche.
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Affiliation(s)
- Matilde Fernández
- Bio-Iliberis Research and Development, I+D Department, 18210, Peligros, Granada, Spain
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Messing SAJ, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease. Nucleic Acids Res 2012; 40:9964-79. [PMID: 22885300 PMCID: PMC3479197 DOI: 10.1093/nar/gks741] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation of certain bacterial functions, such as Integration Host Factor recruitment and mRNA turnover. Although a new clade of putative transposases (RAYTs or TnpAREP) is often associated with an increase in these repeats, it is not clear how these proteins might have directed amplification of REPs. We report here the structure to 2.6 Å of TnpAREP from Escherichia coli MG1655 bound to a REP. Sequence analysis showed that TnpAREP is highly related to the IS200/IS605 family, but in contrast to IS200/IS605 transposases, TnpAREP is a monomer, is auto-inhibited and is active only in manganese. These features suggest that, relative to IS200/IS605 transposases, it has evolved a different mechanism for the movement of discrete segments of DNA and has been severely down-regulated, perhaps to prevent REPs from sweeping through genomes.
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Affiliation(s)
- Simon A J Messing
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 2012; 78:5104-10. [PMID: 22582075 PMCID: PMC3416403 DOI: 10.1128/aem.00619-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/04/2012] [Indexed: 01/16/2023] Open
Abstract
In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.
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Affiliation(s)
| | | | - Susana Conde
- Bio-Iliberis Research and Development, Granada, Spain
| | - Juan Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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21
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Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 2012; 8:e1002784. [PMID: 22792073 PMCID: PMC3390384 DOI: 10.1371/journal.pgen.1002784] [Citation(s) in RCA: 398] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022] Open
Abstract
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire. We sequenced the genomes of seven strains of the Pseudomonas fluorescens group that colonize plant surfaces and function as biological control agents, protecting plants from disease. In this study, we demonstrated the genomic diversity of the group by comparing these strains to each other and to three other strains that were sequenced previously. Only about half of the genes in each strain are present in all of the other strains, and each strain has hundreds of unique genes that are not present in the other genomes. We mapped the genes that contribute to biological control in each genome and found that most of the biological control genes are in the variable regions of the genome, which are not shared by all of the other strains. This finding is consistent with our knowledge of the distinctive biology of each strain. Finally, we looked for new genes that are likely to confer antimicrobial traits needed to suppress plant pathogens, but have not been identified previously. In each genome, we discovered many of these new genes, which provide avenues for future discovery of new traits with the potential to manage plant diseases in agriculture or natural ecosystems.
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Affiliation(s)
- Joyce E Loper
- Agricultural Research Service, US Department of Agriculture, Corvallis, Oregon, United States of America.
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22
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Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G, Chandler M. Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences. Nucleic Acids Res 2011; 40:3596-609. [PMID: 22199259 PMCID: PMC3333891 DOI: 10.1093/nar/gkr1198] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
REPs are highly repeated intergenic palindromic sequences often clustered into structures called BIMEs including two individual REPs separated by short linker of variable length. They play a variety of key roles in the cell. REPs also resemble the sub-terminal hairpins of the atypical IS200/605 family of insertion sequences which encode Y1 transposases (TnpA(IS200/IS605)). These belong to the HUH endonuclease family, carry a single catalytic tyrosine (Y) and promote single strand transposition. Recently, a new clade of Y1 transposases (TnpA(REP)) was found associated with REP/BIME in structures called REPtrons. It has been suggested that TnpA(REP) is responsible for REP/BIME proliferation over genomes. We analysed and compared REP distribution and REPtron structure in numerous available E. coli and Shigella strains. Phylogenetic analysis clearly indicated that tnpA(REP) was acquired early in the species radiation and was lost later in some strains. To understand REP/BIME behaviour within the host genome, we also studied E. coli K12 TnpA(REP) activity in vitro and demonstrated that it catalyses cleavage and recombination of BIMEs. While TnpA(REP) shared the same general organization and similar catalytic characteristics with TnpA(IS200/IS605) transposases, it exhibited distinct properties potentially important in the creation of BIME variability and in their amplification. TnpA(REP) may therefore be one of the first examples of transposase domestication in prokaryotes.
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Affiliation(s)
- Bao Ton-Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, 118, Route de Narbonne, 31062 Toulouse Cedex, France.
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Valls M, Silva-Rocha R, Cases I, Muñoz A, de Lorenzo V. Functional analysis of the integration host factor site of the σ54Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol Microbiol 2011; 82:591-601. [DOI: 10.1111/j.1365-2958.2011.07835.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (TIR) sequences, the nonautonomous miniature inverted-repeat transposable element (MITE). In addition, there are the repetitive extragenic palindromic (REP) sequences that fold into a small stem loop rich in G–C bonding. And the clustered regularly interspaced short palindromic repeats (CRISPRs) display similar small stem loops but are an integral part of a complex genetic element. Other classes of repeats such as the REP2 element do not have TIRs but show other signatures. With the current availability of a large number of whole-genome sequences, many new repeat elements have been discovered. These sequences display diverse properties. Some show an intimate linkage to integrons, and at least one encodes a small RNA. Many repeats are found fused with chromosomal open reading frames, and some are located within protein coding sequences. Small repeat units appear to work hand in hand with the transcriptional and/or post-transcriptional apparatus of the cell. Functionally, they are multifaceted, and this can range from the control of gene expression, the facilitation of host/pathogen interactions, or stimulation of the mammalian immune system. The CRISPR complex displays dramatic functions such as an acquired immune system that defends against invading viruses and plasmids. Evolutionarily, mobile repeat elements may have influenced a cycle of active versus inactive genes in ancestral organisms, and some repeats are concentrated in regions of the chromosome where there is significant genomic plasticity. Changes in the abundance of genomic repeats during the evolution of an organism may have resulted in a benefit to the cell or posed a disadvantage, and some present day species may reflect a purification process. The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, State University of New York, Stony Brook, NY, USA.
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25
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Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW. Pseudomonasgenomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652-80. [DOI: 10.1111/j.1574-6976.2011.00269.x] [Citation(s) in RCA: 578] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Bertels F, Rainey PB. Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria. PLoS Genet 2011; 7:e1002132. [PMID: 21698139 PMCID: PMC3116915 DOI: 10.1371/journal.pgen.1002132] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 05/02/2011] [Indexed: 12/31/2022] Open
Abstract
Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT–containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA. DNA sequences that copy themselves throughout genomes, and make no specific contribution to reproductive success, are by definition “selfish.” Such DNA is a feature of the genomes of all organisms and evident by virtue of its repetitive nature. In bacteria the predominant repetitive sequences are short (∼20 bp), extragenic, and palindromic. These so-called REP sequences may occur many hundreds of times per genome, but their origins and means of dissemination have been a longstanding mystery. We show that REPs are components of higher-order replicative entities termed REPINs, which are themselves thought to be derived from REP sequences that flanked an ancestral autonomous selfish element. In this ancestral state the REP sequences were likely to have been critical for the movement of the selfish element, but were devoid of any capacity to replicate independently. REPINs, on the other hand, have evolved to have a life of their own, albeit one that exploits—even enslaves—a genetic element upon which their existence depends. REPINs are the ultimate non-autonomous, super-streamlined, selfish element and are widespread among bacteria.
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Affiliation(s)
- Frederic Bertels
- New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University at Albany, Auckland, New Zealand.
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27
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Rocco F, De Gregorio E, Di Nocera PP. A giant family of short palindromic sequences in Stenotrophomonas maltophilia. FEMS Microbiol Lett 2010; 308:185-92. [PMID: 20528935 DOI: 10.1111/j.1574-6968.2010.02010.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genome of Stenotrophomonas maltophilia is peppered with palindromic elements called SMAG (Stenotrophomonas maltophilia GTAG) because they carry at one terminus the tetranucleotide GTAG. The repeats are species-specific variants of the superfamily of repetitive extragenic palindromes (REPs), DNA sequences spread in the intergenic space in many prokaryotic genomes. The genomic organization and the functional features of SMAG elements are described herein. A total of 1650 SMAG elements were identified in the genome of the S. maltophilia K279a strain. The elements are 22-25 bp in size, and can be sorted into five distinct major subfamilies because they have different stem and loop sequences. One fifth of the SMAG family is comprised of single units, 2/5 of elements located at a close distance from each other and 2/5 of elements grouped in tandem arrays of variable lengths. Altogether, SMAGs and intermingled DNA occupy 13% of the intergenic space, and make up 1.4% of the chromosome. Hundreds of genes are immediately flanked by SMAGs, and the level of expression of many may be influenced by the folding of the repeats in the mRNA. Expression analyses suggested that SMAGs function as RNA control sequences, either stabilizing upstream transcripts or favoring their degradation.
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Affiliation(s)
- Francesco Rocco
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università FEDERICO II, Napoli, Italy
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de Eugenio LI, Galán B, Escapa IF, Maestro B, Sanz JM, García JL, Prieto MA. The PhaD regulator controls the simultaneous expression of thephagenes involved in polyhydroxyalkanoate metabolism and turnover inPseudomonas putidaKT2442. Environ Microbiol 2010; 12:1591-603. [DOI: 10.1111/j.1462-2920.2010.02199.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nunvar J, Huckova T, Licha I. Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. BMC Genomics 2010; 11:44. [PMID: 20085626 PMCID: PMC2817692 DOI: 10.1186/1471-2164-11-44] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 01/19/2010] [Indexed: 02/08/2023] Open
Abstract
Background Bacterial repetitive extragenic palindromes (REPs) compose a distinct group of genomic repeats. They usually occur in high abundance (>100 copies/genome) and are often arranged in composite repetitive structures - bacterial interspersed mosaic elements (BIMEs). In BIMEs, regularly spaced REPs are present in alternating orientations. BIMEs and REPs have been shown to serve as binding sites for several proteins and suggested to play role in chromosome organization and transcription termination. Their origins are, at present, unknown. Results In this report, we describe a novel class of putative transposases related to IS200/IS605 transposase family and we demonstrate that they are obligately associated with bacterial REPs. Open reading frames coding for these REP-associated tyrosine transposases (RAYTs) are always flanked by two REPs in inverted orientation and thus constitute a unit reminiscent of typical transposable elements. Besides conserved residues involved in catalysis of DNA cleavage, RAYTs carry characteristic structural motifs that are absent in typical IS200/IS605 transposases. DNA sequences flanking rayt genes are in one third of examined cases arranged in modular BIMEs. RAYTs and their flanking REPs apparently coevolve with each other. The rayt genes themselves are subject to rapid evolution, substantially exceeding the substitution rate of neighboring genes. Strong correlation was found between the presence of a particular rayt in a genome and the abundance of its cognate REPs. Conclusions In light of our findings, we propose that RAYTs are responsible for establishment of REPs and BIMEs in bacterial genomes, as well as for their exceptional dynamics and species-specifity. Conversely, we suggest that BIMEs are in fact a special type of nonautonomous transposable elements, mobilizable by RAYTs.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic.
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Genomic analysis of the aromatic catabolic pathways fromSilicibacter pomeroyi DSS-3. ANN MICROBIOL 2009. [DOI: 10.1007/bf03179225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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31
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Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SAC, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 2009; 10:R51. [PMID: 19432983 PMCID: PMC2718517 DOI: 10.1186/gb-2009-10-5-r51] [Citation(s) in RCA: 283] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/21/2009] [Accepted: 05/11/2009] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
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Affiliation(s)
- Mark W Silby
- Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Ana M Cerdeño-Tárraga
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Georgios S Vernikos
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen R Giddens
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Robert W Jackson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Xue-Xian Zhang
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
| | - Christina D Moon
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| | - Stefanie M Gehrig
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Scott AC Godfrey
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: School of Life Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Christopher G Knight
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jacob G Malone
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Zena Robinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Andrew J Spiers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: SIMBIOS Centre, Level 5, Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
| | - Simon Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Alice M Yaxley
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - David Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathy Seeger
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Lee Murphy
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Rutter
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rob Squares
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael A Quail
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Konstantinos Mavromatis
- Genome Biology Program, Department of Energy's Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Stephen D Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Joanne Hothersall
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton Stephens
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stuart B Levy
- Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Auckland, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
| | - Nicholas R Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Davenport CF, Wiehlmann L, Reva ON, Tümmler B. Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides. Environ Microbiol 2009; 11:1092-104. [PMID: 19161433 DOI: 10.1111/j.1462-2920.2008.01839.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Under- and over-represented mono- to hexanucleotides are signatures of bacterial genomes, but the compositional biases of octa- to tetradecanucleotides have not yet been explored. Thirteen completely sequenced genomes of the Pseudomonas genus were searched for highly overrepresented 8-14mers. Between 59-989 overrepresented 8-14mers were found to exceed the applied threshold value. All genomic data sets of the 13 strains showed a consistent pattern, with individual oligomers clustering in either non-coding or coding regions. Non-coding oligonucleotides were typically part of longer repeats. Coding oligonucleotides were evenly distributed in the core genome, preferred one reading frame and matched with the local tetranucleotide usage patterns. Genomic islands were recognized by the depletion of overrepresented oligonucleotides. Several mainly coding 8-14mers occurred in genomes on average every 10 000 bp or less. Such frequently occurring 8-14mers could become useful markers for species identification. In the future of next-generation ultra-high throughput DNA sequencing, the composition of bacterial metagenomes may be quantified by scanning the primary sequence reads for these 8-14mer markers.
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Affiliation(s)
- Colin F Davenport
- Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, Hanover, Germany.
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Genomic analysis of the role of RNase R in the turnover of Pseudomonas putida mRNAs. J Bacteriol 2008; 190:6258-63. [PMID: 18641145 DOI: 10.1128/jb.00630-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNase R is a 3'-5' highly processive exoribonuclease that can digest RNAs with extensive secondary structure. We analyzed the global effect of eliminating RNase R on the Pseudomonas putida transcriptome and the expression of the rnr gene under diverse conditions. The absence of RNase R led to increased levels of many mRNAs, indicating that it plays an important role in mRNA turnover.
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Cozzuto L, Petrillo M, Silvestro G, Di Nocera PP, Paolella G. Systematic identification of stem-loop containing sequence families in bacterial genomes. BMC Genomics 2008; 9:20. [PMID: 18201379 PMCID: PMC2267715 DOI: 10.1186/1471-2164-9-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 01/17/2008] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure. RESULTS The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. 25 of them include all well-known SLS containing repeats and others reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions. CONCLUSION Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that, even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at the RNA level.
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Affiliation(s)
- Luca Cozzuto
- CEINGE Biotecnologie Avanzate scarl, Via Comunale Margherita 482, 80145 Napoli, Italy.
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Magnusson M, Tobes R, Sancho J, Pareja E. Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9. THE JOURNAL OF IMMUNOLOGY 2007; 179:31-5. [PMID: 17579017 DOI: 10.4049/jimmunol.179.1.31] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacterial DNA exerts immunostimulatory effects on mammalian cells via the intracellular TLR9. Although broad analysis of TLR9-mediated immunostimulatory potential of synthetic oligonucleotides has been developed, which kinds of natural bacterial DNA sequences are responsible for immunostimulation are not known. This work provides evidence that the natural DNA sequences named repetitive extragenic palindromic (REPs) sequences present in Gram-negative bacteria are able to produce innate immune system stimulation via TLR9. A strong induction of IFN-alpha production by REPs from Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, and Neisseria meningitidis was detected in splenocytes from 129 mice. In addition, the involvement of TLR9 in immune stimulation by REPs was confirmed using B6.129P2-Tlr9(tm1Aki) knockout mice. Considering the involvement of TLRs in Gram-negative septic shock, it is conceivable that REPs play a role in its pathogenesis. This study highlights REPs as a potential novel target in septic shock treatment.
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MESH Headings
- Adjuvants, Immunologic/genetics
- Adjuvants, Immunologic/physiology
- Animals
- Cells, Cultured
- DNA, Bacterial/metabolism
- DNA, Bacterial/physiology
- Escherichia coli K12/genetics
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/immunology
- Humans
- Immunity, Innate/genetics
- Ligands
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neisseria meningitidis, Serogroup B/genetics
- Pseudomonas aeruginosa/genetics
- Repetitive Sequences, Nucleic Acid
- Salmonella typhi/genetics
- Toll-Like Receptor 9/deficiency
- Toll-Like Receptor 9/genetics
- Toll-Like Receptor 9/metabolism
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Affiliation(s)
- Mattias Magnusson
- Department of Rheumatology and Inflammation Research, Göteborg University, Göteborg, Sweden
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36
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Jomantiene R, Davis RE. Clusters of diverse genes existing as multiple, sequence-variable mosaics in a phytoplasma genome. FEMS Microbiol Lett 2006; 255:59-65. [PMID: 16436062 DOI: 10.1111/j.1574-6968.2005.00057.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Phytoplasmas are cell wall-less prokaryotes living as obligate parasites and pathogens of plants and insects, making them attractive subjects for studies to gain a greater understanding of transkingdom parasitism and pathogenicity. During a study of two phytoplasma genomes, we obtained evidence for previously unreported clustering of genes, pseudogenes, mobile genetic elements, intergenic repeat units, and repetitive extragenic palindromes that occur in multiple, homologous clusters in some phytoplasma genomes. The clusters represent previously unrecognized mosaics, possibly assembled through multiple events of targeted mobile element attack, duplication, recombination, and rearrangement. Multiple clusters could conceivably afford potential for genome reduction through homologous recombination. Differences in the sizes and multiplicity of such clusters possibly account for some of the previously reported but unexplained variations in genome size among closely related phytoplasma strains.
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Petrillo M, Silvestro G, Di Nocera PP, Boccia A, Paolella G. Stem-loop structures in prokaryotic genomes. BMC Genomics 2006; 7:170. [PMID: 16820051 PMCID: PMC1590033 DOI: 10.1186/1471-2164-7-170] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 07/04/2006] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of sequence elements controlling gene expression. RESULTS Systematic analysis of the distribution of stem-loop structures (SLSs) in 40 wholly-sequenced bacterial genomes is presented. SLSs were searched as stems measuring at least 12 bp, bordering loops 5 to 100 nt in length. G-U pairing in the stems was allowed. SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and composition. The large majority of SLSs fall within protein-coding regions but enrichment of specific, non random, SLS sub-populations of higher stability was observed within the intergenic regions of the chromosomes of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs. Some intergenic SLS regions are members of novel repeated sequence families. CONCLUSION In depth analysis of SLS features and distribution in 40 different bacterial genomes showed the presence of non random populations of such structures in all species. Many of these structures are plausibly transcribed, and might be involved in the control of transcription termination, or might serve as RNA elements which can enhance either the stability or the turnover of cotranscribed mRNAs. Three previously undescribed families of repeated sequences were found in Yersiniae, Bordetellae and Enterococci.
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Affiliation(s)
- Mauro Petrillo
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giustina Silvestro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Pier Paolo Di Nocera
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
- Dipartimento SAVA Università del Molise Via De Sanctis, 86100 Campobasso, Italy
- Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
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Vodovar N, Vallenet D, Cruveiller S, Rouy Z, Barbe V, Acosta C, Cattolico L, Jubin C, Lajus A, Segurens B, Vacherie B, Wincker P, Weissenbach J, Lemaitre B, Médigue C, Boccard F. Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila. Nat Biotechnol 2006; 24:673-9. [PMID: 16699499 DOI: 10.1038/nbt1212] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 04/07/2006] [Indexed: 11/08/2022]
Abstract
Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified.
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Affiliation(s)
- Nicolas Vodovar
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France
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Tobes R, Pareja E. Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. BMC Genomics 2006; 7:62. [PMID: 16563168 PMCID: PMC1525189 DOI: 10.1186/1471-2164-7-62] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 03/24/2006] [Indexed: 02/04/2023] Open
Abstract
Background Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP) elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements. Results This global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates. Conclusion Our findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for genome manipulation.
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Affiliation(s)
- Raquel Tobes
- Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud – Armilla Granada 18100, Spain
| | - Eduardo Pareja
- Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud – Armilla Granada 18100, Spain
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40
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Ramos-González MI, Campos MJ, Ramos JL, Espinosa-Urgel M. Characterization of the Pseudomonas putida mobile genetic element ISPpu10: an occupant of repetitive extragenic palindromic sequences. J Bacteriol 2006; 188:37-44. [PMID: 16352819 PMCID: PMC1317595 DOI: 10.1128/jb.188.1.37-44.2006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have characterized the Pseudomonas putida KT2440 insertion element ISPpu10. This insertion sequence encodes a transposase which exhibits homology to the transposases and specific recombinases of the Piv/Moov family, and no inverted repeats are present at the borders of its left and right ends, thus constituting a new member of the atypical IS110/IS492 family. ISPpu10 was found in at least seven identical loci in the KT2440 genome, and variants were identified having an extra insertion at distinct loci. ISPpu10 always appeared within the core of specific repetitive extragenic palindromic (REP) sequences TCGCGGGTAAACCCGCTCCTAC, exhibiting high target stringency. One intragenic target was found associated with the truncation of a GGDEF/EAL domain protein. After active in vitro transposition to a plasmid-borne target, a duplication of the CT (underlined above) at the junction as a consequence of the ISPpu10 insertion was experimentally demonstrated for the first time in the IS110/IS492 family. The same duplication was observed after transposition of ISPpu10 from a plasmid to the chromosome of P. putida DOT-T1E, an ISPpu10-free strain with REPs similar to those of strain KT2440. Plasmid ISPpu10-mediated rearrangements were observed in vivo under laboratory conditions and in the plant rhizosphere.
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Affiliation(s)
- María Isabel Ramos-González
- Department of Plant Biochemistry and Molecular and Cellular Biology, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain.
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Suyama M, Lathe WC, Bork P. Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii. FEBS Lett 2005; 579:5281-6. [PMID: 16182294 DOI: 10.1016/j.febslet.2005.08.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/02/2005] [Accepted: 08/18/2005] [Indexed: 11/26/2022]
Abstract
We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.
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Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, Land M, Richardson PM, Kyrpides NC, Ivanova N, Lindow SE. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A 2005; 102:11064-9. [PMID: 16043691 PMCID: PMC1182459 DOI: 10.1073/pnas.0504930102] [Citation(s) in RCA: 368] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of P. syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism.
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Affiliation(s)
- Helene Feil
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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43
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Abstract
Through the analysis of 57 bacterial genomes we have detected repetitive extragenic palindromic DNA sequences (REPs) in 11 species. For a sequence to be considered as REP, the following criteria should be met: (i) It should be extragenic, (ii) palindromic, (iii) of a length between 21 and 65 bases and (iv) should constitute more than 0.5% of the total extragenic space. Species-specific REPs have been found in human pathogens such as Escherichia coli, Salmonella enterica, Neisseria meningitidis, Mycobacterium tuberculosis, Rickettsia conorii and Pseudomonas aeruginosa, the plant pathogen Agrobacterium tumefaciens and the soil bacteria Deinococcus radiodurans, Pseudomonas putida and Sinorhizobium meliloti.
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Affiliation(s)
- Raquel Tobes
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín. Department of Plant Biochemistry and Molecular and Cellular Biology. Profesor Albareda number 1, E-18008 Granada, Spain
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44
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Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS, Thomashow LS, Loper JE. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2005; 23:873-8. [PMID: 15980861 PMCID: PMC7416659 DOI: 10.1038/nbt1110] [Citation(s) in RCA: 421] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 05/04/2005] [Indexed: 12/11/2022]
Abstract
Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
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Affiliation(s)
- Ian T Paulsen
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Caroline M Press
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Donald Y Kobayashi
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA
| | | | - Dmitri V Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington USA
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Rekha Seshadri
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - A Scott Durkin
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | | | | | | | | | - Liwei Zhou
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Davd J Schneider
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | - Samuel W Cartinhour
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | | | - Janice Weidman
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kisha Watkins
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kevin Tran
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - Leland S Pierson
- Department of Plant Sciences, University of Arizona, Tucson, Arizona USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, Washington USA
| | - Joyce E Loper
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
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45
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Tobes R, Pareja E. Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. Res Microbiol 2005; 156:424-33. [PMID: 15808947 DOI: 10.1016/j.resmic.2004.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 10/06/2004] [Accepted: 10/13/2004] [Indexed: 11/24/2022]
Abstract
Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears to be disseminated in more than 300 copies in the Pseudomonas syringae DC3000 genome. The finding of REP sequences in P. syringae confirms the broad presence of this type of repetitive sequence in bacteria. We analyzed the distribution of REP sequences and the structure of the clusters, and we show that palindromy is conserved. REP sequences appear to be allocated to the extragenic space, with a special preference for the intergenic spaces limited by convergent genes, while their presence is scarce between divergent genes. Using REP sequences as markers of extragenicity we re-annotated a set of genes of the P. syringae DC3000 genome demonstrating that REP sequences can be used for refinement of annotation of a genome. The similarity detected between virulence genes from evolutionarily distant pathogenic bacteria suggests the acquisition of clusters of virulence genes by horizontal gene transfer. We did not detect the presence of P. syringae REP elements in the principal pathogenicity gene clusters. This absence suggests that genome fragments lacking REP sequences could point to regions recently acquired from other organisms, and REP sequences might be new tracers for gaining insight into key aspects of bacterial genome evolution, especially when studying pathogenicity acquisition. In addition, as the P. syringae REP sequence is species-specific with respect to the sequenced genomes, it is an exceptional candidate for use as a fingerprint in precise genotyping and epidemiological studies.
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Affiliation(s)
- Raquel Tobes
- Bioinformatics Unit, Era7 Information Technologies, C/Río Tajo 49, Las Gabias, Granada 18110, Spain.
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46
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Bartolomé-Martín D, Martínez-García E, Mascaraque V, Rubio J, Perera J, Alonso S. Characterization of a second functional gene cluster for the catabolism of phenylacetic acid in Pseudomonas sp. strain Y2. Gene 2005; 341:167-79. [PMID: 15474299 DOI: 10.1016/j.gene.2004.06.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 05/27/2004] [Accepted: 06/21/2004] [Indexed: 10/26/2022]
Abstract
Pseudomonas sp. strain Y2 is a styrene degrading bacterium that mineralises this compound through its oxidation to phenylacetic acid (PAA). We previously identified a complete gene cluster (paa1 cluster) for the degradation of phenylacetate, but, surprisingly, some paa1 deletion mutants were still able to catabolize styrene (STY) suggesting that this strain contained a second catabolic pathway. We report here the characterization of a second and novel paa2 gene cluster comprising 17 genes related to the catabolism of phenylacetate. We have identified a new gene (paaP) that is most likely involved in a transport process. Remarkably, the organization of the paa2 gene cluster is more similar to that of Pseudomonas putida KT2440 than to the paa1 gene cluster. Two new genes of undefined function were located inside the paa2 cluster. Sequence comparison between the paa2 genes and the paa1 and paa clusters of Pseudomonas sp. strain Y2 and P. putida KT2440, respectively, revealed a similar degree of divergence among the three sets of genes. Differences in the gene organization between paa1 and paa2 clusters of Pseudomonas sp. strain Y2 can be explained by an independent evolutionary history, probably associated with the adjacent sty genes. Deletion of either the first (paa1) or the second (paa2) gene cluster did not affect the ability of strain Y2 to grow in phenylacetate, whereas the deletion of both clusters led to the loss of this ability. The co-existence of two functional gene clusters for the degradation of phenylacetic acid in a bacterium has not been reported so far.
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Affiliation(s)
- David Bartolomé-Martín
- Departmento de Bioquímica y Biología Molecular, I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Ciudad Universitaria, s/n. 28040 Madrid, Spain
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47
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Dos Santos VAPM, Heim S, Moore ERB, Strätz M, Timmis KN. Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 2004; 6:1264-86. [PMID: 15560824 DOI: 10.1111/j.1462-2920.2004.00734.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.
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Affiliation(s)
- V A P Martins Dos Santos
- Department of Environmental Microbiology, GBF - German Research Centre for Biotechnology, Braunschweig, Germany.
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48
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Regenhardt D, Heuer H, Heim S, Fernandez DU, Strömpl C, Moore ERB, Timmis KN. Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ Microbiol 2002; 4:912-5. [PMID: 12534472 DOI: 10.1046/j.1462-2920.2002.00368.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- D Regenhardt
- Division of Microbiology, GBF - German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
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49
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Jiménez JI, Miñambres B, García JL, Díaz E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 2002; 4:824-41. [PMID: 12534466 DOI: 10.1046/j.1462-2920.2002.00370.x] [Citation(s) in RCA: 352] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of the catabolic potential of Pseudomonas putida KT2440 against a wide range of natural aromatic compounds and sequence comparisons with the entire genome of this microorganism predicted the existence of at least four main pathways for the catabolism of central aromatic intermediates, that is, the protocatechuate (pca genes) and catechol (cat genes) branches of the beta-ketoadipate pathway, the homogentisate pathway (hmg/fah/mai genes) and the phenylacetate pathway (pha genes). Two additional gene clusters that might be involved in the catabolism of N-heterocyclic aromatic compounds (nic cluster) and in a central meta-cleavage pathway (pcm genes) were also identified. Furthermore, the genes encoding the peripheral pathways for the catabolism of p-hydroxybenzoate (pob), benzoate (ben), quinate (qui), phenylpropenoid compounds (fcs, ech, vdh, cal, van, acd and acs), phenylalanine and tyrosine (phh, hpd) and n-phenylalkanoic acids (fad) were mapped in the chromosome of P. putida KT2440. Although a repetitive extragenic palindromic (REP) element is usually associated with the gene clusters, a supraoperonic clustering of catabolic genes that channel different aromatic compounds into a common central pathway (catabolic island) was not observed in P. putida KT2440. The global view on the mineralization of aromatic compounds by P. putida KT2440 will facilitate the rational manipulation of this strain for improving biodegradation/biotransformation processes, and reveals this bacterium as a useful model system for studying biochemical, genetic, evolutionary and ecological aspects of the catabolism of aromatic compounds.
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Affiliation(s)
- José Ignacio Jiménez
- Departmento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Velázquez 144, 28006 Madrid, Spain
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50
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Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Düsterhöft A, Tümmler B, Fraser CM. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 2002; 4:799-808. [PMID: 12534463 DOI: 10.1046/j.1462-2920.2002.00366.x] [Citation(s) in RCA: 975] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.
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Affiliation(s)
- K E Nelson
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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