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Sverchkova NV, Akhremchuk AE, Valentovich LN, Kolomiets EI. A Molecular Genetic Analysis of the Bacterial Genome of Bacillus velezensis BIM B‑454 D: The Basis of a Probiotic Preparation for Veterinary Practice. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Mohapatra B, Malhotra H, Phale PS. Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICE nahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86 T Suggest Probable Role in Colonization and Adaptation. Front Microbiol 2022; 13:928848. [PMID: 35875527 PMCID: PMC9298801 DOI: 10.3389/fmicb.2022.928848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic and functional analyses revealed the presence of three genomic islands (GIs, >50 Kb size): ICEnahCSV86, Pseudomonas bharatica genomic island-1 (PBGI-1), and PBGI-2 in the preferentially aromatic-degrading soil bacterium, Pseudomonas bharatica CSV86T. Site-specific genomic integration at or near specific transfer RNAs (tRNAs), near-syntenic structural modules, and phylogenetic relatedness indicated their evolutionary lineage to the type-4 secretion system (T4SS) ICEclc family, thus predicting these elements to be integrative conjugative elements (ICEs). These GIs were found to be present as a single copy in the genome and the encoded phenotypic traits were found to be stable, even in the absence of selection pressure. ICEnahCSV86 harbors naphthalene catabolic (nah-sal) cluster, while PBGI-1 harbors Co-Zn-Cd (czc) efflux genes as cargo modules, whereas PBGI-2 was attributed to as a mixed-function element. The ICEnahCSV86 has been reported to be conjugatively transferred (frequency of 7 × 10–8/donor cell) to Stenotrophomonas maltophilia CSV89. Genome-wide comparative analyses of aromatic-degrading bacteria revealed nah-sal clusters from several Pseudomonas spp. as part of probable ICEs, syntenic to conjugatively transferable ICEnahCSV86 of strain CSV86T, suggesting it to be a prototypical element for naphthalene degradation. It was observed that the plasmids harboring nah-sal clusters were phylogenetically incongruent with predicted ICEs, suggesting genetic divergence of naphthalene metabolic clusters in the Pseudomonas population. Gene synteny, divergence estimates, and codon-based Z-test indicated that ICEnahCSV86 is probably derived from PBGI-2, while multiple recombination events masked the ancestral lineage of PBGI-1. Diversifying selection pressure (dN-dS = 2.27–4.31) imposed by aromatics and heavy metals implied the modular exchange-fusion of various cargo clusters through events like recombination, rearrangement, domain reshuffling, and active site optimization, thus allowing the strain to evolve, adapt, and maximize the metabolic efficiency in a contaminated niche. The promoters (Pnah and Psal) of naphthalene cargo modules (nah, sal) on ICEnahCSV86 were proved to be efficient for heterologous protein expression in Escherichia coli. GI-based genomic plasticity expands the metabolic spectrum and versatility of CSV86T, rendering efficient adaptation to the contaminated niche. Such isolate(s) are of utmost importance for their application in bioremediation and are the probable ideal host(s) for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Berezhnaya AV, Evdokimova OV, Valentovich LN, Sverchkova NV, Titok MA, Kolomiyets EI. Molecular Genetic and Functional Analysis of the Genome of Bacteria Bacillus velezensis BIM B-439D. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819040033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Clasen FJ, Pierneef RE, Slippers B, Reva O. EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes. BMC Genomics 2018; 19:323. [PMID: 29724163 PMCID: PMC5934851 DOI: 10.1186/s12864-018-4724-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/25/2018] [Indexed: 11/17/2022] Open
Abstract
Background Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes. Results SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za, was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface. Conclusions SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4724-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederick Johannes Clasen
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa. .,Forestry and Agricultural Biotechnology Institute; Department of Biochemistry , Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - Rian Ewald Pierneef
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa
| | - Bernard Slippers
- Forestry and Agricultural Biotechnology Institute; Department of Biochemistry , Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, Private Bag X20, Hatfield, 0028, South Africa
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Yu X, Reva ON. SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees. Evol Bioinform Online 2018; 14:1176934318759299. [PMID: 29511354 PMCID: PMC5826093 DOI: 10.1177/1176934318759299] [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: 11/14/2017] [Accepted: 01/24/2018] [Indexed: 11/17/2022] Open
Abstract
Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.
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Affiliation(s)
- Xiaoyu Yu
- Department of Biochemistry, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Oleg N Reva
- Department of Biochemistry, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
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Oliveira Alvarenga D, Moreira LM, Chandler M, Varani AM. A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes. Methods Mol Biol 2018; 1704:213-242. [PMID: 29277867 DOI: 10.1007/978-1-4939-7463-4_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses.
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Affiliation(s)
- Danillo Oliveira Alvarenga
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho"-UNESP, Jaboticabal, SP, Brazil
| | - Leandro M Moreira
- Departamento de Ciências Biológicas-Núcleo de Pesquisas em Ciências Biológicas-NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS 118, Route de Narbonne, 31062, Toulouse Cedex, France
| | - Alessandro M Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho"-UNESP, Jaboticabal, SP, Brazil.
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Martin-Cuadrado AB, Pašić L, Rodriguez-Valera F. Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi. BMC Genomics 2015; 16:603. [PMID: 26268990 PMCID: PMC4535781 DOI: 10.1186/s12864-015-1794-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 07/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Haloquadratum walsbyi represents up to 80% of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid library and recovered seven novel version of its cell-wall associated genomic island. The fosmid inserts were sequenced and analysed. RESULTS The novel cell-wall associated islands delineated two major clades within H. walsbyi. The islands predominantly contained genes putatively involved in biosynthesis of surface layer, genes encoding cell surface glycoproteins and genes involved in envelope formation. We further found that these genes are maintained in the population and that the diversity of this region arises through homologous recombination but also through the action of mobile genetic elements, including viruses. CONCLUSIONS The population of H. walsbyi in the studied saltern brine is composed of numerous clonal lineages that differ in surface structures including the cell wall. This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating viruses.
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Affiliation(s)
- Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, Alicante, Spain.
| | - Lejla Pašić
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, Alicante, Spain. .,Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, Alicante, Spain.
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Pierneef R, Cronje L, Bezuidt O, Reva ON. Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015. [PMID: 26200753 PMCID: PMC5630688 DOI: 10.1093/database/bav058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries.
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Affiliation(s)
- Rian Pierneef
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Louis Cronje
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Oliver Bezuidt
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Oleg N Reva
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
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The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment. J Bacteriol 2013; 195:4793-803. [PMID: 23995634 DOI: 10.1128/jb.00825-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.
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He P, Hao K, Blom J, Rückert C, Vater J, Mao Z, Wu Y, Hou M, He P, He Y, Borriss R. Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. J Biotechnol 2013; 164:281-91. [PMID: 23357245 DOI: 10.1016/j.jbiotec.2012.12.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/21/2012] [Accepted: 12/22/2012] [Indexed: 11/29/2022]
Abstract
The plant-associated Bacillus amyloliquefaciens subsp. plantarum strain B9601-Y2, isolated from wheat rhizosphere, is a powerful plant growth-promoting rhizobacterium. Its relative large genome size of 4.24Mbp, exceeding that of other representatives of the B. amyloliquefaciens subsp. plantarum taxon, is mainly due to the presence of 18 DNA-islands containing remnants of phages, a unique restriction modification system, a gene cluster for mersacidin synthesis, and an orphan gene cluster devoted to non-ribosomal synthesis of an unidentified peptide. Like other members of the taxon, the Y2 genome contains giant gene clusters for non-ribosomal synthesis of the polyketides macrolactin, difficidin, and bacillaene, the antifungal lipopeptides bacillomycin D, and fengycin, the siderophore bacillibactin, and the dipeptide bacilysin. A gene cluster encoding enzymes for a degradative pathway with 2-keto-3-deoxygluconate and 2-keto-3-deoxy-phosphogluconate as intermediates was explored by genome mining and found as being a unique feature for representatives of the plantarum subspecies. A survey of the Y2 genome against other B. amyloliquefaciens genomes revealed 130 genes only occurring in subsp. plantarum but not in subsp. amyloliquefaciens. Notably, the surfactin gene cluster is not functional due to a large deletion removing parts of the Srf synthetases B and C. Expression of polyketides, lipopeptides, mersacidin, and of the growth hormone indole-3-acetic acid in Y2 was demonstrated by matrix-assisted laser desorption ionization-time of flight mass spectroscopy and high-performance liquid chromatography, respectively.
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Affiliation(s)
- Pengfei He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
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Bezuidt O, Pierneef R, Mncube K, Lima-Mendez G, Reva ON. Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS One 2011; 6:e25702. [PMID: 22022434 PMCID: PMC3195076 DOI: 10.1371/journal.pone.0025702] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/08/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. PRINCIPAL FINDINGS The study revealed oscillations of gene exchange in enterobacteria, which originated from marine γ-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective 'vehicles' ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of β-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. CONCLUSIONS Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed.
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Affiliation(s)
- Oliver Bezuidt
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Rian Pierneef
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Kingdom Mncube
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Gipsi Lima-Mendez
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Oleg N. Reva
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
- * E-mail:
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Klockgether J, Cramer N, Wiehlmann L, Davenport CF, Tümmler B. Pseudomonas aeruginosa Genomic Structure and Diversity. Front Microbiol 2011; 2:150. [PMID: 21808635 PMCID: PMC3139241 DOI: 10.3389/fmicb.2011.00150] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/27/2011] [Indexed: 12/23/2022] Open
Abstract
The Pseudomonas aeruginosa genome (G + C content 65–67%, size 5.5–7 Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5–0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.
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Affiliation(s)
- Jens Klockgether
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Klinische Forschergruppe Hannover, Germany
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Norberg P, Bergström M, Jethava V, Dubhashi D, Hermansson M. The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination. Nat Commun 2011; 2:268. [PMID: 21468020 PMCID: PMC3104523 DOI: 10.1038/ncomms1267] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/08/2011] [Indexed: 01/24/2023] Open
Abstract
Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species. Plasmids are present in many bacteria and are often transferred between different species causing horizontal gene transfer. By comparing the sequences of 25 plasmid DNA backbones, the authors show that homologous recombination is prevalent in plasmids and that the plasmids have adapted to persist in different host bacteria.
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Affiliation(s)
- Peter Norberg
- Department of Cell and Molecular Biology, Microbiology, University of Gothenburg, Box 462, SE 413 46, Gothenburg, Sweden.
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Beloqui A, Nechitaylo TY, López-Cortés N, Ghazi A, Guazzaroni ME, Polaina J, Strittmatter AW, Reva O, Waliczek A, Yakimov MM, Golyshina OV, Ferrer M, Golyshin PN. Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol 2010; 76:5934-46. [PMID: 20622123 PMCID: PMC2935051 DOI: 10.1128/aem.00902-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/01/2010] [Indexed: 11/20/2022] Open
Abstract
The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha-arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).
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Affiliation(s)
- Ana Beloqui
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Taras Y. Nechitaylo
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Nieves López-Cortés
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Azam Ghazi
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - María-Eugenia Guazzaroni
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Julio Polaina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Axel W. Strittmatter
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Oleg Reva
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Agnes Waliczek
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Michail M. Yakimov
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Olga V. Golyshina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Manuel Ferrer
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Peter N. Golyshin
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
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15
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Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Dønsvik T, Skjerve E, Ussery DW. Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics 2010; 11:464. [PMID: 20691090 PMCID: PMC3091660 DOI: 10.1186/1471-2164-11-464] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 08/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity. RESULTS The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content was also found but appears to be non-linear and varies greatly among phyla. CONCLUSIONS Our findings show that GCVAR is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that GCVAR should be used as a complement to mean GC content.
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Affiliation(s)
- Jon Bohlin
- Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P,O, Box 8146 Dep, NO-0033 Oslo, Norway.
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16
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Davenport C, Ussery DW, Tümmler B. Comparative genomics of green sulfur bacteria. PHOTOSYNTHESIS RESEARCH 2010; 104:137-152. [PMID: 20099081 DOI: 10.1007/s11120-009-9515-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO(2) fixation. Whole-genome gene family and single gene sequence comparisons yielded similar phylogenetic trees of the sequenced chromosomes indicating a concerted vertical evolution of large gene sets. Chromosomal synteny of genes is not preserved in the phylum Chlorobi. The accessory genome is characterized by anomalous oligonucleotide usage and endows the strains with individual features for transport, secretion, cell wall, extracellular constituents, and a few elements of the biosynthetic apparatus. Giant genes are a peculiar feature of the genera Chlorobium and Prosthecochloris. The predicted proteins have a huge molecular weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment.
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Affiliation(s)
- Colin Davenport
- Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie und Neonatologie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover, Germany
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17
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Differential decay of parent-of-origin-specific genomic sharing in cystic fibrosis-affected sib pairs maps a paternally imprinted locus to 7q34. Eur J Hum Genet 2010; 18:553-9. [PMID: 20051989 DOI: 10.1038/ejhg.2009.229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease characterized by a high variability of disease severity and outcome that points to the role of environmental factors and modulating genes that shape the course of this multiorgan disease. We genotyped families of cystic fibrosis sib pairs homozygous for F508del-CFTR who represent extreme clinical phenotypes at informative microsatellite markers spanning a 38 Mb region between CFTR and 7qtel. Recombination events on both parental chromosomes were compared between siblings with concordant clinical phenotypes and siblings with discordant clinical phenotypes. Monitoring parent-of-origin-specific decay of genomic sharing delineated a 2.9-Mb segment on 7q34 in which excess of recombination on paternal chromosomes in discordant pairs was observed compared with phenotypically concordant sibs. This 2.9-Mb core candidate region was enriched in imprinting-related elements such as predicted CCCTC-binding factor consensus sites and CpG islands dense in repetitive elements. Moreover, allele frequencies at a microsatellite marker within the core candidate region differed significantly comparing mildly and severely affected cystic fibrosis sib pairs. The identification of this paternally imprinted locus on 7q34 as a modulator of cystic fibrosis disease severity shows that imprinted elements can be identified by straightforward fine mapping of break points in sib pairs with informative contrasting phenotypes.
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18
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Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. Community-wide analysis of microbial genome sequence signatures. Genome Biol 2009; 10:R85. [PMID: 19698104 PMCID: PMC2745766 DOI: 10.1186/gb-2009-10-8-r85] [Citation(s) in RCA: 373] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/10/2009] [Accepted: 08/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. RESULTS We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH approximately 5) versus extracellular (pH approximately 1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. CONCLUSIONS An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Current address: Department of Geological Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI 48109-1005, USA
| | - Anders F Andersson
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Current address: Evolutionary Biology Centre, Department of Limnology, Uppsala University, Norbyv. 18 D, SE-75236, Uppsala, Sweden
- Current address: Department of Bacteriology, Swedish Institute for Infectious Disease Control, Nobels väg 18 SE-17182 Solna, Sweden
| | - Brett J Baker
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Sheri L Simmons
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - A Pepper Yelton
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Hilgard Hall, Berkeley, CA 94720, USA
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Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens. J Biotechnol 2009; 140:27-37. [DOI: 10.1016/j.jbiotec.2008.10.011] [Citation(s) in RCA: 301] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/23/2008] [Accepted: 10/21/2008] [Indexed: 11/18/2022]
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20
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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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21
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Ganesan H, Rakitianskaia AS, Davenport CF, Tümmler B, Reva ON. The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 2008; 9:333. [PMID: 18687122 PMCID: PMC2528017 DOI: 10.1186/1471-2105-9-333] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2008] [Accepted: 08/07/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visualization. The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package. RESULTS The SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional variation of DNA sequences. The applet is also used for identification of divergent genomic regions both in annotated sequences of bacterial chromosomes, plasmids, phages and viruses, and in raw DNA sequences prior to annotation by comparing local and global OU patterns. The applet allows fast and reliable identification of clusters of horizontally transferred genomic islands, large multi-domain genes and genes for ribosomal RNA. Within the majority of genomic fragments (also termed genomic core sequence), regions enriched with housekeeping genes, ribosomal proteins and the regions rich in pseudogenes or genetic vestiges may be contrasted. CONCLUSION The SWGB applet presents a range of comprehensive OU statistical parameters calculated for a range of bacterial species, plasmids and phages. It is available on the Internet at http://www.bi.up.ac.za/SeqWord/mhhapplet.php.
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Affiliation(s)
- Hamilton Ganesan
- Dep of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Lynnwood road, Hillcrest, Pretoria, 0002, South Africa.
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22
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Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF. Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism. FEMS Microbiol Lett 2008; 281:87-97. [DOI: 10.1111/j.1574-6968.2008.01083.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Durand PM, Coetzer TL. Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes. Bioinform Biol Insights 2008; 2:101-17. [PMID: 19812769 PMCID: PMC2735952 DOI: 10.4137/bbi.s430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Apoptosis is the phenotypic result of an active, regulated process of self-destruction. Following various cellular insults, apoptosis has been demonstrated in numerous unicellular eukaryotes, but very little is known about the genes and proteins that initiate and execute this process in this group of organisms. A bioinformatic approach presents an array of powerful methods to direct investigators in the identification of the apoptosis machinery in protozoans. In this review, we discuss some of the available computational methods and illustrate how they may be applied using the identification of a Plasmodium falciparum metacaspase gene as an example.
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Affiliation(s)
- Pierre Marcel Durand
- Department of Molecular Medicine and Haematology, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
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24
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25
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Bohlin J, Skjerve E, Ussery DW. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics 2008; 9:104. [PMID: 18307761 PMCID: PMC2289816 DOI: 10.1186/1471-2164-9-104] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 02/28/2008] [Indexed: 11/22/2022] Open
Abstract
Background The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. A set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. The statistical methods we are concerned with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. These methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, which can be determined by genomic nucleotide content, smaller oligonucleotide frequencies, or be based on specific statistical distributions. Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/conserved DNA, and homology searches. Our aim was to explore the reliability and best suited applications for some popular methods, which include relative oligonucleotide frequencies (ROF), di- to hexanucleotide zero'th order Markov methods (ZOM) and 2.order Markov chain Method (MCM). Tests were performed on distant homology searches with large DNA sequences, detection of foreign/conserved DNA, and plasmid-host similarity comparisons. Additionally, the reliability of the methods was tested by comparing both real and random genomic DNA. Results Our findings show that the optimal method is context dependent. ROFs were best suited for distant homology searches, whilst the hexanucleotide ZOM and MCM measures were more reliable measures in terms of phylogeny. The dinucleotide ZOM method produced high correlation values when used to compare real genomes to an artificially constructed random genome with similar %GC, and should therefore be used with care. The tetranucleotide ZOM measure was a good measure to detect horizontally transferred regions, and when used to compare the phylogenetic relationships between plasmids and hosts, significant correlation (R2 = 0.4) was found with genomic GC content and intra-chromosomal homogeneity. Conclusion The statistical methods examined are fast, easy to implement, and powerful for a number of different applications involving genomic sequence comparisons. However, none of the measures examined were superior in all tests, and therefore the choice of the statistical method should depend on the task at hand.
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Affiliation(s)
- Jon Bohlin
- Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway.
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26
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Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tümmler B, Ussery DW. Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol 2007; 10:614-25. [PMID: 18081853 DOI: 10.1111/j.1462-2920.2007.01483.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The global feature of the completely sequenced Alcanivorax borkumensis SK2 type strain chromosome is its symmetry and homogeneity. The origin and terminus of replication are located opposite to each other in the chromosome and are discerned with high signal to noise ratios by maximal oligonucleotide usage biases on the leading and lagging strand. Genomic DNA structure is rather uniform throughout the chromosome with respect to intrinsic curvature, position preference or base stacking energy. The orthologs and paralogs of A. borkumensis genes with the highest sequence homology were found in most cases among gamma-Proteobacteria, with Acinetobacter and P. aeruginosa as closest relatives. A. borkumensis shares a similar oligonucleotide usage and promoter structure with the Pseudomonadales. A comparatively low number of only 18 genome islands with atypical oligonucleotide usage was detected in the A. borkumensis chromosome. The gene clusters that confer the assimilation of aliphatic hydrocarbons, are localized in two genome islands which were probably acquired from an ancestor of the Yersinia lineage, whereas the alk genes of Pseudomonas putida still exhibit the typical Alcanivorax oligonucleotide signature indicating a complex evolution of this major hydrocarbonoclastic trait.
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Affiliation(s)
- Oleg N Reva
- Klinische Forschergruppe, OE6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
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27
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Lang DM. Circuit assemblages derived from net dinucleotide values provide a succinct identity for the HIV-1 genome and each of its genes. Virus Genes 2007; 36:11-26. [PMID: 17987374 DOI: 10.1007/s11262-007-0128-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 06/05/2007] [Indexed: 10/22/2022]
Abstract
Dinucleotide composition has been recognized as a species-specific characteristic of organisms for more than 20 years. Lang (2000, Bioinformatics, 16, 212-221), found that in Monilinia rRNA a species-specific identity is conserved when dinucleotide counts are compressed into net dinucleotide counts (e.g., 50AC + 20CA = 30nAC) and clusters of net dinucleotides of equal value (e.g., 30nAC + 30nCT + 30nTA = 30ACTA) which were called circuits. This study evaluates circuit assemblages (CAs)--the collection of all net dinucleotide circuits derived from a sequence--in a diverse set of 110 HIV-1 genomes. The circuit composition, which is often based on <or= 15% of the total dinucleotides of a sequence, uniquely characterizes each gene and genome, although the pairwise similarity of the sequences is as low as 70%. Variations in net dinucleotide distributions are associated with structural and functional features of the genome and its proteins. Circuit values of the env signal sequence are different between subtypes that have remained localized and those that have become pandemic. CAs of complete genomes of HIV-1 are similar to other retro-transcribing viruses, and distinct from viroids and single- and double-stranded DNA and RNA viruses. CAs provide a succinct, quantitative, and species-specific description of DNA composition that is consistent with the results of traditional analytic methods at multiple levels of genome organization.
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Affiliation(s)
- Dorothy M Lang
- School of Contemporary Sciences, University of Abertay-Dundee, Bell Street, Dundee DD1 1HG, Scotland, UK.
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Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2007; 2:e214. [PMID: 17194220 PMCID: PMC1713258 DOI: 10.1371/journal.pgen.0020214] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/02/2006] [Indexed: 01/24/2023] Open
Abstract
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals. Soil systems contain the greatest diversity of microorganisms on earth, with 5,000–10,000 species of microorganism per gram of soil. Arthrobacter sp. strains have a primitive life cycle and are among the most frequently isolated, indigenous soil bacteria, found in common and deep subsurface soils, arctic ice, and environments contaminated with industrial chemicals and radioactive materials. To better understand how these bacteria survive in environmentally harsh conditions, the authors used a structural genomics approach to identify genes involved in soil survival of Arthrobacter aurescens strain TC1, a bacterium originally isolated for its ability to degrade the herbicide atrazine. They found that the genome of this bacterium comprises a single circular chromosome and two plasmids that encode for a large number proteins involved in stress responses due to starvation, desiccation, oxygen radicals, and toxic chemicals. A. aurescens' metabolic versatility is in part due to the presence of duplicated catabolic genes and its ability to funnel plasmid-derived intermediates into chromosomally encoded pathways. Arthrobacter's array of genes that allow for survival in stressful conditions and its ability to produce a temperature-tolerant “cyst”-like resting cell render this soil microorganism able to survive and prosper in a variety of environmental conditions.
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Affiliation(s)
- Emmanuel F Mongodin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Nir Shapir
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Sean C Daugherty
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Joanne B Emerson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Alla Shvartzbeyn
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jessica Vamathevan
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Florenta Riggs
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Viktoria Grinberg
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Karen E Nelson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 2007; 25:1007-1014. [PMID: 17704766 DOI: 10.1002/9781118297674.ch83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/09/2007] [Indexed: 05/24/2023]
Abstract
Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis 168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal synthesis of secondary metabolites, we identified four giant gene clusters absent in B. subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core skeleton.
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Affiliation(s)
- Xiao Hua Chen
- Bakteriengenetik, Institut für Biologie, Humboldt Universität, Chausseestrasse 117, D-10115 Berlin, Germany
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30
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Klockgether J, Würdemann D, Reva O, Wiehlmann L, Tümmler B. Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 2007; 189:2443-59. [PMID: 17194795 PMCID: PMC1899365 DOI: 10.1128/jb.01688-06] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 01/08/2007] [Indexed: 12/27/2022] Open
Abstract
The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNA(Lys) (pKLC102) or tRNA(Gly) (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.
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Affiliation(s)
- Jens Klockgether
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
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31
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Fieseler L, Hentschel U, Grozdanov L, Schirmer A, Wen G, Platzer M, Hrvatin S, Butzke D, Zimmermann K, Piel J. Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges. Appl Environ Microbiol 2007; 73:2144-55. [PMID: 17293531 PMCID: PMC1855645 DOI: 10.1128/aem.02260-06] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid genes were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping genes, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS genes from complex sponge-symbiont associations.
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Affiliation(s)
- Lars Fieseler
- Research Center for Infectious Diseases, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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