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Beard S, Moya-Beltrán A, Silva-García D, Valenzuela C, Pérez-Acle T, Loyola A, Quatrini R. Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology. Front Microbiol 2023; 14:1271138. [PMID: 37817747 PMCID: PMC10561277 DOI: 10.3389/fmicb.2023.1271138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.
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Affiliation(s)
- Simón Beard
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ana Moya-Beltrán
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Danitza Silva-García
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Cesar Valenzuela
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Tomás Pérez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Alejandra Loyola
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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Chen J, Liu Y, Diep P, Mahadevan R. Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129456. [PMID: 35777147 DOI: 10.1016/j.jhazmat.2022.129456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.
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Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2019; 73:1121-1137. [PMID: 29370371 DOI: 10.1093/jac/dkx488] [Citation(s) in RCA: 514] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
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Affiliation(s)
- M Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M S M Brouwer
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - B Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - D J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Abstract
The omnipresence of Arthrobacter species in polluted and toxic soils indicates their great potential in environmental biotechnologies, but practical applications of these bacteria are scarce mainly due to the availability of useful genetic engineering tools. Although many fully sequenced Arthrobacter genomes have been deposited in GenBank, little is known about the biology of their plasmids, especially the core functions: replication and partition. In this study the available Arthrobacter plasmid sequences were analyzed in order to identify their putative replication origin. At least the oris from the cryptic plasmids pXZ10142, pCG1, and pBL1 appear to work in this genus. Based on ParA homolog sequences, the Arthrobacter specific plasmids were classified into 4 clades. Iteron-like sequences were identified on most of the plasmids, indicating the position of the putative Arthrobacter specific oris. Although attempts were made to identify the core gene set required for plasmid replication in this genus, it was not possible. The plasmid proteomes showed a rather low similarity.
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Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One 2013; 8:e78237. [PMID: 24250794 PMCID: PMC3826726 DOI: 10.1371/journal.pone.0078237] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. PRINCIPAL FINDINGS Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. SIGNIFICANCE For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
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Affiliation(s)
- Lillian G. Acuña
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | | | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingenieria, Universidad de Talca, Talca, Chile
| | | | - Jorge Valdés
- Center for Systems Biotechnology, Fraunhofer Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Douglas E. Rawlings
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - David S. Holmes
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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6
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Bustamante P, Covarrubias PC, Levicán G, Katz A, Tapia P, Holmes D, Quatrini R, Orellana O. ICE Afe1, an Actively Excising Genetic Element from the Biomining Bacterium Acidithiobacillus ferrooxidans. J Mol Microbiol Biotechnol 2013; 22:399-407. [DOI: 10.1159/000346669] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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7
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Loftie-Eaton W, Rawlings DE. Diversity, biology and evolution of IncQ-family plasmids. Plasmid 2011; 67:15-34. [PMID: 22037393 DOI: 10.1016/j.plasmid.2011.10.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 11/16/2022]
Abstract
Plasmids of IncQ-family are distinguished by having a unique strand-displacement mechanism of replication that is capable of functioning in a wide variety of bacterial hosts. In addition, these plasmids are highly mobilizable and therefore very promiscuous. Common features of the replicons have been used to identify IncQ-family plasmids in DNA sequence databases and in this way several unstudied plasmids have been compared to more well-studied IncQ plasmids. We propose that IncQ plasmids can be divided into four subgroups based on a number of mutually supportive criteria. The most important of these are the amino acid sequences of their three essential replication proteins and the observation that the replicon of each subgroup has become fused to four different lineages of mobilization genes. This review of IncQ-family plasmid diversity has highlighted several events in the evolution of these plasmids and raised several questions for further research.
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Affiliation(s)
- Wesley Loftie-Eaton
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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8
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Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms. Appl Microbiol Biotechnol 2010; 88:605-20. [DOI: 10.1007/s00253-010-2795-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 07/22/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
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9
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Poirel L, Carattoli A, Bernabeu S, Bruderer T, Frei R, Nordmann P. A novel IncQ plasmid type harbouring a class 3 integron from Escherichia coli. J Antimicrob Chemother 2010; 65:1594-8. [DOI: 10.1093/jac/dkq166] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Fondi M, Bacci G, Brilli M, Papaleo MC, Mengoni A, Vaneechoutte M, Dijkshoorn L, Fani R. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome. BMC Evol Biol 2010; 10:59. [PMID: 20181243 PMCID: PMC2848654 DOI: 10.1186/1471-2148-10-59] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 02/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online. RESULTS By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed. CONCLUSIONS We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.
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Affiliation(s)
- Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Dept, of Evolutionary Biology, Via Romana 17-19, University of Florence, I-50125 Florence, Italy
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Matcher GF, Rawlings DE. The effect of the location of the proteic post-segregational stability system within the replicon of plasmid pTF-FC2 on the fine regulation of plasmid replication. Plasmid 2009; 62:98-107. [PMID: 19481568 DOI: 10.1016/j.plasmid.2009.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/11/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The broad host-range IncQ-2 family plasmid, pTF-FC2, is a mobilizable, medium copy number plasmid that lacks an active partitioning system. Plasmid stability is enhanced by a toxin-antitoxin (TA) system known as pas (plasmid addiction system) that is located within the replicon between the repB (primase) and the repA (helicase) and repC (DNA-binding) genes. The discovery of a closely related IncQ-2 plasmid, pRAS3, with a completely different TA system located between the repB and repAC genes raised the question of whether the location of pas within the replicon had an effect on the plasmid in addition to its ability to act as a TA system. In this work we demonstrate that the presence of the strongly expressed, autoregulated pas operon within the replicon resulted in an increase in the expression of the downstream repAC genes when autoregulation was relieved. While deletion of the pas module did not affect the average plasmid copy number, a pas-containing plasmid exhibited increased stability compared with a pas deletion plasmid even when the TA system was neutralized. It is proposed that the location of a strongly expressed, autoregulated operon within the replicon results in a rapid, but transient, expression of the repAC genes that enables the plasmid to rapidly restore its normal copy number should it fall below a threshold.
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Affiliation(s)
- Gwynneth F Matcher
- Department of Microbiology, University of Stellenbosch, Matieland, South Africa
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12
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Garcillán-Barcia MP, Francia MV, de la Cruz F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 2009; 33:657-87. [PMID: 19396961 DOI: 10.1111/j.1574-6976.2009.00168.x] [Citation(s) in RCA: 375] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB1T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families:MOB(F), MOB(H), MOB(Q), MOB(C), MOB(P) and MOB(V). The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.
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Affiliation(s)
- María Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC-IDICAN, Santander, Spain
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Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 2008; 9:597. [PMID: 19077236 PMCID: PMC2621215 DOI: 10.1186/1471-2164-9-597] [Citation(s) in RCA: 325] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 12/11/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
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Affiliation(s)
- Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile.
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14
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Sevastsyanovich YR, Krasowiak R, Bingle LEH, Haines AS, Sokolov SL, Kosheleva IA, Leuchuk AA, Titok MA, Smalla K, Thomas CM. Diversity of IncP-9 plasmids of Pseudomonas. MICROBIOLOGY (READING, ENGLAND) 2008; 154:2929-2941. [PMID: 18832300 PMCID: PMC2885752 DOI: 10.1099/mic.0.2008/017939-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 04/30/2008] [Accepted: 06/30/2008] [Indexed: 11/18/2022]
Abstract
IncP-9 plasmids are important vehicles for degradation and resistance genes that contribute to the adaptability of Pseudomonas species in a variety of natural habitats. The three completely sequenced IncP-9 plasmids, pWW0, pDTG1 and NAH7, show extensive homology in replication, partitioning and transfer loci (an approximately 25 kb region) and to a lesser extent in the remaining backbone segments. We used PCR, DNA sequencing, hybridization and phylogenetic analyses to investigate the genetic diversity of 30 IncP-9 plasmids as well as the possibility of recombination between plasmids belonging to this family. Phylogenetic analysis of rep and oriV sequences revealed nine plasmid subgroups with 7-35 % divergence between them. Only one phenotypic character was normally associated with each subgroup, except for the IncP-9beta cluster, which included naphthalene- and toluene-degradation plasmids. The PCR and hybridization analysis using pWW0- and pDTG1-specific primers and probes targeting selected backbone loci showed that members of different IncP-9 subgroups have considerable similarity in their overall organization, supporting the existence of a conserved ancestral IncP-9 sequence. The results suggested that some IncP-9 plasmids are the product of recombination between plasmids of different IncP-9 subgroups but demonstrated clearly that insertion of degradative transposons has occurred on multiple occasions, indicating that association of this phenotype with these plasmids is not simply the result of divergent evolution from a single successful ancestral degradative plasmid.
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Affiliation(s)
| | - Renata Krasowiak
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Lewis E. H. Bingle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S. Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sergey L. Sokolov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Irina A. Kosheleva
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Anastassia A. Leuchuk
- Genetics Department, Biology Faculty, Belarus State University, 6 Kurchatova St, Minsk 220064, Belarus
| | - Marina A. Titok
- Genetics Department, Biology Faculty, Belarus State University, 6 Kurchatova St, Minsk 220064, Belarus
| | - Kornelia Smalla
- Julius Kühn Institute – Federal Research Centre for Cultivated Plants (JKI), Messeweg 11/12, 38104 Braunschweig, Germany
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15
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Comparative analysis of eight Arthrobacter plasmids. Plasmid 2008; 59:73-85. [DOI: 10.1016/j.plasmid.2007.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 10/18/2007] [Accepted: 12/17/2007] [Indexed: 01/28/2023]
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Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother 2008; 52:1472-80. [PMID: 18268088 PMCID: PMC2292564 DOI: 10.1128/aac.00982-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA sequence analysis of five IncW plasmids (R388, pSa, R7K, pIE321, and pIE522) demonstrated that they share a considerable portion of their genomes and allowed us to define the IncW backbone. Among these plasmids, the backbone is stable and seems to have diverged recently, since the overall identity among its members is higher than 95%. The only gene in which significant variation was observed was trwA; the changes in the coding sequence correlated with parallel changes in the corresponding TrwA binding sites at oriT, suggesting a functional connection between both sets of changes. The present IncW plasmid diversity is shaped by the acquisition of antibiotic resistance genes as a consequence of the pressure exerted by antibiotic usage. Sequence comparisons pinpointed the insertion events that differentiated the five plasmids analyzed. Of greatest interest is that a single acquisition of a class I integron platform, into which different gene cassettes were later incorporated, gave rise to plasmids R388, pIE522, and pSa, while plasmids R7K and pIE321 do not contain the integron platform and arose in the antibiotic world because of the insertion of several antibiotic resistance transposons.
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Bönemann G, Stiens M, Pühler A, Schlüter A. Mobilizable IncQ-related plasmid carrying a new quinolone resistance gene, qnrS2, isolated from the bacterial community of a wastewater treatment plant. Antimicrob Agents Chemother 2006; 50:3075-80. [PMID: 16940104 PMCID: PMC1563527 DOI: 10.1128/aac.00378-06] [Citation(s) in RCA: 80] [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
Plasmid-encoded quinolone resistance was previously reported for different bacteria isolated from patients not only in the United States and Asia but also in Europe. Here we describe the isolation, by applying a new selection strategy, of the quinolone resistance plasmid pGNB2 from an activated sludge bacterial community of a wastewater treatment plant in Germany. The hypersensitive Escherichia coli strain KAM3 carrying a mutation in the multidrug efflux system genes acrAB was transformed with total plasmid DNA preparations isolated from activated sludge bacteria and subsequently selected on medium containing the fluoroquinolone norfloxacin. This approach resulted in the isolation of plasmid pGNB2 conferring decreased susceptibility to nalidixic acid and to different fluoroquinolones. Analysis of the pGNB2 nucleotide sequence revealed that it is 8,469 bp in size and has a G+C content of 58.2%. The plasmid backbone is composed of a replication initiation module (repA-repC) belonging to the IncQ-family and a two-component mobilization module that confers horizontal mobility to the plasmid. In addition, plasmid pGNB2 carries an accessory module consisting of a transposon Tn1721 remnant and the quinolone resistance gene, qnrS2, that is 92% identical to the qnrS gene located on plasmid pAH0376 from Shigella flexneri 2b. QnrS2 belongs to the pentapeptide repeat protein family and is predicted to protect DNA-gyrase activity against quinolones. This is not only the first report on a completely sequenced plasmid mediating quinolone resistance isolated from an environmental sample but also on the first qnrS-like gene detected in Europe.
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Affiliation(s)
- Gabriele Bönemann
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA. Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol Adv 2005; 24:197-211. [PMID: 16288845 DOI: 10.1016/j.biotechadv.2005.09.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2005] [Indexed: 10/25/2022]
Abstract
The use of acidophilic, chemolithotrophic microorganisms capable of oxidizing iron and sulfur in industrial processes to recover metals from minerals containing copper, gold and uranium is a well established biotechnology with distinctive advantages over traditional mining. A consortium of different microorganisms participates in the oxidative reactions resulting in the extraction of dissolved metal values from ores. Considerable effort has been spent in the last years to understand the biochemistry of iron and sulfur compounds oxidation, bacteria-mineral interactions (chemotaxis, quorum sensing, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. All of these are considered key phenomena for understanding the process of biomining. The use of genomics, metagenomics and high throughput proteomics to study the global regulatory responses that the biomining community uses to adapt to their changing environment is just beginning to emerge in the last years. These powerful approaches are reviewed here since they offer the possibility of exciting new findings that will allow analyzing the community as a microbial system, determining the extent to which each of the individual participants contributes to the process, how they evolve in time to keep the conglomerate healthy and therefore efficient during the entire process of bioleaching.
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Affiliation(s)
- Lissette Valenzuela
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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