The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
Shui-feng Chang - One of the best experts on this subject based on the ideXlab platform.
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Two new gene Cassettes, dfr17 (for trimethoprim resistance) and aadA4 (for spectinomycin/streptomycin resistance), inserted in an Escherichia coli class 1 integron
Journal of Antimicrobial Chemotherapy, 2000Co-Authors: Chung-yu Chang, Lin-li Chang, Yu-hung Chang, Tsong-ming Lee, Shui-feng ChangAbstract:Two new gene Cassettes, dfr17 and aadA4, inserted in a class 1 integron of Escherichia coli EC107, are described here. The dfr17 Cassette encodes trimethoprim resistance and has 91% identity with the dfrVII dihydrofolate reductase gene. The aadA4 Cassette confers resistance to spectinomycin and streptomycin and shows 94% identity with the aadA3 gene. The integron carrying the dfr17 and aadA4 Cassettes was located on a conjugative plasmid, pEC1072.
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two new gene Cassettes dfr17 for trimethoprim resistance and aada4 for spectinomycin streptomycin resistance inserted in an escherichia coli class 1 integron
Journal of Antimicrobial Chemotherapy, 2000Co-Authors: Chung-yu Chang, Lin-li Chang, Yu-hung Chang, Tsong-ming Lee, Shui-feng ChangAbstract:Two new gene Cassettes, dfr17 and aadA4, inserted in a class 1 integron of Escherichia coli EC107, are described here. The dfr17 Cassette encodes trimethoprim resistance and has 91% identity with the dfrVII dihydrofolate reductase gene. The aadA4 Cassette confers resistance to spectinomycin and streptomycin and shows 94% identity with the aadA3 gene. The integron carrying the dfr17 and aadA4 Cassettes was located on a conjugative plasmid, pEC1072.
Ruth M Hall - One of the best experts on this subject based on the ideXlab platform.
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Integrons and gene Cassettes: hotspots of diversity in bacterial genomes.
Annals of the New York Academy of Sciences, 2012Co-Authors: Ruth M HallAbstract:Integrons are genetic units found in many bacterial species that are defined by their ability to capture small mobile elements called gene Cassettes. Cassettes usually contain only one gene, potentially any gene, and an attC recombination site, and thousands of Cassettes have been sequenced. A specialized IntI site-specific recombinase encoded by the integron recognizes attC and incorporates Cassettes into an attI site located adjacent to the intI gene. Over 100 types of integrons have been found, most in bacterial chromosomes. They can all potentially share the same Cassettes and, as recombination between attC in a Cassette and an attI can occur repeatedly, an integron can contain from zero to hundreds of Cassettes. Cassette arrays that are not located next to an intI gene, or solo Cassettes at apparently random sites, are also seen. Hence, integrons contribute to generation of diversity in bacterial, plasmid, and transposon genomes and facilitate extensive sharing of information among bacteria.
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Gene Cassette encoding a 3-N-aminoglycoside acetyltransferase in a chromosomal integron.
Antimicrobial agents and chemotherapy, 2006Co-Authors: Liam D. H. Elbourne, Ruth M HallAbstract:The large number and variety of antibiotic resistance genes found in gene Cassettes associated with class 1 integrons in multiply antibiotic-resistant organisms have always indicated the existence of a large pool of gene Cassettes from which they are drawn (10). The discovery of integrons, sometimes harboring very large arrays of gene Cassettes, in the chromosomes of many different bacteria has confirmed the existence of this pool, but to date very few Cassettes containing resistance genes have been found among these Cassettes. Known examples are the catB9 (12) and blaP7 (blaP9) (7, 8) Cassettes found in the Cassette arrays of different Vibrio cholerae strains. Though 3-N-aminoglycoside acetyltransferases [AAC(3) enzymes] have been classified into several groups based on differences in the spectrum of aminoglycosides they modify, they fall into only two groups based on the relationships between the proteins (6). The five characterized aacC genes found in gene Cassettes (see Table Table1)1) encode proteins of 154 to 158 amino acids that are related to one another and form family A (6). They belong to the aac(3)-I phenotypic group and confer resistance to gentamicin, sisomicin, and fortimicin but not to tobramycin, amikacin, or kanamycin (1, 3, 6, 11, 13, 15). TABLE 1. aacC-A genes and gene Cassettes Our recent searches have revealed further potential aacC-A-type genes (Table (Table1).1). One is in a Cassette found in a class 1 integron, but three of them are in draft sequences of bacterial genomes. The aacC-A7 gene in the complete Saccharophagus degradans (formerly Microbulbifer degradans) genome also lies within an identifiable gene Cassette. The putative AacC-A7 [AAC(3)-Ig] acetyltransferase encoded by this Cassette is 51 to 60% identical to other Cassette-encoded AacC-A enzymes and most closely related to AacC-A5 [AAC(3)-Ie]. Alignment of the established and putative AacC-A sequences (Fig. (Fig.1)1) reveals 45 completely conserved amino acids, or 62 if only AacC-A1 to AacC-A7 are considered. It therefore seems reasonable to assume that aacC-A7 also confers resistance to aminoglycoside antibiotics. FIG. 1. Alignment of proteins in the AacC-A [AAC(3)-I] family. Amino acids completely conserved in all sequences are shown as white on black and are indicated by uppercase letters below the sequence. Amino acids conserved in 9 of the 10 sequences are indicated ... This represents only the third identification of a potential antibiotic resistance gene associated with a gene Cassette that is part of the genome of a microorganism that harbors an integron. Though each aacC-A Cassette has an identifiable 59-be (sometimes called an attC site) made up of two simple sites and a central region as is characteristic for 59-be (14), in most cases they are not close relatives of one another and some are not closely related to ones found in any other known Cassette (6, 11). The 59-be of the Saccharophagus aacC-A7 Cassette is not closely related to a 59-be in any of the many Cassettes in that organism's genome. Its closest relative is in a Cassette from Nitrosococcus oceani. Thus, if, as is generally assumed, Cassettes that arose in a particular organism have very similar 59-be, it is unlikely that the aacC-A7 Cassette was originally formed in S. degradans.
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recombination between the dfra12 orff aada2 Cassette array and an aada1 gene Cassette creates a hybrid Cassette aada8b
Antimicrobial Agents and Chemotherapy, 2005Co-Authors: Alicia M Gestal, H. W. Stokes, Sally R Partridge, Ruth M HallAbstract:Homologous recombination between closely related gene Cassettes, such as aadA1 and aadA2, which are 89% identical, can create hybrid Cassettes and hybrids of existing Cassette arrays. A new Cassette array, dfrA12-orfF-aadA8b, which was created by such a recombination event occurring within the aadA2 Cassette in the dfrA12-orfF-aadA2 array, has been identified.
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Plasmid evolution by acquisition of mobile gene Cassettes: plasmid pIE723 contains the aadB gene Cassette precisely inserted at a secondary site in the IncQ plasmid RSF1010
Molecular microbiology, 1995Co-Authors: Gavin D. Recchia, Ruth M HallAbstract:Gene Cassettes are mobile DNA elements which contain a specific recombination site, a 59-base element, recognized by the site-specific recombination system of integrons. Gene Cassettes are normally found inserted at a unique site in an integron, downstream of a promoter which directs transcription of the Cassette-associated genes. However, insertion of a gene Cassette into a secondary site in a plasmid which does not contain an integron is also formally possible. Sequence analysis of the aadB gene in pIE723, a plasmid closely related to the IncQ plasmid RSF1010, revealed the presence of the complete aadB Cassette inserted at a secondary site downstream of a known RSF1010 promoter. The site of insertion of the aadB Cassette in RSF1010 conformed to the consensus for secondary sites recognized by the integron integrase (Int), and it is likely that the Cassette was inserted via a single Int-mediated recombination event between the 59-base element of a free, circular aadB Cassette and a secondary site in RSF1010. The Cassette-associated recombination site was inactivated by the insertion, and Int-mediated excision of the aadB Cassette from this non-specific location was not detectable, indicating that the Cassette is stably inserted. The movement of gene Cassettes to secondary sites is likely to play an important role in the acquisition of new genes by bacterial and plasmid genomes.
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Expression of antibiotic resistance genes in the integrated Cassettes of integrons.
Antimicrobial agents and chemotherapy, 1995Co-Authors: Christina M Collis, Ruth M HallAbstract:Plasmids containing cloned integron fragments which differ only with respect to either the sequence of the promoter(s) or the number and order of inserted Cassettes were used to examine the expression of resistance genes encoded in integron-associated gene Cassettes. All transcripts detected commenced at the common promoter P(ant), and alterations in the sequence of P(ant) affected the level of resistance expressed by Cassette genes. When both P(ant) and the secondary promoter P2 were present, transcription from both promoters was detected. When more than one Cassette was present, the position of the Cassette in the array influenced the level of antibiotic resistance expressed by the Cassette gene. In all cases, the resistance level was highest when the gene was in the first Cassette, i.e., closest to P(ant), and was reduced to different extents by the presence of individual upstream Cassettes. In Northern (RNA) blots, multiple discrete transcripts originating at P(ant) were detected, and only the longer transcripts contained the distal genes. Together, these data suggest that premature transcription termination occurs within the Cassettes. The most abundant transcripts appeared to contain one or more complete Cassettes, and is possible that the 59-base elements found at the end of the Cassettes (3' to the coding region) not only function as recombination sites but may also function as transcription terminators.
H. W. Stokes - One of the best experts on this subject based on the ideXlab platform.
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Deletion of integron-associated gene Cassettes impact on the surface properties of Vibrio rotiferianus DAT722.
PloS one, 2013Co-Authors: Rita A. Rapa, H. W. Stokes, Ronald Shimmon, Steven P. Djordjevic, Maurizio LabbateAbstract:Background The integron is a genetic recombination system that catalyses the acquisition of genes on mobilisable elements called gene Cassettes. In Vibrio species, multiple acquired gene Cassettes form a Cassette array that can comprise 1–3% of the bacterial genome. Since 75% of these gene Cassettes contain genes encoding proteins of uncharacterised function, how the integron has driven adaptation and evolution in Vibrio species remains largely unknown. A feature of Cassette arrays is the presence of large indels. Using Vibrio rotiferianus DAT722 as a model organism, the aim of this study was to determine how large Cassette deletions affect vibrio physiology with a view to improving understanding into how Cassette arrays influence bacterial host adaptation and evolution. Methodology/Principal Findings Biological assays and proteomic techniques were utilised to determine how artificially engineered deletions in the Cassette array of V. rotiferianus DAT722 affected cell physiology. Multiple phenotypes were identified including changes to growth and expression of outer membrane porins/proteins and metabolic proteins. Furthermore, the deletions altered cell surface polysaccharide with Proton Nuclear Magnetic Resonance on whole cell polysaccharide identifying changes in the carbohydrate ring proton region indicating that gene Cassette products may decorate host cell polysaccharide via the addition or removal of functional groups. Conclusions/Significance From this study, it was concluded that deletion of gene Cassettes had a subtle effect on bacterial metabolism but altered host surface polysaccharide. Deletion (and most likely rearrangement and acquisition) of gene Cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Biofilm formation was shown to be altered in one of the deletion mutants used in this study. Reworking surface properties may provide an advantage to the bacterium’s interactions with organisms such as bacteriophage, protozoan grazers or crustaceans.
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Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene Cassettes in polluted sediments from Suez and Tokyo Bays.
The ISME journal, 2011Co-Authors: Hosam E. Elsaied, H. W. Stokes, Keiko Kitamura, Yasurou Kurusu, Yoichi Kamagata, Akihiko MaruyamaAbstract:In order to understand the structure and biological significance of integrons and associated gene Cassettes in marine polluted sediments, metagenomic DNAs were extracted from sites at Suez and Tokyo Bays. PCR amplicons containing new integrase genes, intI, linked with novel gene Cassettes, were recovered and had sizes from 1.8 to 2.5 kb. This approach uncovered, for the first time, the structure and diversity of both marine integron attachment site, attI, and the first gene Cassette, the most efficiently expressed integron-associated gene Cassette. The recovered 13 and 20 intI phylotypes, from Suez and Tokyo Bay samples, respectively, showed a highly divergence, suggesting a difference in integron composition between the sampling sites. Some intI phylotypes showed similarity with that from Geobacter metallireducens, belonging to Deltaproteobacteria, the dominant class in both sampling sites, as determined by 16S rRNA gene analysis. Thirty distinct families of putative attI site, as determined by the presence of an attI-like simple site, were recovered. A total of 146 and 68 gene Cassettes represented Suez and Tokyo Bay unsaturated Cassette pools, respectively. Gene Cassettes, including a first Cassette, from both sampling sites encoded two novel families of glyoxalase/bleomycin antibiotic-resistance protein. Gene Cassettes from Suez Bay encoded proteins similar to haloacid dehalogenases, protein disulfide isomerases and death-on-curing and plasmid maintenance system killer proteins. First gene Cassettes from Tokyo Bay encoded a xenobiotic-degrading protein, cardiolipin synthetase, esterase and WD40-like β propeller protein. Many of the first gene Cassettes encoded proteins with no ascribable function but some of them were duplicated and possessed signal functional sites, suggesting efficient adaptive functions to their bacterial sources. Thus, each sampling site had a specific profile of integrons and Cassette types consistent with the hypothesis that the environment shapes the genome.
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The Integron/gene Cassette system : an active player in bacterial adaptation
Methods in molecular biology (Clifton N.J.), 2009Co-Authors: Maurizio Labbate, Rebecca J. Case, H. W. StokesAbstract:The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene Cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in Cassettes is extraordinarily high, suggesting that the integron/gene Cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene Cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene Cassettes and gene Cassette arrays are discussed.
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the integron gene Cassette system an active player in bacterial adaptation
Methods of Molecular Biology, 2009Co-Authors: Maurizio Labbate, Rebecca J. Case, H. W. StokesAbstract:The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene Cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in Cassettes is extraordinarily high, suggesting that the integron/gene Cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene Cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene Cassettes and gene Cassette arrays are discussed.
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integron associated gene Cassettes in halifax harbour assessment of a mobile gene pool in marine sediments
Environmental Microbiology, 2008Co-Authors: Jeremy E Koenig, H. W. Stokes, Yan Boucher, Camilla L Nesbø, Michael J Joss, Robert L Charlebois, Olga Zhaxybayeva, Eric Bapteste, Matthew Spencer, W F DoolittleAbstract:Summary The integron/gene Cassette systems identified in bacteria comprise a class of genetic elements that allow adaptation by acquisition of gene Cassettes. Integron gene Cassettes have been shown to facilitate the spread of drug resistance in human pathogens but their role outside a clinical setting has not been explored extensively. We sequenced 2145 integron gene Cassettes from four marine sediment samples taken from the vicinity of Halifax Nova Scotia, Canada, increasing the number of gene Cassettes obtained from environmental microbial communities by 10-fold. Sequence analyses reveals that the majority of these Cassettes encode novel proteins and that this study is consistent with previous claims of high Cassette diversity as we estimate a Chao1 diversity index of ~3000 Cassettes from these samples. The functional distribution of environmental Cassettes recovered in this study, when compared with that of Cassettes from the only other source with significant sampling (Vibrio genomes) suggests that alternate selection regimes might be acting on these two gene pools. The majority of Cassettes recovered in this study encode novel, unknown proteins. In instances where we obtained multiple alleles of a novel protein we demonstrate that non-synonymous versus synonymous substitution rates ratios suggest relaxed selection. Cassetteencoded proteins with known homologues represent a variety of functions and prevalent among these are isochorismatases; proteins involved in iron scavenging. Phylogenetic analysis of these isochorismatases as well as of Cassette-encoded acetyltransferases reveals a patchy distribution, suggesting multiple sources for the origin of these Cassettes. Finally, the two most environmentally similar sample sites considered in this study display the greatest overlap of Cassette types, consistent with the hypothesis that Cassette genes encode adaptive proteins.
Chung-yu Chang - One of the best experts on this subject based on the ideXlab platform.
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Variable Gene Cassette Patterns of Class 1 Integron-Associated Drug-Resistant Escherichia Coli in Taiwan
The Kaohsiung journal of medical sciences, 2007Co-Authors: Lin-li Chang, Tsung-ming Chang, Chung-yu ChangAbstract:This study characterized class 1 integrons in Escherichia coli in Taiwan. The stability and changes in gene Cassettes inserted into integrons were also evaluated. The study included 436 clinical strains of E. coli isolated in 2002. Class 1 integrons were characterized by polymerase chain reaction and direct sequencing. Genetic localization of class 1 integrons was determined by conjugal transfer and Southern hybridization. The results indicated that 64% of E. coli isolates carried class 1 integrons. Molecular analysis revealed that the class 1 integrons harbored 13 different antimicrobial resistance gene Cassettes and two unknown gene Cassettes; the predominant Cassettes were aadA and dfrA. Novel gene Cassettes first recovered from E. coli were aacA4 and linF. Cassette arrays orfD-aacA4-catB8 and aadA1-linF were also observed. Gene Cassette dfrA12-orfF-aadA2 was stable. The class 1 integron and dfrA17-aadA5 gene Cassette were located on the same transferable plasmids and were capable of transmission. Therefore, the increased drug resistance of clinical isolates may be explained by antibiotic selective pressure and widespread presence of integrons. Under antibiotic selective pressure, gene Cassette-mediated resistance may not be easily lost. The potential role of integrons in the uptake and dissemination of resistance genes by plasmid between species of bacteria may decrease the therapeutic effectiveness of antibiotics.
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Two new gene Cassettes, dfr17 (for trimethoprim resistance) and aadA4 (for spectinomycin/streptomycin resistance), inserted in an Escherichia coli class 1 integron
Journal of Antimicrobial Chemotherapy, 2000Co-Authors: Chung-yu Chang, Lin-li Chang, Yu-hung Chang, Tsong-ming Lee, Shui-feng ChangAbstract:Two new gene Cassettes, dfr17 and aadA4, inserted in a class 1 integron of Escherichia coli EC107, are described here. The dfr17 Cassette encodes trimethoprim resistance and has 91% identity with the dfrVII dihydrofolate reductase gene. The aadA4 Cassette confers resistance to spectinomycin and streptomycin and shows 94% identity with the aadA3 gene. The integron carrying the dfr17 and aadA4 Cassettes was located on a conjugative plasmid, pEC1072.
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two new gene Cassettes dfr17 for trimethoprim resistance and aada4 for spectinomycin streptomycin resistance inserted in an escherichia coli class 1 integron
Journal of Antimicrobial Chemotherapy, 2000Co-Authors: Chung-yu Chang, Lin-li Chang, Yu-hung Chang, Tsong-ming Lee, Shui-feng ChangAbstract:Two new gene Cassettes, dfr17 and aadA4, inserted in a class 1 integron of Escherichia coli EC107, are described here. The dfr17 Cassette encodes trimethoprim resistance and has 91% identity with the dfrVII dihydrofolate reductase gene. The aadA4 Cassette confers resistance to spectinomycin and streptomycin and shows 94% identity with the aadA3 gene. The integron carrying the dfr17 and aadA4 Cassettes was located on a conjugative plasmid, pEC1072.
Michael R Gillings - One of the best experts on this subject based on the ideXlab platform.
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Impact of Wastewater Treatment on the Prevalence of Integrons and the Genetic Diversity of Integron Gene Cassettes.
Applied and environmental microbiology, 2018Co-Authors: Qing-lin Chen, Dong Zhu, Yong-guan Zhu, Michael R GillingsAbstract:ABSTRACT The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene Cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance genes; however, knowledge about the impacts of wastewater treatment on integrons and their gene Cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding gene Cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron gene Cassettes, whereas class 3 integron gene Cassettes exhibited highest diversity in activated sludge. Most of the gene Cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance genes were highly prevalent in class 1 integron gene Cassettes, while class 3 integrons mainly carried beta-lactam resistance gene Cassettes. A core class 1 integron resistance gene Cassette pool persisted during wastewater treatment, implying that these resistance genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance genes within both class 1 and 3 integrons. IMPORTANCE Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and genes spreading into environments. Integrons are important genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their gene Cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze gene Cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their gene Cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated gene Cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments.
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Recovery and evolutionary analysis of complete integron gene Cassette arrays from Vibrio
BMC Evolutionary Biology, 2006Co-Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle, H. W. StokesAbstract:Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene Cassettes. Gene Cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated Cassette arrays. The most striking examples are found in Vibrio , where such Cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene Cassette arrays from bacterial strains. Results The complete Vibrio sp . DAT722 integron Cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene Cassette encoded genes). It differs extensively in terms of genomic context as well as gene Cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene Cassette pool suggests frequent transfer of Cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene Cassettes and others where Cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene Cassette arrays. Comparative analysis of the Vibrio sp . DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phylogenetic distance separating two species and the rate at which they exchange gene Cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio gene Cassette pool as well as intragenomic translocation events of integrons in vibrios.
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Recovery and evolutionary analysis of complete integron gene Cassette arrays from Vibrio
BMC evolutionary biology, 2006Co-Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle, H. W. StokesAbstract:Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene Cassettes. Gene Cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated Cassette arrays. The most striking examples are found in Vibrio, where such Cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene Cassette arrays from bacterial strains. The complete Vibrio sp. DAT722 integron Cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene Cassette encoded genes). It differs extensively in terms of genomic context as well as gene Cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene Cassette pool suggests frequent transfer of Cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene Cassettes and others where Cassettes have been inserted into chromosomal locations outside integrons. Our systematic approach greatly facilitates the isolation and annotation of large integrons gene Cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phylogenetic distance separating two species and the rate at which they exchange gene Cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio gene Cassette pool as well as intragenomic translocation events of integrons in vibrios.
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Mobile gene Cassettes : a fundamental resource for bacterial evolution
The American naturalist, 2004Co-Authors: Carolyn A. Michael, Michael R Gillings, Andrew J. Holmes, Nigel R. Andrew, Lesley Hughes, Marita Holley, H. W. StokesAbstract:Abstract: Horizontal gene transfer increases genetic diversity in prokaryotes to a degree not allowed by the limitations of reproduction by binary fission. The integron/gene Cassette system is one of the most recently characterized examples of a system that facilitates horizontal gene transfer. This system, discovered in the context of multidrug resistance, is recognized in a clinical context for its role in allowing pathogens to adapt to the widespread use of antibiotics. Recent studies suggest that gene Cassettes are common and encode functions relevant to many adaptive traits. To estimate the diversity of mobile Cassettes in a natural environment, a molecular technique was developed to provide representative distributions of Cassette populations at points within a sampling area. Subsequently, statistical methods analogous to those used for calculating species diversity were employed to assess the diversity of gene Cassettes within the sample area in addition to gaining an estimate of Cassette pool size...
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The gene Cassette metagenome is a basic resource for bacterial genome evolution.
Environmental microbiology, 2003Co-Authors: Andrew J. Holmes, Bridget C Mabbutt, Michael R Gillings, Blair S Nield, K. M. Helena Nevalainen, Harold W. StokesAbstract:Summary Lateral gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral gene transfer. However, the processes by which disparate genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/gene Cassette system indicate it has the potential to play a role in this process. Gene Cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of gene Cassettes and of the expression of their associated genes. The potential of the integron/gene Cassette system is thus largely determined by the diversity contained within the Cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental gene Cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding genes. Environmental gene Cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this gene pool through tests of recombinational activity with a representative range of EGCs. We propose that gene Cassettes represent a vast, prepackaged genetic resource that could be thought of as a metagenomic template for bacterial evolution.