The Integration and Excision of CTnDOT

Wood, Margaret M.; Gardner, Jeffrey F.

doi:10.1128/9781555819217.ch8

Cited by 9 publications

(10 citation statements)

References 74 publications

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“…Pfam database describes DNA‐binding domain PF12728 in several thousand proteins, and a vast majority (>80%) of them consist of only this single domain. There are few examples of such single domain proteins that have been characterized experimentally, and include excisionases Xis from phage P22 (Mattis et al ., ) and Xis2d from the Bacteroides conjugative transposon CTnDOT (Wood and Gardner, ). These two proteins bind DNA in a sequence‐specific manner, but their binding sites are strikingly different.…”

Section: Resultsmentioning

confidence: 99%

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

Rajeev

Garber

Zane

et al. 2019

Environmental Microbiology

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Summary Bacterial genes for molybdenum‐containing and tungsten‐containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA‐binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate‐specific transporting systems as well as molybdo/tungsto‐enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten‐containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten‐specific ABC‐type transporter tupABC genes under tungsten‐replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.

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Section: Resultsmentioning

confidence: 99%

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

Rajeev

Garber

Zane

et al. 2019

Environmental Microbiology

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“…Several ICEs have been found in the taxa of Bacteroides (29, 61-64), which belong to the family Bacteroidaceae in phylum Bacteroidetes. Of these elements, CTnDOT in B. thetaiotaomicron has been studied extensively (65-68). The ICEs identified in E. anophelis are structurally distinct from CTnDOT.…”

Section: Resultsmentioning

confidence: 99%

In SilicoIdentification of Three Types of Integrative and Conjugative Elements (ICEs) inElizabethkingia anophelisStrains Isolated from Around the World

Pei

Nicholson

et al. 2018

Preprint

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27Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. 28 We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis 29 derived from various environmental settings and human infections from different geographic 30 regions around the world over past decades from 1950s. Thirty-one of these 36 strains harbor 31 integrative and conjugative elements (ICEs). A total of 52 ICEs were identified, and 32 categorized into three ICE types based on the architecture of signature genes in the 33 conjugation module. The type II and III ICEs were found to integrate into regions adjacent to 34 tRNA genes, while type I ICEs used a variety of integration sites, inserting into intergenic 35 regions or even directly into a gene, sometimes disrupting gene function. Integrases such as 36 tyrosine recombinases, serine recombinases and DDE transposases were found in most ICEs. 37 The ICEs carry various cargo genes including transcription regulators and those involved in 38 antibiotic resistance. The CRISPR-Cas system was found in nine strains, including four 39 strains in which CRISPR-Cas machinery and ICEs co-exist. ICE distribution in the strains 40 showed no geographic or temporal patterns. The ICEs in E. anophelis differ in gene structure 41 and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. This is the 42 first set of ICEs identified in the family Flavobacteriaceae. As a prevalent type of mobile 43 genetic elements in various strains of E. anophelis around the world, the categorization of 44 ICEs will facilitate further investigations such as virulence, genome epidemiology and 45 adaptation genomics of E. anophelis. 46 Importance 47Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity 48 between strains from around the world becomes apparent as more genomes are sequenced. 49The Integrative Conjugative Element (ICE), found in many bacterial species, contains genes 50 3 for transfer via conjugation and integration into the chromosome, along with various cargo 51 genes. ICEs are identified in 31 of 36 strains and categorized into three types based on 52 architecture of modular genes, integrases, and integration sites. ICE distribution in different 53 strains displays no spatial and temporal patterns. Several ICE-containing strains also 54 possessed CRISPR-Cas units, considered to be the bacterial adaptive immune system 55 providing protection against phage and predatory mobile genetic elements. This co-existence 56 suggests that ICEs are beneficial or at least not harmful to the bacterial cells they inhabit. 57ICEs as a component of the mobile genetic repertoire enable recipients to resist antibiotics, 58 survive disinfecting agents, and adapt to various ecological niches.

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“…5). Some Bacteroides integrases are known to tolerate a small number of mismatches in the overlap sequence, which may account for this discrepancy (Wood and Gardner, 2015). Combining these data, it is predicted that this integrase recognizes/duplicates a 24-bp sequence ttcgagCCCCAGGCGGATCActca with some tolerance for mismatches (lower case) outside the core region (capitalized).…”

Section: Ga1 and Ga2 Ice Integrate At Different Genomic Sitesmentioning

confidence: 99%

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species sweeps and geographical clustering

García-Bayona

Coyne

Comstock

2021

Preprint

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The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on integrative and conjugative elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population sweeps of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 177 MGE that sweep through multiple Bacteroidales species within individual gut microbiomes. We further show that only eight MGE demonstrate multi-species population sweeps in as many human gut microbiomes as the GA1 and GA2 ICE. These data underscore the ubiquity and rapid dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.

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The Integration and Excision of CTnDOT

Cited by 9 publications

References 74 publications

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

In SilicoIdentification of Three Types of Integrative and Conjugative Elements (ICEs) inElizabethkingia anophelisStrains Isolated from Around the World

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species sweeps and geographical clustering

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