The gain and loss of chromosomal integron systems in the Treponemaspecies

Wu, Yu Wei; Doak, Thomas G.; Ye, Yuzhen

doi:10.1186/1471-2148-13-16

Cited by 17 publications

(17 citation statements)

References 26 publications

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“…Integrons sample cassettes from an extraordinarily diverse pool that encodes functions of potential adaptive significance. Consequently, they are a hot spot of genomic diversity in a range of genera ( Gillings et al, 2005 ; Boucher et al, 2011 ; Hall, 2012 ; Wu et al, 2013 ).…”

Section: The Evolutionary History Of the Class 1 Integronmentioning

confidence: 99%

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

et al. 2014

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Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.

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Section: The Evolutionary History Of the Class 1 Integronmentioning

confidence: 99%

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

et al. 2014

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“…Integrons in the ancestral Treponema appear to have been acquired in a single lateral transfer event and subsequently lost in some members of the genus. In the best-studied species, T. denticola, the number of cassettes in the respective arrays varies between 18 and 45 (22,47). The cassettes in these arrays are extraordinarily dynamic.…”

Section: Diversity Of Chromosomal Integronsmentioning

confidence: 99%

“…1). These reverse integrons have so far been found in members of the Spirochaetes, Planctomycetes, Cyanobacteria, and Chlorobi isolated from a variety of environments (1,21,22).…”

Section: Evolutionary History Of Integronsmentioning

confidence: 99%

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Integrons: Past, Present, and Future

Gillings

2014

Microbiol Mol Biol Rev

563

472

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SUMMARY Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.

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“…However, some integrons have integrase genes transcribed in the same directions as their GCs. These are called unusual integrons or reverse integrons (Fig 1B), and have been identified in Treponema denticola, Chlorobium phaeobacteroides and Blastopirellula marina [5, 6].…”

Section: Introductionmentioning

confidence: 99%

Promoter activity of ORF-less gene cassettes isolated from the oral metagenome

Tansirichaiya

Mullany

Roberts

2018

Preprint

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19Integrons are genetic elements consisting of a functional platform for recombination and expression 20 of gene cassettes (GCs). GCs usually carry promoter-less open reading frames (ORFs), encoding 21 proteins with various functions including antibiotic resistance. The transcription of GCs relies mainly 22 on a cassette promoter (PC), located upstream of an array of GCs. Some integron GCs, called ORF-less 23 GCs, contain no identifiable ORF with a small number shown to be involved in antisense mRNA 24 mediated gene regulation. 25In this study, promoter sequences were identified, using in silico analysis, within GCs PCR amplified 26 from the oral metagenome. The promoter activity of ORF-less GCs was verified by cloning them 27 upstream of a gusA reporter, proving they can function as a promoter, presumably allowing bacteria 28 to adapt to multiple stresses within the complex physico-chemical environment of the human oral 29 cavity. A bi-directional promoter detection system was also developed allowing direct identification of 30 clones with promoter-containing GCs on agar plates. Novel promoter-containing GCs were identified 31 from the human oral metagenomic DNA using this construct, called pBiDiPD. 32 This is the first demonstration and detection of promoter activity of ORF-less GCs and the development 33 of an agar plate-based detection system will enable similar studies in other environments. 34 35 Introduction 36Integrons are bacterial genetic elements able to integrate and express genes present on gene cassettes 37 (GCs) [1][2][3]. They consist of two main components; a functional platform and a variable array of GCs. 38The functional platform, located on the 5' end of an integron, consists of an integrase gene (intI), and 39 its promoter (PintI), an attI recombination site and a constitutive cassette promoter (PC) for the 40 expression of GCs [4]. IntI is a site-specific tyrosine integrase that catalyses the insertion and excision 41 of GCs via recombination mainly at attI and the attC, the latter located at the joint of excised, 42 circularised GCs. The integrase gene; intI, is normally transcribed in the opposite direction to GCs 43 within an integron ( Fig 1A). However, some integrons have integrase genes transcribed in the same 44 directions as their GCs. These are called unusual integrons or reverse integrons ( Fig 1B), and have been 45 identified in Treponema denticola, Chlorobium phaeobacteroides and Blastopirellula marina [5, 6]. 46The second part of an integron is an array of GCs. Each usually contains a single promoterless open 47 reading frame (ORF) and an attC recombination site [7]. The proteins encoded by GCs are diverse and 48 include those associated with antibiotic resistance, virulence, and metabolism [2, 8]. When a GC is 49 excised from integron, it forms a non-replicative mobile genetic element, which can be a substrate for 50 integrase mediated recombination between attI (on the integrons) and attC (on the circular GC). This 51 directionality of recombination is favoured over attC:attC...

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The gain and loss of chromosomal integron systems in the Treponemaspecies

Cited by 17 publications

References 26 publications

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

Integrons: Past, Present, and Future

Promoter activity of ORF-less gene cassettes isolated from the oral metagenome

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