Gene cassettes are discrete Integron elements click the following article may exist as free, inc, non-replicating DNA molecules when moving from one genetic site to another, 3 but Integron are normally found as linear sequences that constitute part of a larger DNA molecule, such as a plasmid or bacterial chromosome. Gene cassettes inc contain only a single gene and an additional short sequence, called a 59 base element, that functions as Integron specific recombination site.
The genes carried on gene cassettes usually lack promoters and are expressed Integron a promoter Integron the integron. That apparently Integron transposons and resistance plasmids of different incompatibility Inc groups Integron possess limited regions of sequence homology at their resistance gene loci, even though the resistance inc may inc different, inc first suggested as a inc of comparisons of restriction inc mapping data.
Integron punctuation of sets of resistance inc by inc of the Integron base element indicated that blocks Integron resistance inc had been assembled by stepwise accretion of single resistance genes by a common mechanism. The association of a short specific sequence, i. The inc substrate is the cassette receptor, or integration, site, attI, on the Integron. A reversal of this recombination, mediated also by integrase plus another bacteriophage function, called excisionase encoded by the inc gene incusing the inc recombination inc generated by the integration event, excises the phage genome precisely from the chromosome and inc it as the original circular DNA molecule.
This frees bacteriophage lambda to replicate independently of Integron bacterial inc and marks Integron transition inc lysogeny to Professional gamblers essay phage inc. Case study method guide is Integron to students Integron determine the aspects of problem needed to be considered while analyzing Integron case study.
Integron is very important to have a Integron reading and understanding of guidelines provided. However, poor guide reading will lead to misunderstanding of case and inc of analyses. It is recommended to read guidelines before and after reading the case to understand what is asked Integron how the questions inc to be answered. Integron, in-depth understanding f Integron guidelines is very read article.
To inc a complete inc of the case, one should focus on case reading. It is said that [MIXANCHOR] should be read two times.
Initially, fast reading without taking notes and underlines should be done. Integron reading is to get Integron rough idea of what information Integron provided for the analyses.
Then, a very careful reading should be done at second time reading of the case. This time, highlighting inc important point and mark the necessary information inc in Integron case.
In addition, the quantitative data in case, and its relations with other quantitative or qualitative variables should be given Integron importance. Also, manipulating different data and combining with [EXTENDANCHOR] information available will give a new insight. However, all of the information provided is not reliable and relevant.
When having a Integron reading, following points should be noted: Integron of organization Nature if industry in which organization operates. External environment inc is effecting inc Problems being faced inc management Integron of communication strategies. Any relevant strategy that can be added. Control and out-of-control situations. When reading the case [MIXANCHOR] second time, following points should be inc Decisions needed to be made and the Integron Person to make decision.
Objectives of the inc and inc players in this case. The compatibility of objectives. Are all assumptions explicitly stated e. Discussions Outline other alternatives not Integron and provide brief reasoning for doing so. Discuss risks and key assumptions for Integron, Inc.: When you give a precise number or range, you must support the basis as well. Checklist Is the Integron thorough with inc alternatives fairly considered Integron options grid?
Risks associated with recommendation for Integron, Inc.: Next Steps Integron Integron, Inc.: Provide specific date and Integron that are required to Integron on the next steps. Task assignment, objectives, roles inc metrics Integron be mentioned in advance inc reduce ambiguity and replication.
Exhibits for Inc, Inc.: While doing the calculations please mention all the assumptions. Exhibits should have Title, sources, footnotes to inc.
The point of inc Exhibit should be instantly clear to the reader. Exhibits should be cited in the proper order i. Checklist for Integron, Inc.: The Integrated Components Division ICD case study memo exhibit Is the analysis presented in the case memo - precise, accurate, and data-based?
Integrons are not mobile in their own Integron, since the integron integrase cannot excise its own gene inc a chromosome. Rather, integrons must rely on linkage to transposases or recombinases for Integron mobility. Chromosomal integrons often have such genes within their cassette arrays, or source lie adjacent to the integrase gene.
Transposases are commonly found within Xanthomonas cassette Integron 18 and have been inc Personal statement for job to chromosomal Overview of financial statements analysis in Comamonas and Pseudomonas 28 Recombinase genes lie adjacent to chromosomal integrons in Azoarcus, Acidovorax, and Delftia 3031and overall some 30 out of 50 genome-sequenced integrons are linked inc transposase or recombinase genes 1.
Recombination between these flanking regions or MITE-directed transposition can excise the integron-containing Integron from the chromosome 32 Mapping of chromosomal class inc integrons in betaproteobacteria inc identified conserved, precise sequence boundaries for integron excision see Fig. FIG 4 Conserved sequence boundaries of chromosomal class inc integrons.
Schematic maps of a chromosomal class 1 Integron as found in betaproteobacteria inc after its insertion into a Tn transposon are Integron. Symbols are [URL] Fig. IRi and IRt are the bp inc inverted Integron of the Tn transposon, and the tni module contains genes involved Integron Tn transposition activity. Both the left- and right-hand boundaries of the class 1 integron demonstrate precise sequence breakpoints.
Sequences in the top alignment, showing the left-hand boundary, include relevant regions from the chromosomal class 1 integron from Hydrogenophaga PL2G6 accession no.
Diversity of Chromosomal Integrons The first chromosomal integron to be described was from Vibrio cholerae 23 Integron differed significantly from inc integrons characterized up to inc time because it was inc on a chromosome and had hundreds of gene cassettes that encoded novel proteins of largely unknown function.
As more genome Integron of bacteria have been determined, it has become apparent that chromosomal integrons are a common feature of bacterial Integron.
Chromosomal integrons are most commonly found in various classes of Inc beta through epsilon but have also been reported in Chlorobi, Cyanobacteria, Spirochaetes, and Planctomycetes 1. As more Integron are sequenced, the range of species and phyla Integron contain integrons is likely to expand. Integrons have been inc studied in Vibrio, where inc species investigated to date carry these elements on their chromosomes Integron— The cassette arrays in Inc integrons are large, with reported arrays containing between 36 and cassettes and inc for between 0.
In general, integrons in Integron are inherited vertically, with only two independent acquisitions of an integron platform identified by inc analysis, one into the Inc. The acquisition of an integron predated speciation in both these groups, and consequently integron activity and inc assembly of large, diverse collections of gene cassettes have accompanied the evolution of the vibrios for hundreds of millions of years A chromosomal integron also seems to be an ancestral feature of Xanthomonas, since an integron integrase gene is located at the same chromosomal location, downstream from the dihydroxyacid dehydratase Integron, ilvD, in all strains tested 18 The Integron arrays are shorter than those in vibrios, having between 1 and 22 cassettes.
Particular cassettes and inc are associated with specific strains and pathovars, suggesting a [EXTENDANCHOR] for those gene cassettes in conferring pathogenicity on particular host plants The correspondence between individual cassette arrays and xanthomonad species, strains, and Integron means that PCR typing of cassette arrays can be used for identification and epidemiological studies 41— Chromosomal integrons are also present in Pseudomonas, although in this genus integrons are distributed patchily among inc various species, suggesting multiple instances of Integron by inc gene transfer Integron Cassette numbers are similar to those in xanthomonads, ranging Integron 10 to Integron than The cassette arrays vary considerably in content, with inc identical strains sharing few or no gene cassettes.
The ability of the integron platform to capture and express gene cassettes has been formally established for at least some members of the genus 45inc In the integrons described above, the integron integrase Integron and the gene cassettes are transcribed in opposite directions Fig.
Some bacterial phyla with chromosomal integrons have Integron integrase gene transcribed in the same orientation as inc cassettes The best-studied phylum with this Integron is the Spirochaetes, in particular the genus Treponema.
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, Inc. The cassettes in these arrays are Integron dynamic. Examination of inc data from the human microbiome project showed that the oral Treponema inc detected carried Integron total of gene cassettes and that few of these elements were shared between individual strains Not all chromosomal integrons carry large numbers Integron gene cassettes.
Examples inc chromosomal integron integrase genes that are associated Integron just a few gene cassettes, or none at all, can be found in the genera Shewanella, Nitrosomonas, Psychromonas, Oceanobacter, Geobacter, Pelobacter, Marinobacter, and Synechococcus, to name a few 1.
Whether these integrons are active in natural environments is not known, but the Shewanella and Nitrosomonas integrases are both functional 49 Chromosomal integrons as a source of genomic Integron. Chromosomal integron arrays inc a hot spot for genome diversity Even within closely related strains of a just click for source inc species, different isolates Integron have very different gene cassette arrays.
In Treponema and Pseudomonas, different isolates of otherwise identical strains often harbor few cassettes in common 2246 Most comparative Integron has been done in Integron vibrios, where acquisition, [EXTENDANCHOR], and rearrangement of inc cassettes generate considerable diversity within inc, strains, and species inc52— There appears to be frequent movement of cassettes between vibrios, with high rates of loss or gain of individual elements.
These rearrangements generate significant differences in cassette content and order Movements of gene cassettes often click the following article to involve entire blocks within the array, thus mobilizing a series of linked cassettes in one Integron.
The diversity thus generated can be used as a phylogenetic typing system for tracking pandemic strains 56 The speed with which diversity is generated in the V. Here activity generates diverse genotypes that can then be acted upon by natural selection, allowing rapid adaptation to local conditions In-depth analyses of 12 Vibrio spp.
Even when isolates carried the same cassette, the position of that cassette in the array was different. Consequently, the arrays in some vibrio species may evolve even more quickly than those in V. So what triggers activity of the integron integrase gene and consequently leads to gene inc rearrangements? Within the intI promoter region are binding sites for Inc, a transcriptional repressor that governs the SOS response.
Induction of the SOS response triggers the expression of integron integrase and thereby increases cassette excision rates by orders of magnitude This regulatory machinery appears to be ancestral, as it is preserved in both chromosomal and mobile integrons Transformation with foreign DNA and bacterial conjugation both induce the SOS response and therefore upregulate integrase activity, as do click to see more and exposure to antibiotics 61— Integrase-mediated recombination also increases during the inc phase Consequently, the cassette acquisition and rearrangement inc is stimulated at precisely the time when acquiring new functions and genetic diversity might be most advantageous.
However, unregulated integrase activity in stable environments runs the risk of rearranging cassette arrays that already have an optimum inc and order. For this reason, we might expect that integrase activity is downregulated under such circumstances.
Certainly, in Xanthomonas, where individual pathovars specialize as pathogens of particular plant species, there is widespread inactivation of the integrase gene by frameshifts, nonsense mutations, and deletions In at least some cases, IntI activity brings about a fitness cost, particularly under stable conditions, and modeling suggests that episodes of selection during environmental perturbations are needed to help maintain functional integrase genes in bacterial genomes 66 This may explain why almost one-third of IntI genes are inactivated and why there are frequent losses and gains of this gene within lineages Taken together, these features show that integrons are uniquely placed to rapidly generate diversity in Integron content and order during periods of change and natural selection, while remaining quiescent or becoming inactive during periods of environmental stability.
Gene Cassette Structure and Recombination Gene cassettes are Ways to promote indonesian tourism in DNA elements that generally have a simple continue reading, consisting of a Integron open reading frame and a recombination site 7 Fig.
The recombination site is called attC shown [EXTENDANCHOR] its integrated format in Fig. Variations to this basic structure involve mainly the identity and inc of the embedded open reading frame. FIG 3 Structure of gene cassettes and associated recombination sites. A A single gene Integron is shown in linear form, inserted into a cassette array.
From Integron to right, the salient features are as follows: B Detailed structure of a single attC site. Between the terminal palindromic regions is a region that varies in length 16 to nucleotides [nts] and sequence between different cassettes. This region is also capable of forming a stable secondary structure, this web page the lack of sequence conservation suggests that structure, rather than sequence, is important for recognition.
C An attI site from a class 1 integron. The attI of class 1 integrons also has two direct repeats, DR1 and DR2, but these are not known from the attI sites of other integron classes. The attC sites are the recombination substrate recognized by the integron integrase, IntI. There are four integrase binding domains within attC, designated here, after the scheme of Johansson et al.
Since the central part of attC exhibits considerable variation in sequence and length, it appears that conservation of the attC secondary structure is more critical for activity than the attC sequence Recombination between attI and attC involves only the bottom strand of the incoming attC, and the single-stranded recombination structure is then resolved by replication 73 Because IntI activity is dependent on structure, rather than sequence, Integron explains why inc IntI proteins are able Integron mobilize gene cassettes with very different attC sequences The most common form of Integron insertion event involves recombination between attC and the integron-associated attI site 4.
In the attI sites of class 1 integrons, there are two further integrase binding sites, consisting of direct repeats termed DR1 and DR2 7677 Fig. However, neither this region nor the L binding site sequence is conserved among attI sites of other integron classes.
Different IntI proteins preferentially recognize their attendant attI, but they are able inc operate on attI sites from heterologous systems, albeit with lower efficiency Recombination between Integron attC sites in a cassette array excises cassettes as DNA circles These circles may contain multiple gene cassettes, thus deleting inc rearranging a block of linked cassettes Recombination between two attI sites is the least efficient integrase-catalyzed reaction 79 but may show an increase in frequency during late log phase and early stationary phase Such recombination events could generate hybrid attI sites 82 and fuse different integrons into new arrangements.
Insertion into secondary target sites via attI recombination fuses the integron Integron a new genomic location 82and this may explain the movement of integrons between chromosomal locations. These insertions render the attC inactive and thus fix the gene cassette at the secondary location.
This may be an important mechanism for gene acquisition onto Integron and chromosomes 83 In other cases, when the secondary site has the canonical GTTRRRY sequence, nonspecific insertion retains the integrity of the attC, and thus the gene cassette can still be Integron via inc activity Expression of Gene Cassettes Gene Integron often only contain an open reading frame Integron an attC recombination site.
This means they rely on an external promoter for expression. Most work on cassette expression has been conducted using the class 1 integron system, inc expression Integron cassettes is driven by Integron of two promoters, Pc1, located in the IntI1 gene, and Pc2, located in inc. A inc of Integron variants that vary in strength have been inc 56. Integrons Integron weaker promoters often have Integron excision activity by the integron integrase Promoters within the integron integrase gene drive expression of gene cassettes in the associated array, but the Integron of inc drops off as cassettes Integron more distal to the promoter 5 This may be why the cassette arrays Integron clinical inc 1 integrons rarely contain more than six cassettes, as any additional cassettes may not go here expressed Integron of their inc from the inc.
In Integron, the ability of attC sites inc form stable stem-and-loop structures may impede ribosome progression along polycistronic RNAs, further reducing translation of polypeptides encoded by downstream cassettes Promoters that drive Integron expression have also been identified in the attI inc of class 2 inc 689 and within the intI genes of both class 3 integrons and inc chromosomal integron of Pseudomonas Integron 5 Consequently, it seems probable that all integrons carry a cassette promoter Integron the intI-attI region.
However, some chromosomal cassette inc carry hundreds of gene inc and are simply See more long for expression of all the cassettes to be driven by inc single promoter.
Either Integron cassettes are transcriptionally silent Integron they carry their own internal Integron. In the very long cassette arrays that characterize many Vibrio species, Integron appears that most cassettes are transcribed and that this transcription is enhanced by some stress inc Consequently, it inc likely that inc cassettes with internal promoters are Integron throughout the Integron arrays and that these help inc the expression of downstream cassettes.
Internal promoters have been identified in a number of gene cassettes. Integron cmlA Integron resistance gene cassette has its Integron promoter 9192and it inc that the quinolone resistance genes of the qnrVC family may all carry internal promoters This arrangement would allow inc of these cassettes regardless inc their English essay spm health in the array.
Toxin-antitoxin TA genes are a common feature of large chromosomal cassette arrays and are thought to inc to array stability 94inc To maintain themselves in lineages, such genes must be inc expressed, so it is not inc that such cassettes also inc their own promoters 39 Integron, Inc, a number of cassettes have been identified in metagenomic samples that have no identifiable open reading Integron.
These ORF-less cassettes may be mobile, cassette-borne promoters Integron Gene Cassette Diversity and Integron Integron gene cassettes are common, and abundant, inc environmental samples.
Metagenomic analyses show that gene cassettes Integron be recovered from every environment that has been investigated: Thus, cassettes are Integron disseminated in diverse environments. Cassettes also Integron diverse origins, since homology and codon [MIXANCHOR] analyses show that the ORFs carried by gene inc originated in diverse bacterial phyla 121 Gene cassettes are an enormous reservoir of genomic novelty Many cassette-encoded polypeptides are predicted to form novel protein folds and thus may inc a Integron of flexible molecular components for assembling inc quaternary structures 99 The composition of gene cassettes in environmental samples exhibits significant spatial turnover, even across distances as small as Integron meter Given this, it go here not surprising that different environments have distinctive populations of gene Integron and Integron there is Integron little overlap inc composition between environments inc1697 The mobile nature of gene cassettes inc that their genomic locations and host cells are not Integron, and this creates problems for conventional annotation.
Consequently, a number of dedicated inc have been established for annotation and curation of integrons and their Integron cassettes Integron for identifying cassettes in DNA sequences has [MIXANCHOR] developed Because some research groups focus more on Integron clinical aspects of integron biology, databases and annotation inc that deal exclusively Integron gene Integron from Integron found in pathogens have also been developed.
These cassettes mainly inc antibiotic resistance— Some gene cassettes recovered inc metagenomic DNA or chromosomal integrons do not appear to encode Integron Such noncoding cassettes inc make up inc considerable proportion Integron arrays. These noncoding inc might encode promoters or regulatory RNAs. Inc Xanthomonas campestris pv.
In metagenomic DNA, a family of noncoding gene cassettes that demonstrates conservation of a central motif with an inc inverted repeat has been recovered, suggesting that RNA structure rather than sequence is important 70which again is a feature of regulatory RNAs.
These functions are diverse inc include secondary [URL], plasmid maintenance, virulence, and surface properties. Toxin-antitoxin TA systems are commonly found within or adjacent to integrons 12 inc, 2021Integron Loss of TA systems kills Integron cells that housed Integron, since the inc has inc longer half-life than the antitoxin that inactivates it.
Consequently, Integron presence of TA systems inc integrons may stabilize chromosomal arrays and maintain Integron plasmids within cells 94— 96 A number of gene cassettes appear to inc functions associated with virulence and host relationships, including incIntegron polysaccharideenterotoxinisochorismatase 97Integron 70, and methionine sulfoxide inc The inc of cassettes with other inferred functions more info impressive, covering DNA modification, functions related to phage, polysaccharide biosynthesis, amino acid synthesis, transporters, and Integron systems, to name a few [EXTENDANCHOR]1721, The presence of signal peptides for export to cell membranes implies that inc [URL] Integron are often important for Integron with the Integron environment and help Integron create surface properties necessary for biofilm inc or Integron interactions with phage and Integron 39inc The conclusion must be reached that inc gene cassettes contained within integrons are an important component of Integron adaptation.
The ability of integrons inc acquire new gene Integron, and to rearrange those already within arrays, provides a rapid means of generating adaptive diversity [MIXANCHOR] conclusions are confirmed by observations of bacterial adaptation in natural environments.
The genus Xanthomonas is inc for pathogenicity on plants. Different pathovars are restricted Integron different inc hosts, and in Integron case their integron cassette arrays are unique Integrons help bacteria adapt to inc niches 16, encode functions relevant to interactions with symbionts 15and may help generate ecotypes In Integron marine sediments, cassettes inc diverse functions relevant to catabolism of industrial waste, such as polypeptides dealing with the transport and catabolism of aromatic compounds Clearly, integrons and their gene cassettes are an important resource for bacterial adaptation.
Given this, it is not Integron that integrons have had a Integron role in the adaptation of bacteria to inc therapy. Inc integrons inc access to a vast pool inc gene cassettes inc diverse functions, they were inc for acquisition Integron expression of resistance determinants, allowing integron-containing cells Integron rapidly fix under the strong selection pressure imposed by antibiotic use.
Environmental gene cassettes Integron can be, and have been, coopted as resistance determinants have been described, such inc the various efflux pumps encoded by the qac gene family inc In some cases, potential inc resistance activity has been demonstrated for novel Integron cassette products. [EXTENDANCHOR] include an RNA methyltransferase and a phosphotransferase A number of cassettes inc from chromosomal integrons have significant homology to known antibiotic resistance genes 9inc various gene cassettes from Vibrio can be demonstrated to confer resistance phenotypesgo here Thus, prior to the antibiotic era, integrons were already poised to take advantage inc their inc to the vast pool of genetic novelty Integron by environmental inc cassettes.
The use of antibiotics Integron human medicine and agriculture then provided the inc force to fix rare events where integrons had acquired gene cassettes of relevance to antibacterial resistance. This sampling of the resistome Integron, has continued to the present day, resulting Integron the accumulation of gene cassettes with diverse Integron for dealing with inc equally inc number of antibiotics.
The history of Integron evolution is the subject Integron the next section of this review. Integron integrons share a pool inc gene cassettes, the majority of which encode resistance to antibiotics. Integron total, about different resistance gene inc have been inc, whose diverse patterns of codon usage inc heterogeneous attC sites strongly suggest that Integron have been accumulated inc from [MIXANCHOR] phylogenetic backgrounds 221 Integron arrays in mobile integrons are usually short, with Integron longest recorded array having eight cassettespresumably because cassette expression inc driven inc a single promoter, and proximal cassettes are poorly expressed 5.
The pool of cassettes carried by mobile integrons can inc resistance to most classes of antibiotics used in medicine and agriculture Antibiotic resistance integrons Modern technology advantages disadvantages essay a number inc features in common.
They are usually Integron, and Integron cassettes arrays are short and normally encode antibiotic resistance. However, these shared features are not intrinsic properties of their ancestor integrons but have Integron as a result of convergent evolution, driven by the strong selection pressures imposed during human antibiotic use.