Identification of<i>Campylobacter jejuni</i>ATCC 43431-Specific Genes by Whole Microbial Genome Comparisons

Poly, Frédéric; Threadgill, Deborah S.; Stintzi, Alain

doi:10.1128/jb.186.14.4781-4795.2004

Cited by 68 publications

(89 citation statements)

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“…The C. jejuni 81-176 shotgun microarray was constructed as previously described for C. jejuni ATCC 43431 (32). Briefly, the construction of this microarray involved four consecutive steps: (i) construction of a genomic library of C. jejuni 81-176, (ii) plasmid extraction and purification, (iii) assessment of the plasmid quality and concentration by agarose gel electrophoresis, and (iv) printing of the whole plasmids on microarray slides.…”

Section: Methodsmentioning

confidence: 99%

“…This genome-wide approach consists of five consecutive steps: (i) construction of a shotgun library representative of the size of the genome, (ii) arraying of the whole plasmids on glass slides, (iii) competitive genomic hybridization, (iv) identification of the plasmids carrying unique DNA segments, and (v) DNA sequencing. A total of 84 kb of new DNA sequences unique to ATCC 43431 were identified (32). These sequences carry up to 130 genes, representing an addition of approximately 7.5% of novel genes to the current set of known C. jejuni genes.…”

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confidence: 99%

“…The addition of new genome information from C. jejuni strains of different origins will facilitate the identification of genotypic markers and improve the power of this genotyping method. Recently, we have described a novel approach to identify nonredundant sequences of C. jejuni ATCC 43431 by combining the construction of a shotgun library and the power of microarray technology (32). This genome-wide approach consists of five consecutive steps: (i) construction of a shotgun library representative of the size of the genome, (ii) arraying of the whole plasmids on glass slides, (iii) competitive genomic hybridization, (iv) identification of the plasmids carrying unique DNA segments, and (v) DNA sequencing.…”

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Genomic Diversity inCampylobacter jejuni: Identification ofC. jejuni81-176-Specific Genes

2005

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Since the publication of the complete genomic sequence of Campylobacter jejuni NCTC 11168 in February 2000, evidence has been compiling that suggests C. jejuni strains exhibit high genomic diversity. In order to investigate this diversity, the unique genomic DNA sequences from a nonsequenced Campylobacter strain, C. jejuni 81-176, were identified by comparison with C. jejuni NCTC 11168 by using a shotgun DNA microarray approach. Up to 63 kb of new chromosomal DNA sequences unique to this pathogen were obtained. Eighty-six open reading frames were identified by the presence of uninterrupted coding regions encoding a minimum of 40 amino acids. In addition, this study shows that the whole-plasmid shotgun microarray approach is effective and provides a comprehensive coverage of DNA regions that differ between two closely related genomes. The two plasmids harbored by this Campylobacter strain, pTet and pVir, were also sequenced, with coverages of 2.5-and 2.9-fold, respectively, representing 72 and 92% of their complete nucleotide sequences. The unique chromosomal genes encode proteins involved in capsule and lipooligosaccharide biosynthesis, restriction and modification systems, and respiratory metabolism. Several of these unique genes are likely associated with C. jejuni 81-176 fitness and virulence. Interestingly, the comparison of C. jejuni 81-176 unique genes with those of C. jejuni ATCC 43431 revealed a single gene which encodes a probable TraG-like protein. The product of this gene might be associated with the mechanism of C. jejuni invasion into epithelial cells. In conclusion, this study extends the repertoire of C. jejuni genes and thus will permit the construction of a composite and more comprehensive microarray of C. jejuni.

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Genomic Diversity inCampylobacter jejuni: Identification ofC. jejuni81-176-Specific Genes

2005

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“…Using sequences from the four Dehalococcoides genomes, a microarray using unique probe sets to target all identified genes was designed, constructed and validated in this study. Microarray technology has successfully been applied in recent years in comparative genomic analyses of related strains of bacteria in a variety of genera (Poly et al, 2004;Witney et al, 2005;Cooke et al, 2008;Boesten et al, 2009;Castellanos et al, 2009), including Dehalococcoides (West et al, 2008). In this study, we report the physiology of two novel Dehalococcoides strains that have been isolated from an enrichment culture (ANAS) that has been stably dechlorinating trichloroethene to ethene for over 10 years (Richardson et al, 2002;Holmes et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray

Lee

Cheng

et al. 2011

The ISME Journal

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Comparative genomics of Dehalococcoides strains and an enrichment were performed using a microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus. The microarray was designed with 4305 probe sets to target 98.6% of the open-reading frames from strains 195, CBDB1, BAV1 and VS. The microarrays were validated and applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2, and their enrichment source (ANAS) to understand the genome-physiology relationships. Strains ANAS1 and ANAS2 can both couple the reduction of trichloroethene, cis-dichloroethene (DCE) and 1,1-DCE, but not tetrachloroethene and trans-DCE with growth, whereas only strain ANAS2 couples vinyl chloride reduction to growth. Comparative genomic analysis showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements or high-plasticity regions. Combined results of the two isolates closely matched the results obtained using genomic DNA of the ANAS enrichment. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny seems to be related to the presence of distinct reductive dehalogenase-encoding genes with assigned chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Overall, the microarrays are a valuable high-throughput tool for comparative genomics of unsequenced Dehalococcoides-containing samples to provide insights into their gene content and dechlorination functions.

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“…Most of the investigated enzymes did not cut the phage DNA at all. Inefficient cleavage might reflect the very low GϩC content of 26.1% determined for CP81 by genome sequencing (see below), which is even lower than the content reported for its host C. jejuni NCTC11168 (30.6%) (38). Indeed, efficient cleavage was achieved using the enzymes DraI (TTTAAA; 455 sites), SmiI (ATTTAAAT; 51 sites), and VspI (ATTAAT; 224 sites) whose recognition sites are exclusively composed of the bases adenine and thymine (Fig.…”

Section: Resultsmentioning

confidence: 67%

Campylobacter jejuni Group III Phage CP81 Contains Many T4-Like Genes without Belonging to the T4-Type Phage Group: Implications for the Evolution of T4 Phages

Hammerl¹,

Jäckel²,

Reetz³

et al. 2011

J Virol

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CP81 is a virulent Campylobacter group III phage whose linear genome comprises 132,454 bp. At the nucleotide level, CP81 differs from other phages. However, a number of its structural and replication/recombination proteins revealed a relationship to the group II Campylobacter phages CP220/CPt10 and to T4-type phages. Unlike the T4-related phages, the CP81 genome does not contain conserved replication and virion modules. Instead, the respective genes are scattered throughout the phage genome. Moreover, most genes for metabolic enzymes of CP220/CPt10 are lacking in CP81. On the other hand, the CP81 genome contains nine similar genes for homing endonucleases which may be involved in the attrition of the conserved gene order for the virion core genes of T4-type phages. The phage apparently possesses an unusual modification of C or G bases. Efficient cleavage of its DNA was only achieved with restriction enzymes recognizing pure A/T sites. Uncommonly, phenol extraction leads to a significant loss of CP81 DNA from the aqueous layer, a property not yet described for other phages belonging to the T4 superfamily.Campylobacteriosis is a worldwide zoonosis. There are probably more than two million Campylobacter infections in humans annually in the United States. Also, in developing countries, infections with Campylobacter jejuni are very frequent in children, and symptomatic infections early in life are followed later by asymptomatic infections. The bacteria are common commensals of the gastrointestinal tract of various mammals and birds. Consumption of undercooked meats, especially poultry, has been associated with Campylobacter infections (44). The prevalence of Campylobacter-positive chicken is generally high, and transmission of Campylobacter from bird to bird occurs rapidly (25). Intervention strategies mainly focus on biosecurity measures (e.g., improvement of personal hygiene, avoiding of mixed farming, and control of rodents and insects) and postslaughter decontamination of poultry carcasses (19). Since these measures are expensive and not always efficient and since suitable vaccines are not available, bacteriophages have been proposed to reduce the Campylobacter counts on chicken. Indeed, phage administration in the laboratory reduced C. jejuni colonization of the broiler gut and the contamination on chicken skin by several orders of magnitude (3,6,16,20,29,50).Phages intended for therapeutic applications or for the control of pathogens in food production have to fulfill a number of requirements. First and foremost, phages have to be safe in order to avoid any undesired side effect. Therefore, a basic understanding of the biology and genetics of the phage to be used is mandatory. A minimal standard is the acquisition of the genome sequence of the phage to exclude undesired genes. Unfortunately, up to now, genome sequences of Campylobacter phages are scarce. Most Campylobacter phages have been investigated only with respect to their host ranges, morphology, and genome size (3,4,11,16,22,26,30). Almost all Campyloba...

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Identification ofCampylobacter jejuniATCC 43431-Specific Genes by Whole Microbial Genome Comparisons

Cited by 68 publications

References 49 publications

Genomic Diversity inCampylobacter jejuni: Identification ofC. jejuni81-176-Specific Genes

Genomic Diversity inCampylobacter jejuni: Identification ofC. jejuni81-176-Specific Genes

Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray

Campylobacter jejuni Group III Phage CP81 Contains Many T4-Like Genes without Belonging to the T4-Type Phage Group: Implications for the Evolution of T4 Phages

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