The phylogeny of the genus<i>Yersinia</i>based on 16S rDNA sequences

Ibrahim, Ashraf S.; Goebel, Brett M.; Liesack, Werner; Griffiths, Mansel W.; Stackebrandt, Erko

doi:10.1111/j.1574-6968.1993.tb06569.x

Cited by 80 publications

(5 citation statements)

References 22 publications

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“…Y. enterocolitica is the root of the Yersinia clade. In general, the Genomic-TSSR correlation scheme of this group of bacteria is in line with other phylogenetic scheme proposed [28]. However, some slight differences are noticed.…”

Section: Resultssupporting

confidence: 73%

Bacterial phylogenetic tree construction based on genomic translation stop signals

Kuo

Liu

et al. 2012

Microb Informatics Exp

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BackgroundThe efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found on the second and third reading-frames of a gene. They are called premature stop codons (PSC). Like stop codons, the PSC in bacterial genomes are also highly bias in terms of their quantities and qualities on the genes. Phylogenetically related species often share a similar PSC profile. We want to know whether the selective forces that influence the stop codons and the PSC usage biases in a genome are related. We also wish to know how strong these trimers in a genome are related to the natural history of the bacterium. Knowing these relations may provide better knowledge in the phylogeny of bacteriaResultsA 16SrRNA-alignment tree of 19 well-studied α-, β- and γ-Proteobacteria Type species is used as standard reference for bacterial phylogeny. The genomes of sixty-one bacteria, belonging to the α-, β- and γ-Proteobacteria subphyla, are used for this study. The stop codons and PSC are collectively termed “Translation Stop Signals” (TSS). A gene is represented by nine scalars corresponding to the numbers of counts of TAA, TAG, and TGA on each of the three reading-frames of that gene. “Translation Stop Signals Ratio” (TSSR) is the ratio between the TSS counts. Four types of TSSR are investigated. The TSSR-1, TSSR-2 and TSSR-3 are each a 3-scalar series corresponding respectively to the average ratio of TAA: TAG: TGA on the first, second, and third reading-frames of all genes in a genome. The Genomic-TSSR is a 9-scalar series representing the ratio of distribution of all TSS on the three reading-frames of all genes in a genome. Results show that bacteria grouped by their similarities based on TSSR-1, TSSR-2, or TSSR-3 values could only partially resolve the phylogeny of the species. However, grouping bacteria based on thier Genomic-TSSR values resulted in clusters of bacteria identical to those bacterial clusters of the reference tree. Unlike the 16SrRNA method, the Genomic-TSSR tree is also able to separate closely related species/strains at high resolution. Species and strains separated by the Genomic-TSSR grouping method are often in good agreement with those classified by other taxonomic methods. Correspondence analysis of individual genes shows that most genes in a bacterial genome share a similar TSSR value. However, within a chromosome, the Genic-TSSR values of genes near the replication origin region (Ori) are more similar to each other than those genes near the terminus region (Ter).ConclusionThe translation stop signals on the three reading-frames of the genes on a bacterial genome are interrelated, possibly due to frequent off-frame recombination facilitated by translational-associated recombination (TSR). However, TSR may not occur randomly in a bacterial chromosome. Genes near the Ori region are often highly expressed and a bacterium always maintains multiple copies of Ori. Frequent collis...

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Section: Resultssupporting

confidence: 73%

Bacterial phylogenetic tree construction based on genomic translation stop signals

Kuo

Liu

et al. 2012

Microb Informatics Exp

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“…Isolated symbiotic bacteria were identified by nucleotide sequence analysis of 16S ribosomal DNA (rDNA). The universal primer set used was a forward 27F (5′-AGA GTT TGA TCC TGG CTC AG-3′) and a reverse 1492R (5′-GGT TAC CTT GTT ACG ACT T-3′) (Ibrahim et al 1993). Polymerase chain reaction (PCR) was performed with genomic DNA as a template in a total volume of 50 μl containing 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 2 mM MgCl 2 , 0.2 mM dNTPs, 0.2 pmol of each primer, and Taq DNA polymerase (Promega ® ).…”

Section: Methodsmentioning

confidence: 99%

Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates

et al. 2017

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Five bacterial strains were isolated from the hemocoel of the greater wax moth larvae (Galleria mellonella) infected with the entomopathogenic nematodes: Heterorhabditis bacteriophora HP88, Heterorhabditis indicus RM1 and Heterorhabditis sp (S1), Steinernema abbasi and Steinernema sp. (S II). Strains were identified as Photorhabdus luminescens HRM1, P. luminescens HS1, P. luminescens HP88, Xenorhabdus indica and X. nematophila ATTC19061 using 16S rDNA sequence analysis. To reveal the genetic diversity among these strains, three molecular markers (RAPD, ISSR and SRAP) were employed. RAPD analysis showed 73.8 and 54.5 polymorphism percentages for the Photorhabdus and Xenorhabdus strains, respectively. ISSR analysis resulted in 70.1 and 75.2 polymorphism percentages among the Photorhabdus and Xenorhabdus strains, respectively. The SRAP analysis indicated that 75.6 and 61.2% genetic polymorphism was detected among Photorhabdus and Xenorhabdus strains, respectively. The cluster analysis grouped the three Photorhabdus strains together in one cluster and the two Xenorhabdus strains together in another cluster indicating the phylogenetic relationships among them. The genotype-specific markers detected from the three molecular markers (RAPD, ISSR and SRAP) were sufficient to distinguish between the different bacterial strains tested and can be used in the future IBM program that could be built on the use of these strains.

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“…For example, Yersinia pestis is very closely related to E. coli K-12, 21 and we found that Y. pseudotuberculosis IP2666, a strain most closely related to Y. pestis, is fully susceptible to the T7 phage. 22 We were not able to test Y. pestis due to regulatory limitations. Y. enterocolitica is slightly further from Y. pestis and is highly resistant toward T7 phage.…”

Section: ■ Discussionmentioning

confidence: 99%

“…pseudotuberculosis IP2666, a strain most closely related to Y. pestis, is fully susceptible to the T7 phage . We were not able to test Y.…”

Section: Discussionmentioning

confidence: 99%

Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity

Liang¹,

Zhang

Tan³

et al. 2022

ACS Synth. Biol.

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In the fight against antimicrobial resistance, bacteriophages are a promising alternative to antibiotics. However, due to their narrow spectra, phage therapy requires the careful matching between the host and bacteriophage to be effective. Despite our best efforts, nature remains as the only source of novel phage specificity. Directed evolution can potentially open an avenue for engineering phage specificity and improving qualities of phages that are not strongly selected for in their natural environments but are important for therapeutic applications. In this work, we present a strategy that generates large libraries of replication-competent phage variants directly from synthetic DNA fragments, with no restriction on their host specificity. Using the T7 bacteriophage as a proof-of-concept, we created a large library of tail fiber mutants with at least 107 unique variants. From this library, we identified mutants that have broadened specificity as evidenced by their novel lytic activity against Yersinia enterocolitica, a strain that the wild-type T7 was unable to lyse. Using the same concept, mutants with improved lytic efficiency and characteristics, such as lytic condition tolerance and resistance suppression, were also identified. However, the observed limitations in altering host specificity by tail fiber mutagenesis suggest that other bottlenecks could be of equal or even greater importance.

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The phylogeny of the genusYersiniabased on 16S rDNA sequences

Cited by 80 publications

References 22 publications

Bacterial phylogenetic tree construction based on genomic translation stop signals

Bacterial phylogenetic tree construction based on genomic translation stop signals

Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates

Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity

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