Genomic Comparison between <em>Salmonella</em> Gallinarum and Pullorum: Differential Pseudogene Formation under Common Host Restriction

<div><p>Background</p><p><i>Salmonella</i> serovars Enteritidis and Gallinarum are closely related, but their host ranges are very different: the former is host-promiscuous and the latter can infect poultry only. Comparison of their genomic sequences reveals that Gallinarum has undergone much more extensive degradation than Enteritidis. This phenomenon has also been observed in other host restricted <i>Salmonella</i> serovars, such as Typhi and Paratyphi A. The serovar Gallinarum can be further split into two biovars: Gallinarum and Pullorum, which take poultry as their common host but cause distinct diseases, with the former eliciting typhoid and the latter being a dysentery agent. Genomic comparison of the two pathogens, with a focus on pseudogenes, would provide insights into the evolutionary processes that might have facilitated the formation of host-restricted <i>Salmonella</i> pathogens.</p> <p>Methodologies/Principal Findings</p><p>We sequenced the complete genome of Pullorum strains and made comparison with Gallinarum and other <i>Salmonella</i> lineages. The gene contents of Gallinarum and Pullorum were highly similar, but their pseudogene compositions differed considerably. About one fourth of pseudogenes had the same inactivation mutations in Gallinarum and Pullorum but these genes remained intact in Enteritidis, suggesting that the ancestral Gallinarum may have already been restricted to poultry. On the other hand, the remaining pseudogenes were either in the same genes but with different inactivation sites or unique to Gallinarum or Pullorum, reflecting unnecessary functions in infecting poultry.</p> <p>Conclusions</p><p>Our results support the hypothesis that the divergence between Gallinarum and Pullorum was initiated and facilitated by host restriction. Formation of pseudogenes instead of gene deletion is the major form of genomic degradation. Given the short divergence history of Gallinarum and Pullorum, the effect of host restriction on genomic degradation is huge and rapid, and such effect seems to be continuing to work. The pseudogenes may reflect the unnecessary functions for <i>Salmonella</i> within the poultry host.</p> </div

Relationship between bvPu str. CDC1983-67 and other <i>Salmonella</i> strains.

<p>(A) Association between dN/dS (y axis) and dS (x axis). dS represents synonymous substitution rate and dN represents non-synonymous substitution rate. (B) Association between indel/dS (y axis) and dS (x axis). The points in the plot are: bvPu, bvPu str. RKS5078; bvGa, bvGa str. 287/91; SEN, Enteritidis str. P125109; SDU, Dublin str. CT_02021853; SAR, <i>S. arizonae</i> str. RSK2980; other points represent the <i>S. enterica</i> subspecies I strains used for comparison in this study.</p

Pseudogene Recoding Revealed from Proteomic Analysis of <i>Salmonella</i> Serovars

Recoding refers to the reprogramming of mRNA translation by nonstandard read-out rules. In this study, we used stable isotope labeling with amino acids in cell culture (SILAC) technology to investigate the proteome of host-adapted <i>Salmonella</i> serovars, which are characteristic of accumulation of pseudogenes. Interestingly, a few annotated pseudogenes were indeed able to express peptides downstream of the inactivation site, suggesting the occurrence of recoding. Two mechanisms of recoding, namely, programmed frameshifting and codon redefinition, were both found. We believe that the phenomena of recoding are not rare in bacteria. More studies are required for a better understanding of bacterial translation and the implication of pseudogene recoding in <i>Salmonella</i> serovars

Maximum Likelihood Tree for <i>Salmonella enterica</i> strains.

<p>Genes that are conserved in all strains were aligned and concatenated for tree construction. In the brackets are the accession numbers of these genomes downloaded from NCBI database. A scale bar for the genetic distance is shown at the bottom.</p

Circular Map of Pullorum str. CDC1983-67 genome.

<p>Circles range from 1 (inner circle) to 8 (outer circle): 1, coordinates of the genome; 2, GC content; 3, GC skew; 4–8, comparison of gene content with bvPu strain RKS5078, bvGA, Enteritidis, Dublin and Typhimurium, respectively. The locations of seven rRNA operons are indicated by the small outer orange blocks. The outmost arcs represent the chromosomal rearrangements between bvGa and bvPu (the larger one) and between bvGa and Enteritidis (the smaller one).</p

Immobilization-Free Photoelectrochemical Aptasensor for Atrazine Based on Bifunctional Graphene Signal Amplification and a Controllable Sulfhydryl-Assembled BiOBr/Ag NP Microinterface

Immobilization-free sensors (IFSs), with no requirement of fixing the recognition element to the electrode surface, have received increasing attention due to their unique advantages of reusable electrodes, not being limited by the load of the recognition element, and not being easily changed to the structure of the probe. In the present work, an effective visible light-driven immobilization-free photoelectric aptasensor for ultrasensitive detection of atrazine (ATZ) was proposed based on a reusable BiOBr/Ag NP substrate electrode with ultrafast charge transfer. Controllable thiols were used as conditioning agents for the photoelectric signal. The ingeniously designed bifunctional graphene can act as not only a molecular “bridge” for the ATZ aptamer through a strong π–π stacking effect, obtaining a graphene–aptamer complex, serving as a homogeneous recognition element, but also a switch for signal modulation for quantitative detection of target substances. Benefiting from the synergistic effect of the above-mentioned factors, the proposed sensor is capable of ultrasensitive and highly selective detection of ATZ in real water samples with a low detection limit of 1.2 pM and a wide linear range from 5.0 pM to 10.0 nM. Furthermore, it shows high stability, good selectivity, and strong anti-interference ability. Thus, this work has provided a fresh perspective for designing advanced immobilization-free photoelectric sensors and convenient detection of environmental pollutants

Additional file 1: of Clinical study of children with Takayasu arteritis: a retrospective study from a single center in China

Brief comparison of PVAS and ITAS-2010. (DOCX 16 kb

Species Distribution of Clinical <i>Acinetobacter</i> Isolates Revealed by Different Identification Techniques

<div><p>A total of 2582 non-duplicate clinical <i>Acinetobacter</i> spp. isolates were collected to evaluate the performance of four identification methods because it is important to identify <i>Acinetobacter</i> spp. accurately and survey the species distribution to determine the appropriate antimicrobial treatment. Phenotyping (VITEK 2 and VITEK MS) and genotyping (16S rRNA and <i>rpoB</i> gene sequencing) methods were applied for species identification, and antimicrobial susceptibility test of imipenem and meropenem was performed with a disk diffusion assay. Generally, the phenotypic identification results were quite different from the genotyping results, and their discrimination ability was unsatisfactory, whereas 16S rRNA and <i>rpoB</i> gene sequencing showed consistent typing results, with different resolution. Additionally, <i>A. pittii</i>, <i>A. calcoaceticus</i> and <i>A. nosocomialis</i>, which were phylogenetically close to <i>A. baumannii</i>, accounted for 85.5% of the non-<i>A. baumannii</i> isolates. One group, which could not be clustered with any reference strains, consisted of 11 isolates and constituted a novel <i>Acinetobacter</i> species that was entitled <i>genomic species 33YU</i>. None of the non-<i>A. baumannii</i> isolates harbored a <i>bla</i>_OXA-51-like gene, and this gene was disrupted by IS<i>Aba19</i> in only one isolate; it continues to be appropriate as a genetic marker for <i>A. baumannii</i> identification. The resistance rate of <i>non-A. baumannii</i> isolates to imipenem and/or meropenem was only 2.6%, which was significantly lower than that of <i>A. baumannii</i>. Overall, <i>rpoB</i> gene sequencing was the most accurate identification method for <i>Acinetobacter</i> species. Except for <i>A. baumannii</i>, the most frequently isolated species from the nosocomial setting were <i>A. pittii</i>, <i>A. calcoaceticus</i> and <i>A. nosocomialis</i>.</p></div

The difference identification results of 409 <i>Acinetobacter</i> isolates by three different methods.

<p>Note: * indicates mis-identification.</p

The <i>rpoB</i> gene similarity between <i>A. baumannii</i> ATCC 17978 and reference strains of different species.

<p>Note: The column A and C indicated the complete <i>rpoB</i> gene sequences. The column B and D indicated the trimmed partial <i>rpoB</i> gene sequences where our designed primers located.</p