Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome

A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suis

Streptococcus suis, an important zoonotic pathogen, is known to have an open pan-genome and to develop a competent state. In S. suis, limited genetic lineages are suggested to be associated with zoonosis. However, little is known about the evolution of diversified lineages and their respective phenotypic or ecological characteristics. In this study, we performed comparative genome analyses of S. suis, with a focus on the competence genes, mobile genetic elements, and genetic elements related to various defense systems against exogenous DNAs (defense elements) that are associated with gene gain/loss/exchange mediated by horizontal DNA movements and their restrictions. Our genome analyses revealed a conserved competence-inducing peptide type (pherotype) of the competence system and large-scale genome rearrangements in certain clusters based on the genome phylogeny of 58 S. suis strains. Moreover, the profiles of the defense elements were similar or identical to each other among the strains belonging to the same genomic clusters. Our findings suggest that these genetic characteristics of each cluster might exert specific effects on the phenotypic or ecological differences between the clusters. We also found certain loci that shift several types of defense elements in S. suis. Of note, one of these loci is a previously unrecognized variable region in bacteria, at which strains of distinct clusters code for different and various defense elements. This locus might represent a novel defense mechanism that has evolved through an arms race between bacteria and invading DNAs, mediated by mobile genetic elements and genetic competence.

Distribution of Type I Restriction-Modification Systems in Streptococcus suis: An Outlook

Streptococcus suis is a porcine commensal and pathogen with zoonotic potential. We recently identified a novel Type I restriction-modification (R-M) system in a zoonotic S. suis clone which has emerged in the Netherlands. Here, we describe the DNA inversions in the specificity subunit of this system in S. suis serotype 2, clonal complex 20 and explain the absence of domain movement by the absence of repeats. In addition, we identified a core Type I R-M system present in 95% of the isolates and found an association of the distribution of Type I R-M systems in the S. suis genome with population structure. We speculate on the potential role of Type I R-M systems in S. suis given the recently described associations of Type I R-M systems with virulence and propose future research directions.

Role of SraP in adherence of Staphylococcus aureus to the bovine mammary epithelia

SraP, a platelet-binding surface protein of Staphylococcus aureus, is involved in the pathogenesis of infective endocarditis. In this study, we investigated the importance of SraP in the pathogenesis of bovine mastitis. By means of PCR, sraP was detected in all the isolates tested from bovine bulk milk and humans. However, SraP was not expressed on the cell surface in half of the bovine isolates. Moreover, disruption of sraP did not affect the ability of S. aureus to adhere to cultured bovine mammary epithelial cells. These results suggest that SraP does not seem to be an important factor for S. aureus to adhere to the bovine mammary epithelia.

Detecting key structural features within highly recombined genes

Many microorganisms exhibit high levels of intragenic recombination following horizontal gene transfer events. Furthermore, many microbial genes are subject to strong diversifying selection as part of the pathogenic process. A multiple sequence alignment is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, such as phylogenetics; however, an accurate alignment is not always possible to attain. In this study, a new analytic approach was developed in order to better quantify the genetic organization of highly diversified genes whose alleles do not align. This BLAST-based method, denoted BLAST Miner, employs an iterative process that places short segments of highly similar sequence into discrete datasets that are designated “modules.” The relative positions of modules along the length of the genes, and their frequency of occurrence, are used to identify sequence duplications, insertions, and rearrangements. Partial alleles of sof from Streptococcus pyogenes, encoding a surface protein under host immune selection, were analyzed for module content. High-frequency Modules 6 and 13 were identified and examined in depth. Nucleotide sequences corresponding to both modules contain numerous duplications and inverted repeats, whereby many codons form palindromic pairs. Combined with evidence for a strong codon usage bias, data suggest that Module 6 and 13 sequences are under selection to preserve their nucleic acid secondary structure. The concentration of overlapping tandem and inverted repeats within a small region of DNA is highly suggestive of a mechanistic role for Module 6 and 13 sequences in promoting aberrant recombination. Analysis of pbp2X alleles from Streptococcus pneumoniae, encoding cell wall enzymes that confer antibiotic resistance, supports the broad applicability of this tool in deciphering the genetic organization of highly recombined genes. BLAST Miner shares with phylogenetics the important predictive quality that leads to the generation of testable hypotheses based on sequence data.

Microbial genes that accumulate large amounts of nucleotide sequence diversity through lateral exchanges with other microorganisms are often central to understanding key interactions between the microbe and an ever-changing host or environment. Proper sequence alignment of multiple gene alleles is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, and allow scientists to develop hypotheses on biological processes. However, for some of the most interesting genes, a good quality alignment can be impossible to attain. We introduce a new software program, BLAST Miner, for analyzing genes that cannot be well-aligned. It relies on identifying small gene segments having high levels of sequence homology, irrespective of their relative positions within the different genes. Genes encoding a drug-resistance determinant and a target of host immunity are used as examples to demonstrate the application of BLAST Miner, and a potentially novel mechanism for generating genetic change is uncovered. This new bioinformatics tool provides an avenue for studying genes that are intractable by most other analytic approaches.