Interdisciplinary bacteria and phages

A report of the meeting 'Molecular Genetics of Bacteria and Phages', Cold Spring Harbor, USA, 20-24 August 2008

Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A streptococcus population

Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as “pilin types.” Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies. IMPORTANCE Precision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends

DNA -Protein Interactions in the CTnDOT Excisive Intasome

155 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006.The excision mechanism of CTnDOT is more complicated than any system studied to date. Excision requires multiple accessory proteins. Exc is one protein required for excision, however, its function is unknown. In an attempt to determine a role for Exc, the native wild type Exc protein was purified. These studies indicated that Exc might interact with IntDOT during excision, as determined by electrophoretic mobility shift assays. Further studies of Exc are warranted to answer the many questions that still remain about its function.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Pasteurized Akkermansia Muciniphila Reduces Periodontal and Systemic Inflammation Induced by Porphyromonas Gingivalis in Lean and Obese Mice

AIM: The aim of this study was to evaluate the effect of the administration of pasteurized Akkermansia muciniphila and Amuc_1100 on periodontal destruction in lean and obese mice and to determine the impact of the mode of administration. MATERIALS AND METHODS: Porphyromonas gingivalis-associated experimental periodontitis was induced in lean and obese mice. After 3 weeks, live, pasteurized A. muciniphila or Amuc_1100 was administered by oral or gastric gavage for three additional weeks. Moreover, an evaluation of the interaction between A. muciniphila and P. gingivalis was performed by RNA-sequencing, and cytokines secretion was measured in exposed macrophages. RESULTS: Oral administration of live, pasteurized A. muciniphila or Amuc_1100 significantly decreased P. gingivalis-induced periodontal destruction and inflammatory infiltrate in lean and obese mice and contributed to the reduction of the plasma level of TNF-α and to the increase of IL-10. The co-culture of A. muciniphila and P. gingivalis induced an increased expression of genes linked to the synthesis of monobactam-related antibiotics in A. muciniphila, while a decrease of the gingipains and type IX secretion system was observed in P. gingivalis. In P. gingivalis-infected macrophages, pasteurized A. muciniphila decreased TNF-α and increased IL-10 levels. CONCLUSIONS: Pasteurized A. muciniphila can counteract P. gingivalis-associated periodontal destruction

IntDOT Interactions with Core- and Arm-Type Sites of the Conjugative Transposon CTnDOT

CTnDOT is a Bacteroides conjugative transposon (CTn) that has facilitated the spread of antibiotic resistances among bacteria in the human gut in recent years. Although the integrase encoded by CTnDOT (IntDOT) carries the C-terminal set of conserved amino acids that is characteristic of the tyrosine family of recombinases, the reaction it catalyzes involves a novel step that creates a short region of heterology at the joined ends of the element during recombination. Also, in contrast to tyrosine recombinases, IntDOT catalyzes a reaction that is not site specific. To determine what types of contacts IntDOT makes with the DNA during excision and integration, we first developed an agarose gel-based assay for CTnDOT recombination, which facilitated the purification of the native IntDOT protein. The partially purified IntDOT was then used for DNase I footprinting analysis of the integration site attDOT and the excision sites attL and attR. Our results indicate that CTnDOT has five or six arm sites that are likely to be involved in forming higher-order nucleoprotein complexes necessary for synapsis. In addition, there are four core sites that flank the sites of strand exchange during recombination. Thus, despite the fact that the reaction catalyzed by IntDOT appears to be different from that typically catalyzed by tyrosine recombinases, the protein-DNA interactions required for higher-order structures and recombination appear to be similar

Mapping of internal monophosphate 5 ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

International audienceThe recent findings that the narrow-specificity en-doribonuclease RNase III and the 5 exonuclease RNase J1 are not essential in the Gram-positive model organism, Bacillus subtilis, facilitated a global analysis of internal 5 ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5 monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions appeared to be direct targets of RNase III. These target sites were, in most cases, not associated with a known antisense RNA. The PARE analysis also revealed an accumulation of 3-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. A significant result from the PARE analysis was the discovery of an endonuclease cleavage just 2 nts downstream of the 16S rRNA 3 end. This latter observation begins to answer , at least for B. subtilis, a long-standing question on the exonucleolytic versus endonucleolytic nature of 16S rRNA maturation

Akkermansia Muciniphila and Its Pili-Like Protein Amuc_1100 Modulate Macrophage Polarization in Experimental Periodontitis

Periodontitis is a chronic inflammatory disease triggered by dysbiosis of the oral microbiome. Porphyromonas gingivalis is strongly implicated in periodontal inflammation, gingival tissue destruction, and alveolar bone loss through sustained exacerbation of the host response. Recently, the use of other bacterial species, such as Akkermansia muciniphila, has been suggested to counteract inflammation elicited by P. gingivalis In this study, the effects of A. muciniphila and its pili-like protein Amuc_1100 on macrophage polarization during P. gingivalis infection were evaluated in a murine model of experimental periodontitis. Mice were gavaged with P. gingivalis alone or in combination with A. muciniphila or Amuc_1100 for 6 weeks. Morphometric analysis demonstrated that the addition of A. muciniphila or Amuc_1100 significantly reduced P. gingivalis-induced alveolar bone loss. This decreased bone loss was associated with a proresolutive phenotype (M2) of macrophages isolated from submandibular lymph nodes as observed by flow cytometry. Furthermore, the expression of interleukin 10 (IL-10) at the RNA and protein levels was significantly increased in the gingival tissues of the mice and in macrophages exposed to A. muciniphila or Amuc_1100, confirming their anti-inflammatory properties. This study demonstrates the putative therapeutic interest of the administration of A. muciniphila or Amuc_1100 in the management of periodontitis through their anti-inflammatory properties