The complete genome sequencing ofPrevotella intermediastrain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novelPrevotella-lineage-specific repeat

Abstract

Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria.

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

“…As the IME is assumed to replicate by rolling circle during the transfer, the IME probably reintegrates in the chromosome of the donor cell after transfer. Recently, the analysis of the integration/excision modules of three putative IMEs, MTn Pi1 , MTn Pi2 and MTn Pi3 from Prevotella intermedia , which can excise from the chromosome, indicated that each of them encodes a tandem of two distantly related tyrosine recombinases instead of a single tyrosine integrase [ 44 ].…”

“…Other IMEs, with low integration specificity, prefer AT-rich regions. These elements include Tn 5520 from B. fragilis (an IME encoding a single tyrosine integrase) [ 50 ], the three IMEs MTn Pi1 , MTn Pi2 and MTn Pi3 from P. intermedia encoding a duo of tyrosine integrases [ 44 ] and the two IMEs MTn Sag1 from S. agalactiae [ 28 ] and tIS Cpe8 from C. perfringens encoding a DDE transposase [ 29 ]. The last example is the IME Tn 4451 from C. perfringens and its relatives whose serine integrases also lead to a low specificity of integration of these elements [ 33 ].…”

Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia

“…It is notable that Naito et al previously reported a much larger 34.2 kb prophage-related insertion within the cas2 gene of a homologous CRISPR system in the related clinical isolate P . intermedia OMA14, resulting in the apparent inactivation of that CRISPR system [ 75 ]. The transposon insertion within the ATCC25611F array is likely to interfere with the processing of the pre-crRNA transcript, potentially inactivating protospacers 31 to 39 in ATCC25611F, but determination of the precise impact of this transposon insertion on the function of the entire CRISPR-I system will be important to address in future studies.…”

Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease

“…This may be one explanation why the genomes of P. intermedia and P. nigrescens were not conserved and showed high genomic diversity. The environment under periodontal disease conditions is more diverse than that under healthy conditions (Naito et al, 2016 ). However, in this study, the horizontal transfer events seemed more likely to occur under healthy conditions.…”