Horizontal Gene Transfer in Thermus spp.

Abstract

The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population. The DTA must also contend with the recipient cell's defensive barriers, namely restriction enzymes, a panoply of CRISPR-Cas systems, and the argonaute-like protein TtAgo, which may be bypassed by transjugation, a new class of bidirectional transformation-dependent conjugation. Efficient transjugation depends on the presence of the ICETh1, an integrative and conjugative element which promotes simultaneous, generalized DNA transfer from several points in the genome. Transjugation shows preference for genes located within a megaplasmid replicon, where the main strain-specific adaptive modules are located. Contribution of transformation, vesicle-mediated eDNAs, and transjugation to HGT in this genus is discussed.

Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp.

“…This suggests a major role for the chromosome in coding for conserved core functions, which would act as a major counterselection factor if genes were interrupted by IS transposition. Also, our data are in agreement with the more flexible character of the megaplasmids, which encode adaptive and HGT-prone faculties that are only needed under specific conditions [30]. Our data are consistent with other observations of higher incidence of transposable elements within plasmids [47,48], and also that pTT27 harbors the highest plasticity with low synteny among strains [49].…”

“…In this way, a few cases of active ISs have previously been reported in T. thermophilus , including IS1000B in strain HB8 [33,34] and ISTth7 in strain HB27 [35]. However, more recent genomic data suggest that a much greater frequency of transpositional events than initially though takes place in the genus [30].…”

“…The metabolic capabilities of these strains are very diverse, despite their small genome size, with some strictly aerobic strains and others with anaerobic respiration capacity based on nitrogen oxides or metals, and different abilities to utilize polysaccharides. This assortment of phenotypic traits is frequently encoded by megaplasmids and, thus, may be laterally transferred by different mechanisms, contributing to the fast ecological adaptation of these bacteria to sudden changes in a sort of shared pan-genome [30].…”

Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

“…Thus, although evolving in the same ecological niche, the two bacterial species might have adapted differently with respect to their key functions, as has been described previously (de la Haba et al, 2019 ). Since strain RK1 has large strain-specific genomic attributes that may be phage induced, as has already been documented for many rapidly evolving bacterial genomes (Lopez et al, 2012 ; Blesa et al, 2018 ), we wanted to look for CRISPR elements. While genomes of all three strains except P. composti DSM 22900 harbored CRISPR elements ( Supplementary Table 1 ), only one CRISPR from P .…”

A thermostable DNA primase‐polymerase from a mobile genetic element involved in defence against environmental DNA

“…In an extensive search for a physiological role of Ppol, we found that Ppol acted as a barrier against the DNA acquired by the highly efficient natural competence apparatus of this bacterium (Blesa et al ., 2018), in such a way that mutants lacking Ppol (either insertional or marker free) showed an increased transformability of orders of magnitude, not only with replicative and suicide plasmids (Fig. 5) but also with lineal isogenic DNA (Fig.…”