Noncanonical Cell-to-Cell DNA Transfer in Thermus spp. Is Insensitive to Argonaute-Mediated Interference

Abstract

bHorizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-tocell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals. L ateral gene flow is responsible for the enormous plasticity observed in prokaryotic genomes, which confers on these organisms the ability to adapt rapidly to environmental changes (1-5). Three conserved mechanisms are traditionally associated with lateral gene transfer (LGT) in prokaryotes: phage-mediated transduction, natural transformation, and conjugation. Besides, alternative DNA transfer systems based on nanotubes (6), membrane vesicles, and nanopods in Archaea (7-9), or on the so-called "gene transfer agents" (10), have been described as contributors to genetic exchange among prokaryotes. Among these processes, transformation and conjugation depend only on functions encoded by the bacterial cell. Transformation involves the uptake of naked DNA from the environment and relies entirely on the ability of a competent recipient cell to incorporate DNA. Conjugation, on the other hand, is traditionally seen as the unidirectional transfer of a plasmid DNA molecule from a donor to a recipient cell, where the proteins responsible for DNA transfer are provided exclusively by the donor cell (11).Conjugation differs from transformation not only in the imperative need for a mate for the transfer of DNA but also in the nature of the transferred DNA. While transformation can be envisioned as a mechanism that might have originally evolved in ancestral bacteria, such as Thermus spp., for the acquisition of DNA of any sort and origin as a nutrient, conjugation is more frequently associated with a gain of new capabilities from related species and commonly involves plasmids or megaplasmids that encode all the functions required for conjugation. In fact, transfer of chromosomal genes is apparently less common and in many cases requires the integration of a conjug...

The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation

“…On the other hand efficient transjugation was detected between ΔTTC1879:: kat and ΔpilA :: hyg single mutants (Fig 1, bar n° 2). As two strains defective in competence cannot mate [16,19], this result confirmed that the product of TTC1879 was not involved in natural competence, and provides evidence that TTC1879 is required for DNA donation in transjugation, and not for DNA acquisition. The product of TTC1879 was thus designated the T ransjugation D onor T ranslocase A (TdtA).…”

“…To analyze the role of TTC1879 in DNA donation (pushing step) we introduced the ΔTTC1879:: kat mutation into a ΔpilA4 background, which is unable to serve as a recipient in transjugation assays [16], and mated it with a wild type strain labeled with hygromycin (Hyg) resistance. No transjugants were generated in this mating (Fig 1, bar n° 3), implying that the ΔTTC1879:: kat mutant cannot donate DNA in transjugation.…”

“…This strain can be distinguished from HB27 both by PCR and by differences in the pattern of their membrane proteins, specifically size differences of S-layer proteins (SlpA) [20], which enables inference of the directionality of DNA transfer by parenthood analysis. The NAR1 and HB27 wild type strains transjugate efficiently in both directions [16]. To analyze the role of TdtA, a ΔtdtA :: kat mutant was derived from NAR1 and used in transjugation assays with a Hyg r derivative of the HB27 strain.…”

“…thermophilus relies not only on the competence machinery of recipient cells to take up DNA [16], but also on a transformation-independent process for donor cells to push DNA out DNA. This “push-pull” model is termed “transjugation”, an intermediate process between classical conjugation and transformation.…”

“…In this DNA transfer process, the natural competence machinery of the recipient cell plays an active role that is essential for the transfer, whereas competence is not required at all in the donor. For this reason, we proposed a two-step “push-pull” DNA model [16], where both mates play an active role. In this model, termed “transjugation” (from trans formation-dependent con jugation ), the donor cell actively pumps DNA via a hypothetical DNA translocase that is independent from the transformation machinery.…”