Horizontally acquired quorum sensing regulators recruited by the PhoP regulatory network expand host-adaptation repertoire in the phytopathogen Pectobacterium carotovorum

Abstract

In this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study the phytopathosystem comprised of potato tubers and the soft rot pathogen Pectobacterium carotovorum subsp. brasiliense (Pcb1692). By comparing those two networks with that of PecS obtained from the closely related Dickeya dadantii, we found that: (a) 24-31% of the genes regulated at late infection are genus-specific (GS) (based on Pectobacterium and Dickeya genera), and that (b) of these, 28.1-44.4% were predicted with high confidence as horizontal gene transfer (HGT) candidates. Further, genome simulation and statistical analyses corroborated the bias in late infection regulons towards the transcriptional control of candidate GS-HGT genes by PhoP, SlyA, and PecS, highlighting the prominence of network rearrangements in these late infection regulons. The evidence further supports the circumscription of two horizontally acquired quorum sensing regulators (carR and expR1) by the PhoP network. By recruiting carR and expR1, the PhoP network also impacts certain host adaptation- and bacterial competition-related systems, seemingly in a quorum sensing-dependent manner, such as the type VI secretion system, carbapenem biosynthesis, and plant cell walls degrading enzymes (PCWDE) such as cellulases and pectate lyases. Conversely, polygalacturonases and the type III secretion system (T3SS) exhibit a transcriptional pattern that suggests quorum sensing-independent regulation by the PhoP network. This includes a yet uncharacterized novel phage-related gene family within the T3SS gene cluster that has been recently acquired by two Pectobacterium species. The evidence further suggests a PhoP-dependent regulation of carbapenem and PCWDE-encoding genes based on the synthesized products optimum pH. The PhoP network also controls slyA expression in planta, which seems to impact the carbohydrate metabolism regulation, especially at early infection when 69.6% of the SlyA-regulated genes from that category also require PhoP to achieve normal expression levels.\n\nAUTHOR SUMMARYExchanging genetic material through horizontal transfer is a critical mechanism that drives bacteria to efficiently adapt to host defenses. In this report, we demonstrate that a specific plant pathogenic species (from the Pectobacterium genus) successfully integrated a population density-based behaviour system (quorum sensing) acquired through horizontal transfer into a resident stress-response gene regulatory network controlled by the PhoP protein. Evidence found here underscores that subsets of bacterial weaponry critical for colonization, typically known to respond to quorum sensing, are also controlled by PhoP. Some of these traits include different types of enzymes that can efficiently break plant cell walls depending on the environmental acidity level. Thus, we hypothesize that PhoP ability to elicit regulatory responses based on acidity and nutrient availability fluctuations may have strongly impacted the fixation of its regulatory connection with quorum sensing. In addition, another global gene regulator known as SlyA was found under the PhoP regulatory network. The SlyA regulator controls a series of carbohydrate metabolism-related traits, which also seem to be regulated by PhoP. By centralizing quorum sensing and slyA under PhoP scrutiny, Pectobacterium cells added an advantageous layer of control over those two networks that potentially enhances colonization efficiency.