Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology

Abstract

Mobile Genetic Elements (MGEs) are mosaics of functional gene modules of diverse evolutionary origin and are generally divergent from the hosts´ genetic background. Existing biases in base composition and codon usage of these elements` genes impose transcription and translation limitations that may affect the physical and regulatory integration of MGEs in new hosts. Stable appropriation of the foreign DNA depends on a number of host factors among which are the Nucleoid-Associated Proteins (NAPs). These small, basic, highly abundant proteins bind and bend DNA, altering its topology and folding, thereby affecting all known essential DNA metabolism related processes. Both chromosomally- (endogenous) and MGE- (foreign) encoded NAPs have been shown to exist in bacteria. While the role of host-encoded NAPs in xenogeneic silencing of both episomal (plasmids) and integrative MGEs (pathogenicity islands and prophages) is well acknowledged, less is known about the role of MGE-encoded NAPs in the foreign elements biology or their influence on the host's chromosome expression dynamics. Here we review existing literature on the topic, present examples on the positive and negative effects that endogenous and foreign NAPs exert on global transcriptional gene expression, MGE integrative and excisive recombination dynamics, persistence and transfer to suitable hosts and discuss the nature and relevance of synergistic and antagonizing higher order interactions between diverse types of NAPs.

Keywords: Bacterial nucleoid; HGT; MGE; NAP; Regulatory hierarchies; Xenogeneic silencing.

Fig. 1

Roles of NAPs in bacteria. NAPs alter the topology of the DNA with structural effects on folding of the chromosome and nucleoid organization. Both aspects have significant effects in many DNA transactions occurring within cells. NAPs interact with other NAPs and transcriptional regulators, as well as other cellular effector proteins (e.g. the RNA polymerase) exerting direct and indirect effects at both short and long-range distances determining the higher order structuring of the chromosome and the affecting cell physiology at many different levels.

Fig. 2

Network of acknowledged interactions between endogenous and foreign NAPs occurring in bacteria. Endogenous NAPs are encoded chromosomally (NAP_Chr), whereas foreign NAPs (NAP_Epi; NAP_Int) are encoded in episomal (double line circle) or integrated (beige box) mobile genetic elements. The genes are represented as filled arrows and their cognate protein products as circles. The gene-protein pairs are colored according to their origin: green for endogenous; orange for episomal and blue for integrated. Protein-DNA interactions are represented by connecting lines in the main scheme, and protein-protein interactions are represented as connected circles in the upper corner of the green and blue boxes. The nature of the interaction is represented by positve (synergistic) or negative (antagonistic) symbols colored green or red, respectively. NAP proteins main targets, the types of interactions they establish and the functional outputs of those interactions are indicated in the accopmpaigning text boxes. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)