DNA uptake sequences in Neisseria gonorrhoeae as intrinsic transcriptional terminators and markers of horizontal gene transfer

Abstract

DNA uptake sequences are widespread throughout the Neisseria gonorrhoeae genome. These short, conserved sequences facilitate the exchange of endogenous DNA between members of the genus Neisseria. Often the DNA uptake sequences are present as inverted repeats that are able to form hairpin structures. It has been suggested previously that DNA uptake sequence inverted repeats present 3 ¢ of genes play a role in rho-independent termination and attenuation. However, there is conflicting experimental evidence to support this role. The aim of this study was to determine the role of DNA uptake sequences in transcriptional termination. Both bioinformatics predictions, conducted using TransTermHP, and experimental evidence, from RNA-seq data, were used to determine which inverted repeat DNA uptake sequences are transcriptional terminators and in which direction. Here we show that DNA uptake sequences in the inverted repeat configuration occur in N. gonorrhoeae both where the DNA uptake sequence precedes the inverted version of the sequence and also, albeit less frequently, in reverse order. Due to their symmetrical configuration, inverted repeat DNA uptake sequences can potentially act as bi-directional terminators, therefore affecting transcription on both DNA strands. This work also provides evidence that gaps in DNA uptake sequence density in the gonococcal genome coincide with areas of DNA that are foreign in origin, such as prophage. This study differentiates for the first time, to our knowledge, between DNA uptake sequences that form intrinsic transcriptional terminators and those that do not, providing characteristic features within the flanking inverted repeat that can be identified.Keywords: Gonococcal; DUS; rho-independent transcriptional termination; HGT.Abbreviations: DUS, DNA uptake sequence; IR-DUS, inverted repeat DNA uptake sequence; eDUS, extended 12 bp DNA uptake sequence; vDUS, variant DNA uptake sequence found in commensal non-pathogenic Neisseria spp.; veDUS, extended 12 bp variant DNA uptake sequence; IR-eDUS, inverted repeat extended DNA uptake sequence; IR-vDUS, inverted repeat variant DNA uptake sequence; CREE, Correia repeat enclosed elements; GGI, Gonococcal genetic island.

Molecular Epidemiology of Photobacterium damselae subsp. damselae Outbreaks in Marine Rainbow Trout Farms Reveals Extensive Horizontal Gene Transfer and High Genetic Diversity

“…and Neisseria spp.) contain DNA uptake signal sequences within the base-paired stems of transcriptional terminators ( Smith et al, 1999 ; Ambur et al, 2007 ; Spencer-Smith et al, 2016 ). These repeated sequences might therefore have played a role in the recombination of horizontally acquired DNA in some P. damselae subsp.…”

Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire

“…In the pathogenic Neisseria spp., the spread and increased levels of antibiotic resistance, as well as the evolution of pathogenesis, are as a direct result of their ability to take up and transform DNA from their environment [23,74,78,79].…”

“…This analysis demonstrates additional reservoirs for antigenic variant alleles of NadA and Fhbp not represented in the vaccine that may allow N. meningitidis to escape vaccine-mediated control via HGT from commensal Neisseria spp. In concert with the potential role for commensal capsule loci to provide genetic material for capsule switching [6,101], the scope for evolution of this pathogen, and also for pharyngeal N. gonorrhoeae, through their natural competence preference for the neisserial DNA uptake sequence [78,81,82] likely contributes to genome plasticity [109].…”

Secretion of Chromosomal DNA by the Neisseria gonorrhoeae Type IV Secretion System

“…The GC-content of the GGI, at 44%, is significantly lower than the GC-content of the gonococcal chromosome with 51% (Hamilton et al 2005). Its DNA sequence varies in dinucleotide frequencies and contains a deviant number of DNA-uptake sequences (DUS) in comparison to the rest of the chromosome (Hamilton et al 2005; Spencer-Smith et al 2016). The DUS is a 10 or 12 bp sequence that is specific to a subset of species in the Neisseriaceae and occurs throughout their genomes (Goodman and Scocca 1988; Ambur et al 2007).…”