title: DNA uptake sequences inNeisseria gonorrhoeaeas intrinsic transcriptional terminators and markers of horizontal gene transfer.
abstract: DNA uptake sequences are widespread throughout theNeisseria gonorrhoeaegenome. These short, conserved sequences facilitate the exchange of endogenous DNA between members of the genusNeisseria. 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 inrho-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 inN. gonorrhoeaeboth 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.
authors.affiliation: 1​School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.|2​Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.
authors.forename: Russell
authors.initials: R
authors.lastname: Spencer-Smith
authors.affiliation: 1​School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Roberts
authors.affiliation: 1​School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.
authors.forename: Neesha
authors.initials: N
authors.lastname: Gurung
authors.affiliation: 1​School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.
authors.forename: Lori A S
authors.initials: LAS
authors.lastname: Snyder
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D009344:Neisseria gonorrhoeae / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D057345:Sequence Inversion / Q000235:genetics; D013728:Terminator Regions, Genetic / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D004269:DNA, Bacterial
keywords: DUS; Gonococcal; HGT; rho-independent transcriptional termination