In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes.

Emilio Siena,Romina D'Aurizio,Giulia Torricelli,Silvia Guidotti,Duccio Medini,David Riley,E Richard Moxon,Hervé Tettelin

doi:10.1186/s12864-016-3185-1

Abstract

BackgroundThe Neisseria meningitidis (Nm) chromosome shows a high abundance of simple sequence DNA repeats (SSRs) that undergo stochastic, reversible mutations at high frequency. This mechanism is reflected in an extensive phenotypic diversity that facilitates Nm adaptation to dynamic environmental changes. To date, phase-variable phenotypes mediated by SSRs variation have been experimentally confirmed for 26 Nm genes.ResultsHere we present a population-scale comparative genomic analysis that identified 277 genes and classified them into 52 strong, 60 moderate and 165 weak candidates for phase variation. Deep-coverage DNA sequencing of single colonies grown overnight under non-selective conditions confirmed the presence of high-frequency, stochastic variation in 115 of them, providing circumstantial evidence for their phase variability.We confirmed previous observations of a predominance of variable SSRs within genes for components located on the cell surface or DNA metabolism. However, in addition we identified an unexpectedly broad spectrum of other metabolic functions, and most of the variable SSRs were predicted to induce phenotypic changes by modulating gene expression at a transcriptional level or by producing different protein isoforms rather than mediating on/off translational switching through frameshifts.Investigation of the evolutionary history of SSR contingency loci revealed that these loci were inherited from a Nm ancestor, evolved independently within Nm, or were acquired by Nm through lateral DNA exchange.ConclusionsOverall, our results have identified a broader and qualitatively different phenotypic diversification of SSRs-mediated stochastic variation than previously documented, including its impact on central Nm metabolism.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3185-1) contains supplementary material, which is available to authorized users.

Highlights

The Neisseria meningitidis (Nm) chromosome shows a high abundance of simple sequence DNA repeats (SSRs) that undergo stochastic, reversible mutations at high frequency
Two hundred seventy-seven meningococcal genes are associated with simple sequence repeats that show interstrain length polymorphisms An average of 4243 SSRs were identified in each genome, the majority of which (95 %) were represented by homopolymeric tracts (Additional file 1)
The number of SSRs was similar across genomes and their abundance was found to be significantly higher than random expectation (p = 6.8e-8; Additional file 2: Figure S1)

Summary

Introduction

The Neisseria meningitidis (Nm) chromosome shows a high abundance of simple sequence DNA repeats (SSRs) that undergo stochastic, reversible mutations at high frequency. This mechanism is reflected in an extensive phenotypic diversity that facilitates Nm adaptation to dynamic environmental changes. In order to maximize its fitness in the diverse and changing environments offered by the host-pathogen interplay, Nm has evolved multiple and complementary adaptive strategies [7, 8] One such mechanism is represented by Simple Sequence Repeats (SSRs), contiguous iterations of short DNA motifs, generally assumed to range from 1 to 10 nucleotides in length [9]. A variable number SSR (VNSSR) located within a coding sequence can change

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