Abstract
The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci.
Highlights
With bacterial genome sequencing becoming accessible, the demand for quality genome annotation has increased drastically in recent years
Since we aimed at both promoter and TFBS identification, we looked for the available tools implementing both approaches
There were minor differences between the two search algorithms in detecting ‘‘weak’’ binding sites, both nhmmer and MAST are provided as search engines within SigmoID
Summary
With bacterial genome sequencing becoming accessible, the demand for quality genome annotation has increased drastically in recent years. Manual genome annotation requires a lot of effort and is time-consuming. It is usually beyond the scope of most sequencing projects. As a result, automated approaches are commonly used by researchers while submitting genome sequences to GenBank. The genome annotation pipelines such as Prokka, BASYS, RAST and NCBI Prokaryotic Genome Annotation Pipeline (Van Domselaar et al, 2005; Aziz et al, 2008; Tatusova et al, 2013; How to cite this article Nikolaichik and Damienikan (2016), SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.
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