High quality genome annotation and expression visualisation of a mupirocin-producing bacterium.

Autor: Haines AS; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom., Kendrew SG; Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom., Crowhurst N; Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom., Stephens ER; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom., Connolly J; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom., Hothersall J; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom., Miller CE; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom., Collis AJ; Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom., Huckle BD; Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom., Thomas CM; School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2022 May 05; Vol. 17 (5), pp. e0268072. Date of Electronic Publication: 2022 May 05 (Print Publication: 2022).
DOI: 10.1371/journal.pone.0268072
Abstrakt: Pseudomonas strain NCIMB10586, in the P. fluorescens subgroup, produces the polyketide antibiotic mupirocin, and has potential as a host for industrial production of a range of valuable products. To underpin further studies on its genetics and physiology, we have used a combination of standard and atypical approaches to achieve a quality of the genome sequence and annotation, above current standards for automated pathways. Assembly of Illumina reads to a PacBio genome sequence created a retrospectively hybrid assembly, identifying and fixing 415 sequencing errors which would otherwise affect almost 5% of annotated coding regions. Our annotation pipeline combined automation based on related well-annotated genomes and stringent, partially manual, tests for functional features. The strain was close to P. synxantha and P. libaniensis and was found to be highly similar to a strain being developed as a weed-pest control agent in Canada. Since mupirocin is a secondary metabolite whose production is switched on late in exponential phase, we carried out RNAseq analysis over an 18 h growth period and have developed a method to normalise RNAseq samples as a group, rather than pair-wise. To review such data we have developed an easily interpreted way to present the expression profiles across a region, or the whole genome at a glance. At the 2-hour granularity of our time-course, the mupirocin cluster increases in expression as an essentially uniform bloc, although the mupirocin resistance gene stands out as being expressed at all the time points.
Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Authors specified as employees of GSK have competing interests because this work was part of a project to develop technology which would have value to GSK; all authors associated with the university of Birmingham have competing interests because the university of Birmingham would benefit financially if the joint project with GSK led to a process that was deemed to be profitable to GSK. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
Databáze: MEDLINE
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