... understanding life in molecular detail

Dr Kenneth McDowall

Microbial systems; gene regulation; RNA processing and degradation; molecular biology

Our research themes focus on systems that control gene expression and utilise approaches ranging from structural biology through molecular genetics to transcriptomics. For example, we are actively investigating the role of RNase E in controlling the degradation and processing of RNA in Escherichia coli; characterising transcription factors that control the supply of precursor for antibiotics produced by the streptomyces, using Streptomyces coelicolor as a model; and developing approaches to catalogue the primary and secondary transcriptomics of bacteria, including Propionibacterium acnes. The latter is being done to link what actually happens in the cell with structure-function studies being done in the test-tube.

Current major projects include:
  • The initiation of mRNA degradation via direct entry
  • Mechanisms controlling the production of natural products
  • Whole-cell analyses of life-cycles of functional RNAs in bacteria
  • Specialised ribosomes and the translation of leaderess mRNA

Structural and functional analysis of RNA degradation and processing

Escherichia coli is a fantastic model organism for studying key processes in molecular detail as well as developing systems-level understanding. We are principally interested in the degradation and maturation of RNA, both of which are essential for all forms of life. The former ensures for example that the translational machinery follows programming at the level of transcription, while the latter produces an array of RNAs that would otherwise be non-functional. We focus on determining the molecular basis of key events in both these process. Much of our work in this area centres on RNase E, an evolutionarily endoribonuclease that is essential in E. coli and other enteric bacteria. This enzyme is as central to RNA processing and degradation as the ribosome is to translation and RNA polymerases to transcription.

Our constructs and substrates were instrumental in solving the X-ray crystal structure of E. coli RNase E, which has provided an invaluable platform for structure-function studies by us and others. Recently, we have adopted RNA-sequencing to compare with nucleotide resolution the sites at which RNase E cleaves in living cells and the test-tube. This is approach is revealing the code that determines the specificity of cleavage by RNase E. Although our work in this area is driven largely by scientific curiosity it has application. For example, we now have sufficient knowledge to begin producing ‘biobricks’ that could be used by synthetic biologists to control the degradation of polycistronic mRNAs and direct the processing of synthetic RNAs. We have also selected small molecules and aptamers that should maximise the expression of heterologous genes in E. coli and other bacteria where RNase E initiates the bulk of RNA turnover. Collaborators in this area include Ben Luisi (Cambridge), Anastasia Callaghan (Portsmouth) and Jane Grasby (Sheffield). Work in this area is funded by the BBSRC.

Stages in the life-cycle of RNA: Exploiting RNA-seq to characterise key steps

Determining the sequence of the genomes of non-model bacteria provides considerable insight into their capabilities and evolution. However, it currently provides little in the way of reliable insight into the gene regulation that enables some organisms to have a major impact on human health and wellbeing. To begin to address this situation, we are undertaking genome–wide analyses of gene regulation using a combination of improved differential and global RNA-sequencing approaches. For example, this has approach has been applied to Propionibacterium acnes, which is renown through its associated with acne vulgaris, the most common of all human skin diseases, as well as life-threatening diseases, such as meningitis and endocarditis, and chronic back pain following physical injury.

We have produced nucleotide-resolution transcription maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for ‘pervasive’ transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events that include unusual tRNA processing. Continued expansion of our maps to include different growth conditions and genetic backgrounds will provide the platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease. Our approach is transferable to any bacterial species. The P. acnes work was funded by the Leeds Skin Foundation.  

Detailed research programme                  Close ▲

Associate Professor in Molecular Microbiology (Leeds) 2005-p
BSc (Edinburgh) PhD (Glasgow)

Postdoctoral Fellow in Genetics (Stanford) 1991-1996
Royal Society University Research Fellow (Leeds) 1997-2004

Garstang 8.52d
School of Molecular and Cellular Biology
0113 343 3109

Selected Publications

  1. Watson MR, Lin YF, Hollwey E, Dodds RE, Meyer P, McDowall KJ. (2016) An Improved Binary Vector and Escherichia coli strain for Agrobacterium tumefaciens-Mediated Plant Transformation. G3 (Bethesda). 2016 May 18. pii: g3.116.029405. doi: 10.1534/g3.116.029405. [Epub ahead of print]

  2. Li X, Yu T, He Q, McDowall KJ, et al. (2015) Binding of a biosynthetic intermediate to AtrA modulates the production of lidamycin by Streptomyces globisporus. Mol Microbiol. 96: 1257-71. doi: 10.1111/mmi.13004.

  3. Romero DA, Hasan AH, Lin YF, Kime L, Ruiz-Larrabeiti O, Urem M, Bucca G, Mamanova L, Laing EE, van Wezel GP, Smith CP, Kaberdin VR, McDowall KJ. (2014) A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.  Mol Microbiol. 94: 963-987. doi: 10.1111/mmi.12810.

  4. Clarke JE, Kime L, Romero A D, McDowall KJ. (2014) Breakthrough Article - Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res. 42: 11733-51. doi: 10.1093/nar/gku808.