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Huang, Xiaoluo (2015): Classification and functional characterization of extracytoplasmic function (ECF) σ factors from planctomycetes and actinobacteria. Dissertation, LMU München: Fakultät für Biologie
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Abstract

Bacteria necessitate multiple signal transduction systems to sense the ever-changing environments and mediate the cellular response accordingly. The major bacterial signal transduction systems are one-component system (1CS), two-component system (2CS) and extracytoplasmic function (ECF) σ factor. Compared to 1CSs and 2CSs, ECF σ factors have only been identified much later and therefore the knowledge about their molecular mechanisms and physiological roles is less profound. This thesis mainly focuses on the study of ECF σ factors from the bacterial phyla, Planctomycetes and Actinobacteria.

Abstract

In the first two parts of this study, ECF σ factors from eight planctomycetal genomes and 119 actinobacterial genomes were classified and analyzed in depth. This led to the identification of eight novel ECF groups consisting of 202 protein members from Planctomycetes and 18 novel ECF groups consisting of 427 protein members from Actinobacteria, respectively. Many of these novel ECF groups were found to show unusual properties. For example, five ECF groups (ECF01-Gob, ECF48, ECF52, ECF53 and ECF56) contained extended C-terminal domains. Four ECF groups (STK1-STK4) were genomically adjacent to serine/threonine kinases. Further analyses of these properties suggested novel ECF-dependent signal transduction mechanisms.

Abstract

In the third part of this study, we identified the genes controlled by σE, a conserved ECF σ factor in the actinobacterial genus, Streptomyces. Since σE has been characterized to be important for cell envelope stress response in S. coelicolor, we firstly defined the σE regulon in this organism using a combination of chromatin immunoprecipitation-sequencing (ChIP-seq), DNA microarray and bioinformatic analyses. Thus, 91 target genes were assigned into the σE regulon in S. coelicolor. By in depth analysis of these genes, it was found that approximately half of them encode proteins showing cell envelope related functions. Amongst the remaining target genes, proteins involved in cell regulation and cell metabolism could be identified. Subsequently, 17 of these 91 targets were validated by S1 mapping or in vitro transcription. Using this S1 mapping data set, we identified promoters for all of these 17 targets and established a σE binding consensus, consisting of a conserved “AAC” at -35 region and a “TC” at -10 region. Next, we predicted all the σE binding sites across 19 Streptomyces genomes and established a putative σE regulon for every Streptomyces genome. Finally, we selected those targets that were conserved in at least 9 Streptomyces genomes and built a core σE regulon.