Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans

Abstract

Recently, a comprehensive screening workflow for the filamentous bacterium Streptomyces lividans, a highly performant source for pharmaceutically active agents was introduced. This framework used parallelized cultivation in microtiter plates to efficiently accelerate early upstream process development. Focusing on growth performance, cultivation was successfully scaled-up to 1 L stirred tank reactors. However, metabolic adaptation was observed on the transcriptomic level as among others, several genes incorporated in light response were upregulated during bioreactor cultivation. Despite it was assumed that this was attributed to the fact that reactor cultivations were performed in glass vessels exposed to daylight and artificial room light, this setup did not allow distinguishing exclusively between light and other effects. Upon that, the present study directly investigates the influence of light by defined illumination of microtiter plate cultures. Almost identical growth performance was observed for cultures grown in the dark or with illumination. Transcriptomics revealed the upregulation of seven genes of which 6 have previously been described to be relevant for carotenoid synthesis and its regulation. These pigments are effective quenchers of reactive oxygen species. The seventh transcript coded for a photo-lyase incorporated in UV-damage repair of DNA further confirming induced light response. However, this was fully compensated by metabolic adaptation on the transcriptomic level and overall process performance was maintained. Consequently, environmental conditions need extremely careful control and evaluation during in-depth omics analysis of bioprocesses. Otherwise metabolic adaptation induced by such issues can easily be misinterpreted, especially during studies addressing cultivation system comparisons. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:287-292, 2018.

Genetic Underpinnings of Carotenogenesis and Light-Induced Transcriptome Remodeling in the Opportunistic Pathogen Mycobacterium kansasii

“…The second locus (hereafter referred to as the photolyase locus) with differentially expressed genes included a three-gene cluster predicted to encode a deoxyribodipyrimidine photolyase (MKAN_RS22245), a tryptophan-rich sensory protein/translocator protein family member (MKAN_RS22250), and an MmpL family transporter (MKAN_RS22255) (hereafter referred to as phrB , tspO , and mmpL2 , respectively) ( Figure S2f ). Interestingly, photolyases are critical for repairing light-induced DNA lesions, and light-dependent photolyase upregulation was recently reported in Streptomyces lividans [ 63 ]. TspO proteins are transmembrane, conserved throughout evolution, and involved in a myriad of cell processes through their ability to bind tetrapyrroles such as porphyrins [ 64 , 65 ].…”