Differential RNA sequencing implicates sulfide as the master regulator of S0 metabolism in Chlorobaculum tepidum and other green sulfur bacteria

Jacob M. Hilzinger, Vidhyavathi Raman, Kevin E. Shuman, Brian J. Eddie, Thomas E. Hanson

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

The green sulfur bacteria (Chlorobiaceae) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S0, and thiosulfate) as electron donors for photoautotrophic growth. Chlorobaculum tepidum, the model system for the Chlorobiaceae, both produces and consumes extracellular S0 globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to Cba. tepidum growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e., the specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA sequencing (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S0, and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor-dependent transcriptional regulation. These motifs were conserved across homologous Chlorobiaceae promoters. Two lines of evidence suggest that sulfide-mediated repression is the dominant regulatory mode in Cba. tepidum. First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the Cba. tepidum 1277 (CT1277) gene, encoding a putative regulatory protein, leads to constitutive overexpression of the sulfide: quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in Cba. tepidum and the Chlorobiaceae. Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in Cba. tepidum and perhaps other Chlorobiaceae.

Original languageEnglish (US)
Article numbere01966-17
JournalApplied and environmental microbiology
Volume84
Issue number3
DOIs
StatePublished - Feb 1 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 American Society for Microbiology.

Keywords

  • Chlorobaculum tepidum
  • Chlorobiaceae
  • Energy metabolism
  • Sulfur metabolism
  • Transcriptional regulation
  • dRNA-seq

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