2026/07/27 by Dietrich H. Nies, Jan Grau, Grit Schleuder +1
Biochemistry, Genetics and Molecular Biology · Engineering · Environmental Science · #Bacterial Genetics and Biotechnology #Chromium effects and bioremediation #Gene #Housekeeping gene #Metal Extraction and Bioleaching #Promoter #RNA polymerase #Regulatory sequence #Sigma factor #Transcription (linguistics) #Transcriptional regulation
paper · doi:10.1128/jb.00219-26
openalex publication_date 2026/07/27 · openalex created_date 2026/07/28 · openalex updated_date 2026/08/04
ABSTRACT Cupriavidus metallidurans is able to grow in the presence of transition metal mixtures with high concentrations and varying compositions. This ability is mediated by a multitude of metal transport and repository systems. To reveal the genetic regulation underlying these physiological processes, 12,914 transcriptional start sites (TSSs) in metal-stressed and metal-starved cells were determined, and regulatory tags assigned to each TSS. Subsequently, the sense and antisense transcripts downstream of these TSSs were associated with the respective TSS. In this way, the impact of each TSS on genes via sense and antisense transcripts was derived, and a comprehensive transcriptional landscape of C. metallidurans was created. Depending on the replicon, 42%–65% of the TSSs in C. metallidurans were regulated under conditions of changing metal availability, which resulted in significant reorganization of the transcriptome in the bacterium. Promoter consensus motifs for −10 and −35 sites were identified in a pattern search in the upstream region of the TSSs. The results indicate that 83.6% of the TSSs in C. metallidurans have promoters that are mainly used by the housekeeping sigma factor RpoD. Surprisingly, the majority of these promoters are sba (sliding-blocking-another sigma factor) promoters with a correctly positioned −10 site but a −35 site up- or down-stream of the optimal −35 position. The data indicate that RpoD-dependent RNA polymerases dominate transcription initiation in C. metallidurans, interacting at sba promoters in a complex pattern with additional promoter elements, regulatory proteins, and, in some cases, other sigma factors, which is a previously unknown regulatory mechanism. IMPORTANCE Textbook knowledge suggests that RpoD and related sigma factors use −35 and −10 motifs upstream of a TSS to bind to the promoter, melt the DNA, and initiate RNA synthesis, with different sigma factors recognizing different motifs. This is not the case in Cupriavidus metallidurans . The majority of its promoters have a correctly positioned −10 site but an incorrectly positioned −35 site. At these “sba promoters,” other factors are needed for the correct positioning of the RpoD-bound RNA polymerase (RNAP) at the −10 site. In some cases, alternative sigma factors compete with RpoD-RNAP for promoter-binding. The complete transcriptional landscape revealed in C. metallidurans an altogether novel and complicated regulatory interaction at sba promoters.