Abstract
In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5′ untranslated regions (5′ UTRs). Along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions under the different growth conditions. Interestingly, we observed low GC content in ncRNAs for RNA-based regulation via unstructured forms or interaction with other cellular components. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that transcription of orthologous genes are initiated by highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. These results provide the genetic information of T. onnurineus for its future application in metabolic engineering.
Highlights
Mazei, Methanolobus psychrophilus, and Haloferax volcanii identified the genome-wide location of transcription start site (TSS) and further revealed the significance of post-transcriptional regulation and extensive ncRNA-based regulation[12,13,14,15]
We determined the primary transcriptome of the hyperthermophilic archaeon T. onnurineus NA1 using dRNA-seq so that the cis-regulatory components were cataloged on a genomic scale
In addition to the conserved promoter elements, this is less understood, it has been suggested that archaeal 5′UTRs contain the initiator element motif (INR), with high AT content, which affects promoter strength through interacting with transcription activators or facilitating promoter opening[3,44]
Summary
Mazei, Methanolobus psychrophilus, and Haloferax volcanii identified the genome-wide location of TSS and further revealed the significance of post-transcriptional regulation and extensive ncRNA-based regulation[12,13,14,15]. Extensive analyses were performed to elucidate the cis-encoded determinants of transcription initiation and the upstream regulatory regions around the promoters and 5′UTRs. we generated a map of genome-scale ncRNAs and their differential utilization under formate and CO conditions, which are known to be upregulated for the production of hydrogen gas based on measuring levels of individual transcripts using ssRNA-seq[20]. We generated a map of genome-scale ncRNAs and their differential utilization under formate and CO conditions, which are known to be upregulated for the production of hydrogen gas based on measuring levels of individual transcripts using ssRNA-seq[20] This comprehensive genome-scale view of transcript architecture using upstream regulatory features provides a better understanding of transcriptional and posttranscriptional regulation in archaeal genomes
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