A Global Characterisation of the Archaeal Transcription Machinery

Abstract

Archaea employ a eukaryote-like transcription apparatus to transcribe a bacteria-like genome; while the RNA polymerase, basal factors and promoter elements mirror the eukaryotic RNA polymerase II system, archaeal genomes are densely packed with genes organised into multicistronic transcription units. The molecular mechanisms of archaeal transcription have been studied and characterised in great detail in vitro, but until recently relatively little was known about its global characteristics. In this chapter we discuss an integrated view of transcription from the molecular to the global level. Systems biology approaches have provided compelling insights into promoter and terminator DNA elements, the genome-wide distribution of transcription initiation-and elongation factors and RNA polymerase, the archaeal transcriptome and chromatin organisation. Overall these analyses illuminate transcription from a genome-wide perspective and serve as a resource for the community. In addition, Big Data can often validate mechanistic models based on biochemical and structural information, and generate new working hypotheses that can be thoroughly tested and dissected in vitro. This is an exciting time to study gene expression in the archaea since we are at the brink of a comprehensive yet detailed understanding of transcription.

Characterization of promoters in archaeal genomes based on DNA structural parameters

“…The complete set of promoter sequences was converted into structural parameters through a self‐developed Python script (Supplementary Script S1: https://doi.org/10.5281/zenodo.5137597 ) that adopts the numeric parameters available in Table 1 , except for intrinsic curvature. The curvature calculation hinges on five nucleotides (instead of di and resulted in 4 5 (Smollet et al, 2017 ) possible combinations). The 1024 numeric parameters are the result of BMHT calculations (Bolshoy et al, 1991 ), and they are available in Supplementary Script S2 ( https://doi.org/10.5281/zenodo.5137597 ).…”

“…Additionally, the initiation might be optimized with the presence of a transcription factor E (TFE) protein (Ao et al, 2013 ). Subsequently, an open complex is assembled, followed by the elongation process whereby the RNAP carries out the synthesis of a messenger RNA molecule (mRNA) (Smollet et al, 2017 ; Soppa, 1999 ). In general, three main conserved DNA elements devoted to the transcription process have been identified as common to all archaeal groups: (i) an initiator element (INR) around the transcription start site (TSS); (ii) the TATA box element, centered around −26/27 relative to the TSS; and (iii) an element upstream the TATA box comprising two adenines at −34 and −33, which is designated as “transcription factor B recognition element” (BRE).…”

Machine learning and statistics shape a novel path in archaeal promoter annotation

“…The initiation of transcription in archaea has been reported to need two transcription factor proteins: a TBP and a TFB, homolog to eukaryotic TFIIB [ 7 , 10 ]. Additionally, a second strong signal was observed around positions − 10 and + 1, matching the Proximal Promoter Element.…”

“…Indeed, the eukaryotic model poses as a more specialized version of its archaeal counterpart. For instance, while archaea employs a single RNAP to transcribe all genes, animals and plants make use of three and five different enzymes, respectively [ 7 , 8 ].…”

Explainable Artificial Intelligence as a reliable annotator of archaeal promoter regions

“…When proteins get expressed in a prokaryotic archaeal cell, the DNA-dependent RNA polymerase enzyme (RNAP) transcribes genetic information in an intermediate RNA molecule; this is a conserved process found across all three domains of life (Gehring et al, 2016, Smollet et al, 2017. For RNAP to carry out RNA synthesis, it rstly needs to be recruited to the correct site in the DNA where protein-coding information is located.…”