Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea

Abstract

Transcription termination sets the 3' end boundaries of RNAs and plays key roles in gene regulation. Although termination has been well studied in bacteria, the signals that mediate termination in archaea remain poorly understood. Here, we applied term-seq to comprehensively map RNA 3' termini, with single-base precision, in two phylogenetically distant archaea: Methanosarcina mazei and Sulfolobus acidocaldarius. Comparison of RNA 3' ends across hundreds of genes revealed the sequence composition of transcriptional terminators in each organism, highlighting both common and divergent characteristics between the different archaeal phyla. We find that, in contrast to bacteria, a considerable portion of archaeal genes are controlled by multiple consecutive terminators, generating several alternative 3' untranslated region isoforms for >30% of the genes. These alternative isoforms often present marked length differences, implying that archaea can employ regulation via alternative 3' untranslated regions, similar to eukaryotes. Although most of the terminators are intergenic, we discover numerous cases in which termination of one gene occurs within the coding region of a downstream gene, implying that leaky termination may tune inter-transcript stoichiometry in multi-gene operons. These results provide the first high-throughput maps of transcriptional terminators in archaea and point to an evolutionary path linking bacterial and eukaryal non-coding regulatory strategies.

Factor-dependent archaeal transcription termination

“…Therefore, TBP and TFB alone are capable of assisting RNAP in the formation of the transcription bubble. In all Archaea, TFB is responsible for stabilizing the TBPbound DNA complex and, together, this bipartite protein platform recruits RNAP (46) Several new insights into TFE activity and evolution have been recently described. The archaeal TFE had previously been characterized as a monomer and as a homologue of the alpha subunit of eukaryotic TFIIE, termed TFIIEα (19,47,48).…”

“…TFEα consists of two domains: a winged helix (WH) domain and a zinc ribbon domain (55,56); TFEβ contains a conserved WH domain and an FeS domain (20). The WH domain of TFEα contacts the upstream, nontemplate strand of DNA and helps form the open promoter complex through an unknown mechanism (18,46). Several studies have shown that the presence of the RNAP stalk domain-unique to archaeoeukaryotic RNAPs and comprised of two subunits, RpoE and RpoF in archaea and Rpo4 and Rpo7 in eukaryotes-is essential for the full activity of TFEα (10,54,57).…”

“…10 µl of peak fractions (identified via UV absorbance) are combined with 2 µl 6X SDS-loading buffer and boiled for 3 minutes. The ultimate control of transcription elongation is provided by factors and sequences that can disrupt the normally extremely-stable transcription elongation complex (TEC) to terminate transcription and release the nascent transcript and RNAP from the DNA template (3,(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47).…”

“…DNA sequences encoding poly-U rich sequences are sufficient to disrupt the archaeal TEC both in vivo and in vitro, and although surrounding sequence context can influence intrinsic transcription termination efficiency, there is no requirement for RNA structure for intrinsic termination (38,41,46,48).…”

sRNA41 affects ribosome binding sites within polycistronic mRNAs in Methanosarcina mazei Gö1

“…These include masking RBSs in the 5'UTRs of their targets (J€ ager et al, 2012;Prasse et al, 2017), arguing that those archaeal sRNAs act similarly as their bacterial counterparts. Besides, there are several indications that archaeal sRNAs also target 3'UTRs (Bernick et al, 2012;M€ artens et al, 2013;Babski et al, 2014;Dar et al, 2016). Recently, the first archaeal sRNA was reported to stabilize the targeted transcript by most likely binding and masking RNase binding sites (Prasse et al, 2017).…”