Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

Abstract

Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5′ untranslated regions (5′ UTR, median lengths of 20–40 nt), 51% mRNAs of this methanogen have large 5′ UTR (>50 nt). For 24% of the mRNAs, the 5′ UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5′ UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5′ UTRs, suggesting alternative 5′ UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.

Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene

“…Leaderless transcripts are mRNAs that are completely devoid of 5= untranslated regions (UTRs), and such transcripts are known to occur in S. meliloti (9) as well as in other organisms, including Escherichia coli, Rhodobacter sphaeroides, and Synechocystis sp. strain PCC6803 (10)(11)(12). The 5=-terminal AUG triplet of leaderless mRNAs in E. coli was shown to be competent for ribosome binding (12).…”

The Non-Coding Regulatory RNA Revolution in Archaea

“…volcanii, M. psychrophilus, T. kodakerensis, and P. abyssi [14,[29][30][31]. The dRNA-seq method is based on the selective enrichment of primary transcripts, which in prokaryotes carry a triphosphate at their 5' ends.…”

“…However, it is the unprecedented discovery of more than 2,900 sRNAs in H. volcanii by two recent high-throughput sequencing (HTS) studieswhich is quite remarkable considering that the genome of this organism encode for just over 4,000 proteins [1, 14] -that has permanently altered our view of the archaeal transcriptome. While sRNAs are particularly numerous in haloarchaea genomes [14], they have also been found in a number of other archaea, including Sulfolobus [22], Methanosarcina [23], Pyrobaculum [24], Pyrococcus [29], Thermococcus [30], and Methanolobus [31] ( Table 1). In…”

“…Both cis asRNAs and trans-encoded sRNAs (thereafter called itsRNAs for intergenic sRNAs) have been reported in a number of archaeal species (Fig. 1), as well as cis sense sRNAs that are transcribed within the open reading frame (ORF) of genes [1, 14,[22][23][24][25][26][27]. In addition to these ncRNAs, small UTR, within the coding sequence (CDS), extending past the CDS, and overlapping multiple mRNAs.…”

Molecular Mechanisms of Transcription Initiation—Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation

“…Recent next generation sequencing approaches have enabled the genomewide mapping of TSSs and thereby the sequence determinants of archaeal promoters for a number of organisms [39][40][41][42]. Sequence alignments centred around the TSSs for Sso and Tko confirm that BRE and TATA are the two canonical promoter elements in archaea and that the IMR is generally AT-rich ( Figure 3).…”