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.
Highlights
Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
Previous transcriptomic analysis of R15 indicated that expression of 40% of its genes responded to changes in temperature and that the genes related to RNA degradation were up-regulated in response to cold[6], implying that mRNA turnover may play a role in the cold-responsive gene regulation
Multiple transcription start sites (TSSs) per gene and cold-responsive TSS indicate a dynamic transcriptome in this archaeon, providing a new avenue for exploring archaeal cold adaption and the coordination between transcriptional and posttranscriptional regulation
Summary
Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. 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. The cold shock protein gene cspA of E. coli encodes an RNA chaperone and transcribes a large 59 untranslated region (UTR) of mRNA which determines the transcript’s cold stability and translational conformation in the cold[8]. This unique architecture of the cspA mRNA allows it to function as a RNA thermometer[9]. Our recent work demonstrated that the mRNAs for mtaA and mtaC, which encode the methylcobalamin:coenzyme M methyltransferase and methanol corrinoid proteins that are the www.nature.com/scientificreports key enzymes in methanol-derived methanogenesis of a cold-adaptive methanogen, all have long 59 UTRs, that contribute to the transcripts’ stability at low temperatures[10]
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