Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis

Nucleic Acids Research
Lei QiXiuzhu Dong

Abstract

Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal prote...Continue Reading

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Citations

Sep 13, 2018·Annual Review of Genetics·José Vicente Gomes-FilhoLennart Randau
Apr 24, 2018·FEMS Microbiology Reviews·Béatrice Clouet-d'OrvalLisa-Katharina Maier
Mar 16, 2019·Current Opinion in Biotechnology·Zhe Lyu, William B Whitman
May 18, 2021·Frontiers in Microbiology·Albert WeixlbaumerDina Grohmann

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Methods Mentioned

BETA
RNA-seq
Assay
dRNA-seq
PCR
X-ray
protein assay

Software Mentioned

Rnaviz2
Quantity One
iPSS
MEME
Mfold
uPSS

Related Concepts

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