Related Experiment Video
Updated: Jun 20, 2026
Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy
Published on: July 29, 2019
Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii
1Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
Abstract:
Messenger RNA (mRNA) processing plays important roles in gene expression in all domains of life. A number of cases of mRNA cleavage have been documented in Archaea, but available data are fragmentary. We have examined RNAs present in Methanocaldococcus (Methanococcus) jannaschii for evidence of RNA processing upstream of protein-coding genes. Of 123 regions covered by the data, 31 were found to be processed, with 30 including a cleavage site 12-16 nucleotides upstream of the corresponding translation start site. Analyses with 3'-RACE (rapid amplification of cDNA ends) and 5'-RACE indicate that the processing is endonucleolytic. Analyses of the sequences surrounding the processing sites for functional sites, sequence motifs, or potential RNA secondary structure elements did not reveal any recurring features except for an AUG translation start codon and (in most cases) a ribosome binding site. These properties differ from those of all previously described mRNA processing systems. Our data suggest that the processing alters the representation of various genes in the RNA pool and therefore, may play a significant role in defining the balance of proteins in the cell.
Insights
Messenger RNA (mRNA) processing in Archaea is not well understood. This study reveals a novel endonucleolytic mRNA cleavage upstream of translation start sites in Methanocaldococcus jannaschii, impacting gene expression.
Area of Science:
- Molecular Biology
- Genetics
- Microbiology
Background:
- Messenger RNA (mRNA) processing is crucial for gene expression across all life domains.
- Existing data on mRNA cleavage in Archaea is limited and fragmented.
- Understanding archaeal mRNA processing is key to deciphering gene regulation in this domain.
Purpose of the Study:
- To investigate RNA processing upstream of protein-coding genes in the archaeon Methanocaldococcus jannaschii.
- To characterize the nature and location of identified RNA processing events.
- To identify sequence features or structural elements associated with these processing sites.
Main Methods:
- Analysis of RNA sequencing data from Methanocaldococcus jannaschii.
- Identification of processed RNA regions upstream of translation start sites.
- 3'- and 5'-rapid amplification of cDNA ends (RACE) to determine processing mechanism.
- Sequence and structural analysis of regions surrounding cleavage sites.
Main Results:
- 31 out of 123 examined regions showed evidence of RNA processing.
- A significant majority (30/31) featured a cleavage site 12-16 nucleotides upstream of the start codon.
- Processing was confirmed to be endonucleolytic via RACE analyses.
- No recurring sequence motifs or secondary structures were found, apart from start codons and ribosome binding sites.
Conclusions:
- Methanocaldococcus jannaschii exhibits a unique endonucleolytic mRNA processing system upstream of genes.
- This processing mechanism differs significantly from previously described mRNA processing systems.
- The observed mRNA processing likely regulates gene expression by altering RNA pool representation, influencing cellular protein balance.
Related Concept Videos
02:01pre-mRNA Processing
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
02:01Pre-mRNA Processing
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
02:27Nonsense-mediated mRNA Decay
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
02:27Nonsense-mediated mRNA Decay
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
01:35Pre-mRNA Processing: Modification of pre-mRNA Ends
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...
02:53Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...