The tmRNA Website

Overview

The tmRNA Website is a comprehensive resource for transfer-messenger RNA (tmRNA) and its partner protein SmpB, which together resolve problems arising when bacterial ribosomes reach the end of mRNA with no stop codon through a process called trans-translation.

Database Content

tmRNA Sequences

• 1,716 unique tmRNA sequences: 1,454 one-piece and 262 two-piece tmRNAs
• 9,387 instances across public databases (RefSeq, GenBank, etc.)
• Phylogenetic breakdown: 1,594 bacterial, 0 archaeal, 122 organellar (79 oomycete/jakoid mitochondria, 42 algal plastids, 1 chromatophore)
• 734 unique proteolysis tag sequences

SmpB Sequences

• 2,258 unique SmpB sequences
• 4,125 instances including 24 potentially pseudogenized/frameshifted/truncated sequences
• SmpB proteins linked with their corresponding tmRNA partners

Trans-Translation Biology

tmRNA Function

tmRNA uses both tRNA-like and mRNA-like properties during trans-translation:

1. When a ribosome stalls on non-stop mRNA, alanine-charged tmRNA enters as substrate for peptidyl transfer
2. Ribosome switches from defective mRNA to the ‘resume codon’ of tmRNA
3. Translation continues, adding a peptide tag that signals proteolysis
4. Frees stalled ribosome and marks non-stop mRNA for degradation

SmpB Role

The protein SmpB is a partner throughout trans-translation, bound to tmRNA and occupying space normally occupied by the anticodon stem-loop.

Key Features

Sequence Discovery Pipeline

• Detection tools: tRNAscan-SE, BRUCE, ARAGORN, plus custom rFind.pl
• Processing: tFind.pl wrapper for comprehensive tmRNA identification
• Software availability: Tools freely available for public download

Annotations

• tmRNA features: Length, sequence, genomic location, proteolysis tag, CCA coordinates, introns (when present), two-piece tmRNA structural details
• SmpB annotations: Amino acid sequence, genomic coordinates, orientation relative to ssrA gene
• Secondary structures: Images provided where available

Search and Analysis Tools

• BLAST searches: Available for both tmRNA and SmpB
• Sequence alignments: 632 tmRNA and 2,258 SmpB distinct alignments
• Krona visualization: Modified metagenome taxonomy viewer enabling navigation to individual tmRNA pages while displaying phylogenetic distribution

Data Distribution

• Found in nearly all bacterial genomes (except six recalcitrant genomes)
• Present in some organelles
• SmpB genes found in all bacterial genomes studied (sometimes with severe defects) and in eukaryotic nuclear genomes with signals targeting transport to organelles encoding tmRNA

Data Sources

• Primary genomic data: RefSeq (2,168 organisms plus 1,755 plasmids and 581 viruses)
• Additional sequence databases: NCBI est, gss, htgs, nt, other_genomic, patnt, refseq_genome, tsa_nt, wgs
• Contributions to: RNAcentral, International Nucleotide Sequence Database Archive (GenBank/ENA/DDBJ) as third-party annotation

Related Resources

• tmRDB: Additional tmRNA database
• Rfam: RNA families database including tmRNA
• RNAcentral: Central repository receiving tmRNA Website contributions

Website Status

The tmRNA Website was hosted at Sandia National Laboratories (http://bioinformatics.sandia.gov/tmrna/) but appears to be inactive as of 2025. The database content has been contributed to RNAcentral for continued access.

Funding

Research fully supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.

Citation

Hudson CM, Williams KP. The tmRNA website. Nucleic Acids Research. 2015;43(D1):D138-D140. doi:10.1093/nar/gku1109