ArticleFrontiers in microbiology2014
Ends of the line for tmRNA-SmpB.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- Approaches to Study Proteins Encoded by Essential Genes.Proteins · 2026Review
- Expansion of the tmRNA sequence database and new tools for search and visualization.NAR genomics and bioinformatics · 2025Article
- Cooperative and Independent Functionality of tmRNA and SmpB inInternational journal of molecular sciences · 2025Article
- Article
- RqcH supports survival in the absence of non-stop ribosome rescue factors.bioRxiv : the preprint server for biology · 2024Article
- Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli.Molecular microbiology · 2023Article
- Article
- Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Ribosome Rescue Pathways in Bacteria.Frontiers in microbiology · 2021Review
- Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function.Journal of lipid research · 2019Article
- Article
- How a circularized tmRNA moves through the ribosome.Science (New York, N.Y.) · 2019Article
- Article
- Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue.eLife · 2018Article
- Characterization and induction of prophages in human gut-associated Bifidobacterium hosts.Scientific reports · 2018Article
- KKL-35 Exhibits Potent Antibiotic Activity against Legionella Species Independently ofAntimicrobial agents and chemotherapy · 2018Article
- Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma.Genome biology and evolution · 2017Article
- Trans-translation is essential in the human pathogen Legionella pneumophila.Scientific reports · 2016Article
- Human Cells Require Non-stop Ribosome Rescue Activity in Mitochondria.PLoS genetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes for the RNA tmRNA and protein SmpB, partners in the trans-translation process that rescues stalled ribosomes, have previously been found in all bacteria and some organelles. During a major update of The tmRNA Website (relocated to http://bioinformatics.sandia.gov/tmrna), including addition of an SmpB sequence database, we found some bacteria that lack functionally significant regions of SmpB. Three groups with reduced genomes have lost the central loop of SmpB, which is thought to improve alanylation and EF-Tu activation: Carsonella, Hodgkinia, and the hemoplasmas (hemotropic Mycoplasma). Carsonella has also lost the SmpB C-terminal tail, thought to stimulate the decoding center of the ribosome. We validate recent identification of tmRNA homologs in oomycete mitochondria by finding partner genes from oomycete nuclei that target SmpB to the mitochondrion. We have moreover identified through exhaustive search a small number of complete, but often highly derived, bacterial genomes that appear to lack a functional copy of either the tmRNA or SmpB gene (but not both). One Carsonella isolate exhibits complete degradation of the tmRNA gene sequence yet its smpB shows no evidence for relaxed selective constraint, relative to other genes in the genome. After loss of the SmpB central loop in the hemoplasmas, one subclade apparently lost tmRNA. Carsonella also exhibits gene overlap such that tmRNA maturation should produce a non-stop smpB mRNA. At least some of the tmRNA/SmpB-deficient strains appear to further lack the ArfA and ArfB backup systems for ribosome rescue. The most frequent neighbors of smpB are the tmRNA gene, a ratA/rnfH unit, and the gene for RNaseR, a known physical and functional partner of tmRNA-SmpB.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.