ArticleNucleic acids research2017
Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed, 58 citations in OpenAlex.
- Deep learning-drivenSynthetic and systems biotechnology · 2027Article
- Role of the anti-Shine-Dalgarno sequence of 16S rRNA in Flavobacterium johnsoniae.Nucleic acids research · 2026Article
- Detection of bacterial gene expression elements on Tobacco mosaic virus RNA using cDNA analysis.PloS one · 2026Article
- The -10 region adjacent to open reading frames is a common expression pattern inLife science alliance · 2025Article
- Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.Nucleic acids research · 2025Article
- Molecular basis of mRNA delivery to the bacterial ribosome.Science (New York, N.Y.) · 2024Article
- Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.Microbiome · 2024Article
- Analysis of programmed frameshifting during translation ofRNA (New York, N.Y.) · 2024Article
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria.Nature communications · 2023Article
- Chloroplast gene expression: Recent advances and perspectives.Plant communications · 2023Review
- Identification and validation of ferroptosis-related genes in patients infected with dengue virus: implication in the pathogenesis of DENV.Virus genes · 2023Article
- Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript.Nucleic acids research · 2023Article
- Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae.Nucleic acids research · 2023Article
- Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli.Nucleic acids research · 2023Article
- INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors.Nucleic acids research · 2022Article
- Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients.BMC microbiology · 2022Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Role of aIF5B in archaeal translation initiation.Nucleic acids research · 2022Article
- Identification and Cross-Characterisation of Artificial Promoters and 5' Untranslated Regions inFrontiers in bioengineering and biotechnology · 2022Article
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 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea). We identified distinct nucleotide frequency biases upstream of the initiation codon in bacteria and archaea, likely because of the presence of leaderless mRNAs lacking a 5΄ UTR. Moreover, we observed overall similarities in the nucleotide patterns between upstream and downstream regions of the initiation codon in all examined phyla. Symmetric nucleotide frequency biases might facilitate translation initiation by preventing the formation of secondary structures around the initiation codon. These features are more prominent in species' genomes that harbor large fractions of non-SD sequences, suggesting that a reduced stability around the initiation codon is important for efficient translation initiation in prokaryotes.
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.