ArticleNucleic acids research2022
"Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato.Plant cell reports · 2026Article
- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- Article
- A perspective and demonstration of an approach to screening synthetic nucleic acid orders containing short nucleic acid sequences.Frontiers in bioengineering and biotechnology · 2026Article
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- High quality transcriptome profiling confirms the transcriptional landscape of Treponema pallidum subsp. pallidum.Scientific reports · 2025Article
- Pseudogenes and host specialization in the emergent bacterial plant pathogenApplied and environmental microbiology · 2025Article
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- A genomic and phenotypic investigation of pigeon-adaptive Salmonella.PLoS pathogens · 2025Article
- Serovar-specific genomic features ofFrontiers in molecular biosciences · 2025Article
- Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility.Nucleic acids research · 2024Article
- The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- The Landscape and Perspectives of the Human Gut Metaproteomics.Molecular & cellular proteomics : MCP · 2024Article
- Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection.Microbiology spectrum · 2024Article
- Identification of Campylobacter jejuni and Campylobacter coli genes contributing to oxidative stress response using TraDIS analysis.BMC microbiology · 2024Article
- A large-scale phylogeny-guided analysis of pseudogenes inMicrobiology spectrum · 2023Article
- Genome degradation promotesNational science review · 2023Article
- Nontriplet feature of genetic code inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- One species, different diseases: the unique molecular mechanisms that underlie the pathogenesis of typhoidal Salmonella infections.Current opinion in microbiology · 2023Review
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes' mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
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