ArticleGenome research2013
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 70 citations in OpenAlex.
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- Detection of Known and Novel Small Proteins inAnalytical chemistry · 2023Article
- Unraveling the small proteome of the plant symbiontmicroLife · 2023Article
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- Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.Science (New York, N.Y.) · 2022Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Adaptive Resistance Mutations at Suprainhibitory Concentrations Independent of SOS Mutagenesis.Molecular biology and evolution · 2021Article
- Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungusMicrobial cell (Graz, Austria) · 2021Article
- Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.Microbiome · 2021Article
- An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1.NPJ biofilms and microbiomes · 2020Article
- An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation inFrontiers in microbiology · 2019Article
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.High-throughput · 2018Review
- Article
- Comparative Genomics of Completely SequencedFrontiers in microbiology · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.Applied and environmental microbiology · 2017Article
- A family of genus-specific RNAs in tandem with DNA-binding proteins control expression of the badA major virulence factor gene in Bartonella henselae.MicrobiologyOpen · 2017Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.
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