Quantitative Control for Stoichiometric Protein Synthesis
Open accessAbstract
Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production.
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In B. subtilis, the gene atpI is located immediately prior to the remainder of the ATP synthase coding genes, in the identical order as they appear in JCVI-syn3A.
“When the ATP synthase containing operon is examined in B. subtilis,49 we observe that the gene atpI is located immediately prior the remainder of the ATP synthase coding genes, in the identical order as they appear in JCVI-syn3A.”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [49]
The section “Specifying Differential Expression Through mRNA Processing” mentions a B. subtilis ATP synthase operon, but does not give its gene order. Searches for atpI, ATP synthase gene order, and JCVI-syn3A found no passage establishing that atpI immediately precedes the other genes or that their order matches JCVI-syn3A; page numbers were unavailable in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredGene /0797 is atpI, an ATP synthase component involved in membrane pH gradient.
“atpI/0797 | membrane pH gradient | ATP synthase component”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [49]
The passage on operon translation in “Autonomous Translation and Impact of Neighboring Genes” (page unavailable) discusses protein-production efficiency, not atpI or ATP synthase. Searches for “atpI,” “0797,” and the membrane pH gradient found no passage in our copy identifying the gene or supporting its stated function. (LLM, conf=0.76)
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References 187 · Cited by 17
Research works printed but not linked: 3
- [35]Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, 2009. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteom 8(6): 1350– 60 PMC2690492 19193632
- McCormick DM, Lalanne J-B, Lan TCT, Rouskin S, Li G-W. 2021. Sigma factor dependent translational activation in Bacillus subtilis. RNA In press PMC8208050 33927010
- [168]Urtecho G, Insigne KD, Tripp AD, Brinck M, Lubock NB, 2020. Genome-wide functional characterization of Escherichia coli promoters and regulatory elements responsible for their function. bioRxiv 2020.01.04.894907. 10.1101/2020.01.04.894907 · DOI
- Authors
- Taggart, J. C., Lalanne, J.-B., & Li, G.-W.
- Affiliations
- Massachusetts Institute of Technology (US)
- University of Washington (US)
- Venue
- Annual Review of Microbiology
- Publisher
- Annual Reviews
- Published
- 2021-10-08
- Volume
- 75
- Issue
- 1
- Pages
- 243-267
- ISSN
- 0066-4227 (ISSN-L)
- 1545-3251
- PMC
- PMC8720029
- OpenAlex
- W3189126572
- Cited by
- 17
- References
- 187
- Citations by year
- 2025: 5 · 2024: 2 · 2023: 7 · 2022: 2 · 2021: 1
- FWCI
- 0.31
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (CAREER)
- Howard Hughes Medical Institute
- Searle Scholars Program
- National Institutes of Health
- Natural Sciences and Engineering Research Council of Canada
- National Institute of General Medical Sciences (T32GM007287, R35GM124732)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- protein stoichiometry, bacterial protein synthesis, operon regulation, mRNA secondary structure, transcriptional regulation, translational regulation, RNA turnover
- MeSH terms
- Escherichia coli, Operon, Proteins, RNA, Messenger, Transcription, Genetic, Protein Biosynthesis
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