Defining the Precision and Sequence Determinants of Protein Synthesis Rates
Protein synthesis drives cellular proliferation and produces the primary effectors of biological function. Understanding how protein synthesis rates are controlled is therefore a central question of quantitative biology. In this work, I explore both the degree of precision in protein production and...
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| Format: | Thesis |
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Massachusetts Institute of Technology
2023
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| Online Access: | https://hdl.handle.net/1721.1/147460 https://orcid.org/0000-0002-6853-1583 |
| _version_ | 1811081146733166592 |
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| author | Taggart, James Christopher |
| author2 | Li, Gene-Wei |
| author_facet | Li, Gene-Wei Taggart, James Christopher |
| author_sort | Taggart, James Christopher |
| collection | MIT |
| description | Protein synthesis drives cellular proliferation and produces the primary effectors of biological function. Understanding how protein synthesis rates are controlled is therefore a central question of quantitative biology. In this work, I explore both the degree of precision in protein production and the mechanisms by which protein synthesis rates are encoded in genome sequences. First, I explore whether proportional synthesis of protein complex subunits, a phenomenon widely observed in bacterial protein synthesis, is a strategy adopted by eukaryotes. Using ribosome profiling, I observe proportional synthesis in the budding yeast Saccharomyces cerevisiae and through chromosomal duplications show that the precision in these protein synthesis rates is hard-coded without widespread negative feedback regulation. Proportional synthesis is also seen in large abundant complexes conserved in higher eukaryotes. I additionally present work to unify this understanding of proportional synthesis with evidence of post-translation buffering of protein complex subunit abundance derived from mass spectrometry. In the second half of this thesis, I turn my focus towards understanding how RNA decay and processing rates, two poorly understood processes central to the quantitative tuning of protein synthesis, are encoded in bacterial mRNAs. Using high-resolution RNA end-mapping techniques in combination with genetic perturbations to stabilize intermediates of RNA decay, I generate a global map of positions of endonuclease cleavage in Bacillus subtilis. Coupling this approach with knockouts of specific endonucleases, I greatly expand and refine the known set of targets of RNase Y, its specificity factor YlbF, and RNase III. Through this, I capture sequence and structural features recognized by RNase Y, the primary endonuclease initiating RNA decay in B. subtilis. I additionally provide evidence for a novel RNA 5′ end trimming activity of unknown origin. Finally, I present a system for massively parallel interrogation of the sequence-function relationship of B. subtilis mRNA processing sites. Using this approach, I uncover key sequence determinants of cggR-gapA and glnRA operon processing by RNase Y. Taken together, this work provides insight into the degree of precision achieved in gene expression across life and reveals mechanistic details of how protein synthesis can be tuned through RNA decay in a model Gram- positive bacterium. |
| first_indexed | 2024-09-23T11:42:14Z |
| format | Thesis |
| id | mit-1721.1/147460 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T11:42:14Z |
| publishDate | 2023 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1474602023-01-20T03:37:40Z Defining the Precision and Sequence Determinants of Protein Synthesis Rates Taggart, James Christopher Li, Gene-Wei Massachusetts Institute of Technology. Department of Biology Protein synthesis drives cellular proliferation and produces the primary effectors of biological function. Understanding how protein synthesis rates are controlled is therefore a central question of quantitative biology. In this work, I explore both the degree of precision in protein production and the mechanisms by which protein synthesis rates are encoded in genome sequences. First, I explore whether proportional synthesis of protein complex subunits, a phenomenon widely observed in bacterial protein synthesis, is a strategy adopted by eukaryotes. Using ribosome profiling, I observe proportional synthesis in the budding yeast Saccharomyces cerevisiae and through chromosomal duplications show that the precision in these protein synthesis rates is hard-coded without widespread negative feedback regulation. Proportional synthesis is also seen in large abundant complexes conserved in higher eukaryotes. I additionally present work to unify this understanding of proportional synthesis with evidence of post-translation buffering of protein complex subunit abundance derived from mass spectrometry. In the second half of this thesis, I turn my focus towards understanding how RNA decay and processing rates, two poorly understood processes central to the quantitative tuning of protein synthesis, are encoded in bacterial mRNAs. Using high-resolution RNA end-mapping techniques in combination with genetic perturbations to stabilize intermediates of RNA decay, I generate a global map of positions of endonuclease cleavage in Bacillus subtilis. Coupling this approach with knockouts of specific endonucleases, I greatly expand and refine the known set of targets of RNase Y, its specificity factor YlbF, and RNase III. Through this, I capture sequence and structural features recognized by RNase Y, the primary endonuclease initiating RNA decay in B. subtilis. I additionally provide evidence for a novel RNA 5′ end trimming activity of unknown origin. Finally, I present a system for massively parallel interrogation of the sequence-function relationship of B. subtilis mRNA processing sites. Using this approach, I uncover key sequence determinants of cggR-gapA and glnRA operon processing by RNase Y. Taken together, this work provides insight into the degree of precision achieved in gene expression across life and reveals mechanistic details of how protein synthesis can be tuned through RNA decay in a model Gram- positive bacterium. Ph.D. 2023-01-19T19:52:00Z 2023-01-19T19:52:00Z 2022-09 2022-09-13T20:41:23.013Z Thesis https://hdl.handle.net/1721.1/147460 https://orcid.org/0000-0002-6853-1583 In Copyright - Educational Use Permitted Copyright retained by author(s) https://rightsstatements.org/page/InC-EDU/1.0/ application/pdf Massachusetts Institute of Technology |
| spellingShingle | Taggart, James Christopher Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title | Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title_full | Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title_fullStr | Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title_full_unstemmed | Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title_short | Defining the Precision and Sequence Determinants of Protein Synthesis Rates |
| title_sort | defining the precision and sequence determinants of protein synthesis rates |
| url | https://hdl.handle.net/1721.1/147460 https://orcid.org/0000-0002-6853-1583 |
| work_keys_str_mv | AT taggartjameschristopher definingtheprecisionandsequencedeterminantsofproteinsynthesisrates |