The ribosome is one the most ubiquitously conserved and best characterized of the multi- component cellular RNPs. While much is known about ribosome structure and function, there are still many details to be elucidated especially regarding ribosome assembly and its impact the functional capacity of ribosomes. Thus, our work to address biosynthesis of E. coli small ribosomal subunits (SSUs) will have a significant impact on understanding not only assembly and function of these particles but also on the dynamic assembly and function of other RNPs. Moreover approximately 40% of the total energy production of E. coli is consumed to synthesize ribosomal components. This observation and the direct correlation between the rates of E. coli growth and ribosome biogenesis indicate that an accurately assembled and functional ribosome is of utmost importance for cell viability. Our long term goal is to gain a detailed understanding of ribosome biogenesis and thus reveal the impact of this dynamic process on fundamental aspects of cell physiology, such as growth regulation. This proposal details studies of E. coli SSU biogenesis. The purpose of this work is to gain an in-depth understanding of conformational changes and the factors that modulate these changes during the course of functional SSU assembly.
Three specific aims have been proposed to address these questions. First, conformational changes within 16S rRNA and specific rRNA nucleotides and ribosomal proteins that facilitate these changes during different stages of assembly in vitro and in vivo will be identified. Second, using a combination of genetics and biochemistry, novel SSU assembly intermediates will be identified and characterized. Third, auxiliary factors that facilitate SSU assembly will be analyzed. Factors identified in the current funding period will be explored in detail and additional factors will be identified and characterized. Our progress during the current funding cycle and our preliminary data indicate that all three specific aims will be successful and thus will directly impact understanding of SSU biogenesis and greatly expand understanding of RNA-protein interactions and RNP assembly in general. By revealing aspects that are critical for both assembly and function of SSUs, we may identify novel target sites for antimicrobial action. Given the growing prevalence of antibiotic resistant bacterial strains, the discovery of such targets is critical for human health.

Public Health Relevance

Project Narrative: Known antibiotics share common targets and chemical moieties and given the prevalence of multi-drug resistant bacteria, the identification of additional antibiotics and targets is critical for human health. It has been proposed that bacterial ribosome biogenesis represents promising new ground for development of antimicrobials and thus our studies of ribosome biogenesis in E. coli may result in the identification of novel targets for antibiotic action and may aid in alleviating the problem of bacterial drug resistance as a health concern.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Bender, Michael T
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University of Rochester
Schools of Arts and Sciences
United States
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Napper, Nathan; Culver, Gloria M (2015) Analysis of r-protein and RNA conformation of 30S subunit intermediates in bacteria. RNA 21:1323-34
Gupta, Neha; Culver, Gloria M (2014) Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA. Nat Struct Mol Biol 21:937-43
Connolly, Keith; Culver, Gloria (2013) Overexpression of RbfA in the absence of the KsgA checkpoint results in impaired translation initiation. Mol Microbiol 87:968-81
Desai, Pooja M; Culver, Gloria M; Rife, Jason P (2011) Site-directed mutants of 16S rRNA reveal important RNA domains for KsgA function and 30S subunit assembly. Biochemistry 50:854-63
Calidas, Deepika; Culver, Gloria M (2011) Interdependencies govern multidomain architecture in ribosomal small subunit assembly. RNA 17:263-77
Roy-Chaudhuri, Biswajoy; Kirthi, Narayanaswamy; Culver, Gloria M (2010) Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity. Proc Natl Acad Sci U S A 107:4567-72
Xu, Zhili; Culver, Gloria M (2010) Differential assembly of 16S rRNA domains during 30S subunit formation. RNA 16:1990-2001
Connolly, Keith; Culver, Gloria (2009) Deconstructing ribosome construction. Trends Biochem Sci 34:256-63
Xu, Zhili; Culver, Gloria M (2009) Chemical probing of RNA and RNA/protein complexes. Methods Enzymol 468:147-65
Connolly, Keith; Rife, Jason P; Culver, Gloria (2008) Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA. Mol Microbiol 70:1062-75

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