The fundamental and essential process of translation is catalyzed by the ribosome, and this proposal focuses on biogenesis of the ribosome. Ribosomes are intricate RNPs, whose biogenesis involves the transcription, processing, modification and folding of rRNA and the dynamic binding of r-proteins and at least 40 assembly factors. Ribosomes have long been the benchmark for understanding functional capabilities of complex RNPs, and work to unravel the mechanisms of 30S subunit biogenesis will similarly increase our understanding of biogenesis of all cellular RNPs. Our long-term goal is to gain a detailed understanding of the factors and pathways involved in E. coli ribosomal subunit biogenesis. Since bacterial and eukaryotic ribosome biogenesis share several features, results from these studies will undoubtedly lead to new conserved features and new insights into biogenesis of eukaryotic ribosomes. Furthermore, since ribosome biogenesis is likely to be highly conserved among bacteria and is linked to pathogenicity of some bacteria, discoveries of bacterial- specific biogenesis events will yield a number of new possible antimicrobial targets and likely new insights into possible methodologies for medical manipulation to alter growth of pathogenic bacteria. Our approach involves the isolation of in vivo formed intermediates and subsequent analysis of the components, structures, and processing of these particles. Preliminary results have shown the existence of three distinct complexes, at least 30 potential assembly factors, three of which we have already confirmed as assembly factors. We will use these data to further interrogate ribosome biogenesis and to identify important steps in this process. We will use biochemistry, genetics, molecular biology and proteomics to study ribosomal subunit biogenesis intermediates and factors that are involved in these processes and these data will be used to develop a network of interactions important for this process in bacteria. These studies will not only result in novel targets for antibiotic screening and insights into bacterial drug resistance, but will also yield better understanding of the evolution of ribosome biogenesis, and the interplay of biogenesis with fundamental aspects of cell physiology.

Public Health Relevance

Known antibiotics share common targets and chemical moieties and these characteristics aid in the growing occurrence of multi-drug resistant bacteria. Given the impact of multi-drug resistant bacteria on human health, the identification of additional antibiotics and targets is critical for future treatment of these strains. It has been proposed tha 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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM062432-18
Application #
9406129
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Bender, Michael T
Project Start
2001-03-01
Project End
2018-12-31
Budget Start
2018-01-01
Budget End
2018-12-31
Support Year
18
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of Rochester
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
041294109
City
Rochester
State
NY
Country
United States
Zip Code
14627
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
Xu, Zhili; Culver, Gloria M (2010) Differential assembly of 16S rRNA domains during 30S subunit formation. RNA 16:1990-2001
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
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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