Genetic or age-related defects in mitochondrial gene expression can reduce or eliminate mitochondrial function and cause multiple human pathologies, including neurodegenerative and cardiovascular disease, diabetes and cancer. Mitochondrial transcription is a key process for gene expression, and accordingly some of these pathogenic alterations have been associated with proteins involved in transcription. However, our functional understanding of the different components of the transcription machinery in mitochondria is relatively poor. Characterizing the molecular mechanisms underlying mitochondrial transcription will allow us to understand how small genetic or environmental alterations in this process can result in gene expression deficiencies and the development of mitochondrial pathology. This proposal aims to provide functional insight into the process of mitochondrial transcription and investigate the importance of the rRNA methyltransferase activities present in transcription factors.
We aim to unravel the mechanism of transcription initiation, the connections between transcription and ribosome biogenesis and the relationship between transcriptional defects and mitochondrial disease. The proposal has three aims: (i) to investigate the structural and functional differences between two transcription factors related to 16S rRNA methyltransferases, TFB1M and TFB2M, and to study the specificity of their interaction with their nucleic acid substrates;(ii) to investigate the methyltransferase activitie of TFB1M and TFB2M, their importance for transcription and ribosome biogenesis and their relationship with maternally inherited deafness;(iii) to determine the mechanisms of transcription initiation, the protein-protein interactions necessary for the process and the architecture of the transcription machinery. The proposal will take advantage of substantial preliminary data, including two novel crystal structures, the discovery of a novel interaction critical for initiation and the development of new methods to study the rRNA methyltransferase activities in vitro. We will apply various molecular genetics, biochemical and biophysical techniques to investigate the functional interactions necessary for transcription and the enzymatic activities of TFB1M and TFB2M. Electron microscopy, small angle x-ray scattering and X-ray crystallography will be used to provide additional structural insight and, in turn, facilitate our functional understanding of the process. The expected results will dramatically increase our knowledge of mitochondrial transcription, the individual roles of transcription factors, the relationships between transcription and ribosome biogenesis and the molecular basis of maternally inherited deafness. Ultimately, improving our mechanistic understanding of the transcription process will help clarify the relationship between transcription, mitochondrial dysfunction and disease.

Public Health Relevance

Deficiencies in mitochondrial gene expression affect a large proportion of the population and can cause or contribute to disease development. This proposal will study the molecular mechanisms responsible for transcription, a central process in gene expression, and will improve our understanding of the mechanisms by which deficiencies in this process can lead to mitochondrial pathologies. The expected results will be relevant to our understanding of mitochondrial function, the development of mitochondrial diseases and the contribution of mitochondrial genetic alterations to the onset of age-related pathologies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Membrane Biology and Protein Processing (MBPP)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
State University New York Stony Brook
Schools of Medicine
Stony Brook
United States
Zip Code
Hauser, Kevin; He, Yiqing; Garcia-Diaz, Miguel et al. (2017) Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. J Chem Inf Model 57:864-874
Airola, Michael V; Shanbhogue, Prajna; Shamseddine, Achraf A et al. (2017) Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation. Proc Natl Acad Sci U S A 114:E5549-E5558
Burak, Matthew J; Guja, Kip E; Hambardjieva, Elena et al. (2016) A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. EMBO J 35:2045-59
Guha, Manti; Srinivasan, Satish; Guja, Kip et al. (2016) HnRNPA2 is a novel histone acetyltransferase that mediates mitochondrial stress-induced nuclear gene expression. Cell Discov 2:16045
Byrnes, James; Hauser, Kevin; Norona, Leah et al. (2016) Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion. J Mol Biol 428:2542-2556
Hauser, Kevin; Essuman, Bernard; He, Yiqing et al. (2016) A human transcription factor in search mode. Nucleic Acids Res 44:63-74
Khan, Irfan; Crouch, Jack D; Bharti, Sanjay Kumar et al. (2016) Biochemical Characterization of the Human Mitochondrial Replicative Twinkle Helicase: SUBSTRATE SPECIFICITY, DNA BRANCH MIGRATION, AND ABILITY TO OVERCOME BLOCKADES TO DNA UNWINDING. J Biol Chem 291:14324-39
Aleem, Saadat; Georghiou, George; Kleiner, Ralph E et al. (2016) Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles. Cell Chem Biol 23:1103-1112
Burak, Matthew J; Guja, Kip E; Garcia-Diaz, Miguel (2015) Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda. Nucleic Acids Res 43:8089-99
Yang, Meng; Guja, Kip E; Thomas, Suzanne T et al. (2014) A distinct MaoC-like enoyl-CoA hydratase architecture mediates cholesterol catabolism in Mycobacterium tuberculosis. ACS Chem Biol 9:2632-45

Showing the most recent 10 out of 17 publications