Characterization of an essential mitochondrial rRNA methyltransferase

Summary

Principal Investigator: Kip E Guja
Abstract: DESCRIPTION (provided by applicant): Defects in mitochondrial gene expression can cause a myriad of mitochondrial disorders, including mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, Kearns-Sayre syndrome, and Leber hereditary optic neuropathy. These diseases have a large impact in the population since, when considered as a class, they are estimated to have a prevalence of at least 1 in 5000. Furthermore, a progressive decay in mitochondrial function is associated with human aging and mitochondrial deficiencies are thought to contribute to the onset of age-related diseases. Clear associations exist between deficiencies in mitochondrial function and neurodegenerative diseases such as Alzheimer's and Parkinson's disease, as well as diabetes and cancer. There is extensive evidence linking mitochondrial deficiencies to human pathology, and in particular of the central role that defects in mitochondrial gene expression play in pathogenesis. A crucial requirement for mitochondrial gene expression is proper ribosome biogenesis. This process, which is not well understood, involves several posttranscriptional RNA modifications that are thought to be crucial for ribosome assembly. KsgA and Dim1 methyltransferases dimethylate two adjacent adenine residues in a conserved stem-loop in the small subunit of the bacterial and eukaryotic ribosomes, respectively. Both the stem-loop structure and methylation events are conserved in the human 12S mitochondrial rRNA. Mitochondrial transcription factor B1 (TFB1M) is essential for mammalian development and catalyzes the analogous rRNA modification in mitochondria. Methylation by KsgA is related to bacterial aminoglycoside sensitivity and TFB1M activity could similarly be related to the effect of aminoglycoside antibiotics on the mitochondrial ribosome and aminoglycoside-induced hearing loss. Consistently, aminoglycoside sensitivity in humans is often maternally inherited, and methylation activity by TFB1M modulates the effects of a pathogenic mtDNA mutation linked to deafness. Other TFB1M polymorphisms are associated with reduced insulin secretion and increased risk of type II diabetes mellitus, further highlightin the importance of this modification for normal mitochondrial function. Metazoan mitochondria contain a second TFB family member, TFB2M, in addition to TFB1M. TFB2M was discovered along with TFB1M as a putative mitochondrial transcription factor that associates with the mitochondrial RNA polymerase and promotes initiation of mitochondrial transcription. It is now accepted that TFB2M is essential for the initiation of transcription in mitochondria, yet surprisingly, neither TFB1M nor TFB2M display similarity to any known transcription factor, raising the question of why a protein with a predicted methyltransferase fold plays a central role in transcription initiation. This question remains unanswered, since the mechanism by which TFB2M promotes initiation is not yet known. Both TFB1M and TFB2M are predicted to adopt methyltransferase folds, yet their atomic structures remain unknown. Key structural differences must exist between them that explain their evident functional divergence. The goal of this proposal is to provide a more complete understanding of how TFB proteins influence disease pathogenesis by elucidating the roles that they play in mitochondrial gene expression.
Funding Period: 2013-06-01 - 2015-05-31
more information: NIH RePORT

Top Publications

  1. pmc Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1
    Kip E Guja
    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA, Medical Scientist Training Program, Stony Brook University Medical Center, Stony Brook, NY 11794, USA and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
    Nucleic Acids Res 41:7947-59. 2013
  2. pmc A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site
    Agata Jacewicz
    Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
    PLoS ONE 8:e76700. 2013
  3. pmc Organization of the human mitochondrial transcription initiation complex
    Elena Yakubovskaya
    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, Cryo electron Microscopy Facility, New York Structural Biology Center, New York, NY 10027 and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 42:4100-12. 2014

Research Grants

Detail Information

Publications4

  1. pmc Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1
    Kip E Guja
    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA, Medical Scientist Training Program, Stony Brook University Medical Center, Stony Brook, NY 11794, USA and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
    Nucleic Acids Res 41:7947-59. 2013
    ..Together with mutagenesis studies, these data suggest a model for substrate binding and provide insight into the mechanism of methyl transfer, clarifying the role of this factor in an essential process for mitochondrial function. ..
  2. pmc A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site
    Agata Jacewicz
    Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
    PLoS ONE 8:e76700. 2013
    ..This represents a striking example of an action-at-a-distance interaction. ..
  3. pmc Organization of the human mitochondrial transcription initiation complex
    Elena Yakubovskaya
    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, Cryo electron Microscopy Facility, New York Structural Biology Center, New York, NY 10027 and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 42:4100-12. 2014
    ..Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex. ..

Research Grants30

  1. Mechanisms of transcription initiation in mitochondria
    Dmitry Temiakov; Fiscal Year: 2013
    ..The crystal structure of the core initiation complex that includes mtRNAP, TFAM, TFB2M and promoter DNA will be determined. ..
  2. mtDNA heteroplasmy in development and differentiation: an in-vitro approach
    RAJ RAGHAVENDRA RAO; Fiscal Year: 2013
    ..abstract_text> ..
  3. Mechanisms of mitochondrial transcription
    Miguel Garcia-Diaz; Fiscal Year: 2013
    ..Ultimately, improving our mechanistic understanding of the transcription process will help clarify the relationship between transcription, mitochondrial dysfunction and disease. ..
  4. MECHANISM AND REGULATION OF TRANSCRIPTION INITIATION
    Smita S Patel; Fiscal Year: 2013
    ..abstract_text> ..
  5. Transcribing Activities in N4 Infected E. Coli
    LUCIA B B ROTHMAN-DENES; Fiscal Year: 2013
    ..We will determine its localization on the template in vivo, purify gp1 and analyze its effect on N4 RNAP transcription initiation. ..
  6. Structure determination of reaction intermediates in macromolecular complexes
    Amie K Boal; Fiscal Year: 2013
    ....
  7. DEGENERATIVE AND DEMENTING DISEASES OF AGING
    Stanley B Prusiner; Fiscal Year: 2013
    ..The ultimate goal of all the proposed studies is to define the molecular events that feature in the formation of human prions in order to develop therapeutics that cure the human prion diseases. ..
  8. Hypoxic stabilization of OXPHOS complexes in mitochondrial defects
    Francisca Diaz; Fiscal Year: 2013
    ..Learning how to regulate respiratory complex and supercomplex assemblies will help us devise approaches to minimize free radical formation and further oxidative stress when cells are faced with a bioenergetic or oxygen challenges. ..
  9. Genetic Analysis of the PINK1-Parkin Pathway
    Leo J Pallanck; Fiscal Year: 2013
    ..Insight from our studies should be directly relevant to the etiology and treatment of Parkinson's disease, as well as the many other diseases in which mitochondrial dysfunction is implicated. ..
  10. SPINAL CIRCUITS AND THE MUSCULOSKELETAL SYSTEM
    Arthur W English; Fiscal Year: 2013
    ..This PPG brings together a team of established scientists from diverse backgrounds, with a common goal to continue to strengthen the science base underlying clinical rehabilitation. ..
  11. EARLY EVENTS IN ALZHEIMER PATHOGENESIS
    SUE TILTON GRIFFIN; Fiscal Year: 2013
    ..The synergy between our aims, approaches, and measures will enable us to meet our goal of defining early cellular interactions toward development of rational interventions in AD. ..
  12. Alerations of Sleep and Circadian Timing in Aging
    Eve Van Cauter; Fiscal Year: 2013
    ..Core B (Methods and Analysis) will standard operating procedures for data collection, archival and analysis. Core C will assay peripheral levels of hormones, cytokines and other blood constituents. ..
  13. UCLA Alzheimer's Disease Research Center
    David B Teplow; Fiscal Year: 2013
    ..Innovations in advancing research are proposed in each Core of this proposal. Each core has responded to criticisms and recommendations from the 2008 review in this renewal application. ..
  14. DEVELOPMENT OF NOVEL THERAPIES FOR NIDDM
    Christopher B Newgard; Fiscal Year: 2013
    ..abstract_text> ..
  15. Human Mitochondrial Disease: From Novel Gene Variants to Causality and Function
    VAMSI KRISHNA MOOTHA; Fiscal Year: 2013
    ..Finally, this project promises to have a valuable impact in fundamental biochemistry by revealing new proteins required for the assembly and biogenesis of the OXPHOS system. ..
  16. Structure and Mechanism of the Human Fe-S Cluster Assembly Complex
    David P Barondeau; Fiscal Year: 2013
    ..This fundamental research will establish a framework for emerging genetic results and discoveries and provide a basis for understanding defects in iron-sulfur cluster metabolism relevant to human health and disease. ..
  17. RNA Import into Mitochondria and Neurodegenerative Disorders
    Eriko Shimada; Fiscal Year: 2013
    ..My studies aim to uncover a novel role for RNA import in maintaining neural tissue and its contribution to neurodegenerative diseases when this process is defective. ..