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Postdoc - Biochemistry "University of Texas Southwestern Medical School, Dallas, Texas" - 1983
Ph.D. - Biochemistry University of Iowa, Iowa City, Iowa - 1979
B.A. - Chemistry University of Northern Iowa, Cedar Falls, Iowa - 1969
Dr. Millers research interests include the structure and organization of mitochondrial DNA, mitochondrial gene expression, RNA editing, and mitochondrial biogenesis. He is currently studying the extent and mechanism of RNA editing as a step in the mitochondrial gene expression of Myxomycetes.
Mitochondrial function is essential for the survival of nearly all eukaryotic organisms. Mitochondria are the site of cellular respiration and ATP synthesis and are the location of enzymes involved in such cellular processes as fatty acid synthesis, the urea cycle, apoptosis, and electron transport. Dysfunction of mitochondria is associated with cancer, aging, and a number of maternally inherited genetic diseases. Mitochondrial biogenesis depends on the coordinated expression of two different sets of genes, one set located on DNA in the nucleus and the other set located on DNA in mitochondria (mtDNA). These genes code for RNAs and proteins necessary for mitochondrial biogenesis. RNAs and proteins produced from nuclear genes must be imported into mitochondria where they function either autonomously or by interacting with the products of genes on mtDNA. Genes on mtDNA are transcribed to RNA by the mitochondrial RNA polymerase (mtRNAP). This is a central step in mitochondrial gene expression and is absolutely necessary for mitochondrial biogenesis. The mtRNAP is a single polypeptide which is encoded by a gene on the nuclear DNA. We are studying the mtRNAP of the myxomycete, Physarum polycephalum. This mtRNAP is particularly interesting since it is involved in a unique type of RNA processing called RNA editing.
RNA editing is the insertion or substitution of nucleotides in RNAs so that the RNAs are not identical in sequence to their DNA template. There are numerous examples of RNA editing but the most extensive examples are found in the RNAs of some mitochondria. Physarum polycephalum has a unique type of RNA editing in which mono or dinucleotides are inserted in RNAs at multiple sites relative to their mtDNA template. This process creates the open reading frame coding for proteins in mRNAs and produces structural features necessary for the function of transfer RNAs and ribosomal RNAs. These nontemplated nucleotides must be accurately and efficiently added to RNAs for mitochondrial function in Physarum. Accuracy requires the addition of the proper nucleotide at the proper site. We are currently attempting to understand the mechanism whereby nontemplated nucleotides are accurately and efficiently added to RNAs in mitochondria of Physarum, and to identify the genetic information used to specify nucleotide identity and the site of nucleotide addition. Several lines of evidence lead us to believe that the mtRNAP is an integral part of RNA editing in Physarum mitochondria. Because of this evidence we are presenting the mtRNAP with novel templates in an attempt to reproduce RNA editing in vitro.
Sarcar, S. N. and D. L. Miller A specific, promoter-independent activity of T7 RNA polymerase suggests a general model for DNA/RNA editing in single subunit RNA Polymerases.Nature - Scientific Reports 8, 13885 - 13896. 2018 - publications
Miller, D. L., R. Padmanabhan, S. N. Sarcar Genomics and Gene Expression in Myxomycetes. In: The Myxomycete: Biology, Systematics, Biogeography and Ecology, Steven Stephenson and Carlos Rojas, Eds., Elsevier Press pp. 107 - 143. 2017 - publications
Schaap, P.L., .....D.L. Miller et al. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-component and Metazoan-type Tyrosine Kinase Signaling.Genome Biology and Evolution 8, 109 – 125. 2016 - publications
Miller, D.L. Mitochondrial Genomes in Amoebozoa.In: Molecular Life Sciences, An Encyclopedic Reference, Springer Press. 2014 - publications
Miller, M.L. and D.L. Miller Non-DNA-Templated Addition of Nucleotides to the 3’End of RNAs by the Mitochondrial RNA Polymerase of Physarum polycephalum.Molecular and Cell Biology 28, 5795 – 5802. 2008 - publications
Krishnan, U., A. Barsamian, and D.L. Miller Evolution of RNA Editing Sites in the Mitochondrial Small Subunit rRNA of the Myxomycetes Methods in Enzymology424, 197 – 220. 2007 - publications
Miller, M., T.J. Antes, F. Qian, and D.L. Miller Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: characterization, expression, purification and transcription in vitro.Current Genetics, 49, 259 - 271. 2006 - publications
Estrada-Torres, A., T.W. Gaither, D.L. Miller, C. Lado, and H.W. Keller The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster.Mycologia 97, 139- 149. 2005 - publications
Assistant Professor, Molecular and Cell Biology The University of Texas at Dallas [1983–1988]
Associate Professor, Molecular and Cell Biology The University of Texas at Dallas [1988–Present]
Associate Head, Cell and Molecular Biolgy The University of Texas at Dallas [2007–Present]
Chair of Biotechnology Masters Program The University of Texas at Dallas [2008–Present]
Associate Dean of Undergraduate Studies, NS&M The University of Texas at Dallas [2009–2017]
Graduate and Postdoctoral Advisors
Dr. John Donelson, University of Iowa, Iowa City, Iowa
Dr. Nancy Martin, University of Kentucky, Louisville, Kentucky
Student Degrees Awarded
M.S. DEGREES AWARDED
1984 Ying-Chuan Yang (December) 1991 Anita Ghate (December) 1993 Ning Yang (May) 1993 C. Peyton Hughes (December) 1995 Nathan Abbott (December) 1996 Fang Qian (December) 1999 Arpi Barsamian (December) 2000 Tsui-ling Chang (May)
Ph.D. DEGREES AWARDED
1986 Richard M. Torczynski (Co-Chair) (August) 1988 Young-Won Kang (May) 1989 Gwo-Jen Liaw (December) 1989 Lynn C. Shaw (December) 1990 Elsy P. Jones (May) 1990 Ratha Mahendran (May) 1990 Matthew Spottswood (May) 1990 Hsiao-Hsueh Shu (Co-Chair) (December) 1994 Siqing Wang (December) 1996 Wen-Ju Lin (May) 1997 Catherine Nakagawa (December) 1997 Sung-Tzu Liang (Co-Chair) (May) 1998 Travis John Antes (August) 1999 Uma Krishnan (May) 2005 Mara Miller (December) 2018 Ramesh Padmanabhan (May) 2018 Subha Sarcar (May)