Dennis Miller

Associate Professor - Biological Sciences
Associate Dean of Undergraduate Education - Natural Sciences & Mathematics
dmiller@utdallas.edu
972-883-2539
FO3.218
Tags: Molecular Biology Biology Biochemistry

Professional Preparation

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

Research Areas

Overview
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.

Research Interests
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. 

Publications

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 Enzymology 424, 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
Wang, S., R. Mahendran and D.L. Miller
Editing of cytochrome b mRNA in Physarum mitochondria.Journal of Biological Chemistry 274, 2725-2731. 1999 - publications
Antes, T., H. Costandy, R. Mahendran,  M. Spottswood, and D. L. MillerInsertional editing of mitochondrial tRNAs of  Physarum polycephalum  and  Didymium nigripes.Molecular and Cellular Biology 18, 7521-7527. 1998 - publications

Appointments

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]

Additional Information

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)