Sandra L. Martin, Ph.D.
Professor
Ph.D. (1982), University of California at Berkeley
Molecular Evolutionary Genetics
Two biological questions are presently under investigation in my laboratory. We are interested in the mechanism of L1 retrotransposition and its control in genetic and evolutionary time, as well as in the molecular events that determine the phenotype of a hibernating mammal. Answers to both questions will impact our understanding of genome evolution and the relationship between genotype and phenotype.
LINE-1, or L1, elements populate the genomes of all mammals. Typically, L1 sequences comprise between 10 and 30% of a genome and are interspersed throughout all chromosomes. This highly repetitive L1 DNA family is comprised of a small number of active transposable elements and a large number of their truncated, defective progeny. Movement into new sites in nuclear DNA occurs via reverse transcription of an RNA intermediate, probably by a unique mechanism known as target primed reverse transcription, or tprt. Current efforts in our laboratory are directed towards understanding the biochemical intermediates of L1 retrotransposition and the genetic control points that regulate the dynamics of this process in vivo. LINE-1 retrotransposition begins with transcription of a full-length, sense-strand L1 RNA and requires two L1-encoded polypeptides. These proteins also catalyze the reverse transcription and integration of SINEs (short interspersed repeated sequences) and processed pseudogenes, thereby amplifying the effects of LINE-1 in mammalian genome dynamics. Our long-range goal is to understand the retrotransposition process in detail, including the biochemical intermediates involved as well as its control in genetic and evolutionary time. Specifically, ongoing experiments are designed to enhance understanding of the structure and function of the two essential L1-encoded proteins, ORF1p and ORF2p, and the details of their interaction with each other as well as with both RNA and DNA. We are also working to define the cis- and trans-acting components of translational control that operate upon the two L1-encoded proteins in the naturally-occurring dicistronic L1 mRNA, and how the L1 RNA transitions from its role as a translation template to that of a reverse transcriptase template
We also study hibernation in mammals because it serves as a dramatic example with which to examine the molecular basis of adaptive evolution. Mammals in deep hibernation exhibit profound reductions in their basal metabolic, heart and respiratory rates, along with core body temperature; the identical constellation of physiological parameters is inevitably lethal to a non-hibernating species. At present, very little is known about the mechanisms that permit hibernators to achieve, maintain and survive these profound physiological changes at the molecular level. Hibernating species are widely interspersed among monotremes, marsupials and placentals. The widespread phylogenetic distribution of hibernators suggests that hibernation is an ancestral trait that has been lost numerous times in mammalian evolution, but implies that all mammals share the genes that specify and permit the hibernating phenotype. Thus, our long term goal for this project is to understand how the mammalian genotype is expressed as a hibernating phenotype in some, but not all mammals. This project has two components: the first seeks to identify differentially expressed genes at the mRNA and protein level. The second component tests predictions that derive from the hypothesis that hibernators must rewarm periodically in order to replenish gene products that are catabolized, but not synthesized, at the low body temperatures of torpor. Understanding the molecular mechanisms that control the reversible suppression of various biochemical processes during hibernation is expected to have broad implications for cell function and survival of the hypothermic and/or hypometabolic state, as will elucidation of the molecular signature that underlies the hibernating phenotype. Application of this understanding to human biology is expected to have widespread utility, including: improved storage times for transplant organs, simplification of routine surgery, and improved outcomes for victims of cardiac arrest due to heart failure or trauma.
Publications
van Breukelen, F. and Martin, S.L. (2001) Translational initiation is uncoupled from elongation at 18¡C during mammalian hibernation, Am. J. Physiol. 281, R1374-R1379.
van Breukelen, F. and Martin, S.L. (2002) Reversible depression of transcription during hibernation. J. Comp. Physiol. 172, 355-361.
Epperson, L.E. and Martin, S.L. (2002) Quantitative assessment of ground squirrel mRNA levels in multiple stages of hibernation, Physiol. Genomics 10, 93-102.
van Breukelen, F. and Martin, S.L. (2002) Molecular adaptations in mammalian hibernators: unique adaptations or generalized responses? J. App. Physiol. 92, 2640-2647.
Kolosha, V.O. and Martin, S.L. (2003) High affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1), J Biol Chem. 278, 8112-8117.
Martin, S.L., Branciforte, D., Keller, D. and Bain, D.L. (2003) Novel trimeric structure for an essential protein in L1 retrotransposition, Proc. Natl. Acad. Sci., USA 100, 13815-13820.
van Breukelen, F., Sonenberg, N. and Martin S.L. (2004) Seasonal and state dependent changes of eIF4E and 4E-BP1 during mammalian hibernation: implications for the control of translation during torpor, Am J Physiol Regul Integr Comp Physiol. 287, R349-R353
Epperson, L.E., Dahl, T. and Martin, S.L. (2004) Quantitative analysis of liver protein expression during hibernation in golden-mantled ground squirrel, Mol. Cell. Proteomics. 3, 920-933.
Martin, S.L., Li, W.-l. P., Furano, A.V. and Boissinot, S. (2005) The structures of mouse and human L1 elements reflect their insertion mechanism, Cytogenet. Genome Res. 110, 223-228.
Martin, S.L., Cruceanu, M., Branciforte, D., Li, P. W.-l., Kwok, S.C., Hodges, R.S. and Williams, M.C. (2005) LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein, J. Mol. Biol. 348, 549-561.
Heras, S. R., L—pez, M. C., Garc’a-PŽrez, J. L., Martin, S. L. & Thomas, M. C. (2005). The L1Tc C-terminal domain from a Trypanosoma cruzi non-LTR retrotransposon codes for a protein that bears two C2H2 zinc-finger motifs and is endowed with nucleic acid chaperone activity. Mol. Cell. Biol. 25, 9209-9220.
Williams, D.R., Epperson, L.E., Li, W., Hughes, M.A., Taylor, R., Rogers, J., Martin, S.L., Cossins, A.R., Gracey, A.Y. (2005) The seasonally hibernating phenotype assessed through transcript screening. Physiol. Genomics. 24, 13-22.
Basame, S., Li, P.W-l., Howard, G., Branciforte, D., Keller, D., Martin, S.L. (2006) Spatial assembly and RNA binding stoichiometry of a protein essential for LINE-1 retrotransposition. J. Mol. Biol. 357, 351-7.
Li, P.W.-l., Li, J., Timmerman, S., Krushel, L., Martin, S. L. (2006) The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nuc. Acids Res. 34, 853-64.
