Michael W. Krause, Ph.D.


Laboratory of Molecular Biology, Chief

DIR
DIVISION INTRAMURAL RESEARCH
NIDDK, National Institutes of Health
Building 3 , Room 2W05
3 Center Dr.
Bethesda, MD 20814
Tel: 301-402-4633
Fax: 301-496-0201
Email: michaelkr@niddk.nih.gov


Education / Previous Training and Experience:
B.A., University of Colorado, 1978
Ph.D., University of Colorado, 1986


Research Statement:

My research group has an interest in the transcriptional regulation of cell fate determination during metazoan development. We are using the simplicity of the C. elegans system (genomic, genetic, cellular, etc.) to provide novel insights into the transcriptional control of cell fate specification. The defined and essentially invariant cell lineage in this model organism allows us to precisely determine when and where transcription factor are present throughout development. The genetics of the system allow us to determine the loss- or reduction-of-function phenotypes when one or more of these transcription factors are depleted. Together, this gives us the ability to tease apart the transcriptional hierarchy of cell fate specification from fertilization to adulthood. In recent years, we have extended these studies to include an analysis of transcriptional changes associated with nutrient flux, including the characterization of heme-responsive genes and the study of an under appreciated post-translational modification (O-GlcNAcylation) that influences RNA Pol II behavior.

Transcriptional Control of Cell Fate: Understanding master regulators and the redundant and hierarchical control of developmental programs

Gut: The intestinal developmental program in the worm is one of the simplest among animal models, with all intestinal cells arising clonally from a single precursor blastomere called E. Previous work from others have defined the transcriptional cascade leading to the specification of the E blastomere as a gut precursor and defined the GATA-type transcription factor ELT-2 as the master regulator of this decision. Our recent work has asked whether this single transcription factor 1) operates by activating all intestinal target genes and 2) functions throughout development, from embryo to adult. In collaboration with the McGhee lab in Calgary, we provide convincing evidence that indeed ELT-2 does direct the expression of most (if not all) gut genes directly and that this factor functions in this role throughout development. This work shows how a single transcription factor can act as a master regulator, specifying organ identity and orchestrating a complex pattern of gene expression throughout development.

Muscle: A long-standing area of emphasis for my group is bodywall muscle development during embryogenesis. Previously, we demonstrated that the master regulatory transcription factor HLH-1/MyoD is essential for proper bodywall (striated) muscle fate specification and development. We went on to show that it worked in concert with another factor, UNC-120/SRF, in a positive feed-forward and autoregulatory loop to ensure commitment of blastomeres to the bodywall muscle fate. Moreover, we uncovered a third, partially redundant factor, HND-1/Hand, that operates in a subset of bodywall muscle precursors. We demonstrated that deletion of all three factors, but not any one or two, resulted in animals lacking this muscle type. This work uncovered unexpected redundancy within the muscle cell fate specification program. More importantly, we were able to propose a unified theory of animal muscle development involving a core set of transcription factors, thus solving a long-standing paradox in the muscle development field.

As a follow-up to these studies, we continue to dissect the transcriptional programs operating both upstream and downstream of this core muscle master regulator. We were able to demonstrate that in the posterior bodywall muscle lineages a rather simple program exists to activate the myogenic factor HLH-1/MyoD. Here, a maternally contributed factor (PAL-1/Caudal) works in conjunction with Wnt signaling through defined cis-acting elements in the promoter of hlh-1 to initiate myogenesis. This work clarifies the transcriptional cascade at the molecular level for posterior bodywall muscle cell development and allows us to understand the developmental program for these cells from prior to fertilization until the newly hatched animal. We also characterized the genome-wide distribution of HLH-1 binding sites and analyzed them in light of previously described muscle transcriptomes. In addition to providing technical advances in this type of analysis, this work reveals that the prolific binding of HLH-1/MyoD genome-wide is evolutionarily conserved, implying functions for these factors master regulators beyond simple transcriptional activation.

More recently, we have turned our attention to understanding the regulatory cascade of bodywall muscle cells originating from the early blastomere called MS. Although the 28 MS-derived bodywall muscle cells all eventually activate the core muscle factors HLH-1 and UNC-120, the cascade of regulators leading to the activation of these two transcription factors is complex and variable making this a very challenging developmental question. Using forward and reverse genetics, in combination with reporter genes and antibody staining assays, we find that MS bodywall muscle cell development is driven by at least five transcription factors operating in both distinct and overlapping temporal and spatial patterns of expression. We can now describe the minimal transcriptional cascade needed for essentially all bodywall muscle cells in C. elegans from fertilization onward. Importantly, each of the five transcription factors we identified within the MS lineage has previously been implicated in some aspect of head mesodermal development in frogs and mice. Thus, our results reveal a previously unappreciated conservation of a transcriptional module regulating anterior mesoderm development that is evolutionarily conserved from worms to mammals.

Transcriptional Responses to Nutrient Flux: Sensing nutrient availability and the ensuing gene expression responses

Heme: Heme-containing proteins regulate essential metabolic activities in a variety of cellular compartments. This includes the guanylate cyclases and globins in the cytoplasm, mitochondrial cytochromes, and lysosomal peroxidases. Interestingly, the uptake, intracellular transport, and sequestration mechanisms for heme are very poorly understood in metazoans. In collaboration with Dr. Iqbal Hamza, we capitalized on his observations that nematodes are heme auxotrophs to identify genes responsive to fluctuating heme concentrations in culture. This pioneering work led to the identification of many novel heme-regulated genes (hrgs), some of which were evolutionarily conserved. In addition to uncovering novel regulators of heme homeostasis, this work dissects for the first time in a living organism the complex mechanisms employed by tissues to sense heme levels and activate scavenging, transport and recycling pathways for this important cofactor. Additionally, nematode-specific heme transporters are attractive drug targets in the fight against the devastating health effects from helminth infections world-wide.

O-GlcNAc: The hexosamine signaling pathway is a nutrient sensing mechanism used by cells to modulate a variety of cellular processes (e.g. transcription, translation, protein turnover) in response to changes in nutrient flux. The synthesis of the sugar nucleotide UDP-N-acetyl glucosamine (UDP-GlcNAc) is linked to energy, fatty acid, and glucose metabolism, thus the UDP-GlcNAc pool reflects the nutrient status of the cell. High levels of UDP-GlcNAc drive the addition of a single sugar (O-GlcNAc) to Ser and Thr residues of target nuclear and cytoplasmic proteins via a transferase (OGT). This reaction is in dynamic equilibrium with the removal of the sugar by the O-GlcNAcase (OGA). Thus, the hexosamine pathway can modulate multiple cellular processes by modifying protein activity in response to changes in nutrient status. Roles for these enzymes in modulating insulin-like signaling in C. elegans emerged from our current and previous work done as a long-term collaboration with Dr. John Hanover’s group in NIDDK.

Recently, our study of this dynamic post-translational, single sugar modification of target proteins has focused on transcription. Capitalizing on the unique viability and fertility of loss-of-function mutants in both enzymes in the C. elegans system, we have used chromatin immunoprecipitation (ChIP) and whole-genome array hybridization (chip) to show that O-GlcNAcylated chromatin-associated proteins are discretely located at the promoter region of a subset of genes. We have gone on to show that this chromatin O-GlcNAc mark is responsive to nutritional flux, that RNA Pol II is a target of O-GlcNAcylation, and that disruption of normal O-GlcNAc cycling in mutants results in dramatic changes in RNA Pol II distribution and global changes in gene expression. These results expand our understanding of the integration of nutritional sensing with transcriptional regulation and provide a novel link between nutritional flux and the epigenetic control of gene expression.



Selected Publications:

Krause, M., Love, D.C., Ghosh, S.K., Wang, P., Bentley, D.L., Fukushige, T., and Hanover, J.A. (2011) Nutrient-driven O-GlcNAcylation at promoters impacts genome-wide RNA Pol II distribution and dynamics. (Submitted)

Fukushige, T. and Krause, M. (2011) Myogenic conversion and transcriptional profiling of embryonic blastomeres in C. elegans. Methods (Invited Review – submitted).

Kouns, N.A., Nakielna, J., Behensky, F., Krause, M.W., Kostrouch, Z, and Kostrouchova, M. (2011) NHR-23 dependent collagen and Hedghog-related genes required for molting. BBRC (Accepted).

Krause, M. and Liu, J.K. (2011) Somatic muscle specification during embryonic and post-embryonic development in the nematode C. elegans. WIREs Developmental Biology (accepted).

Mondoux, M.A., Love, D.C., Ghosh, S.K., Fukushige, T., Bond, M., Weerasinghe, G.R., Hanover, J.A., and Krause, M.W. (2011) O-GlcNAc cycling and insulin signaling are required for the glucose stress response in C. elegans. Genetics , 188: 369-382.

Lei, H., Fukushige, T., Niu, W., Sarov, M., Reinke, V. and Krause, M. (2010).  A widespread distribution of geomic CeMyoD binding sites revealed and cross validated by ChIP-chip and ChIP-seq techniques. PLoS ONE 5(12):e15898.

Love, D. C., Krause, M.W., and Hanover, J.A. (2010). O-GlcNAc cycling: Emerging roles in development and epigenetics. Seminars in Cell & Developmental Biology , 21, 646-654.

Vohanka, J., Simeckova, K., Machalova, E., Behensky, F., Krause, M.W., Kostrouch, Z., and Kostrouchova, M. (2010).  Diversification of fasting regulated transcription in a cluster of duplicated nuclear hormone receptors in C. elegans. Gene Expression Patterns , 10, 227-236.

Severance, S., Rajagopal, A., Rao, A.U., Cerqueira, G.C., Mitreva, M., El-Sayed, N.M., Krause, M. and Hamza, I. (2010) Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans. PLoS Genetics , 6, e1001044.

Dona C. Love, Salil Ghosh, Michelle A. Mondoux, Tetsunari Fukushige, Peng Wang, Mark C. Wilson, Wendy B. Iser, Catherine A. Wolkow, Michael W. Krause and John A. Hanover. (2010) Dynamic O-GlcNAc cycling at promoters of C. elegans genes regulating longevity, stress and immunity. Proc. Natl. Acad. Sci. U.S.A ., 107, 7413-7418.

Hanover, J.A., Krause, M. W., and Love, D. C., (2010) The Hexosamine Signaling Pathway:  O-GlcNAc cycling in feast or famine. Biochemica et Biophhysica Acta ,1800, 80-95.

Hanover, J.A., Krause, M. W., and Love, D. C., (2009) The Hexosamine Signaling Pathway:  O-GlcNAc cycling in feast or famine. Biochemica et Biophhysica Acta - General Subjects (in press).

Michelle A. Mondoux, Michael W. Krause, and John A. Hanover. (2009) Insulin Signaling is Only the Beginning: C. elegans Genetic Networks Predict Roles for O-GlcNAc Regulation in Key Signaling Pathways.  CSTT (in press)

Lei, H., Liu, J., Fukushige, T., Fire, A., and Krause, M. (2009) Caudal-like PAL-1 directly activates the bodywall muscle module regulator hlh-1 in C. elegans to initiate the embryonic muscle gene regulatory network. Development , 136, 1241-1249.

McGhee, J.D., Fukushige, T., Krause, M.W., Minnema, S.E., Goszczynski, B., Kohara, Y., Gaudet, J., Bossinger, O., Jones, S.J.M., Zhao, Y., Hirst, M., Ruzanov, P., Marra, M.A., Zapf, R., Moerman, D.G., and Kalb, J.M. (2009) ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol , 327, 551-565.

Cai, T., Hirai, H., Fukushige, T., Yu, P., Zhang, G., Notkins, A.L, and Krause, M.  (2009).  Loss of the transcriptional repressor PAG-3/Gfi-1 results in enhanced neurosecretion that is dependent on the dense-core vesicle membrane protein IDA-1/IA-2. PLOS Genetics , 5: e1000447

Rajagopal, A., Rao, A.U., Amigo, J., Tian, M., Upadhyay,  S.K., Hall, Cl, Uhm, S., Mathew, M.K., Fleming, M.D., Paw, B.H., Krause, M., Hamza, I. (2008)  Haem homeostasis is regulated by the conserved and concerted functions of HRG-1 proteins. Nature , 453, 1127-1131.

Pohludka, M., Simeckova, K., Vohanka, J., Yilma, P., Novak, P., Krause, M.W., Kostrouchova, M. and Kostrouch, Z. (2008)  Proteomic analysis uncovers a metabolic phenotype in C. elegans after nhr-40 reduction of function. BBRC , 12, 49-54.

Fox, R.M., Watson, J.D., Von Stentia, S.E.,  McDermott, J., Brodigan, T.M., Fukushige, T., Krause, M., and Miller, D.M. III (2007). The embryonic muscle transcriptome of C. elegans. Genome Biology, 8, r188.

Simeckova, K., Brozona, E., Vohanka, J., Pohludka, M., Kostrouch, Z., Krause, M., Rall, J.E., and Kostrouchova, M. (2007).  Supplementary nuclear receptor NHR-60 is required for normal embryonic and early larval development of Caenorhabditis elegans. Folia Biologica 53, 85-96.

Fukushige, T., Brodigan, T.M., Schriefer, L., Waterston, R.H., and Krause, M. (2006) Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: Evidence for a unified theory of animal muscle development. Genes & Development 20, 3395-3406.

Michele Forsythe, Dona C. Love, Brooke D. Lazarus, Eun Ju Kim, William A. Prinz, Gilbert Ashwell, Michael W. Krause and John A. Hanover. (2006) C. elegans ortholog of a diabetes susceptibility locus:  oga-1 (O-GlcNAcase) knockout impacts O-GlcNAc cycling, metabolism and dauer formation. Proc. Natl. Acad. Sci . U.S.A. 103, 11952-7.

Okkema, P.G. and Krause, M. (2005) Transcriptional regulation, WormBook , ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.45.1, http://www.wormbook.org., 1-41.

Fukushige, T. and Krause, M. (2005). The myogenic potency of HLH-1 reveals wide-spread developmental plasticity in early C. elegans embryos. Development 132, 1795-1805.

Hanover, J.A., Forsythe, M.E. Hennessey, P., Brodigan, T.M., Love, D.C., Ashwell, G. and Krause, M. (2005). A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout. Proc. Natl. Acad. Sci. U.S.A 102, 11266-11271.

Cai, T., Fukushige, T., Notkins, A.L., and Krause, M. (2004). Insulinoma-Associated Protein IA-2, a vesicle transmembrane protein, genetically interacts with UNC-31/CAPS and affects neurosecretion in Caenorhabditis elegans. J. Neuroscience 24, 3115-3124.

Brodigan, T.M., Liu, J., Park, M., Kipreos, E.T., and Krause, M. (2003).  Cyclin E expression during development in C. elegans. Dev. Biol. 254, 102-115.

Tonkin, L.A., Saccomanno, L., Morse, D.P., Brodigan, T., Krause, M., and Bass, B.L. (2002). RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J . 21, 6025-6035.

Arudchandran, A., Cerritelli, S.M., Krause, M.W., and Crouch, R.J. (2002). Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome. Mol. Biol. & Evol. 19, 1910-1919.

Corsi, A. K., Brodigan, T., Jorgensen, E., and Krause, M. (2002). A dominant negative mutant of C. elegans Twist with implications for Saethre-Chotzen syndrome. Development 129, 2761-2772.

Berke, J.D., Sgambato, V., Zhu, P.-P., Lavoie, B., Vincent, M., Krause, and M., Hyman, S.E. (2001). Dopamine and glutamate induce distinct striatal splice forms of Ania-6, an RNA polymerase II-associated cyclin. Neuron 32, 277-287.

Kostrouchova, M., Krause, M., Kostrouch, Z., and Rall, J.E. (2001). Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 98, 7360-7365.

Cai, T., Krause, M., Odenwald, W.F., Toyama, R., and Notkins, A.L. (2000). The IA-2 gene family: Homologs in C. elegans, Drosophila and zebrafish. Diabetologia 44, 81-88.

Zheng, R., Ghirlando, R., Lee, M.S., Wei, S.-Q., Mizuuchi, K., Krause, M., and Craigie, R. (2000). BAF bridges DNA in a discrete higher order nucleoprotein complex: a possible role in chromosome organization. Proc. Natl. Acad. Sci. U.S.A. 97, 8997-9002.

Dichoso, D., Brodigan, T., Chwoe, K.Y., Lee, J.S., Llacer, R., Park, M., Corsi, A.K., Kostas, S.A., Fire, A., Ahnn, J., and Krause, M. (2000). The MADS box factor CeMef2 is not essential for C. elegans myogenesis and development. Developmental Biology 223, 431-40.

Corsi, A.K., Kostas, S.A., Fire, A., Krause, M. (2000) Caenorhabditis elegans Twist plays an essential role in non-striated muscle development. Development 127, 2041-51.

Fei, Y.-Y., Romero,M.F., Krause, M., Liu, J.-C., Huang, W., Ganpathy, V., and Leibach, F.H. (2000). A novel H -coupled oligopeptide transporter (OPT3) from Caenorhabditis elegans with a predominant function as a H -channel and exclusive expression in neurons. J. Biol. Chem. 275, 9563-71.

Park, M. and Krause, M. (1999). Regulation of postembryonic G1 cell cycle progression in C. elegans by a cyclin/cdk-like complex. Development 126, 4849-4860.

Gladyshev, V.N., Krause, M., Xu, X.M., Korotkov, K.V.. Kryukov, G.V., Sun, Q.A., Lee, B.J., Wooton, J.C., and Hatfield, D.L. (1999). Selenocysteine-containing thioredoxin reductase in C. elegans. Biochem. & Biophys. Res. Com. 259, 244-249.

Zhang, J.-M., Chen, L., Krause, M., Fire, A., and Paterson, B.M. (1999). Evolutionary conservation of MyoD function and differential utilization of E proteins. Dev. Biol. 208, 465-472.

Krause, M. (1999). Cell Fate Determination In C. elegans. In: Development - Genetics, Epigenetics and Environmental Regulation., Enzo Russo, David Cove, Lois Edgar, Rudolf Jaenisch, and Francesco Salamini eds., Springer-Verlag, Heidelberg, 251-267.

Harfe, B.D., Vaz Gomes, A., Kenyon, C., Krause, M., and Fire, A. (1998). Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning. Genes & Dev. 12, 2623-2635.

Harfe, B.D., Branda,C.S., Krause, M., Stern, M.J., and Fire, A. (1998). MyoD and the specification of muscle and non-muscle fates in postembryonic development of the C. elegans mesoderm. Development 125, 2479-2488.

Kostrouchova, M., Krause, M., Kostrouch, Z., and Rall, J.E. (1998). CHR3: a Caenorhabditis elegans orphan nuclear hormone receptor required for proper epidermal development and molting. Development 125, 1617-1626.

Krause, M., Park, M., Zhang, J.-M., Yuan, J., Harfe, B., Xu, S.-Q., Greenwald, I., Cole, M., Paterson, B., and Fire, A. (1997). A C. elegans E/Daughterless bHLH protein marks neuronal but not striated muscle development. Development 124, 2179-2189.

W.A. Lubas, Frank, D.W., Krause, M., and Hanover, J.A. (1997). O-linked GlcNAc transferase is a conserved nucleocytoplasmic protein containing tetratricopeptide repeats. J. Biol. Chem., 272, 9316-9324.

Krause, M. and McGhee, J. (1996). Transcription factors and transcriptional regulation. In: The Nematode C. elegans. ed Don Riddle, Jim Priess, and Tom Blumenthal, Cold Spring Harbor Press (Cold Spring Harbor, NY).

Krause, M.W. (1995). Techniques for analyzing transcription and translation. In: Caenorhabditis elegans: Modern biological analysis of an organism, eds Henry F.Epstein, Diane C.Shakes, Academic Press (San Diego) 513-529.

Krause, M.W. (1995). Regulation of transcription and translation. In: Caenorhabditis elegans: Modern biological analysis of an organism, eds Henry F.Epstein, Diane C.Shakes, Academic Press (San Diego) 483-512.

Krause, M.W. (1995). MyoD and myogenesis in C. elegans. BioEssays 17, 219-228.

Krause, M.W., Harrison, S.W., Xu, S.-Q., Chen, L., and Fire, A. (1994). Elements regulating cell- and stage-specific expression of the C. elegans MyoD family homolog hlh-1. Dev. Biol. 166, 133-148.

Chen, L., Krause, M.W., Sepanski, M., and Fire, A. (1994). The C. elegans MyoD homologue HLH-1 is essential for proper muscle function and complete morphogenesis. Development 120, 1631-1641.

Krause, M.W. and Weintraub, H. (1992). CeMyoD expression and myogenesis in C. elegans. Sem. Dev. Biol. 3, 277-285.

Krause, M.W., Fire, A., Harrison, S.W., Weintraub, H., and Tapscott, S. (1992). Functional conservation of nematode and vertebrate myogenic regulatory factors. J. Cell Sci. , Supp. 16, 111-115.

Mello, C.C., Draper, B.W., Krause, M.W., Weintraub, H., and Priess, J.R. (1992). The pie-1 and mex-1 genes and maternal control of blastomere identity in early C. elegans embryos. Cell 70, 163-176.

Chen, L., Krause, M.W., Draper, B., Weintraub, H., and Fire, A. (1992). Body-wall muscle formation in Caenorhabditis elegans embryos that lack the MyoD homolog hlh-1. Science 256, 240-243.

Weintraub, H., Davis, R., Tapscott, S., Thayer, M., Krause, M., Benezra, R., Blackwell, T.K., Turner, D., Rupp, R., Hollenberg, S., Zhuang, Y., and Lassar, A. (1991). The myoD gene family: Nodal point during specification of the muscle cell lineage. Science 251, 761-766.

Krause, M.W., Fire, A., Harrison, S.W., Priess, J., and Weintraub, H. (1990). CeMyoD accumulation defines the bodywall muscle cell fate during C. elegans embryogenesis. Cell 63, 907-922.

Krause, M.W., Wild, M., Rosenzweig, B.R., and Hirsh, D. (1989). Wild type and mutant actin gene structure in C. elegans. J. Mol. Biol. 208, 381-392.

Dibb, N.J., Maruyama, I., Krause, M.W., and Karn, J. (1989). Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family. J. Mol. Biol. 205, 603-613.

Krause, M.W. and Hirsh, D. (1987). A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49, 753-761.

Krause, M.W. and Hirsh, D. (1986). Actin gene transcription during Caenorhabditis elegans development. In: Cellular and Molecular Biology of the Cytoskeleton, ed. Shay, J.W., Plenum Publishing Corporation (New York).

Krause, M.W. and Hirsh, D. (1984). Actin gene expression in Caenorhabditis elegans. In: Molecular Biology of the Cytoskeleton, eds Murphy, D., Cleveland, D., and Borisy, G., Cold Spring Harbor Press (Cold Spring Harbor, NY).

Landel, C.P., Krause, M.W., Waterston, R., and Hirsh, D. (1984). DNA rearrangements of the actin gene cluster in C. elegans accompany reversion of three muscle mutants. J. Mol. Biol. 180, 497-513.




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