The Department of Biological Chemistry is composed of faculty members that form an intellectually exciting community. The diverse research interests focus on understanding the chemistry and biochemistry of life processes. Faculty members are very active and interactive and work in a culture that encourages the free exchange of ideas while fostering exciting collaborations within and outside the department. Such interactions strongly enhance the ability of each member to make seminal discoveries that cross scientific disciplines.
725 N. Wolfe St. 408 Biophysics BuildingBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-614-1230
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Munns CH, Chung MK, Amzel LM, and Caterina MJ. (2015) Role of the outer pore domain in TRPV1 dynamic permeability to large cations. J. Biol Chem. 290: 5707-5724. PMID: 25568328PubMed ReferencePang Z, Sakamoto T, Kim YS, Yang F, Guan Y, Dong X, Guler A, Caterina MJ. Keratinocyte stimulation is sufficient to evoke nociception in the mouse (2015) Pain Apr;156(4):656-65. (cover article) PMID: 25790456PubMed ReferenceHua ZL, Jeon S, Caterina MJ, and Nathans JN. Frizzled3 is required for the development of multiple axon tracts in the mouse central nervous system. Proc. Natl. Acad. Sci. U.S.A. Jul 22;111(29):E3005-14.PMID: 24799694PubMed ReferenceKim YS, Chu Y, Han L, Li M, Li Z, LaVinka PC, Sun S, Tang Z, Park K, Caterina MJ, Ren K, Dubner R, Wei F and Dong X. Central Terminal Sensitization of TRPV1 by Descending Serotonergic Facilitation Modulates Chronic Pain. Neuron (2014) Feb 19;81(4):873-87. PMID: 24462040PubMed ReferenceCaterina MJ (2014) TRP channel cannabinoid targets and skin inflammation ACS Chem Neurosci. 5(11):1107-16 PMID: 24915599
Park U, Vastani N, Guan Y, Raja S, Koltzenberg M. and Caterina MJ. TRPV2 knockout mice are susceptible to perinatal lethality but display normal thermal and mechanical nociception (2011) J Neurosci. 31(32):11425-36.PubMed Reference
Huang SM, Li X, Yu Y, Wang J, Caterina MJ. TRPV3 and TRPV4 ion channels are not major contributors to mouse heat sensation. (2011) Mol Pain. 2011 May 17;7(1):37.PubMed Reference
Cheng X, Jin, J, Hu L, Shen D, Dong X, Samie MA, Knoff J, Eisinger B, Liu M, Huang SM, Caterina MJ, Dempsey P, Michael E, Dlugosz A, Andrews NC, Clapham DE, and Xu H. A Keratinocyte TRP Channel Controls Hair Morphogenesis and Skin Barrier Formation via EGFR signaling and Transglutaminase Activity. (2010) Cell 141, 331-343.PubMed Reference
Link TM, Park U, Vonakis BM, Raben DM, Soloski MJ, Caterina MJ. TRPV2 has a pivotal role in macrophage particle binding and phagocytosis. (2010) Nature Immunology 11, 232-239.PubMed Reference
Landouré G, Zdebik AA, Martinez TL, Burnett BG, Stanescu HC, Inada H, Shi Y, Taye AA, Kong L, Munns CH, Choo SS, Phelps CB, Paudel R, Houlden H, Ludlow CL, Caterina MJ, Gaudet R, Kleta R, Fischbeck KH, Sumner CJ. Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C Nature Genet. (2010) Feb;42(2):170-4.PubMed Reference
Huang SM, Lee H, Chung MK, Park, U, Yu YY, Bradshaw H, Coulombe PA, Walker JM, and Caterina MJ. Skin keratinocyte TRPV3 ion channels modulate pain sensitivity via prostaglandin E2. (2008) J. Neurosci. 28, 13727-13737.PubMed Reference
Chung MK, Guler AD and Caterina MJ. TRPV1 exhibits dynamic ionic selectivity during agonist stimulation. (2008) Nature Neuroscience 11, 555-564 (Highlighted in Nat Neurosci. 2008 May;11(5):528-9)PubMed Reference
Moussaieff A, Rimmerman N, Bregman T, Straiker A, Felder CC, Shoham S, Kashman Y, Huang SM, Lee H, Shohami E, Mackie K, Caterina MJ, Walker JM, Fride E and Mechoulam R. Incensole acetate, an incense component, elicits psychoactivity by activating TRPV3 channels in the brain (2008) FASEB J 22(8):3024-34.PubMed Reference
Lumpkin EA and Caterina MJ. Mechanisms of Sensory Transduction in the Skin. (2007) Nature 445(7130):858-65.PubMed Reference
Birder L, Negoita F, Lee H, de Groat W, Kanai A, Barrick S, Meyers S, and Caterina, MJ. Activation of Urothelial-TRPV4 by 4a-PDD contributes to altered bladder reflexes in the rat. (2007) J Pharmacol Exp Ther. 323(1):227-35. PubMed Reference
Sidhaye VK, Guler AD, Schweitzer KS, D’Alessio F, Caterina MJ and King LS Transient receptor potential vanilloid 4 regulates aquaporin-5 abundance under hypotonic conditions. (2006) Proc. Natl. Acad. Sci., USA 103(12):4747-52.PubMed Reference
Shimizu I, Iida T, Horiuchi N and Caterina MJ. 5-Iodoresiniferatoxin evokes hypothermia in mice and is a partial TRPV1 agonist in vitro .(2005) J. Pharm. Exp. Ther., 314:1378-85.PubMed Reference
Shimizu I, Iida T, Guan Y, Zhao C, Raja SN, Jarvis MF, Cockayne DA, and Caterina MJ. Enhanced thermal avoidance in mice lacking the ATP receptor P2X3. (2005) Pain, 116, 96-108.PubMed Reference
Pogatzki-Zahn E,, Shimizu I, Caterina MJ and Raja SN. Heat hyperalgesia after incision requires TRPV1 and is distinct from pure inflammatory pain. (2005) Pain, 115, 296-307.PubMed Reference
Chung MK, Guler AD, and Caterina MJ. Biphasic currents evoked by chemical or thermal activation of the heat-gated ion channel, TRPV3. (2005) J. Biol Chem. 280, 15928-15941.PubMed Reference
Lee H, Iida T, Mizuno A, Suzuki M, Caterina MJ. Altered thermal preference in mice lacking TRPV4. (2005) J. Neurosci. 25 1304-10.PubMed Reference
Iida T, Shimizu I, Nealen ML, Campbell, A., and Caterina MJ. Attenuated fever response in mice lacking TRPV1. (2005) Neurosci. Lett. 378, 28-33.PubMed Reference
Chung MK, Lee H, Mizuno A, Suzuki M, Caterina MJ. 2-aminonethoxydiphenyl borate activates and sensitizes the heat-gated ion channel, TRPV3. (2004) J. Neurosci. 24, 5177-5182.PubMed Reference
Suite 371 MRBBaltimore, MD 21205
Office Phone: 410-614-7566
Lab Phone: 410-614-6968
Watkin EE, Arbez N, Waldron-Roby E, O'Meally R, Ratovitski T, Cole RN, and Ross CA (2014) Phosphorylation of mutant huntingtin at serine 116 modulates neuronal toxicity. PLoS One 9: e88284.PubMed Reference
Herbrich SM, Cole RN, West KP, Jr., Schulze K, Yager JD, Groopman JD, Christian P, Wu L, O'Meally RN, May DH, McIntosh MW, and Ruczinski I (2013) Statistical Inference from Multiple iTRAQ Experiments without Using Common Reference Standards. Journal of Proteome Research 12: 594-604.PubMed Reference
Foster DB, Liu T, Rucker J, O'Meally RN, Devine LR, Cole RN, and O'Rourke B (2013) The cardiac acetyl-lysine proteome. PLoS One 8: e67513.PubMed Reference
Cole RN, Ruczinski I, Schulze K, Christian P, Herbrich S, Wu L, Devine LR, O'Meally RN, Shrestha S, Boronina TN, Yager JD, Groopman J, and West KP, Jr. (2013) The plasma proteome identifies expected and novel proteins correlated with micronutrient status in undernourished Nepalese children. Journal of Nutrition 143: 1540-1548.PubMed Reference
Mattis VB, Svendsen SP, Ebert A, Svendsen CN, King AR, Casale M, Winokur ST, Batugedara G, Vawter M, Donovan PJ, Lock LF, Thompson LM, Atwal RS, Zhu Y, Fossale E, Gillis T, Mysore J, Li JH, Seong I, Shen Y, Chen X, Wheeler VC, MacDonald ME, Gusella JF, Akimov S, Arbez N, Juopperi T, Ratovitski T, Chiang JH, Kim WR, Chighladze E, Watkin E, Zhong C, Makri G, Cole RN, Margolis RL, Song H, Ming G, Ross CA, Kaye JA, Daub A, Sharma P, Mason AR, Finkbeiner S, Rushton D, Brazier SP, Battersby AA, Redfern A, Tseng HE, Harrison AW, Kemp PJ, Allen ND, Castiglioni V, Onorati M, Cattaneo E, Yu J, Thomson JA, and Arjomand J (2012) Induced pluripotent stem cells from patients with Huntington's disease show CAG-repeat-expansion-associated phenotypes. Cell Stem Cell 11: 264-278.PubMed Reference
Murray CI, Uhrigshardt H, O'Meally RN, Cole RN, and Van Eyk JE (2012) Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay. Molecular and Cellular Proteomics 11: M111 013441.PubMed Reference
Ratovitski T, Chighladze E, Arbez N, Boronina T, Herbrich S, Cole RN, and Ross CA (2012) Huntingtin protein interactions altered by polyglutamine expansion as determined by quantitative proteomic analysis. Cell Cycle 11: 2006-2021.PubMed Reference
Zizak M, Chen T, Bartonicek D, Sarker R, Zachos NC, Cha B, Kovbasnjuk O, Korac J, Mohan S, Cole RN, Chen Y, Tse CM, and Donowitz M (2012) Calmodulin kinase II constitutively binds, phosphorylates, and inhibits brush border Na+/H+ exchanger 3 (NHE3) by a NHERF2 protein-dependent process. Journal of Biological Chemistry 287: 13442-13456.PubMed Reference
Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, Reedy MC, Zmasek CM, Gucek M, Cole RN, Van Eyk JE, Bodmer R, O'Rourke B, Bernstein SI, and Foster DB (2011) A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster. PLoS One 6: e18497.PubMed Reference
Hartman IZ, Kim A, Cotter RJ, Walter K, Dalai SK, Boronina T, Griffith W, Lanar DE, Schwenk R, Krzych U, Cole RN, and Sadegh-Nasseri S (2010) A reductionist cell-free major histocompatibility complex class II antigen processing system identifies immunodominant epitopes. Nature Medicine 16: 1333-1340.PubMed Reference
Ratovitski T, Gucek M, Jiang H, Chighladze E, Waldron E, D'Ambola J, Hou Z, Liang Y, Poirer MA, Hirschhorn RR, Graham R, Hayden MR, Cole RN, and Ross CA (2009) Mutant Huntingtin N-terminal fragments of specific size mediate aggregation and toxicity in neuronal cells. Journal of Biological Chemistry 284: 10855-10867.PubMed ReferenceGuo Y, Singleton PA, Rowshan A, Gucek M, Cole RN, Graham DR, Van Eyk JE, and Garcia JG (2007) Quantitative proteomic analysis of human endothelial cell membrane rafts: Evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Molecular and Cellular Proteomics 6: 689-696.PubMed Reference
Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, and Hart GW (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Molecular and Cellular Proteomics 1: 791-804.PubMed Reference
Dinkova-Kostova AT, Holtzclaw WD, Cole RN, Itoh K, Wakabayashi N, Katoh Y, Yamamoto M, and Talalay P (2002) Direct evidence that sulfhydryl groups of Keap1 are the sensors regulating induction of phase 2 enzymes that protect against carcinogens and oxidants. Proceedings of the National Academy of Sciences, USA 99: 11908-11013.PubMed Reference
Cole RN and Hart GW (2001) Cytosolic O-glycosylation is abundant in nerve terminals. Journal of Neurochemistry 79: 1080-1089.PubMed Reference
521A Physiology BldgBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-3458
The Fukunaga lab investigates the mechanism and biology of small silencing RNAs. We try to understand how small silencing RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs), are produced and how they function. We use a combination of biochemistry, biophysics, fly genetics, cell culture, X-ray crystallography and next-generation sequencing, in order to understand the biogenesis and function of small silencing RNAs from the atomic to the organismal level.
miRNAs are 21-24 nt long RNA. In fruit fly Drosophila, miRNAs are transcribed as long primary transcripts called pri-miRNAs (Figure 1). The pri-miRNA is cleaved into pre-miRNA in the nucleus by the RNase III enzyme Drosha, aided by the dsRNA-binding partner protein Pasha. The Exportin-5/Ran-GTP complex transports pre-miRNA from the nucleus to the cytoplasm. In cytoplasm, Dicer-1, aided by the dsRNA-binding partner protein Loqs-PA or Loqs-PB, cleaves the pre-miRNA into miRNA duplex. miRNA is then loaded to Argonaute1 and binds target mRNAs through base complementarity of the miRNA sequence at positions 2-8 (called seed sequence). miRNA-Ago1 binding to the target mRNAs causes translational repression and mRNA degradation.
Loqs-PB, but not its alternative splicing isoform Loqs-PA, changes the nucleotide positions at which Dicer-1 cleaves pre-miRNA and produces miRNA with distinct length (Figure 2). These alternatively produced miRNAs can have distinct seed sequences and therefore regulate different target mRNAs. The mammalian Dicer partner protein TRBP, but not its paralogue PACT, changes the length and the seed sequence of miRNAs produced by Dicer in mammals. The Fukunaga lab investigates how Dicer partner proteins (Loqs-PB in fly and TRBP in mammals) change the miRNA length generated by the Dicer enzymes. We also try to uncover biological significance of the alternative miRNA production. Our hypothesis is that the alternative splicing of Loqs-PA/Loqs-PB in fly and the gene expression of TRBP/PACT in mammals are finely regulated in each tissue and developmental stage, leading to regulated production of distinct miRNA isoforms, and that such fine regulation is important for biology. For this end, we are trying to make miR-307a knockout flies and plan to analyze the molecular phenotypes. Furthermore, we are trying to discover novel factors and mechanisms regulating the miRNA production and function.
In another project, as collaboration with a physician scientist, Dr. Roselle Abraham at the Cardiology Division of Department of Medicine, we are studying functional effects of a miRNA SNP mutation found from Hypertrophic cardiomyopathy (HCM) patients. This project may lead to development of novel diagnosis and therapeutics for cardiovascular diseases including HCM in the future.
Drosophila Dicer-2 associates with the dsRNA-binding partner proteins Loqs-PD and R2D2 and produces 21 nt long siRNAs from long dsRNA (Figure 2). siRNA is loaded to Argonaute2 and silences highly complementary target RNAs by cleaving them—a process typically called RNAi. One of the biological functions of the siRNA pathway is to fight against exogenously derived viral infection and against genome encoded transposon invasion. In addition, Dicer-2 produces endogenous siRNAs (endo-siRNAs) derived from genome encoded long hairpin RNA or overlapping mRNAs. The biological functions of these classes of endo-siRNAs are not well understood. We are interested in how viral and endogenously derived RNAs are recognized and cleaved into siRNAs by Dicer-2 and how the produced siRNAs function in biology. We also try to identify and characterize novel factors involved in or regulating the siRNA pathways. We are also interested in understanding how the two Dicer enzymes achieve their respective substrate specificities (pre-miRNA for Dicer-1 and long dsRNA for Dicer-2). Recently, we found that physiological concentration of inorganic phosphate, a small molecule found in all the cells, restricts the substrate specificity of Dicer-2 to long dsRNA by inhibiting Dicer-2 from cleaving pre-miRNA, without affecting cleavage of long dsRNA (Figure 4). We propose that inorganic phosphate occupies the phosphate-binding pocket in Dicer-2 and thereby block access of pre-miRNA. Currently we are investigation the function of the phosphate-binding pocket.
piRNAs (26-31 nt) are mostly produced in gonads (ovaries and testes). Unlike miRNAs and siRNAs, Dicer enzymes are not involved in the piRNA production. piRNAs are produced in the primary processing pathway and the ping-pong pathway, which are not yet fully understood (Figure 5). piRNAs are loaded onto PIWI proteins and function in epigenetic and post-transcriptional gene silencing of transposons and other genetic elements in order to maintain genome integrity of germline cells. Interestingly, piRNAs are recently implicated also in sex determination, neuronal functions in brain, and tumorigenesis in cancer cells. We are interested in the mechanisms for biogenesis and function of piRNAs. We are trying to identify new factors involved in the piRNA pathway, using a fly reporter system.
4. RNA helicase
RNA helicases are involved in almost all the aspects in the RNA biology: RNA transcription, transport, translation, silencing, localization, structural rearrangement, decay, and so on. The Dicer enzymes also have a N-terminal 'helicase' domain. We are studying molecular and physiological roles of DEAD-box RNA helicases. Particularly, we are currently focusing on Drosophila belle, a DEAD-box RNA helicase that essential for fly viability and fertility and is conserved from yeast to human (Figure 6). We are making various mutant Belle and analyzing them genetically and biochemically.
Our lab uses multi-disciplinary approaches to understand the biogenesis and function of small silencing RNAs from the atomic to the organismal level. Small silencing RNAs play crucial roles in various aspects in biology. In fact, mutations in the small RNA genes or in the genes involved in the pathways cause many diseases in human including cancers. Our research projects will answer fundamental biological questions and also potentially lead to therapeutic application to human disease.
Postdoc and student positions are available. Please contact the PI if interested.
Fukunaga R, Colpan C, Han BW, Zamore PD, "Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain" EMBO Journal, 18, 371-84, (2014)PubMed Reference
Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD, "Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals" Cell, 151, 533-46, (2012)PubMed Reference
725 N. Wolfe Street, 520 WBSBBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-502-2361
Sundararajan K, Miguel A, Desmarais SM, Meier EL, Huang KC, and Goley ED. (2015) The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction. Nat Commun. 6:7281. PubMed Reference
Meier EL and Goley ED. (2014) Form and function of the bacterial cytokinetic ring. Curr Opin Cell Biol. 26:19-27.PubMed Reference
Goley ED (2013) Tiny cells meet big questions: a closer look at bacterial cell biology. Mol Biol Cell. 24:1099-102.Pubmed Reference
Biteen JS, Goley ED, Shapiro L, Moerner WE. (2012) Three-Dimensional Super-Resolution Imaging of the Midplane Protein FtsZ in Live Caulobacter crescents cells Using Astigmatism. Chemphyschem. 13:1007-12.PubMed Reference
Goley ED*, Yeh YC*, Hong SH, Fero MJ, Abeliuk E, McAdams HH, Shapiro L. (2011) Assembly of the Caulobacter cell division machine. Mol. Micro. 80:1680-1698.PubMed Reference
Hsiao-lu DL, Lord SJ, Iwanaga S, Zhan K, Xie H, Williams JC, Wang H, Bowman GR, Goley ED, Shapiro L, Tweig RJ, Rao J, Moerner WE. (2010) Superresolution Imaging of Targeted Proteins in Living Cells Using Photoactivatable Organic Fluorophores. J Am Chem Soc. 132:15099-15101.PubMed Reference
Goley ED, Dye NA, Werner JN, Gitai Z, Shapiro L. (2010) Imaging-based identification of a critical regulator of FtsZ protofilament curvature in Caulobacter. Mol. Cell. 39:975-987.PubMed Reference
Goley ED, Comolli LR, Fero KE, Downing KH, Shapiro L. (2010) DipM links peptidoglycan remodeling to outer membrane organization in Caulobacter. Mol. Micro. 77:56-73.PubMed Reference
Goley ED, Toro E, McAdams HH, Shapiro L. (2009) Dynamic Chromosome Organization and Protein Localization Coordinate the Regulatory Circuitry that Drives the Bacterial Cell Cycle. Col Spring Harb. Symp. Quant. Biol. 74:55-64. [Review]PubMed Reference
Goley ED, Iniesta AA, Shapiro L. (2007) Cell cycle regulation in Caulobacter: location, location, location. J. Cell Sci. 120: 3501-7. [Review]PubMed Reference
409 PhysiologyBaltimore, MD 21205
Office Phone: 410-955-0215
Lab Phone: 410-955-3085
Animal cells secrete small vesicles (~50-250 nm diameter) that have the same topology as the cell. These vesicles, known as exosomes and microvesicles (EMVs), can be taken up by neighboring cells, completing a pathway of intercellular vesicle traffic. Our laboratory studies the molecular mechanisms of EMV biogenesis and uptake, and their contributions to cell polarity, cell:cell interactions, and intercellular signaling. Furthermore, we study the ways in which HIV and other retroviruses use the exosome biogenesis pathway for the formation of infectious virions, and the consequences of their EMV origin. Currently, we are investigating the following questions:
Gan X and Gould SJ. (2012) HIV Pol Inhibits HIV Budding and Mediates the Severe Budding Defect of Gag-Pol. PLoS One. 7:e29421. PubMed Reference
Gan X and Gould SJ. (2011) Identification of an inhibitory budding signal that blocks the release of HIV particles and exosome/microvesicle proteins. Mol. Biol. Cell. 22:817-830. PubMed Reference
Shen B, Wu N, Yang JM, and Gould SJ. (2011) Protein targeting to exosomes/microvesicles by plasma membrane anchors. J. Biol. Chem. 286:14383-14395. PubMed Reference
Shen B, Fang Y, Wu N and Gould,SJ. (2011) Biogenesis of the posterior pole is mediated by the exosome/microvesicle protein-sorting pathway. J. Biol. Chem. 286:44162-76. PubMed Reference
725 N. Wolfe Street, 517 WBSBBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-2362
Synapses are specialized cell-cell junctions which connect individual neurons together and are the sites of transmission of information between neurons. While the molecular mechanisms which promote synapse formation have been a subject of intense investigation, little is known about the molecular mechanisms that limit synapse formation so that synapses form at the right time and place and in the correct numbers. We hypothesize that this step in the refinement of synaptic formation is crucial for the fine-tuning of neuronal connectivity and that signaling networks which limit synapses during development are either defective or inappropriately activated in cognitive disorders. Accordingly, our laboratory studies the signaling pathways that regulate synapse formation during normal brain development to begin to understand how, when these pathways go awry, human cognitive disorders develop.
Currently projects include studies of:
1) Ephexin5: Ephexin5 is a guanine nucleotide-exchange factor (GEF) that activates the small G-protein RhoA, a regulator of the actin cytoskeleton. Genetic loss- and gain-of-function studies indicate that Ephexin5 acts to restrict spine growth and synapse development in the developing brain. Upon induction of EphrinB/EphB ligand-receptor signaling, Ephexin5 is rapidly phosphorylated in an EphB-dependent manner and targeted for proteasome-dependent degradation. These findings suggest that Ephexin5 functions as a barrier to excitatory synapse development until its degradation is triggered by EphrinB binding to EphBs. Interestingly, the degradation of Ephexin5 is mediated by Ube3A, a ubiquitin ligase whose expression level is altered in the human cognitive disorder Angelman Syndrome (AS) and in some forms of autism. This suggests that aberrant EphB/Ephexin5 signaling during synaptic development may contribute to the abnormal cognitive function observed in AS and autism.
Using Ephexin5 our laboratory will pursue an understanding of the molecular pathways that regulate restriction of excitatory synapse formation and their relevance to the pathophysiology of Angelman Syndrome by addressing the following questions:
1) What are the molecular determinants critical for Ube3A-mediated control of Ephexin5 degradation?
2) What molecular and cellular events underlie Ephexin5-mediated excitatory synapse restriction important for basic wiring of the nervous system?
3) What additional substrates of Ube3A are important for synapse formation?
1) What are the molecular determinants critical for Ube3A-mediated control of Ephexin5 degradation?
2) What molecular and cellular events underlie Ephexin5-mediated excitatory synapse restriction important for basic wiring of the nervous system?
3) What additional substrates of Ube3A are important for synapse formation?
2) New regulators of synapse formation: The goal of this study will be to identify additional components of the genetic program that restrict synapse numbers using previously developed immunocytochemistry-based assay for neuronal synaptic connections in vitro. Specific targets will be corroborated using electrophysiological and in vivo morphological measurements. We are particularly interested in genes whose products function to restrict synapse formation early in development and are suggested to be defective or inappropriately activated in cognitive disorders.
Margolis SS*, Salogiannis J*, Lipton DM, Mandel-Brehm C, Wills ZP, Mardinly AR, Hu L, Greer PL, Bikoff JB, Ho H-YH, Soskis, MJ , Sahin M, Greenberg ME . EphB mediated degradation of the RhoA GEF Ephexin5 relieves a developmental brake on excitatory synapse formation. Cell. 2010 Nov 29; 143 (4): 442-55.PubMed Reference
Comment in “Cell”: Dalva MB. (2010) Ephecting excitatory synapse development. Cell. 29;143(3):341-2.PubMed Reference
725 N. Wolfe StBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-502-2571
For images of our work
Recent links to our work: Neuroscience Innovations
Videos showing increased mRNA repression (RNA-processing bodies) in live neurons responding to BDNF:Messenger RNA accumulates in a neuronBDNF-treated neuron
Huang*Y-WA, Ruiz*CR, Eyler ECH*, Lin K, and Meffert MK (2012). Dual regulation of miRNA biogenesis generates target specificity in neurotrophin-induced protein synthesis. Cell, 148(5); 933-946.PubMed Reference
Boersma* MC, Dresselhaus*EC, De Biase LM, Mihalas AB, Bergles DE, and Meffert MK (2011), A requirement for NF-kB in developmental and plasticity-associated synaptogenesis. J.Neurosci., 31; 5414-5425.PubMed Reference
Shrum CK, Defrancisco D, and Meffert MK. (2009) Stimulated nuclear translocation of NF-kB and shuttling differentially depend on dynein and the dynactin complex. PNAS, 106; 2647-2652.PubMed Reference
Boersma MC and Meffert MK (2008) Novel roles for the NF-kB signaling pathway in regulating neuronal function. Science Signaling 1, pe7.PubMed Reference
Shrum CK and Meffert MK (2008). The NF- kB Family in Learning and Memory. In J. David Sweatt(Ed.), Molecular Mechanisms of Memory. Vol.  of Learning and Memory: A Comprehensive Reference (J.Byrne Editor), pp. [567-586] Oxford: ElsevierScience Direct
Mattson MP and Meffert MK (2006). Roles for NF-kB in nerve cell survival, plasticity, and disease. Cell Death and Differentiation 13, 852-60.PubMed Reference
Meffert MK and Baltimore D (2005). Physiological functions for brain NF-kB. Trends in Neurosciences 28, 37-43.PubMed Reference
Meffert MK, Chang JM, Wiltgen BJ, Fanselow MS, Baltimore D (2003). NF-kB functions in synaptic signaling and behavior. Nature Neuroscience 6, 1072 - 1078.PubMed Reference
Meffert MK, Calakos NC, Scheller RH, Schulman H (1996). Nitric oxide modulates synaptic vesicle docking / fusion reactions. Neuron 16, 1229-1236.PubMed Reference
Meffert*MK, Haley*JE, Schuman EM, Schulman H, and Madison DV (1994). Inhibition of hippocampal heme oxygenase, nitric oxide synthase and long-term potentiation by metalloporphyrins. Neuron 13, 1225-1233.PubMed Reference
Meffert MK, Premack BA, and Schulman H (1994). Nitric oxide stimulates calcium-independent synaptic vesicle release. Neuron 12, 1235-1244.PubMed Reference
Schuman EM, Meffert MK, Schulman H, Madison DV (1994). An ADP-Ribosyltransferase as a Target for Nitric Oxide Action in Long-Term Potentiation. Proceedings of the National Academy of Sciences 91, 11958-11962.PubMed Reference
510 PhysiologyBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-6918
De Jesus DA, O'Connor TJ, Isberg RR (2013) Analysis of Legionella infection using RNA interference in Drosophila cells. Methods Mol Biol 954:251-264.PubMed ReferenceO'Connor TJ, Boyd D, Dorer M, Isberg RR (2012) Analysis of aggravating genetic interactions allows a solution to redundancy in a bacterial pathogen. Science 338:1440-1444.PubMed Reference
Choy A, Dancourt J, Mugo B, O'Connor TJ, Isberg RR, Melia T, Roy CR (2012) Autophagy inhibition by irreversible deconjugation of Atg8 proteins from membranes. Science 338:1072-1076.PubMed Reference
O'Connor TJ, Adepoju Y, Boyd D, Isberg RR (2011) Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion. Proc Natl Acad Sci 108:14733-14740.PubMed Reference
Huang L, Boyd D, Amyot WM, Hempstead AD, Luo ZQ, O'Connor TJ, Chen C, Machner M, Montminy T, Isberg RR. (2011) The E Block motif is associated with Legionella pneumophila translocated substrates. Cell Microbiol 13:227-245.PubMed Reference
Isberg RR, O’Connor TJ, Heidtman H (2009) The Legionella pneumophila replication vacuole: making a cosy niche inside host cells. Nature Reviews Microbiology 7:13-24.PubMed Reference
725 N. Wolfe St. 400 BiophysicsBaltimore, MD 21205
Office Phone: 410-614-1944
Lab Phone: 410-955-3167
In addition to studies focused on elucidating the structure, mechanism, and regulation of the mammalian mitochondrial ATP synthase, a major disease focus of the Pedersen lab for many years has been cancer because of its well known alterations in energy metabolism. More recently, we have entered also into a study of heart dysfunction as the heart with every beat is totally dependent on energy metabolism, with the mitochondrial ATP synthase being intimately involved. The laboratory uses chemistry, molecular biology, biophysics, immunology, tissue culture and animal models to better understand the energetics/energy metabolism of normal and pathological cells/tissues. A major focus is on the two 'power plants', the mitochondria and the glucose catabolic system (glycolysis), as well as on the interaction between these two systems. The following are active research projects. 1) The mechanism and regulation of ATP synthesis in mammalian mitochondria.This involves the study of the molecular properties of the ATP synthase complex that consists of two nano-motors both of which are necessary to make ATP. In a collaborative study we have obtained the 3-D structure of one of the motors and are now working on the structure of the whole complex that consists of 17 subunit types and over 30 total subunits. Recently, we discovered that the ATP synthase is in complex formation with the transport system (carrier) for phosphate and the transport system for adenine nucleotides (ADP and ATP). We have named this complex the ATP Synthasome and are now carrying out studies to obtain a 3-D structure of the whole complex. It is important to note that the ATP synthasome represents the terminal complex of oxidative phosphorylation in mitochondria and makes most of the ATP needed/day to supply our energy needs. In addition to the above mentioned work, we have also recently discovered that the ATP synthasome contains another key protein originally thought to be within the outer membrane as well as at contact sites between inner and outer membranes. This protein is likely critical for channeling ATP to the cytoplasm.
Work on the ATP synthasome is being vigorously studied.2) Cancer: Regulation and targeting genes and proteins responsible for the most common phenotype and developing a novel potent anticancer agent, 3-bromopyruvate (3BP).The most common metabolic phenotype of malignant cells & tumors including those derived from liver, breast, lung, brain, etc. is their capacity to utilize glucose at high rates even in the presence of oxygen. The pivotal enzyme involved is hexokinase 2 (HK-2) that is markedly elevated and bound at or very near the outer mitochondrial membrane protein named "VDAC" (voltage dependent anion channel). At this location, hexokinase 2 not only helps couple ATP formation in mitochondria to the phosphorylation of glucose to "jump start"glucose catabolism, it also represses this organelle's contribution to cell death. Therefore, hexokinase 2, in addition to its critical metabolic role, also promotes cancer by helping immortalize cancer cells. We are studying both the hexokinase 2 gene and developing novel strategies to target both the gene and the protein. We use both tumor cells growing in tissue culture and animal models, i.e., animals with cancer.
While working in my laboratory at the beginning of this century Dr. Young Ko discovered that the small molecule 3-bromopyruvate (3BP) is a potent anticancer agent. Several years later while working as a new faculty member in collaboration with my laboratory she would lead a team that showed 3BP's capacity to completely cure (eradicate) cancers in 19 out of 19 treated animals, i.e.,100%.
Currently, in collaboration with Dr. Ko, we are now involved in the further development of 3BP while searching for other effective anticancer agents. A limited number of studies conducted in humans with 3BP have proved very promising.
3) Heart Dysfunction: Regulation of the mitochondrial ATP synthase in the normal and ischemic heart. The heart can survive only short periods without oxygen. Conditions where oxygen is limiting can have grave consequences as the mitochondrial membrane potential will collapse and the mitochondrial ATP synthase will switch from synthesizing ATP to hydrolyzing ATP, thus depleting heart cells (cardiomyocytes) of the energy reserves they require for survival. Fortunately, the ATP synthase is well regulated in the heart so that the ATP hydrolytic event is minimized during short periods of ischemia (reduced oxygen). In fact, there are 3 known small peptide regulators of the ATP synthase, one which optimizes ATP synthesis and the other two that suppress ATP hydrolysis. In addition, the ATP synthase is subjected to regulatory signal transduction events that result either in its phosphorylation or dephosphorylation.
We are currently involved in a project designed to understand the relative importance of these and other regulatory events in protecting the heart during sudden ischemic insults. [The laboratory has published over 240 papers of which >150 describe original research while the others refer either to novel methods or represent reviews]
Majkowska-Skrobek G, Augustyniak D, Lis P, Bartkowiak A, Gonchar M, Ko YH, Pedersen PL, Goffeau A, Ułaszewski S. Killing multiple myeloma cells with the small molecule 3-bromopyruvate: implications for therapy. Anticancer Drugs. 2014 Jul;25(6):673-82.PubMed ReferenceDyląg M, Lis P, Niedźwiecka K, Ko YH, Pedersen PL, Goffeau A, Ułaszewski S. 3-Bromopyruvate: a novel antifungal agent against the human pathogen Cryptococcus neoformans. Biochem Biophys Res Commun. 2013PubMed ReferenceDarpolor MM, Kaplan DE, Pedersen PL, Glickson JD. Human Hepatocellular Carcinoma Metabolism: Imaging by Hyperpolarized 13C Magnetic Resonance Spectroscopy. J Liver Disease Transplant. 2012 Sep 1;1(1).PubMed ReferencePedersen PL. Mitochondria in relation to cancer metastasis: introduction to a mini-review series. J Bioenerg Biomembr. 2012 Dec;44(6):615-7.PubMed ReferencePedersen PL. 3-Bromopyruvate (3BP) a fast acting, promising, powerful, specific, and effective "small molecule" anti-cancer agent taken from labside to bedside: introduction to a special issue. J Bioenerg Biomembr. 2012 Feb;44(1):1-6.PubMed ReferenceLis P, Zarzycki M, Ko YH, Casal M, Pedersen PL, Goffeau A, Ułaszewski S. Transport and cytotoxicity of the anticancer drug 3-bromopyruvate in the yeast Saccharomyces cerevisiae. J Bioenerg Biomembr. 2012.PubMed Reference
733 N. BroadwayBaltimore, MD 21205
Office Phone: 443-287-3109
Lab Phone: 443-287-3104
Jattani RP, Tritapoe JM, Pomerantz JL. Cooperative Control of Caspase Recruitment Domain-Containing Protein 11 (CARD11) Signaling by an Unusual Array of Redundant Repressive Elements. J. Biol Chem. 2016. 291(16):8324-8336.PubMed Reference
Jattani RP, Tritapoe JM, Pomerantz JL. Intramolecular Interactions and Regulation of Cofactor Binding by the Four Repressive Elements in the Caspase Recruitment Domain-Containing Protein 11 (CARD11) Inhibitory Domain. J. Biol Chem. 2016. 291(16):8338-8348. PubMed Reference
Hamblet CE, Makowski SL, Tritapoe JM, Pomerantz JL. NK Cell Maturation and Cytotoxicity are Controlled by the Intramembrane Aspartyl Protease SPPL3. J. Immunol. 2016;196:2614-2626.PubMed Reference
Pedersen SM, Chan W, Jattani RP, Mackie dS, Pomerantz JL. Negative Regulation of CARD11 Signaling and Lymphoma Cell Survival by the E3 Ubiquitin Ligase RNF181. Mol Cell Biol. 2016; 36:794-808.PubMed Reference
Makowski, SL, Wang, Z, Pomerantz JL. A Protease-independent Function for SPPL3 in NFAT Activation. Mol Cell Biol. 2015. 35(2):451–467.PubMed Reference
Chan, W., Schaeffer TB, Pomerantz JL. A quantitative signaling screen identifies CARD 11 mutations in the CARD and LATCH domains tht induce Bc110 ubiquitination and human lymphoma cell survival. Mol Cell Biol. 2013. 33(2): 429-443.PubMed Reference
Lamason, R.L., Lew SM, and Pomerantz JL. 2010. Transcriptional target-based expression cloning of immunoregulatory molecules. Immunol. Res. 47:172-178.PubMed Reference
Lamason, R.L., McCully RR, Lew SM, and Pomerantz JL. 2010. Oncogenic CARD11 mutations induce hyperactive signaling by disrupting autoinhibition by the PKC-responsive inhibitory domain. Biochemistry 49:8240-8250.PubMed Reference
Lamason, R.L., Kupfer A, and Pomerantz JL. 2010. The dynamic distribution of CARD11 at the immunological synapse is regulated by the inhibitory kinesin GAKIN. Mol. Cell 40:798-809.PubMed Reference
Yang, H.-C., Shen L, Siliciano RF, and Pomerantz JL. 2009. Isolation of a cellular factor that can reactivate latent HIV-1 without T cell activation. Proc. Natl. Acad. Sci.USA, 106: 6321-6326.PubMed Reference
McCully, R.R. and Pomerantz JL. 2008. The Protein Kinase C-responsive inhibitory domain of CARD11 functions in NF-κB activation to regulate the association of multiple signaling cofactors that differentially depend on Bcl10 and MALT1 for association. Molecular and Cellular Biology 28:5668-5686.PubMed Reference
Sommer, K., Guo B, Pomerantz JL, Bandaranayake AD, Moreno-Garcia ME, Ovechkina YL, and Rawlings DJ. 2005. Phosphorylation of the CARMA1 linker controls NF-kappaB activation. Immunity 23, 561-574.PubMed Reference
Wurtz, N.R., Pomerantz JL, Baltimore D, and Dervan PB. (2002) Inhibition of DNA binding by NF-kB with pyrrole-imidazole polyamides. Biochemistry, 41, 7604-7609.PubMed Reference Pomerantz, J.L., and Baltimore D. (2002) Two pathways to NF-kB. Mol. Cell, 10, 693-695.PubMed Reference Pomerantz, J.L., Denny EM, and Baltimore D. (2002) CARD11 mediates factor-specific activation of NF-kB by the T cell receptor complex. EMBO J., 21, 5184-5194.PubMed Reference
Pomerantz, J.L. and Baltimore D. (2000) Signal transduction ï¿½ A cellular rescue team. Nature, 406, 26-29.PubMed Reference
Pomerantz, J.L. and Baltimore D. (1999) NF-kB activation by a signaling complex containing TRAF2, TANK, and TBK1, a novel IKK-related kinase. EMBO J., 18, 6694-6704.PubMed Reference
Pomerantz, J.L., Wolfe SA, and C.O. Pabo CO. (1998) Structure-based design of a dimeric zinc finger protein. Biochemistry, 37, 965-970.PubMed Reference
Pomerantz, J.L., Pabo CO, and Sharp PA. (1995) Analysis of homeodomain function by structure-based design of a transcription factor. Proc. Natl. Acad. Sci.USA, 92, 9752-9756.PubMed Reference
Pomerantz, J.L., and Sharp PA. (1994) Homeodomain determinants of major groove recognition. Biochemistry, 33, 10851-10858.PubMed ReferencePomerantz, J.L., Kristie TM, and Sharp PA. (1992) Recognition of the surface of a homeo domain protein. Genes & Development 6, 2047-2057.PubMed Reference
Pomerantz, J.L., Mauxion Yoshida FM, Greene WC, and Sen R. (1989) A second sequence element located 3' to the NF-kB binding site regulates IL-2 receptor-alpha gene induction. Journal of Immunology 143, 4275-4281.PubMed Reference Rothenberg, M.E., Pomerantz JL, Owen WF, Jr., Avraham S, Soberman RJ, Austen KF, and Stevens RL. (1988) Characterization of a human eosinophil proteoglycan, and augmentation of its biosynthesis and size by interleukin 3, interleukin 5, and granulocyte/macrophage colony stimulating factor. Journal of Biological Chemistry 263, 13901-13908.PubMed Reference
Hunterian 502Baltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-1410
A major effort in our laboratory is focused on understanding the biochemistry and chemistry underlying the molecular aspects involved in regulating lipid metabolizing signaling enzymes and the physiological roles of this regulation. Control of lipid metabolizing enzymes involves the modulation of two key parameters; their sub-cellular distribution and their intrinsic enzymatic activity. Our studies have concentrated on three families of lipid-metabolizing signaling enzymes: diacylglycerol kinases, phospholipases D, and phospholipases C.
Specific Areas of Interest
Interfacial Enzymology of Lipid Metabolizing Signaling Enzymes: We are particularly interested in identifying the critical modulating proteins, lipids, and post-translational modifications that alter the localization and/or activity of lipid metabolizing enzymes. In these studies we consider the fact that these enzymes act as interfacial enzymes and their regulation includes a number of interfacial-dependent parameters. Our recent studies have identified some of the diacylglycerol metabolizing enzyme DGK-θ (diacylglycerol kinase-theta) interfacial parameters that are altered upon neuronal depolarization. Further, our studies demonstrated that activation of DGK-θ requires a protein that contains a polybasic region. We have recently obtained evidence that identifies at least one, if not only, activator binding domain on DGK-θ.Enzyme Structure/Function Studies: We are also interested in the structural components of these enzymes that are critical for their distribution/re-distribution to specific sub-cellular compartments. Additionally, and to compliment the enzymology studies, we are interested in elucidating the catalytic mechanism(s) of these enzymes. These studies will be conducted partly in collaboration with Dr. Mario Amzel. Our long-term goal is to understand the biochemistry and chemistry of these enzymes and determine how changes in their sub-cellular localization and/or enzymatic activity affect their signaling functions.Physiological Functions of DGKs in Neurons: There is growing evidence that DGKs play physiological roles in mammalian neurons. This evidence includes cellular localization of specific isoforms, and the observations that likely modulate (a) susceptibility to epileptic seizures (DGK-), (b) neuronal spine density (DGK- and DGK-), and (c) pre-synaptic glutamate release during DHPG (3,5-dihydroxyphenylglycine)-induced long-term potentiation (DGK-). We are currently examining the role of DGK-θ in glutamatergic neurons. These studies have initially focused on identifying the physiologic regulator of DGK-θ, and test the hypothesis that this enzyme modulates induced glutamate release in these mammalian neurons. We discovered that DGK-θ modulates glutamate release from cortical and hippocampal neurons in part by modulating synaptic vesicle cycling. These studies are conducted in collaboration with Dr. Rick Huganier’s laboratory.
Tu-Sekine, B., Goldschmidt, H, Raben, D.M. (2015) Diacylglycerol, Phosphatidic Acid, and their Metabolizing Enzymes in Synaptic Vesicle Recycling. Adv. Biol. Reg. Jan;57:147-52.PubMed Reference
Petro E, and Raben DM. (2013) Bacterial expression strategies for several Sus scrofa diacylglycerol kinase alpha constructs: solubility challenges. Scientific Reports 2013;3:160.PubMed Reference
Ueda S, Tu-Sekine B, Yamanoue M, Raben DM, and Shirai Y. (2013) The expression of diacylglycerol kinase theta during the organogenesis of mouse embryos. BMC Developmental Biology 2013, 13:35.PubMed Reference
Bolduc D, Rahdar M, Tu-Sekine B, Sivakumaren SC, Raben DM, Amzel LM, Devreotes P, Gabelli SB, and Cole P. (2013) Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis. Elife 2013 Jul 9;2:e00691.PubMed Reference
Tu-Sekine B, Goldschmidt H, Petro E, and Raben DM. (2013) Diacylglycerol Kinase Theta: Regulation and Stability. Adv. Biol. Reg. Jan;53(1):118-26.PubMed Reference
Tu-Sekine B, and Raben DM. (2012) Dual Regulation of DGK-θ: Polybasic Proteins Promote Activation by Phospholipids and Increase Substrate Affinity. J. Biol. Chem. 287(50):41619-41627.PubMed Reference
Tu-Sekin, B, and Raben DM. (2011) Regulation and Roles of Neuronal Diacylglycerol Kinases: a Lipid Perspective. Crit. Rev. Biochem. Mol. Biol. Oct;46(5):353-64.PubMed Reference
Mohan S, Tse CM, Gabelli SB, Sarker R, Cha B, Fahie K, Nadella M, Zachos NC, Tu-Sekine B, Raben DM, Amzel LM, Donowitz M. (2010) NHE3 Activity Is Dependent on Direct Phosphoinositide Binding at the N Terminus of Its Intracellular Cytosolic Region. J. Biol. Chem. 285(45): 34566-78.PubMed Reference
Tu-Sekine, B. and Raben DM. (2010) Characterization of Cellular DGKΘ. Advances in Enzyme Reg. 50:81-94.PubMed Reference
Link TM, Park U, Vonakis BM, Raben DM, Soloski M.J., Caterina MJ. (2010) TRPV2 plays a pivotal role in macrophage particle binding and phagocytosis. Nature Immunology Mar;11(3):232-9. Epub 2010 Jan 31.PubMed Reference
Tu-Sekine and Raben DM. (2009) Regulation of DGK-Θ J. Cell Physiol. 220(3):548-52.PubMed Reference
Raben DM and Wattenberg BW. (2009) Signaling at the Membrane Interface by the DGK/SK Enzyme Family. J Lipid Res 50th Anniversary Edition: J. Lipid Res. April Supplement: S35-S39.PubMed Reference
Raben DM and Tu-Sekine B. (2008) Nuclear Localization Of Diacylglycerol Kinases: Regulation And Roles. Frontiers in Bioscience 13:590-597.PubMed Reference
Wattenberg BW and Raben DM. (2007) Diacylglycerol Kinases Put the Brakes on Immune Function. Science STKE (398) pe43.PubMed Reference
Tu-Sekine B, Ostroski M, and Raben DM. (2007) Modulation of DGKΘ Activity by α-Thrombin and Phospholipids. Biochemistry, 46(3): 924 -932.PubMed Reference
Rangos 574Baltimore, MD 21205
Understanding the cell biology of genomes and how nuclear architecture controls gene expression is necessary to truly understand biological processes such as development and disease. Although sequencing of the genome and comparative genome analysis have yielded insights into the regulation and dis-regulation of genetic information, these efforts shed little light into how genomes actually work in vivo. The impact of architectural and cellular organization of genomes on gene activity is a next step to unlocking genetic and epigenetic mechanisms in development and disease. Recent evidence is emerging that the non-random organization in the nucleus is a contributing factor in regulating genes important to multiple developmental processes. Moreover, some studies suggest that the non-random organization in the nucleus is a contributing factor in initiating translocations. In mammalian nuclei, chromatin is organized into structural domains by association with distinct nuclear compartments. Such interactions are likely to bring together coordinately regulated genes and to focus proteins and enzymes that regulate DNA based activities such as transcription, recombination, replication and repression. While evidence mounts that genes are regulated by association with distinct nuclear compartments, relatively little is known about how specific loci are directed to different domains. I hypothesize that such “nuclear addressing” requires specific cis elements that interact with a set of sequestered proteins (trans factors) to establish and maintain nuclear architecture and functionality. Such self-reinforcing interactions likely lie at the heart of nuclear structure and function. My recent work has demonstrated that one such compartment that is important for both nuclear structure and gene regulation is the nuclear periphery. In addition to regulation of Immunoglobulin Heavy Chain loci, the nuclear envelope (NE) is also implicated in regulating, among other things, muscle specific genes. The focus of the research in my lab is to begin to understand how the nuclear periphery and other subcompartments contribute to general nuclear architecture and to specific gene regulation. These questions comprise three complementary areas of research: understanding how genes are regulated at the nuclear periphery, deciphering how genes are localized (or “addressed”) to specific nuclear compartments and, finally, how these processes are utilized in development and corrupted in disease.
Harr, J.C, Luperchio, T.R., Wong, X.,
Cohen, E., Sheelan, S.J. and Reddy, K.L. (2015) Directed targeting of
chromatin to the nuclear lamina is mediated by chromatin state and
A-type lamins, Journal of Cell Biology, vol 208(1), 33-52.PubMed Reference
Wong, X., Luperchio, T. R., & Reddy KL. (2014). NET gains and losses: the role of changing nuclear envelope proteomes in genome regulation. Current Opinion in Cell Biology, 28C, 105–120.PubMed Reference
Luperchio, T. R., Wong, X., & Reddy KL. (2014). Genome regulation at the peripheral zone: lamina associated domains in development and disease. Current Opinion in Genetics & Development, 25C, 50–61.PubMed Reference
Mohammad H, Luperchio, T. R., Cutler , J, Mitchell, C. J., Kim, M-S, Pandey, A, Sollner-Webb, B.and Reddy KL (2014) Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis. Journal of Proteomics & Bioinformatics.Link
Harr J. and Reddy KL. (2013) Live Cell imaging of Nuclear Dynamics. Encyclopedia of Biological Chemistry, 2nd Ed., p. 749Link
Reddy KL, & Feinberg, A. P. (2013). Higher order chromatin organization in cancer. Semin Cancer Biol, 23(2), 109–115.PubMed Reference
Zullo, J. M., Demarco, I. a, Piqué-Regi, R., Gaffney, D. J., Epstein, C. B., Spooner, C. J., Reddy KL and Singh, H. (2012). DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell, 149(7), 1474–87.PubMed Reference
Mewborn, S. K., Puckelwartz, M. J., Abuisneineh, F., Fahrenbach, J. P., Zhang, Y., MacLeod, H., Dellefave L, Pytel P, Selig S, Labno CM, Reddy KL, Singh H, McNally E. (2010). Altered chromosomal positioning, compaction, and gene expression with a lamin A/C gene mutation. PloS One, 5(12), e14342.PubMed ReferenceJohnson, K., Reddy, KL, & Singh, H. (2009). Molecular pathways and mechanisms regulating the recombination of immunoglobulin genes during B-lymphocyte development. Adv Exp Med Biol, 650(Journal Article), 133–147.PubMed Reference Reddy KL, & Singh, H. (2008). Using molecular tethering to analyze the role of nuclear compartmentalization in the regulation of mammalian gene activity. Methods (San Diego, Calif.), 45(3), 242–251.MethodsReddy KL, Zullo, J. M., Bertolino, E., & Singh, H. (2008). Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature, 452(7184), 243–7. doi:10.1038/nature06727PubMed ReferenceReynaud, D., A, Demarco, I., L Reddy KL, Schjerven, H., Bertolino, E., Chen, Z., Reddy, K. L. (2008). Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros. Nature Immunology, 9(8), 927–936.PubMed ReferenceSchlimgen, R. J., Reddy KL, Singh, H., & Krangel, M. S. (2008). Initiation of allelic exclusion by stochastic interaction of Tcrb alleles with repressive nuclear compartments. Nature Immunology, 9(7), 802–809.PubMed Reference
410 BiophysicsBaltimore, MD 21205
Office Phone: 410-955-5759
513 PhysiologyBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-3424
Consequently, on the theoretical side, efforts to predict protein structure from sequence focus intensively on enforcing these local interactions in fragments built de novo, using short segments of chain taken from high resolution protein structures. Beginning with fragments of length 4 to 8 residues lacking side chain atoms beyond CG, larger fragments are assembled in a hierarchical fashion, using a variety of statistical potentials to enforce protein-like interactions between elements of secondary structure. In the final step, heavy atoms are added to form complete side chains, and several high resolution all atom potential, including one to quantify solvation, are used as fitness functions in a genetic algorithm-based conformational search.
The laboratory has participated in CASPâ€™s 4, 5, and 6 in the new fold category and in CASP 6 in homology modeling. The upcoming CASP 7 challenge (May through August 2006) will provide us an opportunity to evaluate our new explicit side chain methods.
855 N. Wolfe St.Baltimore, MD 21205
Office Phone: 410-614-8033
Lab Phone: 443-287-7214
Our laboratory is interested in understanding the metabolic properties of neurons and glia at a mechanistic level in situ. Some of the most interesting, enigmatic and understudied cells in metabolic biochemistry are those of the nervous system. Defects in these pathways can lead to devastating neurological disease. Conversely, altering the metabolic properties of the nervous system can have surprisingly beneficial effects on the progression of some diseases. However, the mechanisms of these interactions are largely unknown.
We utilize biochemical and molecular genetic techniques to understand the molecular mechanisms that the nervous system uses to sense and respond to metabolic cues. We have uncovered novel neuronal nutrient sensing paradigms that act through unique metabolic enzymes to control body weight and diabetes susceptibility. We continue to explore novel neuron-specific enzyme function in metabolic processes as well as uncovering novel roles of canonical metabolic pathways in the nervous system. Furthermore, the unique makeup of the nervous system requires our laboratory to develop new technology and assays to facilitate our work.
Below are the broad areas that we are currently focusing on.
Ellis JM, Wong GW & Wolfgang MJ. Acyl Coenzyme A Thioesterase 7 regulates neuronal fatty acid metabolism to prevent neurotoxicity. Mol Cell Biol. 2013; 33(9) 1869-1882.PubMed Reference
Miyamoto T, DeRose R, Suarez A, Ueno T, Chen M, Sun T, Wolfgang MJ, Mukherjee C, Meyers DJ and Inoue T. Generation of Intracellular Logic Gates with Two Orthogonal Chemically Inducible Systems. Nature Chemical Biology 2012, Mar 25;8(5):465-70.PubMed Reference
Rodriguez S & Wolfgang MJ. Targeted chemical-genetic regulation of protein stability in vivo. Chemistry & Biology 2012, Mar 23;19(3):391-8.PubMed Reference
Reamy AA & Wolfgang MJ. Carnitine Palmitoyltransferase-1C gain-of-function in the brain results in postnatal microencephaly. Journal of Neurochemistry. 2011 Aug; 118(3) 388-98.PubMed Reference
Cha SH, Wolfgang M, Tokutake Y, Chohnan S, Lane MD. Differential effects of central fructose and glucose on hypothalamic malonyl-CoA and food intake. Proc Natl Acad Sci USA. 2008;105(44):16871-5.PubMed Reference
Wolfgang MJ, Cha SH, Millington DS, Cline G, Shulman GI, Suwa A, Asaumi M, Kurama T, Shimokawa, T & Lane MD. Brain-specific carnitine palmitoyltransferase-1c: Role in CNS fatty acid metabolism, food intake and body weight. J Neurochem 2008; May;105(4):1550-9.PubMed Reference
Wolfgang MJ, Cha SH, Sidhaye A, Chohnan S, Cline G, Shulman GI & Lane MD. Regulation of hypothalamic malonyl-CoA by central glucose and leptin. Proc Natl Acad Sci USA. 2007 Dec; 104(49): 19285-19290.PubMed Reference
Chakravarthy MV, Zhu Y, López M, Yin L, Wozniak DF, Coleman T, Hu Z, Wolfgang M, Vidal-Puig A, Lane MD & Semenkovich CF. Brain fatty acid synthase activates PPARa to maintain energy homeostasis. J Clin Invest. 2007; 117: 2539-2552.PubMed Reference
Wolfgang MJ & Lane MD. The role of hypothalamic malonyl-CoA in energy homeostasis. J. Biol. Chem. 2006; 281(49): 37265-37269.PubMed Reference
Wolfgang MJ, Kurama T, Dai Y, Suwa A, Asaumi M, Matsumoto S, Cha SH, Shimokawa T & Lane MD. The brain-specific carnitine palmitoyltransferase-1c regulates energy homeostasis. Proc. Natl. Acad. Sci. USA 2006 May; 103(19): 7282-7287.PubMed Reference
Gao Q*, Wolfgang MJ*, Neschen S, Morino K, Horvath, TL, Shulman GI, & Fu XY. Disruption of neural signal transducer and activator of transcription 3 causes obesity, diabetes, infertility and thermal dysregulation. Proc. Natl. Acad. Sci. USA 2004 March; 101(13): 4661-4666. (*equal contribution).PubMed Reference
Kano A*, Wolfgang MJ*, Gao Q*, Jacoby J, Chai GX, Hansen W, Iwamoto Y, Pober JS, Flavell RA, & Fu XY. Endothelial cells require STAT3 for protection against endotoxin-induced inflammation. J Exp Med. 2003; 198(10): 1517-1525. (*equal contribution).PubMed Reference
725. N. Wolfe Street, WBSB 408Baltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-502-3210
In response to multiple forms of cellular stress, levels of the O-GlcNAc protein modification are elevated rapidly and dynamically on myriad nuclear, mitocohdrial and cytoplasmic proteins. Several studies demonstrate that elevation of O-GlcNAc prior to heat stress, oxidative stress, hypoxia, trauma hemorrhage, and ischemia reperfusion injury is protective, suggesting that increased O-GlcNAc in response to stress is a survival response of cells injury. However, the mechanisms by which O-GlcNAc regulates protein function leading to cell survival have not been defined. Our long-term goal is to determine how stress-induced changes in the O-GlcNAc protein modification lead to increased cell/tissue survival in response to injury, in order to develop novel strategies for the treatment of numerous diseases, including ischemia reperfusion injury. Current research in the lab focus's on: 1) Characterizing the molecular mechanisms by which O-GlcNAc regulates heat shock protein expression; 2) The development of novel cells lines and tools for studying the O-GlcNAc modification; 3) Identifying proteins that are O-GlcNAc modified in response to different forms of cellular injury; 4) Understanding the signal transduction pathways that regulate O-GlcNAc modification in response to cellular injury; 5) Determining how O-GlcNAc regulates other stress-induced signaling pathways such as protein-phosphorylation. Together these studies will define a molecular road map from which we, and others, can determine the mechanism(s) by which O-GlcNAc promotes cell survival in diverse models, highlighting new targets for the development of alternative strategies that enhance stress-tolerance and promotes survival relevant models such as ischemic reperfusion injury. In addition, these studies will form a foundation for determining how dysregulation of the “O-GlcNAc-mediated stress response” contributes to pathologies such as type II diabetes and aging.
Zachara NE. (2012) The Roles of O-Linked β-N-Acetylglucosamine (O-GlcNAc) in Cardiac Physiology and Disease. AJP Heart and Circulatory Physiology, 302(10):H1905-18. PubMed Reference