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参考文献
The ABCs of Floral Homeotic Genes
A short history of MADS-box genes in plants
Phylogenetic distribution and evolution of mycorrhizas in land plants
Arbuscular mycorrhiza: the mother of plant root endosymbioses
Phylogeny and evolution of charophytic algae and land plants
Maize AMEIOTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis
往届参考文献
Hao Y 1 2 3 4 5 6 7 8 9
Li Jianming 1 2 3 4
Ma Hong1 2 3
Qi Xie 1 2 3 4 5 6 7 8
Xuemei Chen 1 2 3 4 5 6 7 8 9 10 11 12 13
Yunde Zhao 1 2 3 4 5 6 7 8 9 10 11
others 1 2 3 4 5 6
专家介绍
Dr. Yunde Zhao
Associate Professor
Section of Cell and Developmental Biology, UCSD
e-mail: yzhao@biomail.ucsd.edu
Lab Homepage: http://www-biology.ucsd.edu/labs/zhao/
The goal of our research is to elucidate the mechanisms by which the plant hormone auxin regulates plant growth and development. Although auxin has been studied for over a century, the biochemical mechanisms that govern auxin-regulated processes have remained elusive. One of the major obstacles in auxin research has been a lack of knowledge of the details of the various auxin biosynthetic pathways. In order to help bridge this gap, our efforts had initially been focused on auxin biosynthesis; however, results from these studies have enabled us to investigate auxin-mediated signal transduction from a completely different perspective. Research in our laboratory is multidisciplinary, in that it draws on techniques rooted in classical genetics, chemical genetics, biochemistry, physiology, molecular biology, and bioinformatics. We currently use Arabidopsis as the model system.
We have identified and characterized an auxin overproducing Arabidopsis mutant named yucca (Zhao et al. (2001), Science 291, 306-309). This mutant displays typical auxin-mediated phenotypes, namely, light grown yucca has long hypocotyls and epinastic cotyledons, whereas dark grown yucca has short hypocotyls and lacks an apical hook. The protein encoded by YUCCA is a flavin-containing monooxygenase that catalyzes the N-hydroxylation of tryptamine, a key step in tryptophan dependent auxin biosynthesis. Based on the detailed characterization of yucca phenotypes, we have been able to carry out a genetic screen for yucca-like mutants that should enable us to identify new components in both the auxin biosynthesis and signal transduction pathways. We have also initiated a genetic screen for mutants that can suppress yucca phenotypes. The cloning and characterization of the mutants already identified by these screens is one of our current priorities. In addition, we have undertaken the biochemical characterization of YUCCA and its associated proteins.
We have also initiated a chemical genetics approach to elucidate gene functions in Arabidopsis, with the initial focus on genes that are involved in auxin homeostasis and signal transduction. We have identified a small molecule sirtinol that constitutively activates auxin signal transduction. Analysis of sirtinol resistant mutants led to the discovery of a key auxin signaling component SIR1 (Zhao et al. (2003), Science 301, 1107-1110). We are currently characterizing other sirtinol resistant mutants and analyzing the biochemical mechanisms of SIR1.
Selected Publications:
♦Li, L., Qin, G., Tsuge, T., Hou, X., Ding, M., Aoyama, T., Oka, A., Chen, Z., Gu, H., Zhao, Y . & Qu, L. J. (2008) SPOROCYTELESS modulates YUCCA expression to regulate the development of lateral organs in Arabidopsis New Phytologist 179(3):751-64.
♦McSteen P and Zhao Y (2008). Plant hormones and signaling: common themes and new developments. Dev Cell 14(4):467-73.
♦Zhao, Y. (2008) The role of local biosynthesis of auxin and cytokinin in plant development. Curr Opin Plant Biol . 11(1):16-22.
♦Tao Y, Ferrer JL, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y , Ballaré CL, Sandberg G, Noel JP, Chory J (2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell 133(1):164-76.
♦Wollers S, Heidenreich T, Zarepour M, Zachmann D, Kraft C, Zhao Y , Mendel RR, Bittner F (2008). Binding of Sulfurated Molybdenum Cofactor to the C-terminal Domain of ABA3 from Arabidopsis thaliana Provides Insight into the Mechanism of Molybdenum Cofactor Sulfuration. J Biol Chem 283(15):9642-50.
♦Breuer C, Stacey NJ, West CE, Zhao Y , Chory J, Tsukaya H, Azumi Y, Maxwell A, Roberts K, Sugimoto-Shirasu K (2008). BIN4, a novel component of the plant DNA topoisomerase VI complex, is required for endoreduplication in Arabidopsis. Plant Cell 19(11):3655-68.
♦Li L, Hou X, Tsuge T, Ding M, Aoyama T, Oka A, Gu H, Zhao Y , Qu LJ (2008). The possible action mechanisms of indole-3-acetic acid methyl ester in Arabidopsis. Plant Cell Rep 27(3):575-84
♦Cheng Y., Qin G., Dai X., and Zhao Y (2007). A role for a BTB-NPH3-like protein in auxin-regulated organogenesis in Arabidopsis. PNAS 104, 18825-18829.
♦Cheng Y., Dai X., and Zhao Y. (2007) Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. Plant Cell 19(8): 2430-9
♦Cheng, Y. and Zhao Y. (2007). A role for auxin in flower development. Journal of Integrative Plant Biology 49 (1): 99-104
♦Moon J, Zhao Y , Dai X, Zhang W, Gray WM, Huq E, Estelle M (2007). A New CUL1 Mutant has Altered Responses to Hormones and Light in Arabidopsis. Plant Physiol 142
♦Koussevitzky S, Stanne TM, Peto CA, Giap T, Sjogren LL, Zhao Y , Clarke AK, Chory J (2007). An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development. Plant Mol Biol. 63(1): 85-96.
♦Bowers, A.K. and Zhao, Y. (2006) Recent Advances in Auxin Biosynthesis and Conjugation, in Recent Advances in Phytochemistry: Integrative Plant Biochemistry. J. Romeo, Ed. (2006), vol. 40, pp. 271-285.
♦Cheng, Y., Dai, X., and Zhao, Y. (2006) Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev. 20 (13), 1790-1799. Abstract Full Text PDF Supplemental Material Science News
♦Li, J., Dai, X., and Zhao, Y. (2006) A Role for Auxin Response Factor 19 in Auxin and Ethylene Signaling in Arabidopsis. Plant Physiol. 140, 899-908. Abstract Full Text PDF
♦Qin, G., Gu, H., Zhao, Y., Ma, Z., Shi, G., Yang, Y., Pichersky, E., Chen, H., Liu, M., Chen, Z. and Qu, L. J. (2005) An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development. Plant Cell. 17(10), 2693-2704. Abstract Full Text PDF
♦Dai, X., Hayashi, K., Nozaki, H., Cheng, Y., and Zhao, Y. (2005) Genetic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. PNAS. 102(8), 3129-3134. Abstract Full Text PDF
♦Perry, J., Dai, X., and Zhao, Y. (2005) A Mutation in the Anticodon of a Single tRNAala Is Sufficient to Confer Auxin Resistance in Arabidopsis.
♦Plant Physiol. 139, 1284-1290. Abstract Full Text PDF
♦Cheng, Y., Dai, X., and Zhao, Y. (2004) AtCAND1, A HEAT-Repeat Protein That Participates in Auxin Signaling in Arabidopsis. Plant Physiol. 135, 1020-1026. Abstract Full Text PDF
♦Perry, J. and Zhao, Y. (2003) The CW domain, a structural module shared amongst vertebrates, vertebrate-infecting parasites and higher plants. Trends Biochem. Sci. 281(11), 576-580. Abstract PDF Supplemental Material
♦Blackwell, H.E., and Zhao, Y. (2003) Chemical Genetic Approaches to Plant Biology. Plant Physiol. 133, 456-461. Full Text PDF
♦Zhao, Y., Dai, X., Blackwell, H.E., Schreiber, S.L., and Chory, J. (2003) SIR1, an upstream auxin signaling component identified by chemical genetics. Science 301, 1107-1110. Abstract PDF
♦Zhao, Y., Hull, A. K., Gupta, N., Goss, K.A., Alonso, J., Ecker, J. R., Normanly, J., Chory, J., and Celenza, J. L. (2002). Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes & Development 16, 3100-3112. Abstract
♦Ballou, D. P., Zhao, Y., Brandish, P. E., and Marletta, M.A. (2002). Revisiting the kinetics of nitric oxide binding to soluble guanylate cyclase: the simple NO-binding model is incorrect. PNAS 99, 12097-12101
♦Yin, Y., Cheong, H., Friedrichsen, D., Zhao, Y., Hu, J., Mora-Garcia, S., and Chory, J (2002). A crucial role for the putative Arabidopsis topoisomerase VI in plant growth and development. PNAS 99, 10191-10196. Abstract
♦Zhao, Y. and Chory, J (2001). A link between the light and gibberellin signaling cascades. Development Cell 1, 315-316.
♦Gil, P., Dewey, E., Friml, J., Zhao, Y., Snowden, K. C., Putterill, J., Palme, K., Estelle, M., and Chory, J (2001). BIG: a calossin-like protein required for polar auxin transport in Arabidopsis. Genes & Development 15, 1985-1997. Abstract
♦Zhao, Y., Christensen, S. K., Fankhauser, C., Cashman, J. R., Cohen, J. D., Weigel, D., and Chory, J (2001). A Role for Flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291, 306-309. Abstract
Dr. Yang, Zhenbiao
Professor of Cell Biology & Cell Biologist
Background
My laboratory has focused on two inter-linked areas in plant cell biology: molecular basis for cell polarity development/cell shape formation and signaling networks controlled by a plant-specific GTPase switch called Rop.
A Global Study of Rop Signaling Networks in Arabidopsis
Although our knowledge of plant signal tranduction has leaped over the last few years owing to genetic studies in Arabidopsis, intracellular signaling pathways linking cell surface receptors to nuclear componentracellular signaling pathways by cycling between GTP-bound active and GDP-bound inactive forms.nts remain poorly understood. In animals and yeast, G proteins or GTPases are pivotal switches that turn on and off i The Arabidopsis genome sequence reveals that plants lack many of the signaling G proteins used by animals and yeast; instead, plants contain a unique family of small GTPases, termed Rop. Evidence has emerged from my laboratory and several other laboratories that Rop acts as a versatile switch in signal transduction in plants. We have been interested in elucidating the function of 11 ROP genes and identifying various Rop-dependent pathways in Arabidopsis. Towards this goal, we have used an integrated approach by investigating Rop gene expression and protein localization, by characterizing phenotypes of rop knockout mutants and transgenic plants expressing dominant rop mutants, and by identifying Rop-interacting proteins. From these studies, we have concluded that Rop participates in various signaling pathways that control a wide variety of processes during plant growth, development, and responses to the environment (see Figure 1). This functional diversity of the Rop GTPasse family is further supported by our identification of receptor Ser/Thr kinases as putative Rop interactors and by our demonstration that the Arabidopsis genome contains 11 genes encoding putative Rop targets called RICs (Rop-interacting CRIB motif-containing proteins). RICs are divergent novel proteins containing a CRIB (Cdc42/Rac-interactive binding) motif required for the interaction with the GTP-bound active form of Rop. Subcellular localization and overexpression in pollen tubes suggest distinct functions for different RICs. With the aid of knockout mutants and analysis of Rop-RIC differential interaction, we are aiming to determine whether each Rop and RIC are functionally distinct or redundant and whether specific Rop-RIC pairs act in distinct Rop signaling pathways.
Figure 1. A generalized scheme illustrating the functional diversity of Rop GTPasesCell Polarity Development and Cell Shape Formation. GEF, guanine nucleotide exchange factor; GDI, guanine nucleotide dissociation inhibitor; RopGAP, Rop GTPase activating protein. RIC, Rop-interacting CRIB-containing proteins.
Cell Polarity Development and Cell Shape Formation
Cell polarity is fundamentally important to plant growth and development. Some well-known examples of polarity in plant cells include asymmetric distribution of auxin carriers in the plasma membrane (PM) that is essential for polar auxin transport, asymmetric cell division (generally preceded by polar cytoplasmic distribution) that is critical for cell differentiation (e.g., zygote division of zygotes and division of precursors for guard cells), and polar cell expansion that is important for cell shape formation. Unlike single-celled yeast or cultured mammalian cell lines, cell polarity in higher plants is generally expressed in multi-cellular context and is not expressed normally in cultured cells. This contributes to the difficulties in studying the molecular basis of cell polarity control in higher plants, which remained mysterious until recent studies of Rop GTPases. We have used the "single-celled" tip-growing pollen tube as a model to generate hypotheses about the Rop-dependent pathways leading to polar cell expansion and extended these hypotheses to other cell types including non-tip-growing cells in intact tissues.
A spatially-regulated Rop signaling network controls polar growth in pollen tubes.
Pollen tubes provide an ideal model system for the study of cell polarity. As a male gametophyte, pollen tube growth is controlled by the haploid genome. In culture, pollen tubes develop a uniform cylindrical shape through an extreme form of polar growth--tip growth, a process involving continuous targeting and fusion of Golgi vesicles to a defined region of the plasma membrane, termed tip growth domain (Figure 2). What are the mechanisms that define the tip growth domain and control localized vesicle targeting and fusion is of significant interests. Our studies have demonstrated that the tip-localized Rop1 is a central component of these mechanisms and have allowed us to develop a model for a Rop-dependent network in the control of tip growth (Figure 3). Our unpublished data suggest that PM-localized Rop1 is activated by an unknown localized cue and that the active Rop1 promotes the localization of Rop1 to the PM, forming a positive feedback loop of Rop activation and recruitment. The localized activation of this loop and subsequent lateral amplification and global inhibition of this loop allows the formation of a tip-high gradient of active Rop (Figure 3). This active Rop gradient defines the tip growth domain and controls localized exocytosis. Our evidence suggests that Rop controls localized exocytosis through both actin dynamics and cytoslic calcium accumulation at the tip. This model will be further tested by addressing the following questions: 1) What is the localized cue? 2) How does it activate Rop1 and how does active Rop promote Rop recruitment? 3) How does active Rop regulate actin dynamics and calcium accumulation?
Figure 2. The pollen tube as a model system for cell polarity studies. A. In vitro-cultured pollen tubes show uniformly cylindrically-shaped cells. B. Schematics showing polar distribution of the cytoplasm in pollen tubes. Note the apex contains dynamic F-actin and Golgi vesicles.
Figure 3. A model for spatial regulation of a Rop signaling network and its role in the control of tip growth in pollen tubes. A. The localization of GFP-tagged RIC1 indicating the distribution of active Rop as a tip-high gradient in the plasma membrane of pollen tubes. The localization coincides with the tip growth domain (see Figure 2). B. This Rop activity gradient is formed by an elaborate spatial regulation of Rop recruitment and activation at the tip, defines the tip growth domain, and controls polar exocytosis.
Rop signaling to cell shape formation during organogenesis.
The Rop-dependent tip growth mechanism provides a paradigm for understanding cell polarity control and cell shape formation in plants. By investigating the role of Rop signaling in various other cell types, including root hairs (also tip-growing cells) and various non-tip-growing cells in intact tissue, we conclude that Rop signaling provides a general mechanism for the control of cell polarity and cell shape formation. Furthermore, we have demonstrated that cell shape formation in intact tissues involves two phases with distinct mechanisms. In the Rop-dependent early phase cell expansion occurs in various directions defined by the localization of cortical fine actin as in tip growth, whereas in the Rop-independent late phase cells expand only the longitudinal direction that is determined by transverse cortical microtubules. Cell expansion in developing tissues is controlled by developmental and hormonal signals and likely involves inter-cellular communication between neighboring cells. Using epidermal pavement cells with unique wavy shape and combined genetic and biochemical approaches, we are identifying signals that regulate Rop-dependent directional cell expansion and other components in the Rop-dependent pathways.
Selected Publications
♦Fu, Y., Li, H., Yang, Z. 2002. The Rop2 GTPase controls the formation of cortical fine F-actin and the early phase of directional cell expansion during Arabidopsis organogenesis. Plant Cell. Vol. 14: p.763-776.
♦Jones, M.A., Shen, J., Li, H., Fu, Y., Yang, Z., Grierson, C.S. 2002. The Arabidopsis Rop2 GTPase is a positive regulator of both root hair initiation and tip growth. Plant Cell. Vol. 14: p.777-794.
♦Zheng, Z.L., Nafisi, M., Li, H., Tam, A., Crowell, D.N., Chary, S.N., Shen, J., Schroeder, J.I., Yang, Z. 2002. The Arabidopsis small GTPase ROP10 is a specific negative regulator of phytohormone abscisic acid ABA responses. Plant Cell. Vol. 14: p.2787-2797.
♦Gu, Y., Vernoud, V., Fu, Y., Yang, Z. 2003. ROP GTPase regulation of pollen tube growth through the dynamics of tip-localized F-actin. J. Exp. Bot. Vol. 54: p.93-101.
♦Vernoud, V., Horton, A.C., Yang, Z., Nielson, E. 2003. Analysis of the small GTPase gene family of Arabidopsis thaliana. Plant Physiol. Vol. 131: p.1191-1208.
♦Li, S., Blanchoin, L., Yang, Z., Lord, E.M. 2003. The putative Arabidopsis Arp2/3 complex controls leaf cell morphogenesis. Plant Physiol. Vol. 132: p.2034-2044.
♦Park, J., Gu, Y., Lee, Y., Yang, Z., Lee, Z. 2004. Phosphatidic acid induces leaf cell death in Arabidopsis by activating the Rho-related small G protein GTPase-mediated pathway of reactive oxygen species generation. Plant Physiol. Vol. 134: p.129-136.
♦Bao, F., Shen, J., Brady, S.R., Muday, G.K., Asami, T., Yang, Z. 2004. Brassinosteroids interact with auxin to promote lateral root development in Arabidopsis. Plant Physiol. Vol. 134: p.1624-1631.
♦Gu, Y., Fu, Y., Dowd, P., Li, S., Vernoud, V., Gilroy, S., Yang, Z. 2005. A Rho-family GTPase controls actin dynamics and tip growth via two counteracting downstream pathways in pollen tubes. Journal of Cell Biology. Vol. 169: p.127-139.
♦Fu, Y., Gu, Y., Zheng, Z., Wasteneys, G., Yang, Z. 2005. Arabidopsis interdigitating cell growth requires two antagonistic pathways with opposing action on cell morphogenesis. Cell. Vol. 120: p.687-700.
♦Hwang, J -U., Gu, Y., Lee, Y.J., Yang, Z. 2005. Oscillatory ROP GTPase activation leads the oscillatory polarized growth of pollen tubes. Mol. Biol. Cell. Vol. 16: p.5385-99.
♦Gu, Y., Li, S., Lord, E., Yang, Z. 2006. Members of a novel class of Arabidopsis Rho guanine nucleotide exchange factor (RopGEFs) control Rop GTPae-dependent polar growth. Plant Cell. Vol. 18: p.366-381.
♦Jones, M.A., Raymond, M.J., Yang, Z., Smirnoff, N. 2007. NADPH oxidase-dependent reactive oxygen species formation required for root hair growth depends on ROP GTPase. J. Exp. Bot. Vol. 58: p.1261-1270.
♦Chang, F., Yan, A., Zhao, L., Wu, W., Yang, Z. 2007. A putative calcium-permeable cyclic nucleotide-gated channel, CNGC18, regulates polarized pollen tube growth . J. Int. Plant Biol. Vol. 49: p.1261-1270.
Alumni:
♦Junxian He, Assistant Professor, the Chinese University of Hong Kong
Soo-Hwan Kim, Assistant Professor, Yonsei University, Korea
Srinivas Gampala, Edenspace, Kansas
Ying Sun, Professor, Hebei Normal University, China
Joshua Gendron, Postdoc, UCSD
Brassinosteroid signal transduction and proteomics
We are interested in the signal transduction pathways through which hormonal and environmental signals regulate plant growth and development. To gain a comprehensive understanding of the biological system and to provide inter-disciplinary training to students and postdocs, we use a wide range of approaches, including molecular genetics, biochemistry, proteomics, genomics, and cell biology. Our research focuses on the brassinosteroid (BR) signal transduction pathway and proteomic study of signal transduction.
BRs are plant steroid hormones that regulate a wide range of developmental and physiological processes. BR deficient mutants, such as det2, show dramatic developmental alterations such as dwarfism, male sterility, delayed flowering, reduced apical dominance, and development of light-grown morphology in the dark. One goal of our research is to gain a complete understanding of the signaling and regulatory pathways through which BRs regulate various developmental and physiological processes.
Studies in the last decade have established the BR pathway as one of the best-studied signal transduction pathways in plants. BRs are perceived by the cell-surface receptor kinase BRI1, which initiates a signal transduction cascade that leads to nuclear gene expression and cellular responses. Another receptor kinase, BAK1, interacts with and facilitates activation of BRI1 upon BR binding. BR response is negatively regulated by the GSK3-like kinase BIN2 and positively regulated by the nuclear proteins BZR1 and its homolog BZR2 (also named BES1). In the absence of BRs, BIN2 phosphorylates BZR1 and BZR2 at multiple residues, and phosphorylation inhibits the transcription factors through multiple mechanisms, including degradation by the proteasome, cytoplasmic retention by the 14-3-3 proteins, and inhibiting DNA binding. BR treatment causes dephosphorylation and activation of the BZR1 and BZR2 proteins, most likely by inhibiting BIN2 or activating a phosphatase such as BSU1. Upon dephosphorylation and nuclear localization, BZR1 and its homologs bind specifically to the BR response element (BRRE) and regulate BR responsive gene expression. Our recent proteomic studies using 2-D DIGE and mass spectrometry identified new components of the BR signaling pathway, include the BR-signaling kinases (BSKs) which are substrates of BRI1 that transduce the signal to cytoplasmic components. Using proteomics and genomics tools, we are assembling the complete BR signal transduction pathway from receptor binding at the cell surface to thousands of target genes in the nucleus and to specific developmental and physiological processes.
Current research projects include: (1) functional study of proteins that interact with known BR signaling proteins (such as BZR1), which have been identified using yeast two-hybrid screen and tandem affinity purification; (2) Genomic study of BZR1 target genes using chromatin immunoprecipitation-microarray and systems biology study of the BR regulatory pathway; (3) Molecular genetic studies of BR functions in specific plant developmental processes; (4) Proteomic studies of new BR signal transduction components; (5) Biochemical and cell biological studies of BR signaling mechanisms; (6) Proteomic studies of other signaling pathways that regulate plant growth and development.
Our studies using molecular genetic, genomic, and proteomic approaches are yielding a detailed understanding of how BR signal is transduced from the cell surface receptor kinase to nuclear transcription factors and how the transcriptional network mediates BR regulation of specific cellular and developmental processes. The powerful proteomic and genomic methods are now used in the lab and through collaborations to dissect additional signal transduction pathways that regulate plant growth.
Identification of Brassinosteroid regulated proteins(left) and plasma membrane proteins(right) using 2-D DIGE
Proteins of BR treated and untreated Arabidopsis were labeled with Cy3 and Cy5 dyes and separate by two-dimensional gel electrophoresis.
Selected Publications:
♦Wenqiang Tang, Tae-Wuk Kim, Juan A Oses-Prieto, Yu Sun, Zhiping Deng, Shengwei Zhu, Ruiju Wang, Alma L. Burlingame, and Zhi-Yong Wang (2008). BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis. Science, 321, 557-560.
♦Gendron, J. M., Haque, A., Gendron, N., Chang, T., Asami, T. Wang, Z-Y. (2008). Chemical genetic dissection of brassinosteroid-ethylene interaction. Molecular Plant 1, 368-379.
Wenqiang Tang, Zhiping Deng, Juan A Oses-Prieto, Nagi Suzuki, Shengwei Zhu, Xin Zhang, Alma L. Burlingame, and Zhi-Yong Wang. Proteomic studies of brassinosteroid signal transduction using prefractionation and 2-D DIGE (2008). Molecular Cellular Proteomics 7, 728-738
♦Zhiping Deng, Xin Zhang, Wenqiang Tang, Juan A Oses-Prieto, Nagi Suzuki, Joshua M Gendron, Huanjing Chen, Shenheng Guan, Robert J. Chalkley, T. Kaye Peterman, Alma L. Burlingame, and Zhi-Yong Wang. A Proteomic Study of Brassinosteroid Response in Arabidopsis. Molecular Cellular Proteomics, in press.
♦Joshua M. Gendron and Zhi-Yong Wang (2007). Multiple mechanisms modulate Brassinosteroid signaling. Current Opinion in Plant Biology, 10, 436-441.
♦Srinivas S. Gampala, Tae-Wuk Kim, Jun-Xian He, Wenqiang Tang, Zhiping Deng, Ming-Yi Bai, Shenheng Guan, Sylvie Lalonde, Ying Sun, Joshua M. Gendron, Huanjing Chen, Nakako Shibagaki, Robert J. Ferl, David Ehrhardt, Kang Chong, Alma L. Burlingame, and Zhi-Yong Wang (2007). An Essential Role for 14-3-3 Proteins in Brassinosteroid Signal Transduction in Arabidopsis. Developmental Cell 13, 177-189
♦Ming-Yi Bai, Li-Ying Zhang, Srinivas S. Gampala, Sheng-Wei Zhu, Wen-Yuan Song, Kang Chong, and Zhi-Yong Wang (2007). Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice. Proc Nat Acad Sci 104, 13839-44
♦Zhang X, Chen Y, Wang ZY, Chen Z, Gu H, Qu LJ. (2007) Constitutive expression of CIR1 (RVE2) affects several circadian-regulated processes and seed germination in Arabidopsis. The Plant Journal, 51(3), 512-525
♦Wang ZY, Wang Q, Chong K, Wang F, Wang L, Bai M, Jia C. (2006). The brassinosteroid signal transduction pathway. Cell Res. 16(5): 427-34.
♦Shi, Y-H., Zhu, S-W., Mao, X-Z., Feng, J-X., Zhang, L., Cheng, J., Wei, L-P., Wang, Z-Y., Zhu, Y-X. (2006) Transcriptome Profiling, Molecular Biological and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Cell Elongation. Plant Cell, in press.
♦He, J-X., Gendron, J. M., Sun, Y., Gampala, S. S. L., Gendron, N., Sun, C. Q. and Wang, Z-Y. (2005). BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. Science 307, 1634-1638.
♦Wang Z-Y and He, J-X. (2004). Brassinosteroid signal transduction: choices of signals and receptors. Trends in Plant Science 9 (2), 91-96.
♦He, J-X., Gendron, J. M., Yang, Y. Li, J., Wang, Z-Y. (2002). The GSK3-like kinase BIN2 phosphorylates and destabilizes BZR1, a positive regulator of the brassinosteroid signaling pathway in Arabidopsis. Proc. Nat. Acad. Sci, 99, 10185-10990.
♦Wang, Z-Y., Nakano, T., Gendron, J. M., He, J., Chen, M., Vafeados, D., Yang, Y., Fujioka, S, Yoshida, S., Asami, T., Chory, J. (2002). Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev. Cell, 2, 505-513.
Wang, Z-Y., Setu, H., Fujioka, S., Yoshida, S., and Chory, J. (2001). BRI1 is a critical component of a plasma membrane receptor for plant steroids. Nature, 410, 380-382.
♦He, Z., Wang, Z-Y., Li, J., Zhu, Q., Lamb, C., Ronald, P., and Chory, J. (2000) Perception of brassinosteroids by the extracellular domain of the receptor kinase BRI1. Science, 288, 2360-3
Wang, Z-Y, Tobin, E. M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93, 1207-1217.
♦Wang, Z-Y., Kenigsbuch, D., Sun, L., Harel, E., Ong, M.S., Tobin, E.M. (1997). A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9, 491-507.
Dr. Yin-Long Qiu
Associate Professor
Associate Curator, University of Michigan Herbarium
Ph.D., University of North Carolina, Chapel Hill, 1993
Postdoc, Indiana University (NIH postdoctoral fellowship), 1997
U-M affiliation(s)
Department of Ecology and Evolutionary Biology
University of Michigan Herbarium
Contact information
University of Michigan
2052 Kraus Natural Science Bldg.
830 N. University
Ann Arbor, MI 48109-1048
Phone: (734) 764-8279
Fax: (734) 763-0544
Email: ylqiu@umich.edu
PUBLICATIONS
I. Peer-reviewed Journal Articles (* indicates representative publications):
* 55. Li, L., B. Wang, Y. Liu, & Y.-L. Qiu. 2008. The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus reveals a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. Journal of Molecular Evolution (submitted).
* 54. Jobson, R. W. & Y.-L. Qiu. 2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biology Direct (in press).
53. McManus, H. A. & Y.-L. Qiu. 2008. Life cycles in major lineages of photosynthetic eukaryotes, with a special reference to the origin of land plants. Fieldiana (in press).
52. Liu, Y., Y. Jia, W. Wang, Z.-D. Chen, E. C. Davis, & Y.-L. Qiu. 2008. Phylogenetic relationships of two endemic genera from eastern Asia: Trichocoleopsis and Neotrichocolea (Hepaticae). Annals of the Missouri Botanical Garden 95: 459-470.
51. Nie, Z.-L., J. Wen, H. Sun, Y.-L. Qiu, H. Azuma, W.-B. Sun, & E. A. Zimmer. 2008. Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets. Molecular Phylogenetics and Evolution 48: 1027-1040.
* 50. Qiu, Y.-L. 2008. Phylogeny and evolution of charophytic algae and land plants. Journal ofSystematics and Evolution 46:287-306. PDF
49. Qiu, Y.-L. & G. F. Estabrook. 2008. Inference of phylogenetic relationships among key angiosperm lineages using a compatibility method on a molecular data set. Journal of Systematics and Evolution 46: 130-141. PDF
48. Jian, S., P. S. Soltis, M. A. Gitzendanner, M. J. Moore, R. Li, T. A. Hendry, Y.-L. Qiu, A. Dhingra, C. D. Bell, & D. E. Soltis. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 38-57.
47. Liu, H. M., X. C. Zhang, Z. D. Chen, S. Y. Dong, & Y.-L. Qiu. 2007. Polyphyly of the fern family Tectariaceae sensu Ching: Insights from cpDNA sequence data. Science in China, Series C: Life Sciences 50: 789-798.
46. Zhu, X.-Y.,M. W. Chase, Y.-L. Qiu, H.-Z. Kong, J.-H. Li,D. L. Dilcher, & Z.-D. Chen. 2007. Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids. BMC Evolutionary Biology 7: 217.
46. Liu, H.-M., X.-C. Zhang, W. Wang, Y.-L. Qiu, & Z.-D. Chen. 2007. Molecular phylogeny of the fern family Dryopteridaceae inferred from chloroplast rbcL and atpB genes. International Journal of Plant Sciences 168: 1311-1323.
44. Hendry, T. A., B. Wang, Y. Yang, E. C. Davis, J. E. Braggins, R. M. Schuster, & Y.-L. Qiu. 2007.Evaluating phylogenetic positions of four liverworts from New Zealand, Neogrollea notabilis, Jackiella curvata, Goebelobryum unguiculatum and Herzogianthus vaginatus, using three chloroplast genes. The Bryologist 110: 738-751.
* 43. Qiu, Y.-L., L. Li, B. Wang, Z. Chen, O. Dombrovska, J. Lee, L. Kent, R. Li, R. W. Jobson, T. A. Hendry, D. W. Taylor, C. M. Testa, & M. Ambros. 2007. A non-flowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial and nuclear genes. International Journal of Plant Sciences 168: 691-708. PDF
42. Liu, H. M., X. C. Zhang, Z. D. Chen, & Y.-L. Qiu. 2007. Inclusion of the eastern Asia endemic genus Sorolepidium in Polystichum (Dryopteridaceae): evidence from the chloroplast rbcL gene and morphological characteristics. Chinese Science Bulletin 52: 631-638.
* 41. Qiu, Y.-L., L. Li, T. A. Hendry, R. Li, D. W. Taylor, M. J. Issa, A. J. Ronen, M. L. Vekaria, & A. M. White. 2006. Reconstructing the basal angiosperm phylogeny: evaluating information content of the mitochondrial genes. Taxon 55: 837-856. PDF
* 40. Qiu, Y.-L., L. Li, B. Wang, Z. Chen, V. Knoop, M. Groth-Malonek, O. Dombrovska, J. Lee, L. Kent, J. Rest, G. F. Estabrook, T. A. Hendry, D. W. Taylor, C. M. Testa, M. Ambros, B. Crandall-Stotler, R. J. Duff, M. Stech, W. Frey, D. Quandt, & C. C. Davis. 2006. The deepest divergences in land plants inferred from phylogenomic evidence.Proceedings of the National Academy of Sciences, USA 103: 15511-15516. PDF
39. Leebens-Mack, J., T. Vision, E. Brenner, J. E. Bower, S. Cannon, M. J. Clement, C. W. Cunningham, C. W. dePamphilis, R. deSalle, J. J. Doyle, J. A. Eisen, X. Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H. Philippe, J. C. Pires, Y.-L. Qiu, S. Y. Rhee, K. Sjolander, D. E. Soltis, P. S. Soltis, D. W. Stevenson, K. Wall, T. Warnow, & C. Zmasek. 2006. Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA). OMICS, A Journal of Integrative Biology 10: 231-237.
* 38. Wang, B. & Y.-L. Qiu. 2006. Phylogenetic distribution and evolution of mycorrhizas in land plants. Mycorrhiza 16: 299-363. PDF
37. Parkinson, C. L., J. P. Mower, Y.-L. Qiu, A. J. Shirk, K. Song, N. D. Young, C. W. dePamphilis, & J. D. Palmer. 2005. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evolutionary Biology 5: 73.
36. Liu, Y., Y. Jia, W. Wang, Z.-D. Chen, & Y.-L. Qiu. 2005. A taxonomic reassessment of Microdendron inferred from molecular and morphological evidence. The Bryologist 108:591-599.
* 35. Qiu, Y.-L., O. Dombrovska, J. Lee, L. Li, B. A. Whitlock, F. Bernasconi-Quadroni, J. S. Rest, C. C. Davis, T. Borsch, K. W. Hilu, S. S. Renner, D. E. Soltis, P. S. Soltis, M. J. Zanis, J. J. Cannone, R. R. Gutell, M. Powell, V. Savolainen, L. W. Chatrou, & M. W. Chase. 2005. Phylogenetic analysis of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. International Journal of Plant Sciences 166: 815-842. PDF
34. Cho, Y., J.P. Mower, Y.-L. Qiu, & J. D. Palmer. 2004.Mitochondrial substitution rates are extraordinarily elevated and variable iHhin a genus of flowering plants. Proceedings of the National Academy of Sciences, USA 101: 17741-17746.
33. Nickrent, D. L., A. Blarer, Y.-L. Qiu, R. Vidal-Russell, & F. E. Anderson. 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: 40.
32. Soltis, D. E., V. A. Albert, V. Savolainen, K. Hilu, Y.-L. Qiu, M. W. Chase, J. S. Farris, J. D. Palmer, & P. S. Soltis. 2004. Angiosperm relationships, genome-scale data, and “ending incongruence”: a cautionary tale in phylogenetics. Trends in Plant Science 9: 477-483.
31. Kocyan, A., Y.-L. Qiu, P. K. Endress, & E. Conti. 2004. A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trnL-F and matK sequences. Plant Systematics and Evolution 247: 203-213.
* 30. Qiu, Y.-L. & J. D. Palmer. 2004. Many independent origins of trans-splicing of a plant mitochondrial group II intron. Journal of Molecular Evolution 59: 80-89. PDF
* 29. Dombrovska O. & Y.-L. Qiu. 2004. Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Molecular Phylogenetics and Evolution 32: 246-263. PDF
28. Zanis, M. J., P. S. Soltis, Y.-L. Qiu, E. A. Zimmer, & D. E. Soltis. 2003. Phylogenetic analyses and perianth evolution in basal angiosperms. Annals of the Missouri Botanical Garden 90: 129-150.
27. Qiu, Y.-L. & J. Yu. 2003. Azolla: a model organism for plant genomic studies. Genomics, Proteomics, and Bioinformatics 1: 15-25.
26. Nickrent, D. L, A. Blarer, Y.-L. Qiu, D. E. Soltis, P. S. Soltis, & M. Zanis. 2002. Molecular data place Hydnoraceae with Aristolochiaceae. American Journal of Botany 89: 1809-1817.
25. Adams, K. L., Y.-L. Qiu, M. Stoutemyer, & J. D. Palmer. 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer during angiosperm evolution. Proceedings of the National Academy of Sciences, USA 99: 9905-9912.
24. Gugerli, F., C. Sperisen, U. Büchler, I. Brunner, S. Brodbeck, J. D. Palmer, & Y.-L. Qiu. 2001. The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny. Molecular Phylogenetics and Evolution 21: 167-175.
* 23. Qiu, Y.-L., J. Lee, B. A. Whitlock, F. Bernasconi-Quadroni, & O. Dombrovska. 2001. Was the ANITA rooting of the angiosperm phylogeny affected by long branch attraction? Molecular Biology and Evolution 18: 1745-1753. PDF
22. Adams, K. L., M. Rosenblueth, Y.-L. Qiu, & J. D. Palmer. 2001. Multiple losses and transfers to the nucleus of two mitochondrial respiratory genes during angiosperm evolution. Genetics 158: 1289-1300.
* 21. Qiu, Y.-L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen, V. Savolainen, & M. W. Chase. 2000. Phylogeny of basal angiosperms: analyses of five genes from three genomes. International Journal of Plant Sciences 161: S3-S27. pdf
20. Qiu, Y.-L. & J. Lee. 2000. Transition to a land flora: a molecular phylogenetic perspective. Journal of Phycology 36: 799-802. PDF
19. Adams, K. L., D. O. Daley, Y.-L. Qiu, J. Whelan, & J. D. Palmer. 2000. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408: 354-357.
18. von Balthazar, M., P. K. Endress, & Y.-L. Qiu. 2000. Molecular phylogenetics of Buxaceae based on nuclear ITS and plastid ndhF sequences. International Journal of Plant Sciences 161: 785-792.
17. Palmer, J. D., K. L. Adams, Y. Cho, C. L. Parkinson, Y.-L. Qiu, & K. Song. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns, and highly variable mutation rates. Proceedings of the National Academy of Sciences, USA 97: 6960-6966.
16. Savolainen, V., M. W. Chase, S. B. Hoot, C. M. Morton, D. E. Soltis, C. Bayer, M. F. Fay, A. Y. de Bruijn, S. Sullivan, & Y.-L. Qiu. 2000. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Systematic Biology 49: 306-362.
15. Hoertensteiner, S., S. Rodoni, M. Schellenberg, F. Vicentini, O. I. Nandi, Y.-L. Qiu, & P. Matile. 2000. Evolution of chlorophyll degradation: the significance of RCC reductase. Plant Biology 2: 63-67.
14. Besendahl, A., Y.-L. Qiu, J. Lee, J. D. Palmer, & D. Bhattacharya. 2000. The endosymbiotic origin and vertical evolution of the plastid tRNALeu group I intron. Current Genetics 37: 12-23.
* 13. Qiu, Y.-L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen, V. Savolainen, & M. W. Chase. 1999. The earliestangiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404-407. PDF
12. Qiu, Y.-L. &J. D. Palmer. 1999. Phylogeny of basal land plants: insights from genes and genomes. Trends in Plant Science 4: 26-30. PDF
11. Cho, Y., Y.-L. Qiu, P. Kuhlman, &J. D. Palmer. 1998. Explosive invasion of plant mitochondria by a group I intron. Proceedings of the National Academy of Sciences, USA 95: 14244-14249.
* 10. Qiu, Y.-L., M. W. Chase, S. Hoot, E. Conti, P. R. Crane, K. J. Sytsma, & C. R. Parks. 1998. Phylogenetics of the Hamamelidae and their allies: parsimony analyses of nucleotide sequences of the plastid gene rbcL. International Journal of Plant Sciences 159: 891-905. PDF
* 9. Qiu, Y.-L.,Y. Cho, J. C. Cox, &J. D. Palmer. 1998. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature 394: 671-674. PDF
8. Qiu, Y.-L., M. W. Chase, & C. R. Parks. 1995. A chloroplast DNA phylogenetic study of the eastern Asia-eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae). American Journal of Botany 82: 1582-1588. PDF
* 7. Qiu, Y.-L., C. R. Parks, & M. W. Chase. 1995. Molecular divergence in the eastern Asia-eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae). American Journal of Botany 82: 1589-1598. PDF
6. Qiu, Y.-L. & C. R. Parks. 1994. Disparity of allozyme variation levels in three Magnolia species from the southeastern United States. American Journal of Botany 81: 1300-1308. PDF
5. Parks, C. R., J. F. Wendel, M. M. Sewell, & Y.-L. Qiu. 1994. The significance of allozyme variation and introgression in Liriodendron tulipifera complex (Magnoliaceae). American Journal of Botany 81: 878-889.
4. Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, R. A. Price, H. G. Hills, Y.-L. Qiu, K. A. Kron, J. H. Rettig, E. Conti, J. D. Palmer, J. R. Manhart, K. J. Sytsma, H. J. Michaels, W. J. Kress, K. G. Karol, W. D. Clark, M. Hedren, B. S. Gaut, R. K. Jansen, K.-J. Kim, C. F. Wimpee, J. F. Smith, G. R. Furnier, S. H. Strauss, Q.-Y. Xiang, G. M. Plunkett, P. S. Soltis, S. Swensen, S. E. Williams, P. A. Gadek, C. J. Quinn, L. E. Eguiarte, E. Golenberg, G. H. Learn, Jr., S. W. Graham, S. C. H. Barrett, S. Dayanandan & V. A. Albert. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 528-580.
3. Sewell, M. M., Y.-L. Qiu, C. R. Parks, & M. W. Chase. 1993. Genetic evidence for trace paternal transmission of plastids in Liriodendron and Magnolia (Magnoliaceae). American Journal of Botany 80: 854-858.
* 2. Qiu, Y.-L., M. W. Chase, D. H. Les, & C. R. Parks. 1993. Molecular phylogenetics of the Magnoliidae: cladistic analyses of nucleotide sequences of the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 587-606. PDF
1. Parks, C. R., J. F. Wendel, M. M. Sewell, & Y.-L. Qiu. 1990. Genetic control of isozyme variation in the genus Liriodendron L. (Magnoliaceae). Journal of Heredity 81: 317-323.
II. Volumes Edited:
2. Hong, D.-Y., Z.-D. Chen, Y.-L. Qiu, and M. J. Donoghue. 2008. Patterns of Evolution and the Tree of Life (a symposium volume). Journal of Systermatics and Evolution 46 (3).
1. Endress, P. K., E. M. Friis, Y.-L. Qiu, and E. A. Zimmer. 2000. Current Perspectives on Basal Angiosperms (a symposium volume). International Journal of Plant Sciences 161 (6) Supplement.
III. Book Chapters:
5. Wang, B. & Y.-L. Qiu. 2007. Phylogeny of bryophytes. McGraw-Hill 2007 Yearbook of Science & Technology 178-180, McGraw-Hill, New York.
4. Knoop, V., Y.-L. Qiu, & K. Yoshinaga.2004. Molecular phylogeny of bryophytes and peculiarities of chloroplast and mitochondrial DNAs. In New Frontiers in Bryology: Physiology, Molecular Biology and Functional Genomics (eds. A. J. Wood, M. J. Oliver, and D. J. Cove), Kluwer, Dordrecht, The Netherlands, pp 1-16.
3. Qiu, Y.-L. 2003. Phylogeny of early land plants. McGraw-Hill 2003 Yearbook of Science & Technology 339-341, McGraw-Hill, New York.
2. Adams, K. L., K. Song, Y.-L. Qiu, A. Shirk, Y. Cho, C. L. Parkinson, and J. D. Palmer. 1998. Evolution of flowering plant mitochondrial genomes: gene content, gene transfer to the nucleus, and highly accelerated mutation rates. Pp. 13-18, in Plant Mitochondria: From Gene to Function (eds. Ian M. Moller, P. Gardestrom, K. Glimelius, and E. Glaser), Backhuys Publishers, Leiden, The Netherlands.
1. Cho, Y., Adams, K. L., Y.-L. Qiu, P. Kuhlman, J. C. Vaughn, and J. D. Palmer. 1998. A highly invasive group I intron in the mitochondrial cox1 gene. Pp. 19-23, in Plant Mitochondria: From Gene to Function (eds. Ian M. Moller, P. Gardestrom, K. Glimelius, and E. Glaser), Backhuys Publishers, Leiden, The Netherlands.
IV. Book Reviews:
3. Qiu, Y.-L. 2004. 1 + 1 > 2 in the biological system! - a book review of "Acquiring Genomes: A Theory of the Origin of Species", by Lynn Margulis and Dorion Sagan. Plant Systematics and Evolution 244: 260-263.
2. Qiu, Y.-L. 2003. Time to expand the evolutionary theory with newly discovered macroevolutionary processes? - a book review of "Genetics, Paleontology, and Macroevolution, 2nd ed.", by Jeffrey S. Levinton. Plant Systematics and Evolution 237: 110-114.
1. Qiu, Y.-L. 2000. a book review of "Molecular Evolution - a phylogenetic approach", by Roderic D. M. Page & Edward C Holmes. Plant Systematics and Evolution 221: 130-131.
Dr. Hong Ma
Distinguished Professor of Biology
Education
•Ph.D., MIT, 1988
•B.A., Temple, 1983
Postdoc Training
•Caltech, 1988-1990
Honors and Awards
•Faculty Scholars Medal in Life and Health Sciences, 2005
•Guggenheim Fellowship 2004-2005
•American Cancer Society Junior Faculty Research Award 1994-1997
•Helen Hay Whitney Post-Doctoral Fellowship (resigned 7/90-3/91) 1988-1991
•Gosney Post-doc Fellowship, Division of Biology, Calif. Inst. of Techn. 1988
•Graduate Fellowship, Department of Biology, Mass. Inst. of Tech. 1983-1984
Research Interests
Flower development and its evolution; meiosis and pollen development
Our lab is interested in understanding plant reproductive development at the molecular level, using the laboratory plant Arabidopsis thaliana as the experimental system. We approach this problem largely with molecular and genetic tools. In flowering plants, reproductive development encompasses a range of stages from floral meristem formation to fertilization.
One of our research emphases is the analysis of regulatory genes controlling early flower development using both mutants and transgenic plants carrying altered genes. Some of these genes encode putative transcription factors; in particular, we are interested in understanding the function of the AGAMOUS gene at the molecular level. In addition, we are studying a family of genes (called ASK genes) that may regulate protein turnover during development. One of them, ASK1, regulates both vegetative and flower development. We have recently begun to examine flower development from an evolutionary perspective, in collaboration with Prof. Claude dePamphilis in our department and others. A second focus in our lab is aimed at understanding genes important for male meiosis and pollen development. Meiosis is an important reproductive process in eukaryotes. We have discovered several new genes important for Arabidopsis meiosis. Although these genes share sequence similarity with genes in other eukaryotes, their functions in meiosis were not previously revealed. Therefore, we may have discovered novel regulators of meiosis. We are very excited about the opportunities to study meiotic genes using genetic and molecular tools, as well as cytological approaches. We are also interested in signal transduction and G protein function in plant development. We previously isolated genes encoding putative alpha and beta subunits of heterotrimeric G proteins. We are particularly interested in their potential roles during reproductive development.
We welcome interactions from members of the biological science community about topics of mutual interests, including collaborations of various extents. We encourage graduate and undergraduate students to visit our lab to learn more about our research, and we have research opportunities at different levels. Inquiries about positions at various levels are welcome.
Selected Publications
♦Quan, L.*, Xiao, R.*, Li, W., Oh, S.-A., Ambrose, J.C., Cyr, R., Twell, D., Ma, H. 2008. Functionally divergence of the duplicated Arabidopsis AtKIN14a and AtKIN14b genes: critical roles in meiosis and gametophyte development. Plant J. 53: 1013-1026. (Equal contribution)
Hord, C.L.H., Ma, H. 2007. Genetic control of anther cell division and differentiation. In Verma, D.P.S, Hong, Z. Eds. Cell Division Control in Plants. Springer-Verlag, Heidelberg. (invited book chapter).
♦Ito, T., Nagata, N., Yoshiba, Y., Ohme-Takagi, M., Ma, H.*, Shinozaki, K.* 2007. The Arabidopsis MALE STERILITY1 (MS1) gene encoding a PHD-type transcription factor regulates pollen exine development. Plant Cell. 19: 3549-3562. (* Co-corresponding authors)
♦Kong, H., Frohlick, M., Leebens-Mack, J., Ma, H. dePamphilis, C. 2007. Rapid birth of plant SKP1 genes by tandem duplication and retrotransposition. Plant J. 50: 873-885.
♦Lin, Z. Nei, M., Ma, H. 2007. Evolution of MutS -like genes: Multiple ancient subfamilies and co-evolution between MutS and MutL genes. Nucleic Acids Res. 35: 7591-7603.
♦Soltis, D.E., Ma, H., Frohlich, M.W., Soltis, P.S., Albert, V.A., Oppenheimer, D.G., Altman, N.S., dePamphilis, C.W., Leebens-Mack, J.H. 2007. The Floral Genome: An evolutionary history of gene duplications and shifting patterns of gene expression. . Trends Plant Sci. 12: 358-367.
♦Sun, Y. Hord, C. L.H., Chen, C., Ma, H. 2007. Regulation of Arabidopsis early anther development by putative cell-cell signaling molecules and transcriptional regulators. J. Intg. Plant Biol. 49: 60-68.
♦Sun, Y., Zhou, X., Ma, H. 2007. Genome wide analysis of Kelch repeat-containing F-box family (KFB). J. Intg. Plant Biol. 49: 940-952.
♦Wijeratne, A.J., Ma, H. 2007. Genetic analyses of meiotic recombination in Arabidopsis. J. Intg. Plant Biol. 49: 1199-1207.
♦Wijeratne, A.J., Zhang, W., Sun, Y., Liu, W., Albert, R., Zheng, Z., Oppenheimer, D.G, Zhao, D., Ma, H. 2007. Differential gene expression in Arabidopsis wild-type and mutant anthers: Insights into cell differentiation and regulatory networks during anther development. Plant J. 52: 14-29.
♦Yao, X., Ma, H., Wang, J., Zhang, D. 2007. Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa. J. Intg. Plant Biol. 49: 885-897.
♦Hord, C.L.H.*, Chen, C.*, DeYoung, B.J., Clark, S.E., Ma, H. 2006. The BAM1/BAM2 receptor-like kinases are important regulators of early Arabidopsis anther development. Plant Cell 18: 1667-1680. (* Equal contribution)
♦Hu, W., Ma, H. 2006. Characterization of a novel putative zinc-finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. Plant J. 45: 399-422. (cover)
Li, W., Ma, H. 2006. Double-strand DNA breaks and gene functions in meiosis and recombination. Cell Res . 16: 402-412.
♦Lin, Z., Kong, H., Nei, M.*, Ma, H.* 2006. Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiont gene transfer. Proc. Natl. Acad. Sci. USA. 103: 10328-10333. (* corresponding authors)
♦Ma, H. 2006. A molecular portrait of Arabidopsis meiosis. In The Arabidopsis Book . (Eds. Somerville, C.R., Meyerowitz, E.M., Dangl, J., and Stitt, M.), American Society of Plant Biologists, Rockville , MD , doi/10.1199/tab.0009, http://www.aspb.org/publications/arabidopsis/
Wijeratne, A.*, Chen, C.*, Zhang, W.*, Timofejeva, L., Ma, H. 2006. The Arabidopsis thaliana PARTING DANCERS gene encoding a novel protein is important for normal homologous recombination. Mol . Biol . Cell 17 : 1331-1343. (* Equal contribution)
♦Zahn, L. M., Leebens-Mack, J., Arrington, J. M., Hu, Y., Landherr, L.L., dePamphilis, C. W., Becker, A., Theissen, G., and Ma, H. 2006. Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: Evidence for independent sub- and neofunctionalization events. Evol. Dev . 8: 30-45. (cover)
♦Zhang, W.*, Sun, Y.*, Timofejeva, L., Chen, C., Grossniklaus, U., Ma, H. 2006. Control of Arabidopsis tapetum development by DYSFUNCTIONAL TAPETUM 1 (DYT1) encoding a putative bHLH transcription factor. (* Equal contribution) Development , 133: 3085-3095.
♦Cui, L., Wall, P.K., Leebens-Mack, J., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S., Carlson, J., Arumuganathan, A., Barakat, A., Albert, V., Ma, H., dePamphilis, C.W. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res . 16: 738-749. (cover)
♦Duarte , J.M., Cui, L., Wall, K., Zhang, Q., Zhang, X., Leebens-Mack, J., Ma, H., Altman, N., dePamphilis, C.W. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol. 23: 469-478.
♦Hamant, O., Ma, H., Cande, Z.W. 2006. Genetics of meiotic prophase I in plants. Annu. Rev. Plant Biol. 57: 267-302. (Invited review)
♦Li, C., Liang, Y., Chen, C., Li, J., Xu, Y., Xu, Z., Ma, H., Chong, K. 2006. Cloning and expression analysis of TSK1, a wheat SKP1 homologue, and functional comparison with Arabidopsis ASK1 in male meiosis and auxin signaling. Functional Plant Biol. 33: 381-390.
♦Ru, P., Xu, L., Ma, H., Huang, H. 2006. Plant fertility defects induced by the enhanced expression of microRNA167. Cell Res. 16: 457-465.
♦Wang, X., Ni, W., Ge, X.*, Zhang, J., Li, N., Ma, H.*, Cao, K. 2006. Proteomic identification of potential target proteins regulated by an ASK1-mediated proteolysis pathway. Cell Res. 16: 489-498. (* Corresponding authors)
♦Chen, C.*, Zhang, W.*, Timofejeva, L., Gerardin, Y., Ma, H . 2005. The Arabidopsis ROCK-N-ROLLERS gene encodes a homolog of the yeast ATP-dependent DNA helicase MER3 and is required for normal meiotic crossover formation. Plant J . 43 : 321-334. (* equal contribution)
♦Li, W., Yang, X., Lin, Z., Timofejeva, L., Makaroff, C., Ma, H . 2005. The AtRAD51C gene is required for normal meiotic chromosome synapsis and double-stranded break repair in Arabidopsis. Plant Physiol . 138 : 965-976.
♦Ma, H . 2005. Molecular genetic analysis of microsporogenesis and microgametogenesis. Annu. Rev. Plant Biol. 56 : 393-434.
♦Zahn, L. M.*, Kong, H.*, Leebens-Mack, J., Kim, S., Soltis, P.S., Landherr, L.L., Soltis, D.E., dePamphilis, C. W., Ma, H . 2005. The evolution of the SEPALLATA subfamily of MADS-box genes: A pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169 : 2209-2223 . (* equal contribution)
♦Zhang, X., Feng, B., Zhang, Q., Zhang, D., Altman, N., Ma, H . 2005. Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis . Plant Mol. Biol . 58 : 401-419.
♦Albert, V.A., Soltis, D.E., Carlson, J.E., Farmerie, W.G., Wall, P.K., Ilut, D.C., Mueller, L.A., Landherr, L.L., Hu, Y., Buzgo, M., Kim , S., Yoo, M.-J., Frohlich, M.W., Perl-Treves, R., Schlarbaum, S.E., Bliss, B., Zhang, X., Tanksley, S., Oppenheimer, D.G., Soltis, P.S., Ma, H. , dePamphilis, C.W., Leebens-Mack, J.H. 2005. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology . http://www.biomedcentral.com/1471-2229/5/5 .
♦Ambrose, J. C., Li, W. Marcus, A., Ma, H ., Cyr. R. 2005. A minus-end directed kinesin with +TIP activity is involved in spindle morphogenesis. Mol. Biol. Cell , 16 :1584-1592.
♦Kim, S., Koh, J., Ma, H ., Hu, Y., Endress, P., Hauser, B., Soltis, P.S., Soltis, D.E. 2005. Sequence and expression studies of A-, B-, and E-class MADS-box genes in Eupomatia (Eupomatiaceae): Support for the bracteate origin of the calyptra. Intl . J . Plant Sci . 166 :185-198. (cover)
♦Kim, S., Koh, J., Yoo, M.-J., Kong, H., Hu, Y., Ma, H . Soltis, P.S., Soltis, D.E . 2005. Expression of flo ral MADS-box genes in basal angiosperms: Implications on evolution of floral regulators and the perianth . Plant J . 43 : 724-744. (cover)
♦Zahn, L. M., Leebens-Mack, J., dePamphilis, C. W., Ma, H ., Theissen, G. 2005. To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J . Hered . 96 : 225-240.
♦Kong, H.-Z., Leebens-Mack, J., Ni, W., dePamphilis, C. W., Ma, H . 2004. Highly heterogeneous rates of evolution in the SKP1 gene family in animals and plants: functional and evolutionary implications. Mol. Biol. Evol . 21 : 117-128.
♦Li, W., Chen, C., Markmann-Mulisch, U., Timofejeva, L., Schmelzer, E., Ma, H .*, and Reiss, B.* 2004. The Arabidopsis RAD51 gene is dispensable for vegetative growth but required for meiosis . Proc. Natl. Acad. Sci. USA. 101 : 10596-10601. (* Corresponding authors)
♦Liu, F.*, Ni, W.*, Griffith , M.E. *, Huang, Z., Peng, W., Ma, H .#, Xie, D.# 2004. ASK1 and ASK2 genes are essential for Arabidopsis early development. Plant Cell 1 6 : 5-20. (* equal contribution; # corresponding authors)
♦Ma, H . Arabidopsis thaliana genetics. 2004. In Genetics . Virtual Text (http://www.ergito.com/index.jsp)
♦Ni, W., Xie, D., Hobbie, L., Feng, B., Zhao, D., Akkara, J., Ma, H . 2004. Regulation of flower development in Arabidopsis by SCF complexes. Plant Physiol. 134 : 1574-1585.
♦Wang, G.*, Kong, H.*, Sun, Y.*, Zhang, X., Zhang, W., Altman, N., dePamphilis, C. W., Ma, H . 2004. Genome-wide analysis of cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiol . 135 : 1084-1099. (* equal contribution)
Yang, X., Ma, H .*, Makaroff, C.* 2004. Characterization of an unusual Ds transposable element in Arabidopsis thaliana : evidence for insertion by a circular transposition intermediate. ♦Plant Mol. Biol . 55 : 905-917. (* Corresponding authors)
Buzgo, M., Soltis, D. E., Soltis, P. S., Ma, H . 2004. Towards a comprehensive integration of morphological and genetic studies of floral development. Trends Plant Sci . 9 : 164-173.
♦Nam, J., Kim, J., Lee, S., An, G., Ma, H ., Nei, M. 2004. Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. USA . 100 : 1910-1915.
♦Hu, W., Wang, Y., Bowers, C., Ma, H . 2003. Isolation, sequence analysis, and expression studies of florally expressed genes in Arabidopsis . Plant Mol. Biol. 53 : 545-563.
♦Yang, X.-H., Makaroff, C.*, Ma, H .* 2003. The Arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-finger protein that is required for male meiosis. Plant Cell 15 : 1281-1295. (*# corresponding authors)
♦Zhao, D.*, Ni, W.*, Feng, B., Han, T., Petrasek, M.G., Ma, H . 2003. Members of the Arabidopsis-SKP1-like gene family exhibit a variety of expression patterns and may play diverse roles in Arabidopsis . Plant Physiol. 133 : 203-217. (* equal contribution)
♦Zhao, D., Han, T., Risseeuw, E. P., Crosby, W. L., Ma, H . 2003. Conservation and divergence of ASK1 and ASK2 gene functions during male meiosis in Arabidopsis thaliana . Plant Mol. Biol. 53 : 163-173.
♦Marcus, A.I. Li, W., Ma, H ., Cyr, R.J. 2003. A kinesin mutant with an atypical bipolar spindle in mitosis undergoes normal cell division. Mol. Biol. Cell . 14 :1717-1726.
♦Nam, J., dePamphilis, C. W., Ma, H ., Nei, M. 2003. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol. Biol. Evol . 20 : 1435-1447.
♦Zhang, S., Raina, S., Li, H., Li, J., Dec, E., Ma, H ., Huang, H., Fedoroff, N.V. 2003. Resources for targeted insertional and deletional mutagenesis in Arabidopsis . Plant Mol. Biol . 53 : 133-150.
♦Azumi, Y., Liu, D., Zhao, D., Li, W., Wang, G., Hu, Y., Ma, H. 2002. Homolog interaction during meiotic prophase I in Arabidopsis requires the SOLO DANCERS gene encoding a novel cyclin-like protein. EMBO J . 21 : 3081-3095.
♦Chen, C., Marcus, A., Li, W., Hu, Y., Vielle Calzada, J.-P., Grossniklaus, U., Cyr, R., Ma, H . 2002. The Arabidopsis ATK1 gene is required for spindle morphogenesis in male meiosis. Development , 129 : 2401-2409. (cover)
♦Zhao, D.-Z., Wang, G.-F., Speal, B., Ma, H . 2002. The EXCESS MICROSPOROCYTES1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther. Genes & Dev . 16 : 2021-2031.
♦Soltis, D.E., Soltis, P.S., Albert, V. A., dePamphilis, C. W., Frohlich, M., H. Ma, Theissen, G. 2002. Missing links: the genetic architecture of the flower and floral diversification. Trends Plant Sciences 7 : 22-31.
♦Xu, L., Liu, F., Lechner, E., Genschik, P., Crosby, W. L., Ma, H ., Peng, W., Huang, D., Xie, D. 2002. The SCFcoi1 ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis. Plant Cell 14 : 1919-1935.
♦Zhao, D., Yu, Q. Chen, M., Ma. H . 2001. The ASK1 gene regulates B function gene expression in cooperation with UFO and LEAFY in Arabidopsis. Development . 128 : 2735-2746.
♦Zhao, D., Yu, Q., Chen, C., Ma, H . 2001. Genetic control of reproductive meristems. In: Meristematic Tissues in Plant Growth and Development . (Eds. McManus, M.T. and Veit, B.) Sheffield Academic Press. Sheffield . pp.89-142.
♦Ma, H ., dePamphilis, C. 2000. The ABCs of floral evolution. Cell 101 : 5-8.
Yang, M., Hu, Y., Lodhi, M., McCombie, W. R., Ma, H . 1999. The Arabidopsis SKP1-LIKE1 gene is essential for male meiosis and may control homologue separation. Proc. Natl. Acad. Sci. USA . 96 : 11416-11421.
♦Zhao, D., Yang, M., Solava, J., Ma, H . 1999. The Arabidopsis ASK1 gene regulates vegetative and floral development and interacts with UFO to control floral organ identity. Develop. Genet. 25 : 209-223.
♦Lev, S., Sharon, A., Hadar, R., Ma, H, Horwitz, B. A. 1999. A MAP kinase of the corn pathogen Cochliobolus heterostrophus involved in conidiation, appressoria formation and pathogenecity: diverse roles of MAPK homologs in foliar pathogens. Proc. Natl. Acad. Sci. USA. 96:13542-13547.
Ma, H. 1997. The on and off of floral regulatory genes. Cell 89: 821-824.
♦Mizukami, Y., Ma, H. 1997. Determination of Arabidopsis floral meristem identity by AGAMOUS. Plant Cell 9: 393-408.
♦Huang, H., Tudor, M., Su, T., Zhang, Y., Hu, Y., Ma, H. 1996. DNA-binding properties of two Arabidopsis MADS-domain proteins: binding consensus and dimer formation. Plant Cell 8: 81-94.
Mizukami, Y., Huang, H., Tudor, M., Hu, Y., Ma, H. 1996. Functional domains of the floral regulator AGAMOUS: characterization of the DNA-binding domain and analysis of dominant negative mutations. Plant Cell 8: 831-845.
♦Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J., Dean, C., Ma, H., Martienssen, R. 1995. Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes & Dev. 9: 1797-1810.
♦Ma, H. 1994. The unfolding drama of flower development: recent results from genetic and molecular analyses. Genes & Dev. 8: 745-756.
♦Weiss, C.A., Garnaat, C., Mukai, K., Hu, Y., Ma, H. 1994. Molecular cloning of cDNAs from maize and Arabidopsis encoding a G protein beta subunit. Proc. Natl. Acad. Sci. USA 91: 9554-9558.
♦Weiss, C.A., Huang, H., Ma, H. 1993. Immunolocalization of the G protein alpha subunit encoded by the GPA1 gene in Arabidopsis. Plant Cell 5: 1513-1528.
♦Mizukami, Y., Ma, H. 1992. Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell 71: 119-131.
♦Mandel, M.A., Bowman, J.L., Kempin, S.A., Ma, H., Meyerowitz, E.M., Yanofsky, M.F. 1992. Manipulation of flower structures in transgenic tobacco. Cell 71: 133-143.
♦Ma, H., Yanofsky, M.F., Meyerowitz, E.M. 1991. AGL1-AGL6, An Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes & Dev. 5: 484-495.
♦Ma, H., Yanofsky, M.F., Meyerowitz, E.M. 1990. Molecular cloning and characterization of GPA1, a G protein alpha subunit gene from Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 87: 3821-3825.
♦Yanofsky, M.F., Ma, H., Bowman, J.L., Drews, G.N., Feldmann, K., Meyerowitz, E.M. 1990. The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346: 35-39.
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