Download 第六届植物分子生物学暑期研讨班专家资料介绍

第六届植物分子生物学暑期研讨班专家资料介绍
(参考专家实验室主页)
Dr. Yunde Zhao
Associate Professor
Section of Cell and Developmental Biology, UCSD
e-mail: [email protected]
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:
1)
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.
2)
McSteen P and Zhao Y (2008). Plant hormones and signaling: common themes and new
developments. Dev Cell 14(4):467-73.
3)
Zhao, Y. (2008) The role of local biosynthesis of auxin and cytokinin in plant development.
Curr Opin Plant Biol . 11(1):16-22.
4)
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.
5)
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.
6)
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.
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7)
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
8)
Cheng Y., Qin G., Dai X., and Zhao Y (2007).
auxin-regulated organogenesis in Arabidopsis.
9)
A role for a BTB-NPH3-like protein in
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
10) Cheng, Y. and Zhao Y. (2007).
Integrative Plant Biology
A role for auxin in flower development. Journal of
49 (1): 99-104
11) 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
12) 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.
13) 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.
14) 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
15) 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
16) 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
17) 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
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18) 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
19) 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
20) 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
21) Blackwell, H.E., and Zhao, Y. (2003) Chemical Genetic Approaches to Plant Biology. Plant
Physiol. 133, 456-461. Full Text PDF
22) 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
23) 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
24) 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
25) 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
26) Zhao, Y. and Chory, J (2001). A link between the light and gibberellin signaling cascades.
Development Cell 1, 315-316.
27) 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
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28) 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
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Dr. Yang, Zhenbiao
Professor of Cell Biology & Cell Biologist
College of Natural and Agricultural Sciences
Botany & Plant Sciences
e-mail: [email protected]
3162 BATCHELOR HALL, KEEN HALL
University of California
Riverside, CA 92521
Personal Web Site: http://cepceb.ucr.edu/members/yang.htm
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 components remain poorly understood. In animals and yeast, G proteins or GTPases are
pivotal switches that turn on and off intracellular signaling pathways by cycling between
GTP-bound active and GDP-bound inactive forms. 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
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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,
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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?
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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
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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
1)
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.
2)
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.
3)
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.
4)
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.
5)
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.
6)
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.
7)
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.
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8)
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.
9)
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.
10) 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.
11) 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.
12) 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.
13) 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.
14) 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.
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Dr. Zhiyong Wang
Department of Plant Biology
Carnegie Institution for Science
260 Panama Street
Stanford, CA 94305
Phone: (650) 325-1321 x205
Fax: (650) 325-6857
Personal Web Site: http://carnegiedpb.stanford.edu/wang-lab
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.
Brassinosteroid is a plant growth hormone
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The brassinosteroid signal transduction pathway
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
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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:
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1) 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.
2) 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.
3) 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
4) 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.
5) Joshua M. Gendron and Zhi-Yong Wang (2007). Multiple mechanisms modulate
Brassinosteroid signaling. Current Opinion in Plant Biology, 10, 436-441.
6) 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
7) 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
8) 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
9) 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.
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10) 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.
11) 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.
12) Wang Z-Y and He, J-X. (2004). Brassinosteroid signal transduction: choices of signals
and receptors. Trends in Plant Science 9 (2), 91-96.
13) 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.
14) 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.
15) 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.
16) 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
17) 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.
18) 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.
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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: [email protected]
Fields of study
Plant evolution
Lab home page: http://sitemaker.umich.edu/qiu.lab/home
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 of
Systematics 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
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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.
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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.
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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.
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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 earliest angiosperms: 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
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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.
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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.
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Dr.
Hong Ma
Distinguished Professor of Biology
Office: 405D Life Sciences
Phone: 863-6414
Lab Address: 416 Life Sciences
Lab Phone: 865-3438
e-mail: [email protected]
Lab home page: http://www.bio.psu.edu/home/directory/homepages/hxm16
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
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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
1)
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)
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2)
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).
3)
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)
4)
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.
5)
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.
6)
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.
7)
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.
8)
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.
9)
Wijeratne, A.J., Ma, H. 2007. Genetic analyses of meiotic recombination in Arabidopsis. J.
Intg. Plant Biol. 49: 1199-1207.
10) 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.
11) 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.
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12) 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)
13) 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)
14) Li, W., Ma, H. 2006. Double-strand DNA breaks and gene functions in meiosis and
recombination. Cell Res . 16: 402-412.
15) 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)
16) 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/
17) 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)
18) 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)
19) 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.
20) 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)
11
21) 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.
22) Hamant, O., Ma, H., Cande, Z.W. 2006. Genetics of meiotic prophase I in plants. Annu. Rev.
Plant Biol. 57: 267-302. (Invited review)
23) 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.
24) Ru, P., Xu, L., Ma, H., Huang, H. 2006. Plant fertility defects induced by the enhanced
expression of microRNA167. Cell Res. 16: 457-465.
25) 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)
26) 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)
27) 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.
28) Ma, H . 2005. Molecular genetic analysis of microsporogenesis and microgametogenesis.
Annu. Rev. Plant Biol. 56 : 393-434.
29) 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)
30) 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.
12
31) 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 .
32) 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.
33) 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)
34) 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)
35) 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.
36) 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.
37) 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)
38) 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)
39) Ma, H . Arabidopsis thaliana genetics. 2004. In Genetics . Virtual Text
(http://www.ergito.com/index.jsp)
13
40) 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.
41) 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)
42) 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)
43) 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.
44) 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.
45) 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.
46) 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)
47) 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)
48) 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.
49) 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.
50) 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.
14
51) 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.
52) 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.
53) 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)
54) 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.
55) 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.
56) 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.
57) 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.
58) 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.
59) Ma, H ., dePamphilis, C. 2000. The ABCs of floral evolution. Cell 101 : 5-8.
60) 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.
15
61) 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.
62) 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.
63) Ma, H. 1997. The on and off of floral regulatory genes. Cell 89: 821-824.
64) Mizukami, Y., Ma, H. 1997. Determination of Arabidopsis floral meristem identity by
AGAMOUS. Plant Cell 9: 393-408.
65) 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.
66) 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.
67) 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.
68) Ma, H. 1994. The unfolding drama of flower development: recent results from genetic and
molecular analyses. Genes & Dev. 8: 745-756.
69) 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.
70) 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.
71) 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.
72) 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.
16
73) 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.
74) 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.
75) 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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