Phase changes in plant development: floral transition and secondary xylem - Luận án tiến sĩ Sookyung Oh
Luận án tiến sĩ nghiên cứu giai đoạn phát triển thực vật, chuyển đổi hoa và hình thành gỗ. Sử dụng genomics chức năng để xác định gene điều hòa và cơ chế phân tử.
Michigan State University
Plant Breeding and Genetics
Luan An
Dissertation
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I. Plant Phase Changes and Developmental Transitions
Plants undergo critical developmental shifts called phase changes throughout their lifecycle. These transitions alter meristem potential and cellular identity. Two major phase changes shape plant architecture: the shift from vegetative to reproductive growth and the transition from primary to secondary growth. Phase changes require meristem competency to respond to internal and external signals. Each developmental phase displays distinct morphological and physiological characteristics. Understanding the molecular mechanisms controlling these transitions remains a fundamental challenge in plant developmental biology.
1.1. Meristem Identity and Developmental Competency
Meristems serve as the foundation for plant growth and development. The shoot apical meristem maintains stem cells that generate new tissues. Developmental competency determines when meristems can respond to specific signals. This competency varies across developmental stages. Environmental cues interact with internal developmental programs. The integration of these signals triggers phase transitions. Meristem identity genes regulate the potential for tissue differentiation.
1.2. Morphological Markers of Phase Transitions
Each developmental phase exhibits unique morphological traits. Vegetative phase produces leaves optimized for photosynthesis. Reproductive phase generates flowers for sexual reproduction. Secondary growth creates woody tissues for structural support. These morphological changes reflect underlying genetic reprogramming. Specific gene expression patterns characterize each phase. Understanding these markers helps identify regulatory mechanisms.
1.3. Molecular Mechanisms of Phase Change
Phase changes involve complex genetic networks. Transcription factors coordinate developmental transitions. Chromatin modifications alter gene accessibility. Epigenetic mechanisms provide cellular memory of developmental states. Hormonal signals integrate environmental information. The molecular basis of phase change remains incompletely understood. Research continues to uncover novel regulatory pathways.
II. Floral Transition and Flowering Time Regulation
The transition from vegetative to reproductive growth represents a critical developmental decision. Multiple pathways control flowering time in response to environmental and developmental signals. The photoperiod pathway responds to day length changes. Vernalization pathway requires prolonged cold exposure. The autonomous pathway promotes flowering independently of environmental cues. Gibberellin signaling integrates hormonal control. These pathways converge on floral integrator genes. FLOWERING LOCUS T serves as a mobile flowering signal. Understanding flowering regulation has agricultural and ecological significance.
2.1. Photoperiod Pathway and Light Sensing
Day length profoundly influences flowering time in many species. Plants measure photoperiod through photoreceptors and circadian clock components. Long-day plants flower when days exceed a critical length. Short-day plants flower when days fall below a threshold. Photoperiod pathway genes regulate FLOWERING LOCUS T expression. This pathway enables plants to synchronize reproduction with favorable seasons. Light quality and intensity also modulate photoperiodic responses.
2.2. Vernalization and Cold Response
Many plant species require prolonged cold exposure before flowering. Vernalization prevents premature flowering during winter. Cold treatment establishes epigenetic memory through chromatin modifications. FLOWERING LOCUS C acts as a major floral repressor. Vernalization silences FLC expression through histone modifications. This silencing persists after return to warm temperatures. The autonomous pathway also regulates FLC independently of cold.
2.3. Floral Integrators and Meristem Identity
Multiple flowering pathways converge on floral integrator genes. FLOWERING LOCUS T encodes a mobile protein that moves to the shoot apical meristem. FT protein triggers floral meristem identity gene expression. Meristem identity genes convert vegetative meristems to floral meristems. This conversion represents an irreversible developmental commitment. Floral meristem genes activate downstream programs for flower development. Understanding these integrators reveals flowering time control mechanisms.
III. Secondary Xylem Formation and Wood Development
Secondary growth produces woody tissues through cambial activity. The vascular cambium generates secondary xylem inward and secondary phloem outward. Wood formation involves coordinated cellular differentiation and cell wall biosynthesis. Secondary xylem provides mechanical support and water transport capacity. Hormones regulate cambial activity and wood formation. Auxin and cytokinin maintain cambial cell division. Gibberellins promote xylem differentiation. Functional genomic approaches identify genes controlling wood formation. Understanding secondary growth has implications for forestry and biofuel production.
3.1. Vascular Cambium and Secondary Growth
The vascular cambium represents a lateral meristem producing secondary tissues. Cambial initials maintain stem cell identity while producing differentiated derivatives. Periclinal divisions generate xylem mother cells and phloem mother cells. Secondary xylem accumulates as wood. Secondary phloem functions in nutrient transport. The transition from primary to secondary growth involves cambial establishment. Cambial activity varies seasonally in temperate species.
3.2. Hormonal Regulation of Wood Formation
Plant hormones coordinate secondary growth processes. Auxin promotes cambial cell division and xylem differentiation. Cytokinin maintains cambial stem cell populations. The auxin-cytokinin ratio influences xylem-phloem balance. Gibberellin signaling enhances fiber elongation. Brassinosteroids affect xylem vessel formation. Wounding triggers localized cambial activation. Hormonal interactions create complex regulatory networks controlling wood development.
3.3. Molecular Mechanisms of Xylem Differentiation
Wood formation requires coordinated gene expression programs. Transcription factors regulate xylem cell fate specification. NAC and MYB family transcription factors control secondary cell wall biosynthesis. Cellulose, hemicellulose, and lignin compose secondary walls. Specific enzymes catalyze cell wall polymer synthesis. Programmed cell death creates functional xylem vessels. Understanding these mechanisms enables manipulation of wood properties.
IV. VIP Proteins and Transcriptional Regulation
VERNALIZATION INDEPENDENCE proteins play essential roles in flowering time control. VIP5 and VIP6 mutants display early-flowering phenotypes. These proteins show similarity to yeast Paf1C complex components. Paf1C assists in establishing transcription-promotive chromatin modifications. VIP proteins regulate FLOWERING LOCUS C and MAF gene family expression. Loss of VIP function causes FLC downregulation. This reveals evolutionary conservation of transcriptional mechanisms. VIP proteins affect histone modifications in a locus-specific manner. They influence RNA polymerase II recruitment and activity.
4.1. VIP Protein Function in Flowering Control
VIP5 and VIP6 were identified through early-flowering mutant screens. Genetic mapping and transcriptional profiling enabled gene cloning. VIP proteins maintain high FLC expression levels. FLC represses floral integrator genes. VIP loss-of-function mutations reduce FLC transcript abundance. This derepresses flowering pathway genes. Early flowering results from premature floral transition. VIP proteins function in the autonomous flowering pathway.
4.2. Chromatin Modifications and Gene Expression
VIP proteins regulate chromatin structure at target loci. Histone modifications mark active or repressed chromatin states. VIP proteins promote transcription-permissive histone marks. Loss of VIP function alters histone methylation patterns. These changes occur in a gene-specific manner. Chromatin modifications provide epigenetic memory of gene expression states. VIP proteins connect transcription factor activity to chromatin remodeling.
4.3. RNA Polymerase II Regulation by VIP Proteins
VIP proteins affect RNA polymerase II recruitment to target genes. Pol II distribution changes in VIP mutants. The carboxyl-terminal domain of Pol II undergoes phosphorylation cycles. CTD phosphorylation status correlates with transcription stages. VIP proteins influence CTD dephosphorylation. This suggests VIP involvement in transcription elongation or termination. Understanding VIP function reveals fundamental transcription mechanisms in plants.
V. Functional Genomics of Plant Development
Functional genomic approaches accelerate gene discovery in plant developmental biology. Transcriptional profiling identifies genes with specific expression patterns. Microarray and RNA-seq technologies enable genome-wide expression analysis. Mutant screens reveal genes essential for developmental processes. Forward genetics identifies mutations causing phenotypic changes. Reverse genetics tests functions of candidate genes. Arabidopsis thaliana serves as a powerful model system. Comparative genomics extends findings to crop species. Integrating multiple approaches provides comprehensive understanding of developmental mechanisms.
5.1. Transcriptional Profiling Strategies
Gene expression analysis reveals regulatory networks controlling development. Microarray technology measures thousands of transcript levels simultaneously. RNA sequencing provides quantitative expression data. Temporal expression profiling tracks developmental progression. Tissue-specific profiling identifies spatially restricted gene expression. Comparing mutant and wild-type expression patterns highlights regulatory relationships. Bioinformatic analysis identifies co-regulated gene groups and regulatory motifs.
5.2. Arabidopsis as a Model System
Arabidopsis thaliana offers numerous advantages for developmental studies. The small genome size facilitates molecular analysis. Short generation time enables rapid genetic studies. Extensive mutant collections provide research resources. Transformation protocols allow functional testing. Secondary growth occurs in Arabidopsis stems. This enables wood formation studies in a tractable system. Findings translate to economically important tree species.
5.3. Identifying Regulatory Networks
Developmental processes involve complex gene regulatory networks. Transcription factors coordinate expression of downstream target genes. Cis-regulatory elements mediate transcription factor binding. Identifying these elements reveals regulatory logic. Functional category analysis groups genes by biological process. This highlights key pathways in developmental transitions. Network analysis maps interactions between regulatory components. Systems biology approaches integrate multiple data types.
VI. Applications and Future Directions
Understanding phase changes has practical applications in agriculture and forestry. Manipulating flowering time optimizes crop adaptation to different environments. Controlling wood formation improves timber quality and biofuel production. Climate change necessitates crops with altered developmental timing. Molecular markers enable breeding for desired flowering characteristics. Genetic engineering offers precise developmental control. Future research will elucidate additional regulatory mechanisms. Single-cell genomics will reveal cell-type-specific programs. Understanding phase change mechanisms benefits both basic science and applied plant improvement.
6.1. Agricultural Applications of Flowering Research
Flowering time control affects crop productivity and adaptation. Early flowering varieties suit short growing seasons. Late flowering types avoid frost damage. Photoperiod-insensitive varieties enable cultivation across latitudes. Vernalization requirement affects winter crop survival. Molecular markers accelerate breeding for optimal flowering time. Understanding gibberellin signaling enables growth regulation. These applications improve food security under changing climates.
6.2. Wood Formation and Bioenergy Production
Secondary xylem provides renewable biomass for biofuels. Understanding wood biosynthesis enables genetic improvement. Modifying lignin composition improves biomass processing. Increasing cellulose content enhances sugar yields. Faster-growing trees provide more biomass. Transgenic approaches target specific wood properties. Functional genomics identifies genes for breeding targets. Sustainable forestry benefits from improved wood formation understanding.
6.3. Emerging Technologies in Developmental Biology
New technologies expand research capabilities in plant developmental biology. CRISPR genome editing enables precise gene modifications. Single-cell RNA sequencing reveals cell-type-specific expression. Live imaging tracks developmental processes in real time. Proteomics and metabolomics complement genomic approaches. Machine learning analyzes complex datasets. These tools will uncover additional phase change mechanisms. Integration across scales reveals system-level developmental control.
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Tải xuống để đọc toàn bộPHASE CHANGES IN PLANT DEVELOPMENT WITH RESPECT TO FLORAL TRANSITION AND SECONDARY XYLEM FORMATION By Sookyung Oh A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Plant Breeding and Genetics Program Department of Horticulture 2006 UMI Number: 3236388 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion.
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Box 1346 Ann Arbor, MI 48106-1346 ABSTRACT PHASE CHANGES IN PLANT DEVELOPMENT WITH RESPECT TO FLORAL _ TRANSITION AND SECONDARY XYLEM FORMATION By Sookyung Oh During development, plants undergo a switch in the potential of meristems, termed “phase change”. Phase changes are initiated by competency of meristems to respond to internal and external developmental cues, and the changes are characterized by a unique set of morphological and physiological traits. Our understanding of how phase change is regulated at the molecular level is less clear. My thesis is to understand the molecular mechanism underlying phase changes in plants, by investigating the transition of vegetative to reproductive and of primary to secondary growth.
First, a functional genomic approach was employed to identify genes involved in sequential events of wood formation using Arabidopsis thaliana as a model. Several candidate genes and potential regulatory cis-elements were identified that may play key roles in the genetic regulation of secondary growth. In addition, functional category analysis of the genes suggests the involvement of specific transcription factors in the transition from primary to secondary growth. Second, to better understand molecular mechanism of flowering, I undertook a genetic and molecular analysis of the early-flowering vernalization independence 5 (vip5) and vip6 mutants.
VIP5 and VIP6 were cloned through mapping and transcriptional profiling. Both proteins are closely related to distinct components of budding yeast Paf1C, a transcription factor that assists in establishment and/or maintenance of transcription-promotive chromatin modifications. Loss of function of VIP5 and VIP6 resulted in downregulation of FLC/MAF MADS-domain gene family. The results suggest that an evolutionary conserved transcriptional mechanism plays an essential role in the floral transition.
Finally, I explored the mechanism of VIP proteins in transcription by characterizing the effects of loss of VIP genes on histone modifications, Pol II distribution, and phosphorylation of carboxyl-terminal domain (CTD) of Pol II. VIP proteins are required for chromatin modifications in a locus-specific manner, recruitment of Pol II, and dephosphorylation of CTD, suggesting a significant role of VIP in Pol H-mediated transcription. ACKNOWLEDGMENTS I would like to acknowledge people for helping me during my doctoral work. First, I would like to especially and sincerely thank my advisor, Dr.
Steven van Nocker for his guidance, encouragement, and support at all levels. I would also like to thank my committee members Dr. Zach Burton, Dr. Rebecca Grumet, Dr.
Jim Hancock and Dr. Amy lezzoni for their continual encouragement and offering constructive comments. I would like to thank colleagues in van Nocker laboratory, including Sunchung Park, Hua Zhang, Philip Ludwig, Lingxia Sun, Ying Yan, and Julissa Ek-Ramos. Finally, I would like to thank my family for their life-long love and encouragement.
I am especially grateful to my husband, Sunchung, for his support. iv TABLE OF CONTENTS LIST OF TABLES. Vili LIST OF FIGURES. ix CHAPTER I: LITERATURE REV HE Y.
Phase change in plants 07. Plants produce wood through secondary growth. Hormones and wounding have positive effects on wood formation. Wood bioSynnth€SIS.
óc TH ng ng TH TT TH Tàn TH 00 001 0g 7 2. Model systems for studying wood formatiOT. Functional genomic approaches to wood formation .cscseecssetseeeeeeeeeeenees 10 P9 on nh. 12 ENjiovrI0svc ii.
Cellular memory and chromatin Structure. Molecular and epigenetic mechanisms mediating vernalization. HH TH ng TH ng HH TT T000 27 li. 28 CHAPTER II: Transcriptional Regulation of Secondary Growth in Arabidopsis HA Í[(HHÁ.
co cọ H1 T9 HN HN 00100 1000400009000400800000009180000091600800086 41 ÂU 2n hố. HT HT HH Hà TT TH TH TT n0 0018130 43 Materials and Methods.- HH HH HT TT Hà Hà tà TH TT ng 1á xe 45 Plant growth and treatment for wood formation in Arabidopsis .- 45 RNA extraction and CDNA synthesis. sóng HH HH tre 46 39/2034: 700ẺẺẼ0Ẻ7Ẻ78e. 47 GeneChip array hybr1d1zafiOT.
-- c1 11911111 111 111g Hà HH nh HH Hy 47 Datta analySis 000Ẽ8ẼẺẼ886. 48 Northern blot analysis of selected R2R3-type MYB genes. 49 Analysis of cis-regulatory elements.ccccesccecscesscssscesecesneecsatestaeseateesetessateeneoes 50 Results and D1SCUSSIOTI. Q19 9T g9 1 HH TT ng kg 51 Secondary xylem formation in ArabidOpsis.
Ăn HH HH Hệ, 51 Differential gene expression in treatment stem, bark and xylem. - «nh HT ng HH Hàn H00 010011111 1101111010111101710 59 Cell wall synthesis. án” TT HH TT HH 1 T11 11 01018101007 60 fan) 7e. 64 Transcriptional regulation of secondary xylem formatiOn.
- 2c ccecceeee 65 Identification of regulatory cis-elements for secondary growth. cscsesesessecsserersecseesseseesecenessassesssssesssssasssssesessasesecsesssessesaeensesseseesseseresneges 78 CHAPTER III: A Mechanism Related to the Yeast Transcriptional Regulator Paf1C Is Required for Expression of the Arabidopsis FLC/MAF MADS Box Gene Familly. ee ececessesesesseseesessecsseseesssasseesensesseeesussessesasscsscessussceecsessessesssensessesseaeees 86 Materials and MethOs.- LH ng HH Tu nu THẾ 89 Plant and Yeast Material and ManipulatiO'iS. sáng 89 Cloning Of VIPG wo.
cecccscsscesscesecssecscceseeeaceseceessseesesesessscsasenssonaesseseesesseeensseaeessaseeen 90 Molecular T'echniQU€S.-- ‹ c1 9T ng ng gu ng 90 šg0)⁄0. c1 9v TT TH nh nọ TH HH HH 92 Rss0i5;1020ir1A4- 0 0ẺẼ 18. 93 Microarray ATiAÌYSIS. ch HH HT TT nọ TH ng gu HH HH 94 TT.
95 VIP5 and VIP6 Function in Concert with VIP3 and WÏP4. sex 95 VIPS and VIP6 Participate in the Regulation of a Heterogeneous Subset of Genes Including Other Members of the FLC/MAF Gene Family .cccsessscesesesesereeeeeees 96 VIP6 Encodes a Plant Homolog of the Paf1C Component Ctr9. --- ‹+- 103 The VIP6 Protein Physically Interacts with VIP3 and VIP4 in Vivo. 109 VIP5 Encodes an Additional Paf1C Subunit Homolog.- -¿- 5-5555: 113 VIP Genes Are Not Required for Global Methylation of Histone H3.
115 The VIP Genes Have a Central Role in Flowering through Activation of the FLC/MAF Gene FamlÏy. nàng HH ng 0010101 k1 010111 HH. 115 VIP5 and VIP6 Define Important Pleiotropic Regulators of Developmert. 118 The VIP Genes Cooperatively Regulate Gene Expression through a Mechanism Related to the Yeast Transcriptional Regulator Paf1C 0.ccssssessersesersesesseeenees 119 9x NA ốm.
125 CHAPTER IV: Global and Locus-Specific Roles for Arabidopsis PafÍC Homologs in Transcription and Chromatin Modifications —¬. G1 ng HH TT TT TH TT Cu no TT gu ng eg 132 Materials and Methods.- -ó- 0 Án TH ng HH ng HH ng ng 136 Plant Materials .- G ch TT TT nu TH HT ng ng cung 136 Isolation of histones .ccssccsessesssscsssssescsscsssscssssesscescsecscescsevscsseeseeaseaecssenseaceasaces 136 vi ˆ9ìiïis (1>.- cv 9T 9T HT TH nh gu ng nàn 137 Electrophoresis and ImmunoblÏOffIngE. «s2 HH Hư 138 Chromatin Immunoprecipitation (CÍP).- ác HH HH HH Hiệu 138 RESUS. 139 VIP3 is not required for global modification of either canonical or variant histone 6.
139 VIP3 is required for H3 methylation in a locus-specific manner.-- -- 140 Mutation of VIP3 is associated with a reduction of Pol If on FLC chromatin. 143 VIP genes are required for modification of CTD of Pol ÏT. HH HT HT HT TT TT TT TT HH TH HH TT TT ch tưng nh 152 CHAPTER V: Perspectives and Future DireCfÏOTS.cscsĂcsĂSSSSSSASessessesee 156 - VỊP complex is required for histone H3 methylation in a locus-specific manner. 157 VIP3 may be a higher eukaryote-specific component of Paf1 C.
--- +2 158 VIP complex is required for Ser-2 and Ser-5 phosphorylation of CTD of Pol H. 164 APPENDIX A: Protocol for extraction of hisfOnS.o-os 525516565555 168 APPENDIX B: Primers for ChIP analysis .cccscssosssesesesssesesssscsssessessssessesseessees 170 APPENDIX C: Protocol for ChIP analysis `. 172 vii LIST OF TABLES Table 2-1. Expression patterns of selected xylogenesis-related genes.
Regulatory cis-element motifs identified from the promoter regions of the genes up-regulated in wood-forming SteMS 0. cece - ch HH Hà Hàn th HH 77 Table 4-1. Partial list of genes down-regulated in both the vip5 and vip6 mutants, relative tO 0): 111. List of primers and S€qU€TC€S.
6 n1 11111 11911811 11191 1 1 ng nh 171 vii LIST OE EIGURES Figure 1-1. Organization of the primary and secondary vascular tissues in Arabidopsis SCheMatically. cs cecsccscssccscsecssseeescceeceseescesecsecscceseeeesesseeeeesssseeseseseeseeseseesseeeaseneeesesseseseeaees 4 Figure 1-2. Flowering time control in Arabidopsis.
Maintenance of active and repressed states of FLC transcription by chromatin „0919514150002. Cross-sections of control and treatment stems of Arabidopsis thaliana. Venn diagram showing up-regulated (22-fold) genes in control and treatment stems, xylem, and bark from the Arabidopsis Genome array analyses. Functional classification of the up-regulated genes in control and treatment Stems, bark and xylem.
R2R3-type MYB transcription factor genes up-regulated in xylem (A) or bark 0 ố ố ốốốố. Northern blot analysis of selected R2R3-type MYB genes that were highly up-regulated in xylem (MYB59 and MYB48) or bark (Ä4YB13). 5 sec cscerseseee 69 Figure 2-6. Phylogenetic tree of homeodomain (HD) genes.
Hierarchical clustering of differentially regulated genes and selection of xylem (Group I) and bark (Group II) up-regulated genes. Flowering Time of vip3, vip4, vip5, and vip6 Single and Double Mutants. Characteristics of Microarray Data Derived from fle, vip5, and vip6 Mutants. Expression of the FLC-Related MAF Genes in flc, vip5, and vip6 Mutants.
Map Position, Structure, and Expression of the VIP6 Gene and Protein. Analysis of VIP6 mRNA and Protein Abundance in Various Genetic Backgrounds and in Response to Vernalization. Coimmunoprecipitation of VIP3, VIP4, VIP5, and VIP6 in Vivo. Structure and Expression Of ƒ/ÏPŠ.
Immunoblot Analysis of Histone H3 Methylation in Strong vip3, vip4, vip5, and vip6 Mutants, the flc-3 Null Mutant, and the Col Ecotype. VIP3 is not required for global modification of either canonical or variant II) 0:06. VIP3 is required for histone H3 methylation in a locus-specific manner. VIP-FLAG proteins do not appear to coprecipitate with Pol II.
VIP genes are required for modification of the CTD of Pol II. The phosphorylation cycle of the CTD of Pol TH. --- c5 +s«c<<ccs<ss+ 162 CHAPTER I LITERATURE REVIEW 1. Phase change in plants During their life cycle, plants go through a succession of developmental phases distinguished from one another by various morphological, physiological, and biochemical traits, and the phenomenon is so-called phase change (Brink, 1962).
The phase changes begin with seed germination, and progress generally through juvenility, maturity, and flowering. The changes are associated with competence of the meristems (a tissue populated by actively dividing and undifferentiated cells) responding to internal and external developmental cues (Bernier, 1981; Steeves and Sussex, 1989). Understanding the mechanisms by which developmental phase changes are regulated will be a perpetual question throughout plant biology because they are controlled by myriad signal transduction pathways. The most obvious example of phase change is the transition from vegetative to reproductive development when leaf development is arrested and meristems are differentiated as flowers (Poethig, 1990).
Although the floral transition has been extensively studied, and as a result, many components of flowering pathways have been identified and characterized, the biochemical roles of them in cellular heredity during floral transition are less studied. Another example of phase change is the transition from primary to secondary growth responsible for lateral growth in most tree species, and the study of molecular mechanism for secondary growth is very limited despite its economical and ecological significance.
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