Transcriptional regulation in wood formation.

Wood (i.e. xylem tissue) in trees is mainly composed of two types of cells, fibres and tracheary elements. Recent molecular studies of various trees, as well as the non-tree species Arabidopsis thaliana and Zinnia elegans, have revealed coordinated gene expression during differentiation of these cells in wood and the presence of several transcription factors that might govern the complex networks of transcriptional regulation. This article reviews recent findings concerning the regulation of genes by transcription factors involved in wood formation such as AUXIN RESPONSE FACTOR (ARF), CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII), KANADI (KAN), MYB and NAM/ATAF/CUC (NAC).

[1]  J. Laroche,et al.  Large-scale statistical analysis of secondary xylem ESTs in pine , 2004, Plant Molecular Biology.

[2]  Kyung-Hwan Han,et al.  Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana , 2006, Molecular Genetics and Genomics.

[3]  R. Napier,et al.  Receptors for auxin: will it all end in TIRs? , 2006, Trends in Plant Science.

[4]  V. Kapur,et al.  Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia , 2003, Plant Molecular Biology.

[5]  T. Demura,et al.  SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis[W] , 2006, The Plant Cell Online.

[6]  Ari Pekka Mähönen,et al.  A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. , 2000, Genes & development.

[7]  Youn-sung Kim,et al.  microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. , 2005, The Plant journal : for cell and molecular biology.

[8]  Etienne Paux,et al.  Transcript profiling of Eucalyptus xylem genes during tension wood formation. , 2005, The New phytologist.

[9]  Y. Helariutta,et al.  Phloem and xylem specification: pieces of the puzzle emerge. , 2005, Current opinion in plant biology.

[10]  H. Fukuda.  Signals that control plant vascular cell differentiation , 2004, Nature Reviews Molecular Cell Biology.

[11]  Kyung-Hwan Han,et al.  Developmental and seasonal expression of PtaHB1, a Populus gene encoding a class III HD-Zip protein, is closely associated with secondary growth and inversely correlated with the level of microRNA (miR166). , 2006, The New phytologist.

[12]  M. Campbell,et al.  The genetic control of lignin deposition during plant growth and development. , 2004, The New phytologist.

[13]  A. Déjardin,et al.  Expressed sequence tags from poplar wood tissues--a comparative analysis from multiple libraries. , 2004, Plant biology.

[14]  E. Wisman,et al.  The arabidopsis ATHB-8 HD-zip protein acts as a differentiation-promoting transcription factor of the vascular meristems. , 2001, Plant physiology.

[15]  E. Meyerowitz,et al.  Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development , 2006, PLoS genetics.

[16]  J. Grima-Pettenati,et al.  EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. , 2005, The Plant journal : for cell and molecular biology.

[17]  D. Galbraith,et al.  Global studies of cell type-specific gene expression in plants. , 2006, Annual review of plant biology.

[18]  Masayuki Higuchi,et al.  Cytokinin Signaling and Its Inhibitor AHP6 Regulate Cell Fate During Vascular Development , 2006, Science.

[19]  Guiliang Tang,et al.  MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region , 2004 .

[20]  J. Bowman.  Class III HD-Zip gene regulation, the golden fleece of ARGONAUTE activity? , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[21]  M. Alves-Ferreira,et al.  Identification and characterization of homeobox genes in Eucalyptus , 2005 .

[22]  Dimitra L. Milioni,et al.  Early Gene Expression Associated with the Commitment and Differentiation of a Plant Tracheary Element Is Revealed by cDNA–Amplified Fragment Length Polymorphism Analysis , 2002, The Plant Cell Online.

[23]  R. Sederoff,et al.  Functional genomics and cell wall biosynthesis in loblolly pine. , 2001 .

[24]  J. Craig,et al.  The Xylem and Phloem Transcriptomes from Secondary Tissues of the Arabidopsis Root-Hypocotyl1[w] , 2005, Plant Physiology.

[25]  Tetsuro Mimura,et al.  Transcription switches for protoxylem and metaxylem vessel formation. , 2005, Genes & development.

[26]  J. Bowman,et al.  Establishment of polarity in lateral organs of plants , 2001, Current Biology.

[27]  T. Demura,et al.  Promotion of transcript accumulation of novel Zinnia immature xylem-specific HD-Zip III homeobox genes by brassinosteroids. , 2002, Plant & cell physiology.

[28]  P. Nilsson,et al.  A genomic approach to investigate developmental cell death in woody tissues of Populus trees , 2005, Genome Biology.

[29]  P. Ranocha,et al.  Novel Markers of Xylogenesis in Zinnia Are Differentially Regulated by Auxin and Cytokinin1[W] , 2005, Plant Physiology.

[30]  T. Demura,et al.  Class III homeodomain leucine-zipper proteins regulate xylem cell differentiation. , 2005, Plant & cell physiology.

[31]  Sunchung Park,et al.  Plant Body Weight-Induced Secondary Growth in Arabidopsis and Its Transcription Phenotype Revealed by Whole-Transcriptome Profiling1[w] , 2004, Plant Physiology.

[32]  J. Bowman,et al.  Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes , 2003, Current Biology.

[33]  J. Grima-Pettenati,et al.  Identification of genes preferentially expressed during wood formation in Eucalyptus , 2004, Plant Molecular Biology.

[34]  K. Shinozaki,et al.  NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis[W][OA] , 2007, The Plant Cell Online.

[35]  H. Fukuda,et al.  HD-zip III homeobox genes that include a novel member, ZeHB-13 (Zinnia)/ATHB-15 (Arabidopsis), are involved in procambium and xylem cell differentiation. , 2003, Plant & cell physiology.

[36]  A. Stokes,et al.  Wood formation in trees. , 2001, Plant physiology.

[37]  J. Bowman,et al.  Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots , 2001, Nature.

[38]  Leonel van Zyl,et al.  Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda) , 2004 .

[39]  Kyung-Hwan Han,et al.  Seasonal changes in gene expression at the sapwood-heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis. , 2004, Tree physiology.

[40]  J. Ecker,et al.  Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Developmentw⃞ , 2005, The Plant Cell Online.

[41]  Chengsong Zhao,et al.  Arabidopsis as a Model for Investigating Gene Activity and Function in Vascular Tissues , 2001 .

[42]  T. Mimura,et al.  Regulation of Secondary Cell Wall Development by Cortical Microtubules during Tracheary Element Differentiation in Arabidopsis Cell Suspensions1[w] , 2005, Plant Physiology.

[43]  K. Yoshida,et al.  Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. , 2000, The Plant journal : for cell and molecular biology.

[44]  R. Sederoff,et al.  Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. , 2004, Plant biology.

[45]  Timothy Nelson,et al.  Laser microdissection of plant tissue: what you see is what you get. , 2006, Annual review of plant biology.

[46]  Lisa McMillan,et al.  Wood Formation from the Base to the Crown in Pinus Radiata: Gradients of Tracheid Wall Thickness, Wood Density, Radial Growth Rate and Gene Expression , 2006, Plant Molecular Biology.

[47]  Shoshi Kikuchi,et al.  Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  B. Sundberg,et al.  A transcriptional roadmap to wood formation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[49]  K. Shinozaki,et al.  The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscencew⃞ , 2005, The Plant Cell Online.

[50]  Christopher D Town,et al.  Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. , 2004, The Plant journal : for cell and molecular biology.

[51]  S. Tabata,et al.  ARR1, a Transcription Factor for Genes Immediately Responsive to Cytokinins , 2001, Science.

[52]  Kyung-Hwan Han,et al.  Transcriptome profiling of vertical stem segments provides insights into the genetic regulation of secondary growth in hybrid aspen trees. , 2005, Plant & cell physiology.

[53]  Ari Pekka Mähönen,et al.  APL regulates vascular tissue identity in Arabidopsis , 2003, Nature.

[54]  Sunchung Park,et al.  Journal of Experimental Botany, Page 1 of 14 DOI: 10.1093/jxb/erg304 , 2003 .

[55]  J. Grima-Pettenati,et al.  Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus. , 2006, The New phytologist.

[56]  Jia Li,et al.  BRL1, a leucine-rich repeat receptor-like protein kinase, is functionally redundant with BRI1 in regulating Arabidopsis brassinosteroid signaling. , 2004, The Plant journal : for cell and molecular biology.

[57]  Kyung-Hwan Han,et al.  Arabidopsiswhole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth , 2004, Plant Molecular Biology.

[58]  R. Sederoff,et al.  Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[59]  N. McHale,et al.  MicroRNA-Directed Cleavage of Nicotiana sylvestris PHAVOLUTA mRNA Regulates the Vascular Cambium and Structure of Apical Meristems , 2004, The Plant Cell Online.

[60]  T. Demura,et al.  Primary phloem-specific expression of a Zinnia elegans homeobox gene. , 2001, Plant & cell physiology.

[61]  Chengsong Zhao,et al.  Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. , 2000, Plant physiology.

[62]  Bernard Henrissat,et al.  Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. , 2006, The Plant journal : for cell and molecular biology.

[63]  H. Fukuda,et al.  Dodeca-CLE Peptides as Suppressors of Plant Stem Cell Differentiation , 2006, Science.

[64]  B. Sundberg,et al.  A Populus EST resource for plant functional genomics. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Ana I. Caño-Delgado,et al.  BRL1 and BRL3 are novel brassinosteroid receptors that function in vascular differentiation in Arabidopsis , 2004, Development.

[66]  M. Sugiyama,et al.  A proteoglycan mediates inductive interaction during plant vascular development , 2004, Nature.

[67]  J. B. Reid,et al.  Genomic Research in Eucalyptus , 2005, Genetica.

[68]  Z. Ye.  Vascular tissue differentiation and pattern formation in plants. , 2002, Annual review of plant biology.

[69]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

[70]  Patrick S Schnable,et al.  Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. , 2003, The Plant cell.

[71]  Jun Zhuang,et al.  Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. , 2005, The Plant journal : for cell and molecular biology.

[72]  J. Dean,et al.  SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). , 2002, Tree physiology.

[73]  N. Chaffey,et al.  Secondary xylem development in Arabidopsis: a model for wood formation. , 2002, Physiologia plantarum.

[74]  D. Galbraith,et al.  Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate , 2004, Plant Physiology.

[75]  D. Pot,et al.  Seasonal variation in transcript accumulation in wood-forming tissues of maritime pine (Pinus pinaster Ait.) with emphasis on a cell wall glycine-rich protein , 2003, Planta.

[76]  R. Zhong,et al.  Amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. , 2004, Plant & cell physiology.

[77]  A. Meijer,et al.  Pattern formation in the vascular system of monocot and dicot plant species. , 2004, The New phytologist.

[78]  James E. Johnson,et al.  Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters , 2005, BMC Genomics.