Plant Transcription Factors: Evolutionary, Structural and Functional Aspects

Plant Transcription Factors: Evolutionary, Structural and Functional Aspects is the only publication that provides a comprehensive compilation of plant transcription factor families and their complex roles in plant biology.

While the majority of information about transcription factors is based on mammalian systems, this publication discusses plant transcription factors, including the important aspects and unifying themes to understanding transcription factors and the important roles of particular families in specific processes.

• Provides an entry point for transcription factor literature
• Offers compilation of information into one single resource for rapid consultation on different plant transcription factor features
• Integrates the knowledge about different transcription factors, along with cross-referencing
• Provides information on the unique aspects surrounding plant transcription factors

• Language: English
• Publisher: Academic Press
• Release date: Jul 7, 2015
• ISBN: 9780128011270

Book preview

Plant Transcription Factors

Evolutionary, Structural and Functional Aspects

Edited by

Daniel H. Gonzalez

Universidad Nacional del Litoral, Santa Fe, Argentina

Table of Contents

Cover

Title page

Copyright

List of Contributors

Preface

A: General aspects of plant transcription factors

Chapter 1: Introduction to Transcription Factor Structure and Function

Abstract

1.1. Introduction: Transcription in Eukaryotes

1.2. Structure of Transcription Factors

1.3. DNA Recognition by Transcription Factors

1.4. DNA-binding Domains

1.5. Protein–protein Interactions

1.6. Regulation of Transcription Factor Action

1.7. Plant Transcription Factors

Acknowledgments

Chapter 2: Methods to Study Transcription Factor Structure and Function

Abstract

2.1. Introduction

2.2. In vivo Functional Studies

2.3. Methods for the Analysis of In Vitro Protein–DNA Interactions

2.4. Methods to Study Protein–DNA Interactions In Vivo

2.5. Analysis of Protein–Protein Interactions

Acknowledgments

Chapter 3: General Aspects of Plant Transcription Factor Families

Abstract

3.1. Introduction

3.2. Overview of the Transcription Cycle in Eukaryotes

3.3. Components Involved in the Formation of the RNAPII Preinitiation Complex in Plants

3.4. Plant Transcription Factor Families

3.5. Major TF Families that are Conserved Across Eukaryotes

3.6. Plant-Specific TF Families

3.7. TFs without DBD but Interacting with DBD-Containing TFs

3.8. Conclusion

Acknowledgments

Chapter 4: Structures, Functions, and Evolutionary Histories of DNA-Binding Domains of Plant-Specific Transcription Factors

Abstract

4.1. Introduction

4.2. Description of Respective DBDs

4.3. Evolutionary History of Plant-Specific TFs

Acknowledgments

Chapter 5: The Evolutionary Diversification of Genes that Encode Transcription Factor Proteins in Plants

Abstract

5.1. Introduction – Distinctive Features of TF Genes in Plants (Arabidopsis and Rice)

5.2. A Comparative Analysis of TF Genes Between Plants and Animals

5.3. A Comparative Analysis of Transcription Factor Genes in 32 Diverse Organisms

5.4. The Appearance of New TF Gene Members During Evolution

5.5. The Different Evolutionary Methods of TF Genes in Animals and Plants

5.6. TF Gene Evolution and Its Biological Function

5.7. Conclusion: The Regulatory Role of Individual Transcription Factors

Acknowledgments

B: Evolution and structure of defined plant transcription factor families

Chapter 6: Structure and Evolution of Plant Homeobox Genes

Abstract

6.1. Introduction

6.2. Structure of the Homeodomain

6.3. Specific Contacts with DNA

6.4. Plant Homeodomain Families

6.5. The Evolution of Plant Homeobox Genes

Acknowledgments

Chapter 7: Homeodomain–Leucine Zipper Transcription Factors: Structural Features of These Proteins, Unique to Plants

Abstract

7.1. Homeoboxes and Homeodomains in Eukaryotic Kingdoms

7.2. Plant Homeoboxes

7.3. The Plant Homeodomain Superfamily

7.4. Different Domains Present in Homeodomain Transcription Factors

7.5. The HD-Zip Family

7.6. Target Sequences Recognized by the HD-Containing Transcription Factors

7.7. What do we Know About the Target Sequences of the HD-Zip Proteins?

7.8. Concluding Remarks

Chapter 8: Structure and Evolution of Plant MADS Domain Transcription Factors

Abstract

8.1. Introduction: Who Cares About MADS Domain Transcription Factors?

8.2. The Structure of MADS Domain Proteins

8.3. Evolution of MADS Domain Transcription Factors

8.4. Concluding Remarks

Acknowledgments

Chapter 9: TCP Transcription Factors: Evolution, Structure, and Biochemical Function

Abstract

9.1. Introduction

9.2. Evolution of TCP Proteins

9.3. The TCP Domain: Structure and Function

9.4. Activation and Repression Domains

9.5. TCP Factors as Intrinsically Disordered Proteins

9.6. Posttranslational Modifications of TCP

9.7. Concluding Remarks

Acknowledgments

Chapter 10: Structure and Evolution of Plant GRAS Family Proteins

Abstract

10.1. Presence of GRAS Proteins in Plants and other Organisms

10.2. Genomic Organization (intron/exon)

10.3. Structure of GRAS Proteins

10.4. Conclusion

Chapter 11: Structure and Evolution of WRKY Transcription Factors

Abstract

11.1. Introduction

11.2. The Structure of the WRKY Domain

11.3. The Evolution of WRKY Genes

11.4. R Protein–WRKY Genes

11.5. Conclusion: A Reevaluation of WRKY Evolution

Acknowledgments

Chapter 12: Structure, Function, and Evolution of the Dof Transcription Factor Family

Abstract

12.1. Discovery and Definition of the Dof Transcription Factor family

12.2. Structure and Molecular Characteristics of Dof Transcription Factors

12.3. Molecular Evolution of the Dof Transcription Factor Family

12.4. Physiological Functions of Dof Transcription Factors

12.5. Perspective

Acknowledgments

Chapter 13: NAC Transcription Factors: From Structure to Function in Stress-Associated Networks

Abstract

13.1. Introduction

13.2. NAC Structure

13.3. Evolution of NAC Proteins

13.4. NAC Proteins: From Structure to Interactions with DNA and Other Proteins

13.5. NAC Networks in Abiotic Stress Responses

13.6. Conclusion

Acknowledgments

C: Functional aspects of plant transcription factor action

Chapter 14: Homeobox Transcription Factors and the Regulation of Meristem Development and Maintenance

Abstract

14.1. Introduction

14.2. KNOX and BELL: TALE Superfamily Homeobox Genes

Acknowledgment

Chapter 15: CUC Transcription Factors: To the Meristem and Beyond

Abstract

15.1. Introduction

15.2. Evolution and Structure of NAM/CUC3 Proteins

15.3. NAM/CUC3 Genes Define Boundaries in Meristems and Beyond

15.4. Multiple Regulatory Pathways Contribute to the Fine Regulation of NAM/CUC3 Genes

15.5. NAM/CUC3 Control Plant Development via Modifications of the Cellular Behavior

15.6. Conclusion

Chapter 16: The Role of TCP Transcription Factors in Shaping Flower Structure, Leaf Morphology, and Plant Architecture

Abstract

16.1. Introduction

16.2. TCP Genes and the Control of Leaf Development

16.3. TCP Genes and the Control of Shoot Branching

16.4. TCP Genes and the Control of Flower Shape

16.5. TCP Genes Affect Flowering Time

16.6. Concluding Remarks

Acknowledgments

Chapter 17: Growth-Regulating Factors, A Transcription Factor Family Regulating More than Just Plant Growth

Abstract

17.1. GROWTH-REGULATING FACTORs, a Plant-specific Family of Transcription Factors

17.2. Control of GRF Activity

17.3. Role of GRFs in Organ Growth and Other Developmental Processes

17.4. Conclusion and Perspectives

Acknowledgments

Chapter 18: The Multifaceted Roles of miR156-targeted SPL Transcription Factors in Plant Developmental Transitions

Abstract

18.1. Introduction to Developmental Transitions

18.2. miR156 and its Targets

18.3. miR156-SPL Module in Timing Embryonic Development

18.4. miR156-SPL Module in Juvenile-to-Adult Phase Transition in Higher Plants

18.5. The miR156-SPL Module Regulates Flowering Time in Higher Plants

18.6. The miR156-SPL Module in Developmental Transitions in Moss

18.7. The miR156-SPL Module in Other Developmental Processes

18.8. Perspectives

Acknowledgments

Chapter 19: Functional Aspects of GRAS Family Proteins

Abstract

19.1. The Role of GRAS Proteins in Development

19.2. The Role of GRAS Proteins in Signaling

19.3. General Principles of GRAS Function

19.4. Conclusion

Chapter 20: DELLA Proteins, a Group of GRAS Transcription Regulators that Mediate Gibberellin Signaling

Abstract

20.1. About DELLAs and Gibberellins

20.2. GA Signaling through DELLAs

20.3. The Molecular Mechanism of DELLA Action: DELLA–Protein Interactions and Target Genes

20.4. Conclusion and Future Perspectives

Acknowledgments

Chapter 21: bZIP and bHLH Family Members Integrate Transcriptional Responses to Light

Abstract

21.1. The Role of Light in the Control of Plant Development: A Brief Introduction

21.2. PIFs: Factors that Link Light Perception, Changes in Gene Expression, and Plant Development

21.3. HFR1 and PAR1: Atypical bHLH Factors that Act as Transcriptional Cofactors

21.4. HY5: A Paradigm of a bZIP Member in Integrating Light Responses

21.5. Conclusions

Acknowledgments

Chapter 22: What Do We Know about Homeodomain–Leucine Zipper I Transcription Factors? Functional and Biotechnological Considerations

Abstract

22.1. HD–Zip Transcription Factors are Unique to Plants

22.2. Brief History of the Discovery of HD-Zip Transcription Factors

22.3. Expression Patterns of HD-Zip I Genes

22.4. Environmental Factors Regulate the Expression of HD-Zip I Encoding Genes

22.5. The Function of HD-Zip I TFs from Model Plants

22.6. HD-Zip I TFs from Nonmodel Species

22.7. Divergent HD-Zip I Proteins from Nonmodel Plants

22.8. Knowledge Acquired from Ectopic Expressors

22.9. HD-Zip I TFs in Biotechnology

22.10. Concluding Remarks

D: Modulation of plant transcription factor action

Chapter 23: Intercellular Movement of Plant Transcription Factors, Coregulators, and Their mRNAs

Abstract

23.1. Introduction to Noncell-autonomous Mobile Signals

23.2. Mobile Transcription Factors of the Shoot Apex in Protein Form

23.3. Mobile Root Transcription Factors

23.4. Transcription Factors and Coregulators that Move Long Distance Through the Sieve Element System

23.5. Full-length Mobile mRNAs and their Roles in Development

23.6. Conclusions

Acknowledgments

Chapter 24: Redox-Regulated Plant Transcription Factors

Abstract

24.1. Introduction

24.2. Concept of Redox Regulation

24.3. Redox Regulation of NPR1 During Plant Immunity

24.4. Redox Regulation of Basic Leucine Zipper Transcription Factors

24.5. Redox Regulation of MYB Transcription Factors

24.6. Redox Regulation of Homeodomain-leucine Zipper Transcription Factors

24.7. Rap2.4a is Under Redox Regulation

24.8. Redox Regulation of Class I TCP Transcription Factors

24.9. Conclusion

Acknowledgments

Chapter 25: Membrane-Bound Transcription Factors in Plants: Physiological Roles and Mechanisms of Action

Abstract

25.1. Introduction

25.2. bZIP Transcription Factors

25.3. NAC Transcription Factors

25.4. Conclusions and Future Perspectives

Chapter 26: Ubiquitination of Plant Transcription Factors

Abstract

26.1. The Ubiquitin Proteasome System

26.2. The Ubiquitin Proteasome System and Regulation of Transcription Factor Function

Index

Copyright

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List of Contributors

Agustín L. Arce,     Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Santa Fe, Argentina

Nicolas Arnaud,     INRA, UMR1318, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France

Cordelia Bolle,     Department Biologie I, Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Biozentrum der LMU München, Planegg-Martinsried, Germany

Matías Capella,     Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Santa Fe, Argentina

Raquel L. Chan,     Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Santa Fe, Argentina

Pilar Cubas,     Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

Juan Manuel Debernardi,     Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina

Farah Deeba,     Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Biochemistry, PMAS Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan

María Florencia Ercoli,     Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina

Marçal Gallemí,     Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Barcelona, Spain

Maria Dolores Gomez,     Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Valencia, Spain

Beatriz Gonçalves,     INRA, UMR1318, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France

Daniel H. Gonzalez,     Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina

Eduardo González-Grandío,     Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

Lydia Gramzow,     Department of Genetics, Friedrich Schiller University Jena, Jena, Germany

Sarah Hake,     U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, Plant Gene Expression Center, University of California at Berkeley, Berkeley, CA, USA

David J. Hannapel,     Plant Biology Major, Iowa State University, Ames, Iowa, USA

Jong Chan Hong,     Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea; Division of Plant Sciences, University of Missouri, Columbia, MO, USA

Aeni Hosaka-Sasaki,     Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan

Yuji Iwata,     Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Nakaku, Sakai, Osaka, Japan

Shoshi Kikuchi,     Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan

Nozomu Koizumi,     Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Nakaku, Sakai, Osaka, Japan

Patrick Laufs,     INRA, UMR1318, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France

Yuan Li,     Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, UK

Gary J. Loake,     Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, UK

Leila Lo Leggio,     Department of Chemistry, University of Copenhagen, Copenhagen, Denmark

Jaime F. Martínez-García,     Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

Aude Maugarny,     INRA, UMR1318, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France

Toshifumi Nagata,     Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan

Michael Nicolas,     Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

Javier F. Palatnik,     Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina

Miguel A. Perez-Amador,     Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Valencia, Spain

Roel C. Rabara,     Texas A and M AgriLife Research and Extension Center, Dallas, TX, USA

Pamela A. Ribone,     Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Santa Fe, Argentina

Charles I. Rinerson,     Texas A and M AgriLife Research and Extension Center, Dallas, TX, USA

Ramiro E. Rodriguez,     Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina

Paul J. Rushton,     Texas A and M AgriLife Research and Extension Center, Dallas, TX, USA

Qingxi J. Shen,     School of Life Sciences, University of Nevada, at Las Vegas, NV, USA

Karen Skriver,     Department of Biology, University of Copenhagen, Copenhagen, Denmark

Sophia L. Stone,     Department of Biology, Dalhousie University, Halifax NS, Canada

Günter Theißen,     Department of Genetics, Friedrich Schiller University Jena, Jena, Germany

Prateek Tripathi,     Molecular and Computational Biology Section, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA

Katsutoshi Tsuda,     U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, Plant Gene Expression Center, University of California at Berkeley, Berkeley, CA, USA

Francisco Vera-Sirera,     Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación (CPI), Valencia, Spain

Ivana L. Viola,     Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina

Jia-Wei Wang,     National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China

Ditte H. Welner,     Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

Kazuhiko Yamasaki,     Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan; RIKEN Quantitative Biology Center, Tsurumi-ku, Yokohama, Japan

Shuichi Yanagisawa,     Laboratory of Plant Functional Biotechnology, Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan

Preface

Transcription factors (TFs) are central regulators of gene expression and, as such, modulate essential aspects of organismal function, including cell differentiation, tissue and organ development, responses to hormones and environmental factors, metabolic networks, and disease resistance, among others. Intrinsic to TF action is their capacity to specifically interact with DNA sequences and with other proteins as part of transcriptional complexes involved in the regulation of gene expression. Accordingly, knowledge of the structure of TFs and of the molecular mechanisms involved in the establishment of these interactions is essential to understand TF action. Plants contain a vast number of TFs (about 10% of plant genes encode TFs) that were acquired at different stages of evolution and were adapted to perform specific functions.

This book is intended as a source of information for those interested in the study of plant TFs and the many processes they regulate. It contains basic information that can be useful to students and researchers entering the field as well as more specific chapters devoted to plant TF families. These specific chapters do not constitute a comprehensive list of what is known about the different TF families but are rather examples of how the study of the different aspects of a specific TF family can be useful to establish the molecular aspects of TF function. Section A deals with general aspects of plant TFs. It contains two introductory chapters that describe the basics of TF action and methods usually employed to study TFs, followed by chapters that discuss structural and evolutionary aspects of plant TF families and plant-specific TF DNA-binding domains. Sections B and C present information about the structure, evolution, and functional aspects of several plant TF families, with examples of families that arose at different stages of organismal evolution and were adapted to modulate specific aspects of plant developmental programs and responses. Finally, Section D contains chapters that discuss aspects of the posttranslational regulation of plant TF action by either intra- or intercellular movement, proteolytic processing, ubiquitination, or redox interconversions. The book is centered on TFs rather than on processes, understanding that there are excellent books that already describe plant regulatory networks and the TFs involved. These books, however, often describe interactions established by TFs in regulatory networks but do not deepen into the structural aspects of the TFs involved. I hope that through this book readers will acquire a general view of different aspects of plant TFs that eventually will help to fill the gap existing between the knowledge of the participation of a TF in a defined process and the establishment of the structural properties related to TF functions. In other words, to establish structural–functional relationships that explain in detail the molecular mechanisms involved in TF action.

I would like to thank all authors who generously contributed their chapters. As experts in the field, their contribution was essential for the assembly of this book. I would also like to thank Mary Preap, from Academic Press/Elsevier, for her valuable assistance, and people from my lab for their contributions along many years. Finally, I also acknowledge support from the Argentine Research Council (Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET) and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) for their support to my research activities.

Daniel H. Gonzalez

A

General aspects of plant transcription factors

Chapter 1: Introduction to Transcription Factor Structure and Function

Chapter 2: Methods to Study Transcription Factor Structure and Function

Chapter 3: General Aspects of Plant Transcription Factor Families

Chapter 4: Structures, Functions, and Evolutionary Histories of DNA-Binding Domains of Plant-Specific Transcription Factors

Chapter 5: The Evolutionary Diversification of Genes that Encode Transcription Factor Proteins in Plants

Chapter 1

Introduction to Transcription Factor Structure and Function

Daniel H. Gonzalez    Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina

Abstract

The transcription of eukaryotic genes is regulated by DNA-binding proteins known as transcription factors. These factors interact specifically with sequences located in the promoter regions of the genes they regulate. Transcription factors are classified in families according to the structure of their DNA-binding domain. Some transcription factor families are present in most eukaryotes, while others are specific to certain lineages, suggesting that they are more recent acquisitions. In addition to the DNA-binding domain, transcription factors possess other domains involved in activating or repressing gene expression, dimerization, and establishing protein–protein interactions. Transcription factor action is finely modulated by mechanisms involving their synthesis, subcellular location and activity, usually through interaction with other proteins and/or posttranslational modifications. In this chapter, we summarize the general properties of eukaryotic transcription factors as an introduction to the specific chapters dealing with the structure and function of plant transcription factors in this book.

Keywords

activation domain

DNA-binding domain

eukaryotic transcription factor

repressor

transcription factor family

transcriptional regulation

Outline

1.1 Introduction: Transcription in Eukaryotes 3

1.2 Structure of Transcription Factors 4

1.3 DNA Recognition by Transcription Factors 4

1.4 DNA-binding Domains 5

1.5 Protein–protein Interactions 6

1.6 Regulation of Transcription Factor Action 7

1.7 Plant Transcription Factors 9

References 9

1.1. Introduction: Transcription in Eukaryotes

In eukaryotes, various RNA polymerases are responsible for the transcription of nuclear genes (Roeder and Rutter, 1969). Particularly, RNA polymerase II is in charge of transcribing all protein-coding genes, in addition to several genes that encode noncoding RNAs (Kornberg, 2007; Cramer et al., 2008). RNA polymerase II promoters are composed of a big number of discrete DNA sequences (also named boxes or elements), usually located upstream of the transcription start site, but also within and downstream of transcribed regions (Lenhard et al., 2012). These sequences can be classified as basal promoter elements, upstream promoter elements, and enhancers, and are the binding sites of proteins named transcription factors, which influence the transcription of genes linked to them (Figure 1.1). Basal promoter elements are usually located near the transcription start site (Juven-Gershon et al., 2008) and are the binding site of general transcription factors that participate in the expression of most genes by promoting the binding of RNA polymerase II (Li et al., 1994; Orphanides et al., 1996; Roeder, 1996; Conaway and Conaway, 1997; Reese, 2003). The most common basal promoter element is the TATA box, recognized by TATA-box binding protein (TBP) (Peterson et al., 1990; Burley, 1996), a component of the general transcription factor II D (TFIID) (Horikoshi et al., 1990). Upstream promoter elements are very diverse. They are located further upstream of basal elements (up to several hundred base pairs of the transcription start site) and are recognized by specific transcription factors according to the type of elements present in each gene (Mitchell and Tjian, 1989; Ptashne and Gann, 1997; Lee and Young, 2000). In most genes, the presence of these elements is necessary for efficient transcription since the sole interaction of general transcription factors with the basal promoter is not enough to assemble a stable transcriptional complex (Gill, 1996; Stargell and Struhl, 1996; Struhl et al., 1998). In addition, many of these elements are required for the transcriptional regulation of gene expression under different circumstances, thus receiving the name of response elements. Enhancers are regions of the genome that affect the expression of particular genes linked to them (Stadhouders et al., 2012; Smallwood and Ren, 2013; Levine et al., 2014). Usually, they are not classified as part of the promoter, although their action is required for the correct transcriptional activity of the corresponding genes. Enhancers contain groups of response elements and have the peculiarity of acting at long distances (up to several thousands of base pairs), through the formation of loops in DNA. The transcription characteristics of a gene will then be established by the nature of the different elements that compose its promoter region, including enhancers, and the interactions established by different proteins with these elements and among themselves. Apart from the obvious presence of the appropriate partners, the interaction of promoter elements with the corresponding binding proteins will be influenced by the structure of the chromatin in that particular region of the genome, which leads to an additional source of complexity (Li et al., 2007; Cairns, 2009; Venters and Pugh, 2009; Voss and Hager, 2014).

Figure 1.1   The structure of eukaryotic promoters.

Eukaryotic gene promoters are composed of discrete binding sites for multiple transcription factors dispersed over long distances (usually several thousands of base pairs). General transcription factors (TFIIX) for RNA polymerase II (Pol II) interact with sequences located near the transcription start site (yellow). Specific transcription factors (TF1 to TF9) recognize particular sequences located in proximal promoter regions (blue; at hundreds of base pairs of the start site) or in enhancers (green; at thousands of base pairs of the start site). The transcriptional activity of a gene will be defined by the nature of the transcription factors bound in different regions of its promoter. The transcription start site is indicated by +1.

1.2. Structure of Transcription Factors

Transcription factors are proteins that influence the transcription of genes by binding to defined regions of the genome (Latchman, 1997). Genes encoding transcription factors constitute 3–10% of all genes in eukaryotic genomes (Levine and Tjian, 2003; Harbison et al., 2004; Reece-Hoyes et al., 2005). A basic feature of transcription factors is that they contain DNA-binding domains that recognize specific sequences within the promoter regions of the genes they regulate (Figure 1.2A; Kummerfeld and Teichmann, 2006). By binding to these sequences they either increase or decrease the transcription of their target genes, thus acting as activators or repressors, respectively. Activation or repression is usually achieved through interaction with other components of the transcription apparatus (Figure 1.2B,C; Takagi and Kornberg, 2006), which makes protein–protein interactions another important feature of transcription factor action (Walhout, 2006). Activation or repression of gene expression can also be achieved through interaction with chromatin-modifying enzymes, which are then directed to modulate the accessibility of the transcription machinery to specific regions of the genome (Figure 1.2B,C). The capability of a transcription factor to act as a repressor or an activator is, in most cases, dependent on domains that are located outside, and act independently of, the DNA-binding domain (Figure 1.2A). This brings transcription factors a modular structure and the possibility of acquiring new properties by domain mixing or shuffling, a process used by evolution and researchers to generate new mechanisms of transcriptional regulation (Gossen and Bujard, 1992; Morgenstern and Atchley, 1999; Beerli et al., 2000; Ansari and Mapp, 2002; Traven et al., 2006; Liu et al., 2013).

Figure 1.2   The general structure of transcription factors.

(A) Most transcription factors have a modular structure. They contain a DNA binding domain involved in the recognition of specific DNA sequences (blue and yellow ovals). Usually, they also contain activation (green arrow) or repressor (red rectangle) domains that increase or decrease, respectively, the transcription of genes to which they bind. (B) Activation can be achieved through stabilizing protein–protein interactions with other components of the transcription machinery or the recruitment of chromatin modifying enzymes, like HAT, that relax nucleosome structure. (C) Repression can be achieved by interfering with activators or recruiting chromatin-modifying enzymes, like histone deacetylases (HDAC), that increase compaction of nucleosomes.

1.3. DNA Recognition by Transcription Factors

The recognition of specific DNA sequences by transcription factors is achieved by interactions established between the side chains of amino acids of the DNA binding domain with nucleotides of the target site (Figure 1.3). For specific recognition, interactions must be established with the nucleotide bases that are located inside the DNA double-helical structure. For this reason, most transcription factors establish connections with DNA by binding to the major groove, although interactions through the minor groove have also been reported in several cases (Figure 1.3). Amino acid side chains of transcription factor DNA-binding domains can establish specific interactions with bases through hydrogen bonding and van der Waals contacts (Figure 1.3B,C; Shimoni and Glusker, 1995; Suzuki et al., 1995; Luscombe et al., 2001; Rohs et al., 2010). While these interactions determine the specificity, the strength, or affinity of the interaction is additionally determined by unspecific contacts established with the sugar phosphate backbone, including ionic interactions between DNA phosphates and positively charged residues of the DNA-binding domain. Another factor that influences the strength and specificity of the interaction is the topology of the DNA around the transcription factor-binding site (Pan et al., 2010). Curvatures in DNA are often required by transcription factors to bind their target genes efficiently (Rohs et al., 2009), and some transcription factors induce DNA bending upon binding (van der Vliet and Verrijzer, 1993), thus leading to changes that facilitate other processes, like DNA melting or the binding of additional proteins.

Figure 1.3   DNA recognition by transcription factors.

(A) Specific interactions of the Drosophila bicoid homeodomain transcription factor with DNA (Baird-Titus et al., 2006) are established by an alpha helix (helix III, in red) that inserts into the major groove of DNA (green). Additional interactions are established by a disordered N-terminal arm (yellow) along the adjacent minor groove (only the path of backbone atoms is shown). (B) For specific recognition, the side arms of bicoid helix III amino acids Ile47, Lys50, Asn51, and Arg54 (red) establish specific contacts with bases of the DNA (yellow). (C) For example, bicoid Arg54 forms hydrogen bonds with G and A of the recognition sequence GGATTA. (D) A dimer of the yeast bZip transcription factor GCN4 (Keller et al., 1995, in red) interacts with DNA through alpha helices that run across two adjacent major grooves. Specific contacts are established mainly by basic amino acids (yellow). (E) Zinc finger transcription factors contain DNA-binding modules formed by adjacent alpha helices and beta hairpins. Each module binds DNA through the major groove and is connected to adjacent modules by a disordered region. The different modules wrap along the major groove of DNA (Kim and Berg, 1996).

1.4. DNA-binding Domains

DNA-binding domains adopt different structures, and the interaction of these domains with DNA can be established through alpha helices, beta sheets, or disordered regions (Figure 1.3; Pabo and Sauer, 1992). Usually, the DNA-binding domain forms a module that can be separated from the rest of the transcription factor structure without losing activity. This facilitates structural studies of the isolated DNA-binding domains or their complexes with DNA using techniques that require low molecular weight proteins, like crystallization or NMR. DNA-binding domains are named according to their structural characteristics, and most organisms contain several transcription factors that share the same type of DNA-binding domain. Accordingly, transcription factors are classified in families that usually receive the name of the respective DNA-binding domain (Table 1.1; Stegmaier et al., 2004; Vaquerizas et al., 2009; Charoensawan et al., 2010). Transcription factors that share the same type of DNA-binding domain (in other words, transcription factors from the same family) tend to have more similar DNA-binding specificities than those that belong to different families. In any case, variations in DNA-binding specificity are often observed within the same family, and these are most often due to changes in specific residues of the DNA-binding domain (Berger et al., 2008; Noyes et al., 2008; Badis et al., 2009). Thus, changes in the amino acid residues of the DNA-binding domain are also used by evolution and researchers to create transcription factors with novel DNA-binding characteristics (Blancafort et al., 2004; Amoutzias et al., 2007; Joung and Sander, 2013).

Table 1.1

Classification of Transcription Factors*

1. Superclass: Basic domains

1.1 Class: Leucine zipper factors (bZIP)

1.2 Class: Helix–loop–helix factors (bHLH)

1.3 Class: Helix–loop–helix/leucine zipper factors (bHLH-ZIP)

1.4 Class: NF-1

1.5 Class: RF-X

1.6 Class: bHSH

2. Superclass: Zinc-coordinating DNA-binding domains

2.1 Class: Cys4 zinc finger of nuclear receptor type

2.2 Class: Diverse Cys4 zinc fingers

2.3 Class: Cys2His2 zinc-finger domain

2.4 Class: Cys6 cysteine–zinc cluster

2.5 Class: Zinc fingers of alternating composition

3. Superclass: Helix–turn–helix

3.1 Class: Homeodomain

3.2 Class: Paired box

3.3 Class: Fork head/winged helix

3.4 Class: Heat shock factors

3.5 Class: Tryptophan clusters

3.6 Class: TEA domain

4. Superclass: beta-Scaffold factors with minor groove contacts

4.1 Class: Rel homology region (RHR)

4.2 Class: STAT

4.3 Class: p53

4.4 Class: MADS box

4.5 Class: beta-Barrel alpha helix transcription factors

4.6 Class: TATA-binding proteins

4.7 Class: HMG

4.8 Class: Heteromeric CCAAT factors

4.9 Class: Grainyhead

4.10 Class: Cold-shock domain factors

4.11 Class: Runt

0. Superclass: Other transcription factors

0.1 Class: Copper fist proteins

0.2 Class: HMGI(Y)

0.3 Class: Pocket domain

0.4 Class: E1A-like factors

0.5 Class: AP2/EREBP-related factors

* From http://www.gene-regulation.com/pub/databases/transfac/clSM.html

1.5. Protein–protein Interactions

Many transcription factors require the formation of dimers to bind DNA (Figure 1.4A,B). These dimers can form between two identical molecules (homodimers) or between different molecules (heterodimers), usually from the same transcription factor family (Amoutzias et al., 2008; Funnell and Crossley, 2012; Pogenberg et al., 2014). Typical transcription factors that require dimerization for binding are those of the bZip and bHLH families (Figure 1.4A,B), which use a basic region to interact with DNA and in which the dimerization domain (either leucine zipper or helix–loop–helix motif) is intrinsic to the DNA-binding module (Massari and Murre, 2000; Amoutzias et al., 2007) (see Chapter 21). Other transcription factors that form dimers or higher order structures are able to bind DNA by themselves, but acquire increased specificity or affinity after complex formation (Goutte and Johnson, 1993; Mann and Chan, 1996; Zhong and Vershon, 1997). In an extreme case, a transcription factor will only be able to specifically bind DNA in the presence of a partner that induces a change to an active conformation (Goutte and Johnson, 1993).

Figure 1.4   Protein–protein interactions and transcription factor function.

bZip (A) and bHLH (B) transcription factors bind DNA only as dimers. Dimerization is facilitated by the interaction of regularly spaced hydrophobic amino acids (yellow) present at the dimer interface. The structures of yeast GCN4 (bZip) and mouse MyoD (bHLH) DNA-binding domains are shown (Ma et al., 1994; Keller et al., 1995). (C) The KIX domain of the coactivator CREB-binding protein (CBP) interacts with many transcription factors. The image shows KIX (green) bound to the activation domains of the transcription factors c-Myb (blue) and mixed lineage leukemia (MLL; red). The binding of each partner to KIX induces conformational changes that promote cooperative ternary complex formation (De Guzman et al., 2006).

Besides interactions that modify the DNA-binding properties of transcription factors, a multitude of other protein–protein interactions, established through regions located either within or outside the DNA-binding domain, are inherent to transcription factor action. Transcriptional complexes are formed by a wealth of transcription factors bound to different regions of a gene (Burley and Kamada, 2002; Ogata et al., 2003). This implies that the protein–protein interactions of transcription factors, established either directly or through bridging proteins (Figure 1.4C; Takagi and Kornberg 2006), are essential to determining the stability of the transcriptional complex and, in this way, the transcription rate of a gene. Protein interaction domains that stabilize the transcriptional complex cause an increase in transcription and are then referred to as activation domains (Figure 1.3B; Blau et al., 1996). Activation domains can be classified according to the kind of amino acids that predominate in their structure, thus giving rise to acidic or hydrophobic activation domains (Hope et al., 1988; Regier et al., 1993; Drysdale et al., 1995). Some of these domains interact with general factors or coactivators (Vashee and Kodadek, 1995; Näär et al., 2001), which means that they function when associated with almost any transcription factor and in many different organisms. Other activation domains are more specific and will only function when the appropriate partner is present within the same cell. Due to the nature of eukaryotic transcriptional complexes, which require stabilization of the general transcription machinery through protein–protein interactions, the presence of activators is often required. In addition, transcription factors can act as repressors, usually interfering with the activity of activators by competing for the same target site in DNA or blocking their action through direct or indirect protein–protein interactions (Figure 1.3C; Gaston and Jayaraman, 2003; Reynolds et al., 2013). In addition, activators and repressors can influence transcription by changing the chromatin structure in the vicinity of their binding sites (Figure 1.3B,C). This is also achieved by protein–protein interactions with enzymes like histone acetylases (HAT) and deacetylases, which modify histones and change the strength of their interactions with DNA and, in this way, the accessibility of the transcription machinery (Wolffe et al., 1997; Deckert and Struhl, 2001).

1.6. Regulation of Transcription Factor Action

The transcriptional regulation of genes is usually brought about by regulation of the activity of transcription factors that influence their expression. The term activity in this context must be regarded in a broad sense, since often what is regulated is rather the presence of the transcription factor in the right place to effect transcription (that is, the nucleus), or its presence in the cell at all (in which case, the synthesis of the transcription factor is regulated; Figure 1.5). The location of transcription factors within the cell can be regulated by the presence of proteins that either retain them in the cytosol or help them to translocate to the nucleus (Whiteside and Goodbourn, 1993; Kaffman and O’Shea, 1999). The translocation of proteins to the nucleus requires the presence of nuclear localization signals (NLS, usually stretches of positively charged residues exposed to the protein surface) in their structure, which are recognized by the nuclear import machinery (Stewart, 2007). While most transcription factors contain NLS in their structure, some of them require the formation of a complex with an NLS-containing partner for nuclear localization. Contrary to that, some transcription factors that contain NLS are retained in the cytosol by partners that block their NLS or their interaction with the import machinery. Interactions with ligands or posttranscriptional modifications that disrupt these complexes, sometimes leading to proteolysis of the inhibitory protein, allow migration to the nucleus and binding to the target gene(s). Retention of transcription factors outside the nucleus is sometimes also achieved by their interaction with membranes (Hoppe et al., 2001; Chapter 25). In this case, the activation of specific proteases leads to separation of the membrane-binding domain from the soluble domain that can migrate to the nucleus and interact with target genes. Interactions with ligands or posttranscriptional modifications can also be used to modulate the stability of transcription factors, which can then be targeted to degradation by the proteasome either in the presence or absence of these signaling events (Geng et al., 2012; Yao and Ndoja, 2012; Chapter 26). Posttranslational modifications can also directly modulate the activity of a transcription factor that is otherwise always present within the nucleus. Known modifications include phosphorylation, acetylation, glycosylation, ubiquitination, sumoylation, and redox-dependent changes, among others (Jackson and Tjian, 1988; Bohmann 1990; Bannister and Miska, 2000; Gill, 2003; Liu et al., 2005; Ndoja et al., 2014) In this case, regulation can be exerted on the DNA-binding capacity of the transcription factor or its ability to modulate transcription, acting on its capacity to interact with other proteins once bound to DNA.

Figure 1.5   Regulation of transcription factor action.

The activity of transcription factors (blue) can be modulated in several ways. (1) The synthesis of transcription factors can be modulated through regulation of their expression at the transcriptional, posttranscriptional, and translational levels. (2) Once synthesized, the DNA-binding activity of transcription factors can be regulated by ligand binding (black triangles) or posttranslational modifications (P for phosphorylation and many others). Not only the activity, but also the interaction with other components of the transcriptional machinery (3) or the proteolytic degradation of transcription factors (4) can be regulated. (5) Some transcription factors are retained outside the nucleus because they contain membrane-binding domains (gray). Regulated proteolytic processing allows migration to the nucleus of the soluble domain, containing the transcription factor activity. (6) Alternatively, transcription factors are retained outside the nucleus by protein partners (red) that inhibit nuclear import. Ligand binding or posttranslational modifications release the transcription factor from the inhibitory protein, which may also be targeted for degradation (7). N, nucleus; C, cytosol; Ub, ubiquitin.

1.7. Plant Transcription Factors

The general characteristics of transcription in plants are similar to those of other eukaryotes. Accordingly, many plant transcription factor families are also present in fungi and animals, suggesting that they are ancient acquisitions. However, plants have also acquired transcription factors with novel characteristics (Chapter 3). Some of these factors, like those of the HD-Zip family (Ariel et al., 2007; Chapter 7), arose from the combination of known transcription factor elements also present in other domains of life (the homeodomain and leucine zipper, in this case), while others contain DNA-binding domains that are not present in transcription factors from other eukaryotes (Yamasaki et al., 2013; Chapter 4). Nevertheless, whether they are related to transcription factor families present in other organisms or not, the characteristics of the different plant transcription factor families, as well as their roles in transcriptional regulation of different processes, makes the study of plant transcription factors a necessary road to understand plant function at the molecular level.

Acknowledgments

I acknowledge support from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina) and Universidad Nacional del Litoral.

References

Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem. Sci. 2008;33:220–229.

Amoutzias GD, Veron AS, Weiner 3rd J, Robinson-Rechavi M, Bornberg-Bauer E, Oliver SG, Robertson DL. One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity. Mol. Biol. Evol. 2007;24:827–835.

Ansari AZ, Mapp AK. Modular design of artificial transcription factors. Curr. Opin. Chem. Biol. 2002;6:765–772.

Ariel FD, Manavella PA, Dezar CA, Chan RL. The true story of the HD-Zip family. Trends Plant Sci. 2007;12:419–426.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, et al. Diversity and complexity in DNA recognition by transcription factors. Science. 2009;324:1720–1723.

Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M. The solution structure of the native K50 bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J. Mol. Biol. 2006;356:1137–1151.

Bannister AJ, Miska EA. Regulation of gene expression by transcription factor acetylation. Cell. Mol. Life Sci. 2000;57:1184–1192.

Beerli RR, Dreier B, Barbas 3rd CF. Positive and negative regulation of endogenous genes by designed transcription factors. Proc. Natl. Acad. Sci. USA. 2000;97:1495–1500.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña- Castillo L, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell. 2008;133:1266–1276.

Blancafort P, Segal DJ, Barbas 3rd CF. Designing transcription factor architectures for drug discovery. Mol. Pharmacol. 2004;66:1361–1371.

Blau J, Xiao H, McCracken S, O’Hare P, Greenblatt J, Bentley D. Three functional classes of transcriptional activation domain. Mol. Cell. Biol. 1996;16:2044–2055.

Bohmann D. Transcription factor phosphorylation: a link between signal transduction and the regulation of gene expression. Cancer Cells. 1990;2:337–344.

Burley SK. The TATA box binding protein. Curr. Opin. Struct. Biol. 1996;6:69–75.

Burley SK, Kamada K. Transcription factor complexes. Curr. Opin. Struct. Biol. 2002;12:225–230.

Cairns BR. The logic of chromatin architecture and remodelling at promoters. Nature. 2009;461:193–198.

Charoensawan V, Wilson D, Teichmann SA. Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res. 2010;38:7364–7377.

Conaway RC, Conaway JW. General transcription factors for RNA polymerase II. Prog. Nucleic Acid Res. Mol. Biol. 1997;56:327–346.

Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, et al. Structure of eukaryotic RNA polymerases. Annu. Rev. Biophys. 2008;37:337–352.

Deckert J, Struhl K. Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol. Cell. Biol. 2001;21:2726–2735.

De Guzman RN, Goto NK, Dyson HJ, Wright PE. Structural basis for cooperative transcription factor binding to the CBP coactivator. J. Mol. Biol. 2006;355:1005–1013.

Drysdale CM, Dueñas E, Jackson BM, Reusser U, Braus GH, Hinnebusch AG. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol. Cell. Biol. 1995;15:1220–1233.

Funnell AP, Crossley M. Homo- and heterodimerization in transcriptional regulation. Adv. Exp. Med. Biol. 2012;747:105–121.

Gaston K, Jayaraman PS. Transcriptional repression in eukaryotes: repressors and repression mechanisms. Cell. Mol. Life Sci. 2003;60:721–741.

Geng F, Wenzel S, Tansey WP. Ubiquitin and proteasomes in transcription. Annu. Rev. Biochem. 2012;81:177–201.

Gill G. Regulation of the initiation of eukaryotic transcription. Essays Biochem. 2001;37:33–43.

Gill G. Post-translational modification by the small ubiquitin-related modifier SUMO has big effects on transcription factor activity. Curr. Opin. Genet. Dev. 2003;13:108–113.

Gossen M, Bujard H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. USA. 1992;89:5547–5551.

Goutte C, Johnson AD. Yeast a1 and alpha 2 homeodomain proteins form a DNA-binding activity with properties distinct from those of either protein. J. Mol. Biol. 1993;233:359–371.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004;431:99–104.

Hope IA, Mahadevan S, Struhl K. Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature. 1988;333:635–640.

Hoppe T, Rape M, Jentsch S. Membrane-bound transcription factors: regulated release by RIP or RUP. Curr. Opin. Cell Biol. 2001;13:344–348.

Horikoshi M, Yamamoto T, Ohkuma Y, Weil PA, Roeder RG. Analysis of structure-function relationships of yeast TATA box binding factor TFIID. Cell. 1990;61:1171–1178.

Jackson SP, Tjian R. O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation. Cell. 1988;55:125–133.

Joung JK, Sander JD. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 2013;14:49–55.

Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT. The RNA polymerase II core promoter – the gateway to transcription. Curr. Opin. Cell Biol. 2008;20:253–259.

Kaffman A, O'Shea EK. Regulation of nuclear localization: a key to a door. Annu. Rev. Cell Dev. Biol. 1999;15:291–339.

Keller W, König P, Richmond TJ. Crystal structure of a bZIP/DNA complex at 2.2 Å: determinants of DNA specific recognition. J. Mol. Biol. 1995;254:657–667.

Kim CA, Berg JM. A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA. Nat. Struct. Biol. 1996;3:940–945.

Kornberg RD. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. USA. 2007;104:12955–12961.

Kummerfeld SK, Teichmann SA. DBD: a transcription factor prediction database. Nucleic Acids Res. 2006;34:D74–D81.

Latchman DS. Transcription factors: an overview. Int. J. Biochem. Cell Biol. 1997;29:1305–1312.

Lee TI, Young RA. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 2000;34:77–137.

Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 2012;13:233–245.

Levine M, Cattoglio C, Tjian R. Looping back to leap forward: transcription enters a new era. Cell. 2014;157:13–25.

Levine M, Tjian R. Transcription regulation and animal diversity. Nature. 2003;424:147–151.

Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell. 2007;128:707–719.

Li Y, Flanagan PM, Tschochner H, Kornberg RD. RNA polymerase II initiation factor interactions and transcription start site selection. Science. 1994;263:805–807.

Liu H, Colavitti R, Rovira II, Finkel T. Redox-dependent transcriptional regulation. Circulation Res. 2005;97:967–974.

Liu W, Yuan JS, Stewart Jr CN. Advanced genetic tools for plant biotechnology. Nat. Rev. Genet. 2013;14:781–793.

Luscombe NM, Laskowski RA, Thornton JM. Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level. Nucleic Acids Res. 2001;29:2860–2874.

Ma PC, Rould MA, Weintraub H, Pabo CO. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell. 1994;77:451–459.

Mann RS, Chan S-K. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet. 1996;12:258–262.

Massari ME, Murre C. Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms. Mol. Cell. Biol. 2000;20:429–440.

Mitchell PJ, Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989;245:371–378.

Morgenstern B, Atchley BR. Evolution of bHLH transcription factors: modular evolution by domain shuffling? Mol. Biol. Evol. 1999;16:1654–1663.

Näär AM, Lemon BD, Tjian R. Transcriptional coactivator complexes. Annu. Rev. Biochem. 2001;70:475–501.

Ndoja A, Cohen RE, Yao T. Ubiquitin signals proteolysis-independent stripping of transcription factors. Mol. Cell. 2014;53:893–903.

Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell. 2008;133:1277–1289.

Ogata K, Sato K, Tahirov TH. Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Curr. Opin. Struct. Biol. 2003;13:40–48.

Orphanides G, Lagrange T, Reinberg D. The general transcription factors of RNA polymerase II. Genes Dev. 1996;10:2657–2683.

Pabo CO, Sauer RT. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 1992;61:1053–1095.

Pan Y, Tsai CJ, Ma B, Nussinov R. Mechanisms of transcription factor selectivity. Trends Genet. 2010;26:75–83.

Peterson MG, Tanese N, Pugh BF, Tjian R. Functional domains, and upstream activation properties of cloned human TATA binding protein. Science. 1990;248:1625–1630.

Pogenberg V, Consani Textor L, Vanhille L, Holton SJ, Sieweke MH, Wilmanns M. Design of a bZip transcription factor with homo/heterodimer-induced DNA-binding preference. Structure. 2014;22:466–477.

Ptashne M, Gann A. Transcriptional activation by recruitment. Nature. 1997;386:569–577.

Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJM. A compendium of C. elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol. 2005;6:R110.

Reese JC. Basal transcription factors. Curr. Opin. Genet. Devel. 2003;13:114–118.

Regier JL, Shen F, Triezenberg SJ. Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator. Proc. Natl. Acad. Sci. USA. 1993;90:883–887.

Reynolds N, O'Shaughnessy A, Hendrich B. Transcriptional repressors: multifaceted regulators of gene expression. Development. 2013;140:505–512.

Roeder RG. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 1996;21:327–335.

Roeder RG, Rutter WJ. Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms. Nature. 1969;224:234–237.

Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem. 2010;79:233–269.

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461:1248–1253.

Shimoni L, Glusker JP. Hydrogen bonding motifs of protein side chains: Descriptions of binding of arginine and amide groups. Prot. Sci. 1995;4:65–74.

Smallwood A, Ren B. Genome organization and long-range regulation of gene expression by enhancers. Curr. Opin. Cell Biol. 2013;25:387–394.

Stadhouders R, van den Heuvel A, Kolovos P, Jorna R, Leslie K, Grosveld F, Soler E. Transcription regulation by distal enhancers: who's in the loop? Transcription. 2012;3:181–186.

Stargell LA, Struhl K. Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet. 1996;12:311–315.

Stegmaier P, Kel AE, Wingender E. Systematic DNA-binding domain classification of transcription factors. Genome Inform. 2004;15:276–286.

Stewart M. Molecular mechanism of the nuclear protein import cycle. Nat. Rev. Mol. Cell. Biol. 2007;8:195–208.

Struhl K, Kadosh D, Keaveney M, Kuras L, Moqtaderi Z. Activation and repression mechanisms in yeast. Cold Spring Harb. Symp. Quant. Biol. 1998;63:413–421.

Suzuki M, Brenner SE, Gerstein M, Yagi N. DNA recognition code of transcription factors. Protein Eng. 1995;8:319–328.

Takagi Y, Kornberg RD. Mediator as a general transcription factor. J. Biol. Chem. 2006;281:80–89.

Traven A, Jelicic B, Sopta M. Yeast Gal4: a transcriptional paradigm revisited. EMBO Rep. 2006;7:496–499.

van der Vliet PC, Verrijzer CP. Bending of DNA by transcription factors. BioEssays. 1993;15:25–32.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 2009;10:252–263.

Vashee S, Kodadek T. The activation domain of GAL4 protein mediates cooperative promoter binding with general transcription factors in vivo. Proc. Natl. Acad. Sci. USA. 1995;92:10683–10687.

Venters BJ, Pugh F. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 2009;19:360–371.

Voss TC, Hager GL. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat. Rev. Genet. 2014;15:69–81.

Walhout AJM. Unraveling transcription regulatory networks by protein-DNA and protein–protein interaction mapping. Genome Res. 2006;16:1445–1454.

Whiteside ST, Goodbourn S. Signal transduction and nuclear targeting: regulation of transcription factor activity by subcellular localisation. J. Cell Sci. 1993;104:949–955.

Wolffe AP, Wong J, Pruss D. Activators and repressors: making use of chromatin to regulate transcription. Genes Cells. 1997;2:291–302.

Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S. DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. 2013;18:267–276.

Yao T, Ndoja A. Regulation of gene expression by the ubiquitin-proteasome system. Semin. Cell Dev. Biol. 2012;23:523–529.

Zhong H, Vershon AK. The yeast homeodomain protein MATα2 shows extended DNA binding specificity in complex with Mcm1. J. Biol. Chem. 1997;272:8402–8409.

Chapter 2

Methods to Study Transcription Factor Structure and Function

Ivana L. Viola

Daniel H. Gonzalez    Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina

Abstract

The study of transcription factors comprises the analysis of their roles in the regulation of gene expression and how these changes in gene expression affect cell/organism functions. A complete view of transcription factor action at the molecular level requires the knowledge of their target genes and binding partners, of the effect these interactions have on gene expression, and of the mechanisms involved in the recognition of specific DNA sequences, among others. In this chapter, we summarize the different methods usually employed to study transcription factor action both in vivo and in vitro and discuss how integration of different approaches can help elucidate the molecular mechanisms involved in this action.

Keywords

chromatin immunoprecipitation

electrophoretic mobility shift assay

footprinting

SELEX

transactivation system

yeast one-hybrid assay

Outline

2.1 Introduction 13

2.2 In Vivo Functional Studies 14

2.2.1 Overexpression or Ectopic Expression of Transcription Factors 14

2.2.2 Transactivation Systems for Expression of Transcription Factors 14

2.2.3 Expression of Dominant Negative Forms of Transcription Factors 16

2.2.4 Expression of Dysregulated Forms of Transcription Factors 16

2.2.5 Gain-of-Function Mutants 16

2.2.6 Expression of Fusions to Activating or Repressor Domains 17

2.2.7 Inducible Systems 17

2.3 Methods for the Analysis of In Vitro Protein–DNA Interactions 18

2.3.1 The EMSA Assay 18

2.3.2 Selex 18

2.3.3 Analysis of Transcription Factor–DNA Complexes by Footprinting Assays 20

2.3.4 Microarray-Based Identification of Transcription Factor Target Genes 21

2.4 Methods to Study Protein–DNA Interactions In Vivo 21

2.4.1 Chromatin Immunoprecipitation (ChIP) Assays 21

2.4.2 ChIP-chip and ChIP-Seq 22

2.4.3 DNA Adenine Methyltransferase Identification (DamID) 22

2.4.4 Identification of Transcription Factors Using the Yeast One-Hybrid Assay 24

2.4.5 Transient Assays to Analyze Protein–DNA Interactions In Vivo 24

2.5 Analysis of Protein–Protein Interactions 25

2.5.1 Methods for Protein–Protein Complex Identification 25

2.5.1.1 Yeast Two-Hybrid Assay (Y2H) 25

2.5.1.2 Tandem and One-step Tag-Based Affinity Purification 27

2.5.2 Methods for Verification of Protein–Protein Interactions 28

2.5.2.1 Coimmunoprecipitation 28

2.5.2.2 In Vivo Split Methods 28

2.5.2.3 Resonance Energy Transfer Methods 28

References 29

2.1. Introduction

The regulation of gene expression is a complex process controlled by a network of interactions between different regulatory proteins and cis-regulatory sequences present in the promoters of their target genes (Harbison et al., 2004). According to the basic combinatorial principles of gene regulation, a given DNA-binding protein contributes to the transcription of many genes with varying expression patterns by acting in conjunction with several other transcription factors, each possessing its own unique expression pattern. In addition, transcription factors can be regulated by posttranscriptional mechanisms, allowing them to be present in an active or inactive state or in different subcellular compartments. Chromatin structure and modification states play key roles in determining the competence of transcription, and most DNA-binding proteins can recognize a broad spectrum of DNA sequences with a wide range of affinities. Furthermore, most DNA-binding proteins are members of protein families, with each cell type containing several family members that recognize similar DNA sequences. Based on these considerations, it is likely that multiple proteins will be capable of binding a defined control element in vitro, including several members of a particular family of proteins, and perhaps members of another family that recognize a similar or overlapping sequence. The challenge is to determine which of these proteins is capable of performing the protein–protein and protein–DNA interactions that allow it to regulate endogenous genes. In conclusion, despite intensive work, deciphering the transcriptional code is proving to be more difficult than the genetic code (Harbison et al., 2004). The development of methodologies that allow the characterization of transcription factor DNA-binding specificities has been crucial to understanding transcriptional regulation. Transcription profiling can be applied to stable loss- and gain-of-function transcription factor mutants to identify the global expression changes that are associated with the mutant phenotype, thereby facilitating placement of the transcription factor in a developmental pathway or process. Combining DNA motif discovery and information on the up- or downregulation of target genes can lead to a deeper understanding of molecular modes of action and the specificity of particular transcription factors. In this chapter, the different strategies that can be used to elucidate transcription factor functions as well as a number of techniques commonly used to determine DNA-binding specificities in vitro and to identify their primary targets in vivo are described.

2.2. In vivo Functional Studies

To study transcription factor action in vivo, the same strategies usually used to study the function of genes, like the analysis of loss-of-function mutants and gene-silencing techniques, for example, can be used. Since many transcription factor families are composed of a large number of members with different degrees of functional overlap, sometimes the analysis of higher order mutants or alternative strategies must be used. Many of these strategies rely on the specific characteristics of transcription factor action and are discussed here.

2.2.1. Overexpression or Ectopic Expression of Transcription Factors

The simplest way to modify the action of a transcription factor in plants is to increase its expression by fusing its coding region to a strong promoter (Figure 2.1A). The most popular promoter for this purpose is the 35SCaMV promoter, which brings about high expression levels in most plant tissues. Thus, the use of this promoter and of most promoters used for a similar purpose not only brings about an increase in expression but also expression in cells where the transcription factor is not usually expressed, thus giving rise to ectopic expression too. The phenotypic or gene expression changes brought about by the overexpression/ectopic expression of the transcription factor can be used to infer what the real function of the transcription factor may be. The utility of this approach is mainly based on its simplicity. However, the results obtained are subject to artifacts and must be regarded with care. First, because many of the effects observed are probably due to the presence of the transcription factor in cells where it is normally absent, thus it is difficult to extrapolate how this refers to the normal function of the transcription factor. In addition, expression in unusually high levels is likely to distort many of the interactions involved in transcription factor action. Since the establishment of specific interactions with other proteins and DNA are essential for correct transcription factor action, any distortion of these interactions is likely to be the cause of many of the changes observed. Expression at high levels is likely to bring about unspecific protein–protein or protein–DNA interactions. In the case of transcription factor families, for example, a member of a family may be forced to interact with transcriptional components or response elements that are usually bound by a different member of the same family. In families that form heterodimers, overexpression of one member may disrupt the entire set of active molecules formed by the different interacting members of the family. Nevertheless, overexpression approaches are useful in many cases, provided that they are combined with other functional data. Overexpression or the ectopic expression of transcription factors is also useful for technological purposes to obtain plants with desired characteristics.

Figure 2.1   Strategies to study transcription factor function.

(A) The expression level/pattern of a transcription factor of interest (blue) can be modified by expressing it from either a strong, constitutively active promoter (like the 35SCaMV promoter) or another type of promoter that brings about its ectopic expression (gray). (B) A two-component transactivation system can be used to modify the expression of a transcription factor. In this case, the promoter of interest (gray) drives the expression of an artificial transcriptional activator (yellow and green); this artificial protein binds to control elements (violet) located upstream of the coding region of the transcription factor under study, thus promoting its expression. (C) The expression of truncated or modified forms of transcription factors can lead to dominant negative effects by competing with the normal functions of endogenous transcription factors or generating constitutively active forms. (D) Fusions of transcription factors to strong activating (green arrow) or repressor (red rectangle) domains can be used to modify/enhance the action of transcription factors. (E) Inducible two-component transactivation systems can also be used. In this case, the artificial transcription factor of a system like the one described in (B) is fused to a steroid hormone-binding domain (orange) that retains the transcription factor in the cytosol. Addition of the steroid hormone (black section) activates the transcription factor that is then able to induce the gene of interest.

(F) Inducible one-component systems are also available. In this case, the steroid hormone-binding domain (orange) is directly fused to the transcription factor under study, which becomes inducible by addition of the hormone (black section).

2.2.2. Transactivation Systems for Expression of Transcription Factors

Besides using expression over all parts of the plant to study transcription factor action, it may be useful to analyze the effect of expressing the transcription factor in defined groups of cells or developmental stages. For this purpose, the coding region of a transcription factor gene may be linked to promoter regions known to drive expression in defined places or stages (Figure 2.1A).