This document discusses plant transcription factors. It begins with a brief history of transcription factor discovery, including the first identified in 1994. It then provides definitions of transcription factors and describes their main function of controlling gene transcription. The document outlines several major plant transcription factor families and the number of members in common plant species. It also reviews various methodologies used to study transcription factors, such as in vivo and in vitro techniques. Several scientific reviews and books on the topic are referenced. Statistics on transcription factor research output in various databases are presented. The document concludes by discussing future research prospects.

1. PLANT
TRANSCRIPTION
FACTORS
BY:
Balázs Levente Nagy (AS76M8)
Imtikhanna Dyanuar Winismasari (BU23YS)
Shahid Jamal (GDWKUX)

2. HISTORY
The first transcription factor WRKY(SPF1) was identified
in 1994 for its involvement of expression of gene in
sucrose regulation of sweet potato (Ipomea batatas)
After a year ago two WRKY transcription factors, ABF1
and ABF2 , established the role of WRKY proteins as a
novel family of transcriptional regulators .

3. In 1996 WRKY transcription factors(WRKY1,WRKY2,
WRKY3) were identified for their role in the
PATHOGENESIS RELATED gene regulation.
By 2000 a review paper published identifying the WRKY
transcription factor family in the model plant Arabidopsis
thaliana,lead to wide spread investigation of WRKY
family member

4. Since then WRKY transcription factors have been
extensively investigated for stress tolerance in many
agronomic and horticulture crops.

5. WHAT IS TRANSCRIPTION FACTOR?
Transcription factor is a type of protein that control the rate of the
transcription of the genetic information from DNA to mRNA by binding to a
specific DNA sequence.
The main function of TF is to turn on or off whether gene transcribed or not
Groups of transcription factor binding sites known as enhancers and
silencers can turn a gene on/off in specific parts of body.
Transcription factors acquiesce cells to execute logic operations and
combine different sources of information to "decide" whether to express a
gene.

6. PLANT TRANSCRIPTION FACTORS FAMILY
AP2 (4461) E2F/DP (1781) LFY (253) SAP (164)
ARF (4578) EIL (1234) LSD (957) SBP (4168)
ARR-B (2354) ERF (21129) MIKC_MADS (6918) SRS (1327)
B3 (10609) FAR1 (7527)
M-
type_MADS (7541)
STAT (214)
BBR-BPC (1256) G2-like (9874) MYB (22032) TALE (4433)
BES1 (1549) GATA (5335)
MYB_related (15369
)
TCP (4187)
bHLH (28698) GeBP (1564) NAC (19997) Trihelix (6256)
bZIP (15498) GRAS (9304) NF-X1 (403) VOZ (635)
C2H2 (17740) GRF (1876) NF-YA (2461) Whirly (530)
C3H (9693)
HB-
other (2277)
NF-YB (3099) WOX (2358)
CAMTA (1343) HB-PHD (477) NF-YC (2446) WRKY (14549)
CO-like (2125) HD-ZIP (8602) Nin-like (2766) YABBY (1719)
CPP (1612) HRT-like (249) NZZ/SPL (109) ZF-HD (2589)
DBB (1651) HSF (4574) RAV (690)
Dof (5655) LBD (7216) S1Fa-like (359)

7. METHODOLOGY
● In Vivo Functional Studies
a. Overexpression or Ectopic Expression
b. Transactivation Systems
c. Expression of Dominant Negative Forms
d. Expression of Dysregulated Forms
e. Gain of Function Mutants
f. Expression of Fussions to Activating or Repressor
Domains
g. Inducible Systems

8. ● Method for the Analysis of In Vitro-Protein-DNA
Interactions
a. The EMSA Assay
b. Selex
c. Footprinting assays
d. Microarray-based identification
● Method to Study Protein-DNA Interaction in Vivo
a. Chromatin immunoprecipitations (ChIP) assays
b. ChIP-chip and ChIP seq
c. DNA adenine methyltransferase identification
(DamID)
d. Yeast one-hybrid assay
e. Transient assays

9. ● Analysis of Protein-protein Interactions
a. Protein-protein complex identification
■ Yeast two-hybrid assay
■ Tandem and one-step tag-based affinity
purification
b. Verification of protein-protein interactions
■ Coimmunoprecipitation
■ In vivo split methods
■ Resonance energy transfer methods

10. REVIEWS
● Epigenetic regulation of agronomical traits in
Brassicaceae
(Itabashi E, Osabe K, Fujimoto R, Kakizaki T, 2018)
● Revisiting the Role of Plant Transcription Factors in the
Battle against Abiotic Stress
(Khan SA, Li MZ, Wang SM, Yin HJ, 2018)
● Making Roots, Shoots, and Seeds: IDD Gene Family
Diversification in Plants
(Coelho CP, Huang P, Lee DY, Brutnell TP, 2018)

11. ● Transcription Factors: Their Role in the Regulation of
Somatic Embryogenesis in Theobroma cacao L. and
Other Species
(Garcia C1, Britto D, Marelli JP., 2018)
● Insights into the regulation of C-repeat binding factors
in plant cold signaling
(Liu J, Shi Y, Yang S, 2018)
● The brassinosteroid-regulated transcription factors
BZR1/BES1 function as a coordinator in multisignal-
regulated plant growth
(Li QF, Lu J, Yu JW, Zhang CQ, He JX, Liu QQ, 2018)
● Roles of R2R3-MYB transcription factors in
transcriptional regulation of anthocyanin biosynthesis
in horticultural plants
(Naing AH, Kim CK, 2018)

12. ● Transcription Factors Involved in Plant Resistance to
Pathogens
(Amorim LLB, da Fonseca Dos Santos R, Neto JPB, Guida-
Santos M, Crovella S, Benko-Iseppon AM, 2017)
● Role and functioning of bHLH transcription factors in
jasmonate signalling
(Goossens J, Mertens J, and Goossens A, 2017)
● Balancing Immunity and Yield in Crop Plants
(Ning Y, Liu W, Wang GL, 2017)

13. BOOKS
●Ed. Gonzalez, D.H. 2015. Plant Transcription
Factors: Evolutionary, Structural and
Functional Aspects. Academic Press. San
Diego, USA
●Ed. Yamaguchi, N. 2018. Plant Transcription
Factors: Methods and Protocols. Humana
Press.

14. DATABASE (Statistic)
Keyword: transcription factors of plant crops (last access 11/02/2018)
Source Result
Google Scholar 223.000
Scopus 2983
Web of Science 2786
PubMed 2264

15. CATEGORY
1.Organs developmental
■ WRKY (root development)
■ MYB (plant
development,metabolism,defense)
1.Biotic and abiotic stress resistance

16. PLANT SPECIES
● Adzuki bean (Vigna angularis)
● Apple (Malus domestica)
● Aubergine (Solanum melongena)
● Banana (Musa acuminata)
● Barley (Hordeum vulgare)
● Beet (Beta vulgaris)
● Cabbage (Brassica oleracea)
● Cassava (Manihot esculenta)
● Chilli pepper (Capsicum annuum)
● Chinese white pear (Pyrus bretschneideri)

17. ● Chinese chestnut (Castanea mollissima)
● Clementina Orange (Citrus clementina)
● Cocoa (Theobroma cacao)
● Cowpea (Vigna unguiculata)
● Cucumber (Cucumis sativus)
● Currant tomato (Solanum pimpinellifolium)
● Date palm (Phoenix dactylifera)
● Euphrates poplar (Populus euphratica)
● False flax (Camelina sativa)
● Green Bean (Phaseolus vulgaris)
● Japanese apricot (Prunus mume)
● Lettuce (Lactuca sativa)
● Maize (Zea mays)
● Melon (Cucumis melo)
● Mung bean (Vigna radiata)

18. ● Oil palm (Elaeis guineensis)
● Papaya (Carica papaya)
● Peach (Prunus persica)
● Peanut (Arachis hypogaea)
● Pigeon pea (Cajanus cajan)
● Pineapple (Ananas comosus)
● Potato (Solanum tuberosum)
● Radish (Raphanus sativus)
● Rape (Brassica napus)
● Rice (Oryza sativa)
● Robusta coffee (Coffea canephora)
● Sorghum (Sorghum bicolor)
● Soybean (Glycine max)
● Spinach (Spinacia oleracea)
● Strawberry (Fragaria x ananassa)

19. ● Sugarcane (Saccharum officinarum)
● Sunflower (Helianthus annuus)
● Tobacco (Nicotiana tabacum)
● Tomato (Solanum lycopersicum)
● Tree cotton (Gossypium arboreum)
● Turnip (Brassica rapa)
● Upland cotton (Gossypium hirsutum)
● Valencia orange (Citrus sinensis)
● Watermelon (Citrullus lanatus)
● Wine grape (Vitis vinifera)

20. SCIENTIFIC TRENDS

21. FUTURE PERSPECTIVE
Most relevant topics in the last 3 years (2016-2018)
Resistance (99500 articles)
Tolerance (40600 articles)

22. INDIA

23. RICE
● Expression of OsDREB2A transcription factor confers
enhanced dehydration and salt stress tolerance in rice
(Oryza sativa L.)
(Garladinne Mallikarjuna,Kokkanti Mallikarjuna,M. K. Reddy,
Tanushri Kau, 2011)
● Stress-inducible expression of AtDREB1A transcription
factor greatly improves drought stress tolerance in
transgenic indica rice
(Ravikumar,P. Manimaran,S. R. Voleti,D. Subrahmanyam,R.
M. Sundaram,K. C. Bansal,B. C. Viraktamath,S. M.
Balachandran;2014)

24. Transcriptional profiling and in silico analysis of Dof
transcription factor gene family for understanding their
regulation during seed development of rice Oryza sativaL.
(Vikram Singh Gaur,U.S. Singh,Anil Kumar 2011)

25. TOBACCO
A MYB transcription factor from the grey mangrove is
induced by stress and confers NaCl tolerance in
tobacco (G,Ganesan,H.M.
Sankararamasubramanian,M.Harikrishnan,G.Ashwin,
Ajay Parida 2012)
Modulation of Transcriptome and Metabolome of Tobacco
by Arabidopsis Transcription Factor, AtMYB12, Leads to
Insect Resistance(Prashant Misra, Ashutosh Pandey, Manish Tiwari, K.
Chandrashekar, Om Prakash Sidhu, Mehar Hasan Asif, Debasis
Chakrabarty, Pradhyumna Kumar Singh, Prabodh Kumar Trivedi,
Pravendra Nath, Rakesh Tuli 2010)

26. Co‐expression of Arabidopsis transcription factor, AtMYB12, and soybean
isoflavone synthase, GmIFS1, genes in tobacco leads to enhanced
biosynthesis of isoflavones and flavonols resulting in osteoprotective
activity(Ashutosh Pandey ,Prashant Misra ,Mohd P. Khan ,
Gaurav Swarnkar ,Mahesh C. Tewari ,Sweta Bhambhani,Ritu
Trivedi,Naibedya Chattopadhyay,Prabodh K. Trived 2013)

27. SUGARCANE
Functional characterization of sugarcane MYB transcription factor gene
promoter (PScMYBAS1) in response to abiotic stresses and
hormones(Gajjeraman Prabu,Doddananjappa Theertha Prasad 2012)

28. INDONESIA

29. RICE
● Characterization of Transcription Factor HD-ZIP for Drough-
Tolerant and Introduction of Salisilic Acid Pathway Biosynthesis
Encoded Genes for Blast-Tolerant in Rice
(S. Purwantoro, A. Suwanto, A. Hartana, M.T Suharto, I.H Slamet-Loedin,
2007)
● Genetic Transformation of Transcription Factor (35S-oshox4) Gene
into Rice Genome and Transformant Analysis of hpt Gene by PCR
and Hygromycin Resistance Test
(E.S Mulyaningsih, R. Hermawan, and I.H Slamet-loedin, 2009)
● Transformation of OsDREB1A Gene Using Agrobacterium
tumefaciens for Regeneration of Drought Tolerant Rice Plants
(B. Santosa, Sobir, S. Sujiprihati, and K.R Trijatmiko, 2011)

30. ● Delivering of Over-Expression Construct OsWRKY76 Candidate Gene in
Rice cv. Nipponbare through Agrobacterium tumefaciens
(A. Apriana, A. Sisharmini, W. Enggarini, Sudarsono, N. Khumaida, and K.R
Trijatmiko, 2011)
● Development of Drought Tolerance Upland Indica Rice by Genetic
Transformation of HD-Zip oshox6 Regulator Gene and Through Selection
on Rice Population Harboring Genetic Marker QTL 12.1.
(E.S Mulyaningsih, H. Aswidinnoor, D. Sopandie, I.H Slamet-loedin, and P.B.F
Ouwerkerk, 2011)
● Response of T1 Generation Transgenic Rice cv. Nipponbare
Containing an Oryza sativa Dehydration-response Element
Binding 1A (OsDREB1A) Gene to Salinity Stress
(T.J Santoso, A. Apriana, A. Sisharmini, and K.R Trijatmiko, 2012)

31. ● Genetic Transformation of Rice using Rhizobium and
Agrobacterium and Functional Analysis of OsHox6
(S. Rahmawati, Suharsono, D. Sopandie, and I.H Slamet-loedin, 2012)
● Functional Analysis of OsNAC6 Gene from Batutegi Rice (Oryza
sativa L.) Cultivar to Enhance Drought Tolerance
(A. Rachmat, H. Aswidinnoor, Sudarsono, D. Sukma and S. Nugroho,
2014)
● Genetic transformation of OsMYB6 and OsMYB7 transcription
factor into Nipponbare rice cultivar for lignin content
manipulation
(V.E Windiastri, C.F Pantouw, D. Astuti, D. Widyajayantie, A. Estiati, and
S. Nugroho, 2018)

32. RUBBER TREE
● The Hevea brasiliensis AP2/ERF superfamily: From ethylene
signalling to latex harvesting and physiological disease response
(R.A Putranto, and P. Montoro, 2016)
● Establishment of Hevea brasiliensis lines overexpressing genes
involved in ethylene signalling pathway
(R. Lestari, M. Rio, F. Martin, J. Leclercq, F. Dessailly, S. Suharsono, P.
Montoro, 2016)
● Functional analysis in Hevea brasiliensis of the HbERF-IXc4 and
HbERF-IXc5 genes, two potential orthologs Arabidopsis ERF1 gene
(R, Lestari, 2016)

33. TOBACCO
●Phenotypic expression of cacao APETALA1 (TcAP1) in
tobacco explant
(T. Chaidamsari, Samanhudi, A. Budiani, R. Poerwanto and D.
Santoso, 2006)
OIL PALM
●Correlation between DNA Methylation and Expression of
the MADS-box Genes on Mantled Fruit of Oil Palm (Elaeis
guineensis Jacq.)
(M. Anischan, Suharsono, N. Toruan-Mathius, and A.S
Kusnandar, 2014)

34. HUNGARY

35. WHEAT
Early response of TaNAC2 to hyperosmotic stresses
(Xinguo M., Hongying Z., Xueya Q., Ang L., Guangyao Z., Ruilian
J., 2012.)
Overexpression of TaAREB3 confers freezing tolerance -
Wheat Transcription Factor TaAREB3 Participates in
Drought and Freezing Tolerances in Arabidopsis
(J. Wang, Q. Li, X. Mao, A. Li, and R. Jing, 2016)

36. WHEAT
A Wheat CCAAT Box-Binding Transcription Factor Increases
the Grain Yield of Wheat with Less Fertilizer Input
(B. Qu, X. He, J. Wang, Y. Zhao, W. Teng, A. Shao, X. Zhao, W.
Ma, J. Wang, B. Li, Z. Li, Y. Tong, 2015)
The target gene of tae‐miR164, a novel NAC transcription
factor from the NAM subfamily, negatively regulates
resistance of wheat to stripe rust
(H Feng, X. Duan, Q. Zhang, X. Li, B. Wang, L. Huang X. Wang Z.
Kang, 2013)

37. MAIZE
FASCIATED EAR4 Encodes a bZIP Transcription Factor That
Regulates Shoot Meristem Size in Maize
(M. Pautler, A. L. Eveland, T. LaRue, F. Yang, R. Weeks, C. Lunde,
B. Il Je, R. Meeley, M. Komatsu, E. Vollbrecht, H. Sakai, D.
Jackson, 2015)
ZmNAC55, a maize stress-responsive NAC transcription
factor, confers drought resistance in transgenic
Arabidopsis
(H.Maoa, L. Yub, R.Hanb Z. Lib, H.Liub, 2016)

38. SUNFLOWER
The sunflower transcription factor HaWRKY76 confers
drought and flood tolerance to Arabidopsis thalianaplants
without yield penalty
(Jesica Raineri,K. F. Ribichich, R. L. Chan, 2015)
A Seed-specific Heat-shock Transcription Factor Involved
in Developmental Regulation during Embryogenesis in
Sunflower
(C. Almoguera, A. Rojas ,J. Dı́az-Martı́n, P. Prieto-Dapena,R.
Carranco, J. Jordanol, 2002)

39. SUMMARY
Transcription factor play a key role in the formation and maintenance of
different types of cell during development.
By using transcription factor we are able to make transgenic crops which
are valuable in the field of agriculture.
We can develop many stress tolerance variety of the main staple crop such
as rice,wheat,millets etc.
In response to abiotic stress such as cold,heat,salinity,drought and
mechanical woundering a lot of genes regulated and their gene products
functions in providing the type of stress tolerance in plants.
By these TF we can develop a drought,heat,salt,cold tolerance if we
understand the mechanism of the plant and develop more transgenic and
increase the productivity.

40. TFs genes in breeding and other crop improvement programs will give us a
clear understanding of abiotic stress related signal transduction events and
will lead us to develop good crop varieties which are superior in stress
tolerance by genetic manipulation

43. THANK YOU FOR YOUR KINDLY ATTENTION