This presentation includes information about transcription factors which are found on plants their classification and different families

1. by
Guruprasad A
PAMB1083
Transcription
factors

2. Transcription
Factor

3. Transcription

4. RNA

5. Factor

6. Factor - Something which has an effect on the result

7. X factor

8. 2 x = 8
x = 8/2
x = 4

9. Nuclear Transcription Factor Y Transcription Initiation Factor

10. General TF / Specific TF

11. General Transcriptional factors
5 I
3 I

12. Pol II
General transcription factors
TATAAA
-30
+1 Transcription Start site
TF II D
TBP
TF II A
TF II B
TF II F
TF II E
TF II H
• TF II D - TBP(Core promoter recognition and recruiting TF II B
• TF II A - Stabilising TBP
• TF II B - Moving of pol II and TF II F to site and determination of transcriptional initiation point by pol II
• TF II F - Fixation of pol II and releasing non specific interaction between pol II and DNA
• TF II E - Moving of TF II H , regulation of activity of TF II H helices, ATPase, kinase
• TF II H - Conversion of Double stranded DNA into Single stranded

13. Specific Transcription Factors

14. Specific Transcriptional factors
5 I
3 I

15. Transcription factors : Total number of genes
4.7%
3.6 %
5 - 10 %

16. Classification of Transcription Factors

17. DNA Binding Domains

18. DNA Binding Domains

19. Classification of Transcription Factors*

20. bZIP Transcription factor family

22. Light signalling
Abiotic stress response
Pathogen defence
Seed maturation
Flower development

24. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group A
Seven members of group A have been studied (AtbZIP39/ABI5, AtbZIP36/ABF2/AREB1,
AtbZIP38/ABF4/AREB2, AtbZIP66/AREB3, AtbZIP40/GBF4, AtbZIP35/ABF1 and AtbZIP37/ABF3)
ABA / Stress signaling

25. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group B
Group-B bZIP proteins include AtbZIP17, AtbZIP28, and AtbZIP49
Endoplasmic reticulum (ER) stress responses

26. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group C
Members of this group share structural features with a well characterized family of plant bZIPs that
includes maize Opaque2 and parsley (Petroselinum crispum) CPFR2
Seed storage protein/ Pathgen response ?

27. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group D
Group D genes participate in two different processes: defence against pathogens and development.
Two group D genes are involved in developmental processes: AtbZIP46 /Perianthia
controls floral organ number in Arabidopsis and Liguleless2 establishes the blade-
sheath boundary during maize leaf development
AtbZIP57/OBF4/TGA4 interacts with AtEBP, which binds the
ethylene response element present in many PR gene promoters
might thus be involved in integrating different systemic signals
(salicylic acid and ethylene) at the PR promoter level in response
to pathogen infection.

28. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group E/F
No functional data.

29. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group G
The group G GBF genes from Arabidopsis and their parsley homologues CPRF1, CPRF3, CPRF4a and CPRF5 have been
mainly linked to ultraviolet and blue light signal transduction and to the regulation of light-responsive promoters

30. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group H
Group H has only two members (AtbZIP56/HY5 and AtbZIP64).
HY5’s role in promoting photomorphogenesis

31. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group I
Studies of group I genes from several species indicate that they might play a role in vascular development
RSG gene from tobacco is specifically expressed in the phloem and
activates the GA3 gene of the gibberellin biosynthesis pathway

32. 75 Putative genes
Clustered into 10 groups
A, B, C, D, E, F, G, H, I, S
Based sequence similarities of their base region
Summary
Group S
Group S is the largest bZIP group in Arabidopsis but only ATBZIP11/ATB2 has been analysed in detail
Transcription of this gene is upregulated by light, in carbohydrate-consuming (i.e. sink) tissue and in the vascular system

33. bHLH Transcription factor family

35. bHLH Tfs contain the bHLH domain of approximately 60 amino acids, with two
functionally distinctive regions, the basic region and the HLH region.
The 15 amino acid basic region at the N-terminus of the bHlH domain functions as a DNA-
binding motif.
The HLH region contains two amphipathic alpha-helices with a linking loop of variable length to
form homo or heterodimmers
Some bHLH proteins bind to sequences containing a consensus core element called the E-box (5I-
CANNTG-3I), with the G-box (5I-CACGTG-3I) being the most common form

36. In Arabidopsis 162 bHLH-coding
genes have been identified
(Bailey et al., 2008).
In Rice167 bHLH-coding
genes have been identified
(Li et al., 2006).
The members of the bHLH Tf family in both
Arabidopsis and rice are divided into two
major groups that contain a canonical bHLH
or lack the basic region required for DNA
binding.
(Li et al., 2006).
They are further classified into
25 subfamilies
(Li et al., 2006).

37. Phytochrome Interacting Factors, (PIFs)
which may directly bind to the
photoactivated phytochromes.
Members of the PIF family have been
shown to control light-regulated gene
expression directly and indirectly.
PIF1, PIF3, PIF4 and PIF5 are degraded
in response to light signals, and physical
interaction of PIF3 with phytochromes is
necessary for the light-induced
phosphorylation

38. The bHLH Tf MYC2 has been described as a
master regulator of the crosstalk between the
signaling pathways of JA and those of other
phytohormones such as abscisic acid (ABA),
salicylic acid (SA), gibberellins (GAs), auxins.
Seed coat differentiation, and trichome/root hair
formation (MYC1, GL3, EGL3, TT8) (GLABRA3
(GL3), ENHANCER of GLABRA3 (EGL3),
TRANSPARENT TESTA8 (TT8)), .

39. MYB Transcription factor family

41. MYB proteins integrate to a superfamily of Tf.
This has the largest number of members of any Arabidopsis Tf family: 197
members with a highly conserved DBD known as the MYB domain
This domain generally consists of up to four imperfect amino acid sequence
repeats (R) of about 52 amino acids, each forming a helix–turn–helix
structure that intercalates in the major groove of the DNA.
MYB proteins can be divided into different classes depending on the number of
MYB repeats (one to four).
I,e R1R2, R1R3, R2R3, R1R2R3 MYB repeats
In plants, the MYB family has selectively expanded, particularly through the
large family of R2R3-MYB (Dubos et al., 2010).
In the Arabidopsis genome, 138 are R2R3-MYB, 5 are R1R2R3- MYB, 52 are MYB-
related, and 2 are atypical MYB genes (Yanhui et al., 2006; Katiyar et al., 2012).

42. Combinatorial interactions among bHLH Tfs and
MYB Tfs are reported to play a key role in flavonoid
biosynthesis in plants
The maize C1 bHLH protein interacts with the
MYB R protein to activate maize flavonoid
pathways.
Arabidopsis GL3 and EGL3 interact with
MYB factors GLABRA1 (Gl1) or
WEREWOLF (WER) to form trichomes
and root hairs.

44. HSF (Heat stress transcription factors)

45. Heat stress transcription factors (HSFs) mediate the rapid accumulation of
heat shock proteins (HSPs) in response to both heat stress and many
chemical stressors
HSF recognize conserved binding motifs, so-called heat stress
elements (HSE: 5I-AGAAnnTTCT-3I) that exist in the promoters of Hsp
genes
HSFs have a modular structure with a DBD and an oligomerization domain
(OD).
In addition, they contain a nuclear localization signal (NLS), a nuclear export
signal (NES), and an activator motif (AHA motif).
Plant HSFs are classified into three classes, A, B, and C, based on the
peculiarities of their ODs.
In the Arabidopsis genome, among 21 HSFs,15 belong to Class A, 5 to Class
B, and 1 to Class C

46. Here functional studies show that HsfA1a has a unique
function as master regulator of acquired
thermotolerance and trigger of the Hs response and
that later on, by interaction with HsfA2 and B1 in a
functional triad, affects different aspects of Hs
response and recovery

47. HsfA2 is the most highly induced HSF in
stressed plants and plays a role in
thermotolerance and a broader role for
expression of general stress-related
nonchaperone-encoding genes like APX2
(ASCORBATE PEROXIDASE2)

48. Plant specific Transcription factors

49. WRKY Transcription factor family

50. WRKY ?

51. WRKYGQK
Tryptophan Arginine Lysine Tyrosine Glycine Glutamine Lysine

52. The WRKY Tf family is one of the best studied plant specific Tf families and
comprises 74 members in Arabidopsis.
The WRKY protein family owes its name to the highly conserved 60 amino acid
long WRKY domain, which contains a conserved amino acid sequence motif
WRKYGQK at the N-terminus and a novel zinc-finger-like motif at the C-terminus.
These two motifs are vital for binding to the consensus cis-acting element
termed the W-box (TTGACT/C).
Based on both the number of WRKY domains and features of the the zinc-
finger motif, WRKY proteins are categorized into three subfamilies:
Group I has two WRKY domains,
Group II has one WRKY domain with the same Cys2–His2 zinc-finger motif
(Group II WRKYs are further divided into a–e based on additional conserved motifs outside the WRKY
domain. )
Group III has one WRKY domain containing a different Cys2–His2 zinc-finger motif.

53. AtWRKY52/ RRs1, a member of Group III that contains TIR–
NBS–lRR (TNl) and WRKY domains, confers immunity on the
bacterial pathogen Ralstonia solanacearum by nuclear
interaction with the type III bacterial effector PopP2

54. AtWRKY52/ RRS1, also interacts with the R protein RPS4 to
provide dual resistance towards fungal (Colletotrichum
higginsianum) and bacterial pathogens

55. AP2/ERF Transcription factor family

56. The AP2 domain was first identified as a repeated motif within the
Arabidopsis homeotic gene APETALA 2 (AP2) involved in flower
development.
The ERF domain was first found in tobacco ethylene-responsive
element binding proteins (EREBPs) as a conserved DNA-binding motif.
AP2/ERF family members are encoded by 145 loci in Arabidopsis and 167 loci
in rice.
Members of AP2/ERF family are categorized into three subfamilies: the AP2,
RAV, and ERF subfamilies.
The ERF family is sometimes further classified two major subfamilies, the ERF
subfamily and the CBF/ DREB subfamily

57. ERF subfamily members are mainly involved in responses to biotic stresses by
recognition of the GCC box (5IAGCCGCC3I), which is a DNA sequence
involved in ethylene-responsive gene transcription
CBF/ DREB subfamily members play crucial roles in abiotic stresses by
recognizing a dehydration-responsive element (DRE) with a core motif
5IA/GCCGAC3I. Members of the DREB1/CBF subgroup
(DREB1A/CBF3, DREB1B/ CBF1, and DREB1C/CBF2) are cold
inducible and are major regulators of cold stress responses, while those
of the DREB2 subgroup (DREB2A and DREB2B) play important roles in
dehydration and heat stress responses

58. Transcription factors without DBD
But
Interacts with TF with DBD

59. AUX / IAA family

60. The AUX/IAA family represents a class of proteins interacting with
auxin response factors (ARFs).
Canonical Aux/IAA proteins share four conserved amino acid
sequence motifs known as Domains I, II, III, and IV.
Domain I is a repressor domain that contains a conserved leucine repeat
motif, similar to the EAR (ethylene-responsive element-binding factor-
associated amphiphilic repression) domain
Domain I is also required for the recruitment of the transcriptional
corepressor TPL
C-terminal Domains III and IV are shared with ARF proteins, and are known to
promote homo and heterodimerization
Domain II confers protein instability, leading to rapid degradation of Aux/IAA
through interaction with the f-box protein TIR1

61. JAZ Protein family

62. https://agris-knowledgebase.org/AtTFDB/

63. References

64. References
Bailey, P.C., Dicks, J., Wang, T.l., Martin, C., 2008. IT3f: a web-based tool for functional analysis of transcription factors in plants. Phytochemistry 69,
2417–2425.
Castillon, A., shen, H., Huq, E., 2007. Phytochrome interacting factors: central players in phytochrome-mediated light signaling networks. Trends Plant sci.
12, 514–521.
Deslandes, l., olivier, J., Peeters, N., feng, D.X., Khounlotham, M., Boucher, C., somssich, I., Genin, s., Marco, Y., 2003. Physical inter- action between
RRs1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc. Natl. Acad. sci. 100, 8024–
8029.
Hahn, A., Bublak, D., schleiff, E., scharf, K.-D., 2011. Crosstalk between Hsp90 and Hsp70 chaperones and heat stress transcription factors in tomato.
Plant Cell online 23, 741–755.
Jakoby, M., Weisshaar, B., Droge-laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., Parcy, f., bZIP Research Group, 2002. bZIP transcription
factors in Arabidopsis. Trends Plant. sci. 7, 106–111.
Kazan, K., Manners, J.M., 2013. MYC2: the master in action. Mol. Plant 6, 686–703.
Li, X., Duan, X., Jiang, H., sun, Y., Tang, Y., Yuan, Z., Guo, J., liang, W., Chen, l., Yin, J., Ma, H., Wang, J., Zhang, D., 2006. Genome-wide analysis of
basic/helix–loop–helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141, 1167–1184.
Narusaka, M., shirasu, K., Noutoshi, Y., Kubo, Y., shiraishi, T., Iwabuchi, M., Narusaka, Y., 2009. RRs1 and RPs4 provide a dual resistance- gene system
against fungal and bacterial pathogens. Plant J. 60, 218–226.
Nishizawa, A., Yabuta, Y., Yoshida, E., Maruta, T., Yoshimura, K., shigeoka, s., 2006. Arabidopsis heat shock transcription factor A2 as a key regulator in
response to several types of environmental stress. Plant J. 48, 535–547.
Ramsay, N.A., Glover, B.J., 2005. MYB–bHlH–WD40 protein com- plex and the evolution of cellular diversity. Trends Plant sci. 10, 63–70.