SUPPLEMENTARY FILE 2 : LIST AND DESCRIPTION OF TRANSCRIPTION FACTORS PREDICTED TO BIND TO IDENTIFIED FAMILY MOTIFS PRESENT IN RICE LEA GENES.
Transciption factor / FunctionERFLP1 , ATERF7, ERF-1,
ERF-2, ERF-3, ERF-4 , ERF-5 / The Ethylene-responsive factors (ERFs) are transcription factors that are unique to higher plants (Guo & Ecker, 2004). They are induced by biotic and abiotic stresses and bind GCC boxes that are present in the promoters of many PR genes (Wu et al., 2002) and have been shown to be activators and repressors of GCC box–mediated gene expression in Arabidopsis (Fujimoto et al., 2000).
DREB1A,
CBF1 , CBF2, CBF17 , CBF5 / The DREB1 (dehydration responsive element binding)/CBF (C-repeat (CRT)-binding factor) and DREB2 transcription factors are a subclass of ERF proteins whose expression is rapidly induced by cold and dehydration respectively (Gilmour et al., 1998) (Medina et al., 1999). The DREB1/CBF TF bind to DRE and CRT cis-elements and activate expression of cold responsive genes (Dubouzet et al., 2003).
EmBP-1a / Wheat EmBP-1 is a basic leucine zipper (bZIP) protein which has been implicated in the mechanisms of abscisic acid (ABA)-mediated expression through its ability to bind specifically to the ABA response element (ABRE) from the wheat Em (LEA) gene (Guiltinan et al., 1990).
DPBF-1 , DPBF-2 / The DPBF1 and 2 (Dc3 Promoter-Binding Factors) are basic leucine zipper binding proteins that were isolated from a immature seed cDNA library and identified in a screen as factors that bind to functional cis-regulatory elements in the Dc3 (carrot LEA class gene) promoter (Kim et al., 1997). They were determined to bind to ABA-responsive and embryo specification elements in the Dc3 promoter and the expression of AtDPBF-1 was found to be induced by exogenous ABA in Arabidopsis seedlings (Kim et al., 2002).
TINY2 / TINY2 may be a new member of the AP2/EREBP transcription factor family involved in activation of down-stream genes in response to environmental stress. In Arabidopsis transcription of TINY2 was rapidly induced in response to abscisic acid, cold, drought, mechanical wounding and high salinity (Wei et al., 2005). In Gel retardation assay TINY2 was able to form a specific complex with the previously characterized DRE element.
Pti4 / Pti4 is a tomato transcription factor that belongs to the ERF family of proteins and binds to GCC box cis-elements that are present in the promoters of many PR genes (Wu et al., 2002). In tomato, Pti4 specifically interacts with the Pto resistance gene, which encodes a Ser/Thr protein kinase (Martin et al., 1993). The Pto kinase phosphorylates Pti4 in vitro, and this phosphorylation enhances the GCC box binding activity of Pti4 (Gu et al., 2000) and expression of Pti4 in Arabidopsis resulted in induction of PR gene expression (Gu et al., 2002).
DREBLP1 / In hot pepper, Ca-DREBLP1 was rapidly induced by dehydration and high salinity. The structural features of Ca-DREBLP1 resemble those of the DREB1-type proteins of Arabidopsis thaliana and rice plants, however, its induction patterns are reminiscent of the DREB2-type proteins, suggesting that Ca-DREBLP1 is a unique class DREB subfamily in hot pepper (Hong & Kim, 2005).
DBF1 , DBF2 / The maize dehydration-responsive element (DRE)-binding factors, DBF1 and 2, are members of the AP2/EREBP transcription factor family. DBF1 is induced during maize embryogenesis and in seedlings after desiccation, salt and ABA treatments. DBF1 functions as an activator of DRE2-dependent transcription of rab17 promoter by ABA, whereas DBF2 overexpression had a repression action downregulating basal and ABA-induced promoter activity. ABA was thus proposed to play a role in the regulation of DBF activity possibly through an ABA-dependent pathway for the regulation of genes through the C-repeat/DRE element (Saleh et al., 2006) (Kizis & Pages, 2002).
TSI1 / The tobacco stress-induced gene 1 (Tsi1) has been implicated as a positive trans-acting factor in the regulation of gene expression in response to biotic and abiotic stresses (Park et al., 2001). Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Tsi1 bound specifically to GCC and the DRE/CRT sequences, with greater affinity to the former.
DOF1 / The DOF (DNA binding with One Finger) are plant specific DNA binding proteins that contain a highly conserved DOF domain with a single zinc finger that is involved in DNA-binding and protein-protein interactions (Umemura et al., 2004; Yanagisawa et al., 2004). DOF1 was originally thought to be involved in light dependent activation of transcription from the C4 phosphoenolpyruvate carboxylase (PEPC) promoter (Yanagisawa and Shenn, 1998) and induction of genes involved in carbon metabolism and nitrogen fixation (Yanagisawa, 2004) however, the role of DOF1 in the control of photosynthetic gene expression has recently been questioned (Cavalar et al., 2006).
PBF / The prolamine-box binding factors (PBFs) are endosperm-specific DOF transcription factors that were isolated from maize (Vicente-Carbajosa et al., 1997). The prolamine-box is one element of the biparate endosperm box that is involved in conferring endosperm specificity in cereals (Wu et al., 2000). In barley, transcripts of the bPBF TF are present during endosperm development and bPBF proteins have been shown to be activators of reserve protein encoding genes during seed development (Mena et al., 2002). A transient expression assay system determined that barley PBF could increase transcription of the rice glutelin gene, Gt1 in developing rice endosperm cells (Hwang et al., 2004).
GAMYB / GAMYB is a MYB class TF and has been shown to activate gene expression during endosperm development through binding to the 5’- AACAA-3’ motif in native Hor2 and Itr1 promoters (Diaz et al., 2002). The 5’- AACAAC-3’ motif has been determined to be the third important motif in regulating endosperm specificity and is present in the rice glutelin gene promoters and is recognized by TFs of the MYB class (Suzuki et al., 1998). In barley, transcripts of GAMYB were detected early in the developing seed and were determined to accumulate in the aleurone layer, starchy endosperm, nuclear projection and vascular tissue, but also in the immature embryo. Evidence indicates that GAMYB is an important TF in the combinatorial regulation of genes specifically expressed in the developing endosperm (Diaz et al., 2002).
MCB1 , MCB2 / The MCB1 gene encodes a R1MYB protein that binds to the 5'TATCCAC-3' (GATA core) box in vitro and is a transcriptional repressor of a GA-induced amylase (Amy6.4) promoter in bombarded aleurone layers (Rubio-Somoza et al., 2006). In barley, MCB1 repressed transcription of the Amy6.4 promoter in GA-treated aleurone layers and reversed the GAMYB-mediated activation of this amylase promoter. In contrast, during endosperm maturation HvMCB1 acted as a transcription activator of the seed-specific Itr1 gene promoter through binding to a 5'-GATAAGATA-3' box (Rubio-Somoza et al., 2006).
CAMTA1
CAMTA3 / The calmodulin-binding transcription activators (CAMTAs) comprise a conserved family of transcription factors in a wide range of multicellular eukaryotes (Bouche et al., 2002). In plants, CAMTAs were identified in a screening of cDNA expression libraries of drought stressed leaves using a recombinant calmodulin probe (Bouche et al., 2002). The proteins were determined to contain a transcription activation domain and two DNA-binding domains, designated the CG-1 domain and the transcription factor immunoglobulin (TIG)-like domain, ankyrin repeats, and a number of calmodulin-binding motifs (Lander et al., 2001) (Bouche et al., 2002). In Arabidopsis six CAMTA genes (AtCAMTA1-AtCAMTA6) that are also referred to as AtSR1–6 (Arabidopsis thaliana signal-responsive genes) have been identified and these genes have been determined to be rapidly and differentially expressed in response to environmental signals including UV, extreme temperatures, high salt, the hormones ethylene and ABA as well as signaling molecules such as methyl jasmonate, H2O2, and salicylic acid (Yang & Poovaiah, 2002). The CAMTAs have been determined to specifically bind to a CGCG box (Chen et al., 2005) (Bouche et al., 2002).
CBT / The OsCBT (Oryza sativa CaM-binding transcription factor) is a putative calmodulin-binding transcription factor that was isolated from a rice cDNA expression library using CaM:horseradish peroxidase as a probe. OsCBT shared similar structural features to Arabidopsis AtSRs/AtCAMTAs factors and was determined to preferentially bind to 5’-TWCG(C/T)GTKKKKTKCG-3’ (W = A or C and K = T or G) DNA sequences and also bind to an oligonucleotide probe containing CGCG motifs that was selected from the stress inducible rice Phenylalanine ammonia-lyase (PAL,ZB8) gene promoter supporting that OsCBT DB binds DNA (Choi et al., 2005).
(VOZ1)2 , (VOZ2)2 / AtVOZ1 and AtVOZ2, are novel transcription factors that bind to a 38-bp cis-acting region of the A. thaliana V-PPase gene (AVP1), which is a vacuolar proton pump that is coupled with PPi hydrolysis (Maeshima, 2001). The transcription of AVP1 is altered in response to various environmental conditions and developmental stages (Maeshima, 2001).
ANT / The AINTEGUMENTA (ANT), gene promotes initiation and growth of lateral organ primordial (Nole-Wilson & Krizek, 2006). Results indicate that ANT acts in combination with the YABBY gene FILAMENTOUS FLOWER (FIL) to promote organ polarity by up-regulating the expression of the adaxial-specifying HD-ZIP gene PHABULOSA and the floral homeotic gene APETALA3.
JAMYC2 / The JAMYC2 gene encodes a MYC regulatory bHLH-Leucine zipper DNA-binding protein that specifically binds Jasmonic acid (JA) responsive elements present in wound-inducable tomato genes including the proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes. JAMYC2 specifically binds to a T/G-box AACGTG motif in the tomato LAP gene promoter which is important for JA-mediated defence responses. Knockouts of the Arabidopsis homolog gene AtMYC2 resulted in JA-insensitivity and the JAMYC/AtMYC2 transcription factors are believed to pay a key role in JA-induced defense gene activation (Boter et al., 2004).
ARR10 / The Arabidopsis response regulators (ARR) comprise a family of 22 response regulators that are classified into type A and B subtypes. The type B ARRs are putative transcription factors and include ARR10. The ARRs are thought to be involved in a multistep phosphorelay signaling pathway in response to cytokinin signaling (Suzuki et al., 2001). A model of action for cytokinin signaling has been proposed that relays the cytokinin signal from the membrane to the nucleus via a multi-step phosphorelay that involves cytokinin receptors, AHP (Arabidopsis His-containing phosphotransfer factor) and type-B ARRs which induce transcription of the type-A genes which may mediate downstream responses to cytokinins (Hwang & Sheen, 2001) (Kakimoto, 2003; Hutchison & Kieber, 2002). It has been proposed that ARR10,-12, and -1 together redundantly play pivotal roles in the AHK-dependent phosphorelay signaling in response to cytokinin in roots (Yokoyama et al., 2007).
GT-1,-2 / GT-1 and GT-2 are are trihelix DNA-binding factors that bind to GT elements found in the promoters of many light responsive plant genes and have been shown to be involved in light-responsive transcription in vivo (Schindler and Cashmore, 1990). Gain-of-function experiments have confirmed a critical role for GT-1 cis-elements in mediating light-responsive and tissue-specific gene expression (Hiratsuka et al., 1994) . The GT-2 TF, that was first cloned from rice, was found to bind to a triplet of positively acting GT-boxes (GT-1, -2, -3 bx) that are present in the rice phytochrome A (PHYA) gene promoter, having greatest affinity for GT2-bx and GT3-bx motifs (Dehesh et al., 1990). Studies with recombinant GT-2 indicate that it functions as a transcriptional activator in vivo(Ni et al., 1996).
GT-3a / The GT-3a factor is a relatively recently identified GT factor belonging to a subgroup that cannot bind to GT-1 or -2 binding sites but can bind to cab2 and rbcS-1A gene promoters via the 5’-GTTAC sequence. It has been determined to be predominantly expressed in floral buds and roots and form homo- or heterodimers (Ayadi et al., 2004).
PF1 / PF1 is a small nuclear protein of the high mobility group (HMG) I/Y type that is involved in the regulation of phytochrome A (PHYA) transcription. The PF1 protein contains 4 repeats of the ‘A/T-hook’ motif that mediates binding to the narrow groove of A/T-rich DNA (Reeves & Nissen, 1990). It binds to a cognate A/T-rich cis-element termed PE1 that is present in the PHYA promoter and positively regulates its transcription (Martinez-Garcia & Quail, 1999). The phytochrome family consists of red- and far-red-light absorbing sensory photoreceptors that regulate adaptational changes in gene expression in response to environmental light signals in plants (Tepperman et al., 2001). PHYA is exclusively responsible for seedling responsiveness to continuous far-red light (Deng & ail, 1999; Whitelam & Devon, 1997) and may regulate seedling photomorphogenesis (Tepperman et al., 2001).
TBP2 / The TATA binding protein (TBP) is a subunit of the TFllD transcription initiation factor that interacts with the TATA box sequence in the promoter of most eukaryotic nuclear protein-encoding genes and performs an early DNA recognition function for RNA polymerase II (Vogel et al., 1993). TBP additionally serves as a critical subunit in the initiation complexes for RNA polymerases I and III (reviewed in (Green, 1992)). TBP and TFIIB play crucial roles in transcription of class II genes (Pan et al., 2000). In yeast, animals, and insects (see (Peterson et al., 1990)) only one TBP encoding gene has been identified while in Arabidopsis and maize two TBP genes encoding distinct TBP isoforms have been isolated (Gasch et al., 1990) (Haass & Feix, 1992). In some maize tissue, quantitative differences in transcript accumulation was observed between TBPl and TBP2 and it was suggested that they could differ in their DNA binding specificity and/or in specific interactions with other transcription proteins (Vogel et al., 1993).
DBP1 / DBP1 is a novel DNA-binding protein from tobacco plants with protein phosphatase activity, which binds in a sequence-specific manner to a cis- acting element of a defense-related gene and participates in its transcriptional regulation (Carrasco et al., 2003).
GCBP-1 , / GCBP-1 binds to the minimum consensus sequence 5'-GC(G/C)CC-3' which is similar to a part of the binding site of the human transcription factor Sp1. Maize GCBP-1 and human Sp1 were determined to have similar recognition properties. Studies implicate a direct role for GCBP-1 in the hypoxic activation of Alcohol dehydrogenase-1 (Adhl) gene expression (Olive et al., 1991).
Sp1 / The human transcription factor Sp1 also binds to the ARE element and has similar DNA recognition sites as GCBP-1 (Olive et al., 1991). Sp1 is essential for early embryonic development in mouse (Martin & PazAres, 1997).
References