TCP Transcription Factors Research Articles

Predicting Characteristics of the Potentially Binding Sites for miRNA in the mRNA of the TCP Transcription Factor Genes of Plants

The expression of the TCP transcription factor family genes depends on miRNA, whose effect on the translation of their mRNA is poorly studied. Interactions between miRNA and mRNA were studied with the MirTarget program, which allows estimating of quantitative characteristics of binding of the whole nucleotide sequence of miRNA to mRNA. The analysis of binding of 125 miRNAs to mRNAs of 28 genes of the TCP family of Triticum aestivum L. revealed eight target genes for miR319-3p, miR444a-3p, miR5086-5p, miR9666a-3p, and miR9780-3p. miRNA binding sites in mRNA of the TCP family genes of T. aestivum were located in the CDS only. Only 12 of 22 mRNAs of the ТСР family genes of Oryza sativa L. bounded to the miR1437b-5p, miR1846a-5p, miR1848-5p, miR1858a-5p, miR1858b-5p, miR1861d-5p, miR1861h-5p, miR2102-3p, miR2102-5p, miR2919, miR2925-5p, miR319a-3, miR408-3p, miR5075-3p, and miR5819-5p out of 738 miRNAs in total. miRNA binding sites were located in the 5'UTR and CDS regions of mRNAs of the TCP family genes of O. sativa. Only 10 of 46 TCP family genes of Zea mays L. were shown to be targets for the miR164g-3p, miR164h-5p, miR166a-5p, miR168a-5p, miR171d-5p, miR399d-3p, and miR408a-3p out of 325 miRNAs of Z. mays. The zma-miR166a-5p was bound to mRNAs of the genes GRMZM2G031905_P01, GRMZM2G055024_P01, GRMZM2G062711_P01, and GRMZM2G170232_P01. Two miRNAs were shown to bind to mRNAs of the genes AC213524.3_FGP003, AC233950.1_FGP002, and GRMZM2G034638_P01. Only one miRNA was bound to mRNAs of the genes GRMZM2G035944_P01, AC190734.2_FGP003, and AC205574.3_FGP006. miRNA binding sites were located in the 5'UTR and CDS regions of mRNAs of the TCP family genes of Z. mays. Ten of 27 TCP family genes of Arabidopsis thaliana (L.) Heynh. were shown to be targets for the miR319-3р, miR4228-5p, miR4228-3p, miR5021-5p, miR5658-5p, and miR8181-5p out of 429 miRNAs of A. thaliana. mRNAs of the AT1G53230 and AT2G31070 genes had binding sites for the miR319c-3p, miR5021-5p, and miR5658-5p, while mRNA of the AT3G15030 gene had binding site for the miR319a-3p and miR4228-3p. Two miRNAs bounded to mRNAs of the genes AT1G69690, AT3G02150, and AT3G47620. One miRNA bounded to mRNAs of the genes AT1G30210, AT4G18390, and AT5G08330. miRNA binding sites were located in the 5'UTR, CDS and 3'UTR regions of mRNA of the TCP gene family of A. thaliana. mRNAs of six groups of the TCP family genes had binding sites for the miR319-3p, miR444a-3p, miR5021-5p, miR5658-5p, and miR2102-5p, which encode the oligopeptides QRGPLQS, STSETS, SSSSSS, HHHHHH, GGGGGG, and AAAAAA conservative in the TCP family proteins of different plant species. Quantitative characteristics of miRNA binding to mRNAs of plant transcription factors of the TCP family, which participate in regulation of growth and development of plants, have been predicted.

DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment

Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.

De Novo Shoot Regeneration Controlled by HEN1 and TCP3/4 in Arabidopsis.

Plants have the ability to regenerate whole plant body parts, including shoots and roots, in vitro from callus derived from a variety of tissues. However, the underlying mechanisms for this de novo organogenesis, which is based on the totipotency of callus cells, are poorly understood. Here, we report that a microRNA (miRNA)-mediated posttranscriptional regulation plays an important role in de novo shoot regeneration. We found that mutations in HUA ENHANCER 1 (HEN1), a gene encoding a small RNA methyltransferase, cause cytokinin-related defects in de novo shoot regeneration. A hen1 mutation caused a large reduction in the miRNA319 (miR319) level and a subsequent increase in its known target (TCP3 and TCP4) transcript levels. TCP transcription factors redundantly inhibited shoot regeneration and directly activated the expression of a negative regulator of cytokinin response ARABIDOPSIS THALIANA RESPONSE REGULATOR 16 (ARR16). A tcp4 mutation at least partly rescued the shoot-regeneration defect and derepression of ARR16 in hen1. These findings demonstrate that the miR319-TCP3/4-ARR16 axis controls de novo shoot regeneration by modulating cytokinin responses.

The Regulation of CIN-like TCP Transcription Factors.

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1 and 2 (TCP) family proteins are the plant-specific transcription factors extensively participating in diverse developmental processes by integrating external cues with internal signals. The roles of CINCINNATA (CIN)-like TCPs are conserved in control of the morphology and size of leaves, petal development, trichome formation and plant flowering. The tight regulation of CIN-like TCP activity at transcriptional and post-transcriptional levels are central for plant developmental plasticity in response to the ever-changing environmental conditions. In this review, we summarize recent progresses with regard to the function and regulation of CIN-like TCPs. CIN-like TCPs are regulated by abiotic and biotic cues including light, temperature and pathogens. They are also finely controlled by microRNA319 (miRNA319), chromatin remodeling complexes and auxin homeostasis. The protein degradation plays critical roles in tightly controlling the activity of CIN-like TCPs as well.

Reprogramming of Stem Cell Activity to Convert Thorns into Branches

Thorns arise from axillary shoot apical meristems that proliferate for a time and then terminally differentiate into a sharp tip. Like other meristems, thorn meristems contain stem cells but, in the case of thorns, these stem cells undergo a programmed cessation of proliferative activity. Using Citrus, we characterize a gene network necessary for thorn development. We identify two Citrus genes, THORN IDENTITY1 (TI1) and THORN IDENTITY2 (TI2), encoding TCP transcription factors, as necessary for stem cell quiescence and thorn identity. Disruption of TI1 and TI2 function results in reactivation of stem cells and concomitant conversion of thorns to branches. Expression of WUSCHEL (WUS) defines the shoot stem cell niche in the apical meristems of many angiosperm species; we show that TI1 binds to the Citrus WUS promoter and negatively regulates its expression to terminate stem cell proliferation. We propose that shifts in the timing and function of components of this gene network can account for the evolution of Citrus thorn identity. Modulating this pathway can significantly alter plant architecture and could be leveraged to improve crop yields.

Class I TCP transcription factors regulate trichome branching and cuticle development in Arabidopsis.

Trichomes and the cuticle are two specialized structures of the aerial epidermis that are important for plant organ development and interaction with the environment. In this study, we report that Arabidopsis thaliana plants affected in the function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 show overbranched trichomes in leaves and stems and increased cuticle permeability. We found that TCP15 regulates the expression of MYB106, a MIXTA-like transcription factor involved in epidermal cell and cuticle development, and overexpression of MYB106 in a tcp14 tcp15 mutant reduces trichome branch number. TCP14 and TCP15 are also required for the expression of the cuticle biosynthesis genes CYP86A4, GPAT6, and CUS2, and of SHN1 and SHN2, two AP2/EREBP transcription factors required for cutin and wax biosynthesis. SHN1 and CUS2 are also targets of TCP15, indicating that class I TCPs influence cuticle formation acting at different levels, through the regulation of MIXTA-like and SHN transcription factors and of cuticle biosynthesis genes. Our study indicates that class I TCPs are coordinators of the regulatory network involved in trichome and cuticle development.

Regulatory pathways of CYC‐like genes in patterning floral zygomorphy exemplified in Chirita pumila

AbstractFloral zygomorphy is thought of as an essential adaptation to specific pollinators. The CYCLOIDEA (CYC)‐like genes belonging to the plant‐specific TCP transcription factor family are the key regulators of floral zygomorphy. Their expression differentiations bring about diverse forms of floral zygomorphy. However, the regulatory mechanism underlying their expression differentiation remains unknown. In this study, we selected Chirita pumila D. Don, a zygomorphic member of Gesneriaceae, as a model to address this question. Mutant analysis shows that the CYC gene in C. pumila (CpCYC) plays an important role in controlling floral zygomorphy. Further functional investigation of CpCYC intron and 5′ regulatory regions indicates that an 899 bp promoter region is a key determinant of the dorsal‐specific expression of CpCYC. In this region, using electrophoretic mobility shift assay and transient expression system, we identified three kinds of cis‐regulatory elements with putative binding factors, that is, auxin responsive element, WRKY binding site, LEAFY binding site, and an element with an unknown binding factor. We undertook functional analyses of the two putative LEAFY binding sites, and found that LEAFY could directly activate and regulate CpCYC for its dorsal‐specific expression in patterning floral zygomorphy. This research would shed significant light on the regulatory and evolutionary pathways underlying the spatial‐specific expression of CYC‐like genes for the development of zygomorphic flowers.

CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium.

The complex capitulum of Chrysanthemum morifolium is often comprised of bilaterally symmetrical ray florets and radially symmetrical disc florets. The TCP transcription factor clade CYCLOIDEA2 (CYC2) appears to play a vital role in determining floral symmetry and in regulating floral organ development in Asteraceae. Our previous study identified six CmCYC2 genes from chrysanthemum and showed that CmCYC2c participated in the regulation of ray floret identity. However, the functions of other CmCYC2 genes and the underlying molecular mechanism of CmCYC2-mediated floral development regulation in chrysanthemums have not been elucidated. In this study, we analysed the function of CmCYC2 genes by ectopic expression of CmCYC2 in Arabidopsis. Then, we examined the protein-protein interaction using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Finally, we analysed the protein-DNA interaction using yeast one-hybrid (Y1H) and dual-luciferase reporter assays. We found that ectopic expression of CmCYC2 genes in the Arabidopsis tcp1 mutant changed its floral symmetry and flowering time. Y2H and BiFC assays confirmed three pairs of interactions between CmCYC2 proteins, that is, CmCYC2b-CmCYC2d, CmCYC2b-CmCYC2e and CmCYC2c-CmCYC2d, suggesting that heterodimeric complexes may form between CmCYC2 proteins to increase their functional specificity. The results of Y1H and dual-luciferase reporter assays indicate that CmCYC2c can bind to the promoter of ClCYC2f. Our findings provided clues that CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in C. morifolium. KEY MESSAGE: CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium.

Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses.

The teosinte branched1, cycloidea, and proliferating cell factor family (TCP) proteins, plant-specific transcription factors, are involved in the regulation of plant development; however, the TCP gene family of legumes has been based primarily on a single crop. Here, a total of 55, 22, 26, 21, and 25 genes containing the VQ motif were identified from the genomes of Glycine max, Cicer arietinum, Phaseolus vulgaris, Medicago truncatula, and Lotus japonicus, respectively. Based on the phylogenetic analysis, we divided these TCP genes into three distinct subfamilies: PCF, CYC/TB1, and CIN. The conserved domain analysis indicated that the TCP gene family members contain the bHLH and R domains. The TCP genes from the same evolutionary branches of legumes shared similar motifs and structures. The promoter analysis revealed that cis-elements were related to stress responses, phytohormone responses, and physical and reproductive growth regulation. In addition, the TCP genes presented different expression patterns in the five legumes. Most of them showed specific expression patterns during development. The results of qRT-PCR indicated that the TCP genes played regulatory roles in both salt and drought stresses. The present study provides novel and detailed information regarding the legume TCP gene family, which aids in functional characterisation of the TCP genes in other plants.

A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.)

To improve several agronomic traits in crisphead lettuce (Lactuca sativa L.) under high-temperature growth conditions, we investigated the correlation among those traits in multiple cultivars and performed genetic mapping of their causal genes. In a field cultivation test of Empire type (serrated leaf) and Salinas type (wavy leaf) cultivars, Empire type cultivars showed increased tipburn susceptibility and late bolting compared with Salinas type cultivars. We attempted genetic mapping of leaf shape and bolting time by ddRAD-seq using the F2 population derived from a cross between ‘VI185’ (Empire type) and ‘ShinanoGreen’ (Salinas type). These analyses suggested that both traits are controlled by a single locus in LG5. Genotyping of 51 commercial lettuce cultivars with a tightly linked marker (LG5_v8_252.743Mbp) at this locus showed an association between its genotype and the serrated leaf phenotype. By further fine mapping and transcriptome analysis, a gene encoding putative CIN-like TCP transcription factor was determined to be a candidate gene at this locus and was designated as LsTCP4. An insertion of retrotransposable element was found in the allele of ‘VI185’, and its transcript level in the leaves was lower than that in ‘ShinanoGreen’. Because shapes of leaf epidermal cells in ‘VI185’ were similar to those in the TCP family mutant of Arabidopsis thaliana, the leaf shape phenotype was likely caused by reduced expression of LsTCP4. Furthermore, because it is known that the TCP family protein also controls flowering time via interaction with FT in A. thaliana, it was highly possible that LsTCP4 gave pleiotropic effects on both leaf shape and bolting time in lettuce.

TCP10, a TCP transcription factor in moso bamboo (Phyllostachys edulis), confers drought tolerance to transgenic plants

TCP transcription factors function as significant regulators in plant development and stress defense. In this study, a TCP transcription factor, TCP10, was isolated from moso bamboo (Phyllostachys edulis), and its expression level was induced under drought and abscisic acid (ABA)-treatment conditions. A distinct role in regulating drought-stress responses was identified. PeTCP10 conferred drought tolerance of transgenic Arabidopsis and rice as determined through phenotypic and stress-associated physiological indicators analysis, including relative water content, root growth, survival rate, germination rate, as well as malondialdehyde content. Additionally, ABA sensitivity decreased in transgenic Arabidopsis and rice compared with wild-type plants; over-expressing PeTCP10 in Arabidopsis promoted stomatal closure under ABA-treatment conditions, and ABA accumulated was non-significant difference between transgenic and wild-type Arabidopsis under drought condition. PeTCP10 inhibited lateral root growth via Me-JA (Methyl jasmonate) dependent pathway, while increasing taproot growth under continuous mannitol treatments during the seedling stage in transgenic Arabidopsis. RNA-sequencing revealed that PeTCP10 regulated the expression of a wide spectrum of stress-responsive DEGs. Yeast one hybrid and EMSA assays showed that stress-/ABA-responsive gene BT2 was the directly target gene of PeTCP10. Thus, PeTCP10 may have positive regulatory functions in the drought tolerance of plants through an ABA-dependent signaling pathway and negative in lateral root growth via Me-JA mediated pathway.

Class-I TCP Transcription Factors Activate the SAUR63 Gene Subfamily in Gibberellin-Dependent Stamen Filament Elongation.

In autogamous plants like Arabidopsis (Arabidopsis thaliana), stamen filament elongation must be finely regulated to ensure that anthers reach the pistil at the correct developmental stage. In this work, we studied the roles of Arabidopsis TEOSINTE BRANCHED1, CYCLOIDEA, PCF15 (TCP15), and related class-I TCP transcription factors in stamen filament elongation. Plants with decreased expression of class-I TCPs and plants that express a fusion of TCP15 to a repressor domain (pTCP15::TCP15-EAR) had shorter stamens, indicating that class-I TCPs stimulate filament growth. These plants also showed reduced expression of several SMALL AUXIN UP RNA (SAUR)63 subfamily genes, which contain TCP target motifs in their promoters. Mutational analysis indicated that the TCP target motif in the SAUR63 promoter is required for expression of SAUR63 in stamen filaments. Moreover, TCP15 directly binds to the SAUR63 promoter region that contains the TCP target motif in vivo, highlighting the role of the TCPs in this process. Class-I TCPs are also required for the induction of SAUR63 subfamily genes by gibberellins (GAs). In addition, overexpression of SAUR63 restores filament growth in pTCP15::TCP15-EAR plants, whereas overexpression of TCP15 rescues the short stamen phenotype of GA-deficient plants. The results indicate that TCP15 and related class-I TCPs modulate GA-dependent stamen filament elongation by direct activation of SAUR63 subfamily genes through conserved target sites in their promoters. This work provides insight into GA-dependent stamen filament elongation.

Homozygous Mutant Construction and Function Analysis of TCP Transcription Factor StBRC1a in Diploid Potato

Homozygous Mutant Construction and Function Analysis of TCP Transcription Factor StBRC1a in Diploid Potato

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots.

Plant iron deficiency (-Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loop-helix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other -Fe-induced genes are FIT independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression clustering, we identified over 100 putative CREs (pCREs) that predicted -Fe-induced gene expression in computational models. To assess pCRE properties and possible functions, we used large-scale in vitro TF binding data, positional bias, and evolutionary conservation. As one example, our approach uncovered pCREs resembling IDE1 (iron deficiency-responsive element 1), a known grass -Fe response CRE. Arabidopsis IDE1-likes were associated with FIT-dependent gene expression, more specifically with biosynthesis of Fe-chelating compounds. Thus, IDE1 seems to be conserved in grass and nongrass species. Our pCREs matched among others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of -Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes that advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems.

Adaptive evolution and response to phytoplasma: A genome‐wide study of TCP transcription factors in Sesamum indicum L.

AbstractIntraspecific divergence study of TCP (teosinte branched [TB1], cycloidea [CYC] and proliferating cell factors [PCF]) transcription factors was conducted in Indian and Chinese varieties including landraces of sesame to understand the effects of breeding and adaptive selection on genomic architecture. The varieties included “Swetha,” a pedigree selection and “Zhongzhi‐13,” a space mutant; whereas the landraces studied were “Baizhima” and “Mishouzhima” adapted to widely different ecological niches. “Swetha” the Indian variety contained 33 TCP genes, including 14 Class‐I and 19 Class‐II genes, whereas “Zhongzhi‐13” the RefSeq variety contained 13 Class‐I and 15 Class‐II genes. Sixteen Class‐I genes and six CYC genes were common in both the landraces whereas an additional gene variant was found in “Baizhima.” Class‐II TCP genes were found more conserved within species while Class‐I genes differed widely within and across species. A cluster of 12 Class‐I genes was found unique to the Chinese genotypes, whereas two of the Class‐I genes in landrace “Baizhima” were found more similar to the Indian variety “Swetha” genes. A varied number of retrocopies and retropseudogenes were also found among Class‐I TCPs, due to insertion of TY1/Copia transposons. A number of active TY1/Copia retrotransposons containing “chimeric retrogenes” with multiple introns were discovered in sesame. One set involved “SiwTCP3” from “Swetha” and its homologues from the landraces with a mutation in the conserved Cys‐20 residue which abolished the redox sensitivity whereas the second set was present only in the landraces without the above mutation. None of the “Zhongzhi‐13” genes contained TY1/Copia insertions. Transposon insertions resulted in heavy methylation of unique genes in “Swetha” while methylation spread was noticed in the upstream and downstream regulatory regions. Although CIN‐TCPs were established as preferred binding partners of phytoplasma effectors, we found many mutations in the functional domains which altered the protein folding mechanisms among the protein homologues, with one set reported unique in the Chinese varieties. More duplication was noted in the CIN‐TCP's of “Swetha” whereas multiple exons and exon fusions resulted in the acquisition of novel functions for sesame TCP genes. The insertions, deletions and the duplications acquired through genome evolution under marginal environment conditions altered the binding abilities of CIN‐TCP transcription factors which ultimately resulted in variable response to sesame phyllody caused by phytoplasma.

Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato.

Viroids are small, non-protein-coding RNAs which can induce disease symptoms in a variety of plant species. Potato (Solanum tuberosum L.) is the natural host of Potato spindle tuber viroid (PSTVd) where infection results in stunting, distortion of leaves and tubers and yield loss. Replication of PSTVd is accompanied by the accumulation of viroid-derived small RNAs (sRNAs) proposed to play a central role in disease symptom development. Here we report that PSTVd sRNAs direct RNA silencing in potato against StTCP23, a member of the TCP (teosinte branched1/Cycloidea/Proliferating cell factor) transcription factor family genes that play an important role in plant growth and development as well as hormonal regulation, especially in responses to gibberellic acid (GA). The StTCP23 transcript has 21-nucleotide sequence complementarity in its 3ʹ untranslated region with the virulence-modulating region (VMR) of PSTVd strain RG1, and was downregulated in PSTVd-infected potato plants. Analysis using 3ʹ RNA ligase-mediated rapid amplification of cDNA ends (3ʹ RLM RACE) confirmed cleavage of StTCP23 transcript at the expected sites within the complementarity with VMR-derived sRNAs. Expression of these VMR sRNA sequences as artificial miRNAs (amiRNAs) in transgenic potato plants resulted in phenotypes reminiscent of PSTVd-RG1-infected plants. Furthermore, the severity of the phenotypes displayed was correlated with the level of amiRNA accumulation and the degree of amiRNA-directed down-regulation of StTCP23. In addition, virus-induced gene silencing (VIGS) of StTCP23 in potato also resulted in PSTVd-like phenotypes. Consistent with the function of TCP family genes, amiRNA lines in which StTCP23 expression was silenced showed a decrease in GA levels as well as alterations to the expression of GA biosynthesis and signaling genes previously implicated in tuber development. Application of GA to the amiRNA plants minimized the PSTVd-like phenotypes. Taken together, our results indicate that sRNAs derived from the VMR of PSTVd-RG1 direct silencing of StTCP23 expression, thereby disrupting the signaling pathways regulating GA metabolism and leading to plant stunting and formation of small and spindle-shaped tubers.

Evolution and expression of genes encoding TCP transcription factors in Solanum tuberosum reveal the involvement of StTCP23 in plant defence

BackgroundThe plant-specific Teosinte branched1/Cycloidea/Proliferating cell factor (TCP) family of transcription factors is involved in the regulation of cell growth and proliferation, performing diverse functions in plant growth and development. In addition, TCP transcription factors have recently been shown to be targets of pathogenic effectors and are likely to play a vital role in plant immunity. No comprehensive analysis of the TCP family members in potato (Solanum tuberosum L.) has been undertaken, however, and whether their functions are conserved in potato remains unknown.ResultsTo assess TCP gene evolution in potato, we identified TCP-like genes in several publicly available databases. A total of 23 non-redundant TCP transcription factor-encoding genes were identified in the potato genome and subsequently subjected to a systematic analysis that included determination of their phylogenetic relationships, gene structures and expression profiles in different potato tissues under basal conditions and after hormone treatments. These assays also confirmed the function of the class I TCP StTCP23 in the regulation of plant growth and defence.ConclusionsThis is the first genome-wide study including a systematic analysis of the StTCP gene family in potato. Identification of the possible functions of StTCPs in potato growth and defence provides valuable information for our understanding of the classification and functions of the TCP genes in potato.

Evolutionary Conservation of the Orchid MYB Transcription Factors DIV, RAD, and DRIF.

The MYB transcription factors DIVARICATA (DIV), DIV-and-RAD-Interacting-Factor (DRIF), and the small interfering peptide RADIALIS (RAD) can interact, forming a regulatory module that controls different plant developmental processes. In the snapdragon Antirrhinum majus, this module, together with the TCP transcription factor CYCLOIDEA (CYC), is responsible for the establishment of floral dorsoventral asymmetry. The spatial gene expression pattern of the OitDIV, OitDRIF, and OitRAD homologs of Orchis italica, an orchid with zygomorphic flowers, has suggested a possible conserved role of these genes in bilateral symmetry of the orchid flower. Here, we have identified four DRIF genes of orchids and have reconstructed their genomic organization and evolution. In addition, we found snapdragon transcriptional cis-regulatory elements of DIV and RAD loci generally conserved within the corresponding orchid orthologues. We have tested the biochemical interactions among OitDIV, OitDRIF1, and OitRAD of O. italica, showing that OitDRIF1 can interact both with OitDIV and OitRAD, whereas OitDIV and OitRAD do not directly interact, as in A. majus. The analysis of the quantitative expression profile of these MYB genes revealed that in zygomorphic orchid flowers, the DIV, DRIF1, and RAD transcripts are present at higher levels in the lip than in lateral inner tepals, whereas in peloric orchid flowers they show similar expression levels. These results indicate that MYB transcription factors could have a role in shaping zygomorphy of the orchid flower, potentially enriching the underlying orchid developmental code.

Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

BackgroundThe plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development.ResultsA total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses.ConclusionsOur study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature

ABSTRACTPeiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (Oryza sativa L.). Micro-RNAs are 21–24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.