Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box

ACRE, a class of AP2/ERF transcription factors, activates the expression of sweet potato ß-amylase and sporamin genes through the sugar-responsible element CMSRE-1

Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and β-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.

Plant-TFClass: a structural classification for plant transcription factors

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.

The transcription factor NtERF13a enhances abiotic stress tolerance and phenylpropanoid compounds biosynthesis in tobacco

The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factors play multiple roles in modulating the biosynthesis of diverse specialized metabolites in response to various environmental stresses. ERF13 has been shown to participate in plant resistance to biotic stress as well as in repressing the synthesis of fatty acid. However, its full roles in regulating plant metabolism and stress resistance still remains to be further studied. In this study, we identified two NtERF genes from N. tabacum genome that belong to Ⅸa subgroup of ERF family. Over-expression and knock-out of NtERF13a showed that NtERF13a could enhance plant resistance to salt and drought stresses, as well as promoted the biosynthesis of chlorogenic acid (CGA), flavonoids, and lignin in tobacco. Transcriptome analysis between WT and NtERF13a-OE plants revealed 6 differentially expressed genes (DEGs) that encode enzymes catalyzing the key steps of phenylpropanoid pathway. Chromatin immunoprecipitation, Y1H, and Dual-Luc assays further clarified that NtERF13a could directly bind to the fragments containing GCC box or DRE element in the promoters of NtHCT, NtF3'H, and NtANS genes to induce the transcription of these genes. Knock-out of NtHCT, NtF3'H, or NtANS in the NtERF13a-OE background significantly repressed the increase of phenylpropanoid compound contents caused by over-expression of NtERF13a, indicating that the promotion of NtERF13a on the phenylpropanoid compound contents depends on the activity of NtHCT, NtF3'H, and NtANS. Our study demonstrated new roles of NtERF13a in promoting plant resistance to abiotic stresses, and provided a promising target for modulating the biosynthesis of phenylpropanoid compounds in tobacco.

JUL1, Ring-Type E3 Ubiquitin Ligase, Is Involved in Transcriptional Reprogramming for ERF15-Mediated Gene Regulation

JAV1-associated ubiquitin ligase 1 (JUL1) is a RING-type E3 ubiquitin ligase that catalyzes ubiquitination of JAV1, a jasmonate signaling repressor, in Arabidopsis thaliana in response to herbivore attack. Here we present a new insight into the nature of JUL1 as a multi-targeting enzyme for not only JAV1 but also transcription factors (TFs) screened using in vitro and in vivo protein interaction assays. Reporter assays using protoplasts showed that the JUL1-interacting TFs (JiTFs), including ERF15, bZIP53 and ORA59, were involved in transcriptional activation of jasmonate-responsive PDF1.2 and abscisic acid-responsive GEA6. Likewise, assays using mutant plants suggested that the 3 JiTFs were indeed responsible for transcriptional regulation of PDF1.2 and/or GEA6, and ERF15 and ORA59 were substantially responsible for the anti-herbivore trait. In vitro protein ubiqutination assays showed that JUL1 catalyzed ubiqutination of JAV1 but not any of the TFs. This was in accord with the finding that JUL1 abolished JAV1's interference with ERF15 function, according to the reporter assay. Moreover, of great interest is our finding that ERF15 but not bZIP53 or ORA59 serves as a scaffold for the JAV1/JUL1 system, indicating that there is narrow selectivity of the transcriptional reprogramming by the JAV1/JUL1 system.

Genome-wide identification of the TGA gene family in kiwifruit (Actinidia chinensis spp.) and revealing its roles in response to Pseudomonas syringae pv. actinidiae (Psa) infection

Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive disease of kiwifruit worldwide. Functional genes in response to Psa infection are needed, as they could be utilized to control disease. TGACG-binding transcription factor (TGA), as an essential regulator, involved in the process of plant against pathogens. However, the function of TGA regulators has not been reported in kiwifruit. It is unclear that whether TGA genes play a role in response to Psa infection. Here, we performed genome-wide screening and identified 13 TGA genes in kiwifruit. Phylogenetic analysis showed that 13 members of the AcTGA gene family could be divided into five groups. AcTGA proteins were mainly located in the nucleus, and significant differences were identified in their 3D structures. Segmental duplications promoted the expansion of the AcTGA family. Additionally, RNA-Seq and qRT-PCR revealed that four genes (AcTGA01/06/07/09) were tissue-specific and responsive to hormones at different levels. Subcellular localization showed that four proteins located in the nucleus, and among them, three (AcTGA01/06/07) had transcriptional activation activity. Lastly, transient overexpression proved that these three genes (AcTGA01/06/07) potentially played a role in the resistance to kiwifruit canker. These results provided a theoretical basis for revealing TGA involved in kiwifruit regulation against Psa.

Genome-wide Investigation and Expression Analysis of the AP2/ERF Family for Selection of Agarwood Related Genes in Aquilaria sinensis (Lour.) Gilg

Aquilaria sinensis is an important non-timber tree species for producing high-value agarwood, which is widely used as a traditional medicine and incense. Agarwood is the product of Aquilaria trees in response to injury and fungal infection. AP2/ERF transcription factors play important roles in plant stress responses and metabolite biosynthesis. In this study, 119 AsAP2/ERF genes were identified from the A. sinensis genome and divided into ERF, AP2, RAV and Soloist subfamilies. Their conserved motif, gene structure, chromosomal localization, and subcellular localization were characterized. A stress/defense-related ERF-associated amphiphilic repression (EAR) motif and an EDLL motif were identified. Moreover, 11 genes that were highly expressed in the agarwood layer in response to whole-tree agarwood induction technique (Agar-Wit) treatment were chosen, and their expression levels in response to MeJA, SA or salt treatment were further analyzed using qRT-PCR. Among the 11 genes, eight belonged to subgroup B-3. All 11 genes were significantly upregulated under salt treatment, while eight genes were significantly induced by both MeJA and SA. In addition, the gene clusters containing these upregulated genes on chromosomes were observed. The results obtained from this research not only provide useful information for understanding the functions of AP2/ERF genes in A. sinensis but also identify candidate genes and gene clusters to dissect their regulatory roles in agarwood formation for future research.

Elbaiomy R, Chen L, Wang Z, Jiao J, Zhu J, Zhou W, Chen B, Soaud SA, Abbas M, Lin N, El-Sappah AH. Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae)

FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family's evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene's functions should take note of the possible presence of various roles in other grass species.

Defense Strategies: The Role of Transcription Factors in Tomato-Pathogen Interaction

Simple Summary

Tomato is one of the most cultivated and economically important vegetable crops throughout the world. It is affected by a panoply of different pathogens that cause infectious diseases that reduce tomato yield and affect product quality, with the most common symptoms being wilts, leaf spots/blights, fruit spots, and rots. To survive, tomato, as other plants, have developed elaborate defense mechanisms against plant pathogens. Among several genes already identified in tomato response to pathogens, we highlight those encoding the transcription factors (TFs). TFs are regulators of gene expression and are involved in large-scale biological phenomena. Here, we present an overview of recent studies of tomato TFs regarding defense responses to pathogen attack, selected for their abundance, importance, and availability of functionally well-characterized members. Tomato TFs’ roles and the possibilities related to their use for genetic engineering in view of crop breeding are presented.

Abstract

Tomato, one of the most cultivated and economically important vegetable crops throughout the world, is affected by a panoply of different pathogens that reduce yield and affect product quality. The study of tomato–pathogen system arises as an ideal system for better understanding the molecular mechanisms underlying disease resistance, offering an opportunity of improving yield and quality of the products. Among several genes already identified in tomato response to pathogens, we highlight those encoding the transcription factors (TFs). TFs act as transcriptional activators or repressors of gene expression and are involved in large-scale biological phenomena. They are key regulators of central components of plant innate immune system and basal defense in diverse biological processes, including defense responses to pathogens. Here, we present an overview of recent studies of tomato TFs regarding defense responses to biotic stresses. Hence, we focus on different families of TFs, selected for their abundance, importance, and availability of functionally well-characterized members in response to pathogen attack. Tomato TFs’ roles and possibilities related to their use for engineering pathogen resistance in tomato are presented. With this review, we intend to provide new insights into the regulation of tomato defense mechanisms against invading pathogens in view of plant breeding.