Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter

The OsZHD1 and OsZHD2, Two Zinc Finger Homeobox Transcription Factor, Redundantly Control Grain Size by Influencing Cell Proliferation in Rice

Grain size is vital determinant for grain yield and quality, which specified by its three-dimensional structure of seeds (length, width and thickness). The ZINC FINGER-HOMEODOMAIN (ZHD) proteins play critical roles in plant growth and development. However, the information regarding the function in reproductive development of ZHD proteins is scarce. Here, we deeply characterized the phenotype of oszhd1, oszhd2, and oszhd1oszhd2. The single mutants of OsZHD1/2 were similar with wild type. Nevertheless, the double mutant displayed dwarfism and smaller reproductive organs, and shorter, narrower, and thinner grain size. oszhd1oszhd2 revealed a significant decrease in total cell length and number, and single cell width in outer parenchyma; reducing the average width of longitudinal epidermal cells, but the length were increased in outer and inner glumes of oszhd1oszhd2 compared with wild-type, oszhd1-1, oszhd2-1, respectively. OsZHD1 and OsZHD2 encoded the nucleus protein and were distributed predominately in stem and the developing spikelets, asserting their roles in grain size. Meanwhile, yeast two-hybrid, bimolecular fluorescence complementation, and Co-immunoprecipitation assay clarified that OsZHD1 could directly interacted with OsZHD2. The differential expression analysis showed that 839 DEGs, which were down-regulated in oszhd1oszhd2 than wild type and single mutants, were mainly enriched in secondary metabolite biosynthetic, integral component of membrane, and transporter activity pathway. Moreover, it is reliable that the altered expression of cell cycle and expansion-related and grain size-related genes were observed in RNA-seq data, highly consistent with the qRT-PCR results. Altogether, our results suggest that OsZHD1/2 are functional redundancy and involved in regulating grain size by influencing cell proliferation in rice.

The members of zinc finger-homeodomain (ZF-HD) transcription factors are associated with abiotic stresses in soybean: insights from genomics and expression analysis

BACKGROUND

Zinc finger homeodomain (ZF-HD) belongs to the plant-specific transcription factor (TF) family and is widely involved in plant growth, development and stress responses. Despite their importance, a comprehensive identification and analysis of ZF-HD genes in the soybean (Glycine max) genome and their possible roles under abiotic stress remain unexplored.

RESULTS

In this study, 51 ZF-HD genes were identified in the soybean genome that were unevenly distributed on 17 chromosomes. All GmZF-HD genes contained a conserved ZF-HD_dimer domain and had diverse physicochemical features. Furthermore, the GmZF-HD gene structures exhibited 3 to 10 conserved motifs, and most of them showed intronless gene structures. Phylogenetic analysis categorized them into eight major groups with the highest closeness to dicots including Brassica rapa and Malus domestica. The cis-element analysis recognized plant growth and development (10%), phytohormones (31%) and stress-responsive (59%) elements. Synteny analysis identified 73 segmental and 1 tandem duplicated genes that underwent purifying selection. The collinearity analysis revealed that GmZF-HD genes showed higher homology with dicot species, indicating common ancestors with close evolutionary relationships. A total of 94 gma-miRNAs from 41 diverse miRNA families were identified, targeting 40 GmZF-HD genes, with GmZF-HD6 being most targeted by 7 miRNAs, and gma-miR4993 emerging as the dominant miRNA family. Different TFs including ERF, LBD, BBR-BPC and MYB, etc., were predicted in all 51 GmZF-HD genes upstream regions and visualized in the network. Expression profiling through RNA-Seq showed diverse expressions of GmZF-HD genes in different tissues including seeds, roots, shoots and leaves under diverse conditions. Further, the qRT-PCR analysis demonstrated that all tested GmZF-HD genes were significantly induced in soybean leaves, mainly the GmZF-HD5/6/13/39 and GmZF-HD45 genes were significantly upregulated (2.5 to 8.8 folds) under the tested stress treatments compared to control, highlighting their potential roles in response to stresses in soybean.

CONCLUSION

Overall, this study reveals comprehensive insights into the ZF-HD genes in soybeans and provides a valuable contribution towards functional studies for soybean improvement under stress conditions.

ZF-HD gene family in rapeseed (Brassica napus L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

BACKGROUND

The zinc finger-homeodomain (ZF-HD) transcription factor family is widely involved in regulating plant growth and fruit filling, as well as responding to various abiotic stress. Rapeseed (Brassica napus L.), the second largest oil-producing crop in the world, is an annual or biennial herb of Brassica in Cruciferae. However, there is currently no systematic study on the evolutionary relationship and stress response of ZF-HD transcription factors in rapeseed.

RESULTS

In this study, 60 ZF-HD genes in B. napus (BnZHDs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these BnZHD genes were systematically analyzed. These 60 BnZHD members were divided into seven groups. According to the phylogenetic tree and repetitive events, subfamilies MIF, and V may have undergone stronger expansions during the evolutionary process. Interestingly, segmental duplications may have a more important contribution, which distinguishes them from other dicotyledon plants. To further investigate the evolutionary relationship of the ZF-HD family, we constructed eleven comparative genomic maps of homologous genes between rapeseed and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression pattern of 15 BnZHD genes from different subfamilies under different tissues, fruit developmental stages, and different abiotic stress were analyzed. The expression profile from real-time quantitative PCR analysis showed different expression patterns of BnZHD gene in B. napus. We found that certain BnZHD genes are preferentially expressed in specific tissues of B. napus, while most genes are expressed in multiple tissues. For example, BnZHD37, BnZHD53, and BnZHD55 may be sensitive to different hormones. Under different stresses, the expression of BnZHD3, BnZHD4, BnZHD7, BnZHD38, BnZD45, and BnZHD53 significantly increased in roots, stems, and leaves within 24 h. These genes may play important roles in the growth, development, and environmental adaptation of rapeseed.

CONCLUSIONS

These findings provide a basis for a comprehensive understanding of the ZF-HD family in rapeseed, which will provide information for further research on the functional characteristics of the BnZHD genes.

Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance

The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.

GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton

Fusarium wilt (FW) is widespread in global cotton production, but the mechanism underlying FW resistance in superior-fiber-quality Sea Island cotton is unclear. This study reveals that FW resistance has been the target of genetic improvement of Sea Island cotton in China since the 2010s. The key nonsynonymous single nucleotide polymorphism (SNP, T/C) of gene Gbar_D03G001670 encoding protein phosphatase 2C 80 (PP2C80) results in an amino acid shift (L/S), which is significantly associated with FW resistance of Sea Island cotton. Silencing GbPP2C80 increases FW resistance in Sea Island cotton, whereas overexpressing GbPP2C80 reduces FW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 exist synergistically in Sea Island cotton accessions with haplotype forms "susceptible-susceptible" (TA) and "resistant-resistant" (CC), and interact with each other. CRISPR/Cas9-mediated knockout of GbWAKL14 enhances FW and Verticillium wilt (VW) resistance in upland cotton and overexpression of GbWAKL14 and GbPP2C80 weakens FW and VW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 respond to FW and VW by modulating reactive oxygen species (ROS) content via affecting MPK3 expression. In summary, two tandem genes on chromosome D03, GbPP2C80, and GbWAKL14, functions as cooperative negative regulators in cotton wilt disease defense, providing novel genetic resources and molecular markers for the development of resistant cotton cultivars.

Systematic Analysis of Zinc Finger-Homeodomain Transcription Factors (ZF-HDs) in Barley (Hordeum vulgare L.)

Zinc finger-homeodomain transcription factors (ZF-HDs) are pivotal in regulating plant growth, development, and diverse stress responses. In this study, we found 8 ZF-HD genes in barley genome. Theses eight HvZF-HD genes were located on five chromosomes, and classified into ZHD and MIF subfamily. The collinearity, gene structure, conserved motif, and cis-elements of HvZF-HD genes were also analyzed. Real-time PCR results suggested that the expression of HvZF-HD4, HvZF-HD6, HvZF-HD7 and HvZF-HD8 were up-regulated after hormones (ABA, GA3 and MeJA) or PEG treatments, especially HvZF-HD6 was significantly induced. These results provide useful information of ZF-HD genes to future study aimed at barley breeding.

Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Cucumber (Cucumis sativus L.): Identification, Evolution, Expression Profiles, and Function under Abiotic Stresses

Cucumber (Cucumis sativus L.) is a globally prevalent and extensively cultivated vegetable whose yield is significantly influenced by various abiotic stresses, including drought, heat, and salinity. Transcription factors, such as zinc finger-homeodomain proteins (ZHDs), a plant-specific subgroup of Homeobox, play a crucial regulatory role in stress resistance. In this study, we identified 13 CsZHDs distributed across all six cucumber chromosomes except chromosome 7. Phylogenetic analysis classified these genes into five clades (ZHDI-IV and MIF) with different gene structures but similar conserved motifs. Collinearity analysis revealed that members of clades ZHD III, IV, and MIF experienced amplification through segmental duplication events. Additionally, a closer evolutionary relationship was observed between the ZHDs in Cucumis sativus (C. sativus) and Arabidopsis thaliana (A. thaliana) compared to Oryza sativa (O. sativa). Quantitative real-time PCR (qRT-PCR) analysis demonstrated the general expression of CsZHD genes across all tissues, with notable expression in leaf and flower buds. Moreover, most of the CsZHDs, particularly CsZHD9-11, exhibited varying responses to drought, heat, and salt stresses. Virus-induced gene silencing (VIGS) experiments highlighted the potential functions of CsZHD9 and CsZHD10, suggesting their positive regulation of stomatal movement and responsiveness to drought stress. In summary, these findings provide a valuable resource for future analysis of potential mechanisms underlying CsZHD genes in response to stresses.

The emerging functions of mini zinc finger (MIF) microproteins in seed plants: A minireview

Mini zinc fingers constitute a class of microproteins that appeared early in evolution and expanded in seeds plants. In this review, the phylogenetic history, the functions and the mode of action of Mini zinc fingers in plants are reported and discussed. It appears that mini zinc fingers play an important role in the control of plant development. They are involved in the control of cell division and expansion, in the switch between the determinate/indeterminate state of the meristems and in the regulation of vegetative growth and floral organ development. Their biochemical mode of action seems to be diverse. In some studies, it has been reported that mini zinc fingers can directly bind to DNA and activate target gene expression, whereas other studies have shown that they can interact with and inhibit the activity of specific zinc finger homeodomain transcription factors or act as adaptor proteins necessary to aggregate polymeric protein complexes corresponding to chromatin remodelling factors negatively regulating the expression of specific genes. The diversity of mode of action for mini zinc finger microproteins suggests a wider range of biological functions than what has been that described in the literature thus far, and their involvement in the response to biotic and abiotic stresses should be further investigated in future studies.

The apple transcription factor MdZF-HD11 regulates fruit softening by promoting Mdβ-GAL18 expression

Fruit ripening and the associated softening are major determinants of fruit quality and post-harvest shelf life. Although the mechanisms underlying fruit softening have been intensively studied, there are limited reports on the regulation of fruit softening in apples (Malus domestica). Here, we identified a zinc finger homeodomain transcription factor MdZF-HD11that trans-activates the promoter of Mdβ-GAL18, which encodes a pectin-degradation enzyme associated with cell wall metabolism. Both MdZF-HD11 and Mdβ-GAL18 genes were up-regulated by exogenous ethylene treatment and repressed by 1-methylcyclopropene treatment. Further experiments revealed that MdZF-HD11 binds directly to the Mdβ-GAL18 promoter and up-regulates its transcription. Moreover, using transgenic apple fruit calli, we found that overexpression of Mdβ-GAL18 or MdZF-HD11 significantly enhanced β-galactosidase activity, and overexpression of MdZF-HD11 induced the expression of Mdβ-GAL18. We also discovered that transient overexpression of Mdβ-GAL18 or MdZF-HD11 in 'Golden Delicious' apple significantly increased the release of ethylene, reduced fruit firmness, promoted the transformation of skin color from green to yellow, and accelerated ripening and softening of the fruit. Finally, the overexpression of MdZF-HD11 in tomato also promoted fruit softening. Collectively, these results indicate that ethylene-induced MdZF-HD11 interacts with Mdβ-GAL18 to promote the post-harvest softening of apple.

Genome-wide identification and expression analysis of the ZF-HD gene family in pea (Pisum sativum L.)

Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.

Investigating Grapevine Red Blotch Virus Infection in Vitis vinifera L. cv. Cabernet Sauvignon Grapes: A Multi-Omics Approach

Grapevine red blotch virus (GRBV) is a recently identified virus. Previous research indicates primarily a substantial impact on berry ripening in all varieties studied. The current study analyzed grapes’ primary and secondary metabolism across grapevine genotypes and seasons to reveal both conserved and variable impacts to GRBV infection. Vitis vinifera cv. Cabernet Sauvignon (CS) grapevines grafted on two different rootstocks (110R and 420A) were analyzed in 2016 and 2017. Metabolite profiling revealed a considerable impact on amino acid and malate acid levels, volatile aroma compounds derived from the lipoxygenase pathway, and anthocyanins synthesized in the phenylpropanoid pathway. Conserved transcriptional responses to GRBV showed induction of auxin-mediated pathways and photosynthesis with inhibition of transcription and translation processes mainly at harvest. There was an induction of plant-pathogen interactions at pre-veraison, for all genotypes and seasons, except for CS 110R in 2017. Lastly, differential co-expression analysis revealed a transcriptional shift from metabolic synthesis and energy metabolism to transcription and translation processes associated with a virus-induced gene silencing transcript. This plant-derived defense response transcript was only significantly upregulated at veraison for all genotypes and seasons, suggesting a phenological association with disease expression and plant immune responses.

Zinc Finger-Homeodomain and Mini Zinc Finger proteins are key players in plant growth and responses to environmental stresses

The ZINC FINGER-HOMEODOMAIN (ZHD) protein family is a plant-specific family of transcription factors containing two conserved motifs: a non-canonical C5H3 zinc finger domain (ZF) and a DNA-binding homeodomain (HD). The MINI ZINC FINGER (MIF) proteins belong to this family, but were possibly derived from the ZHDs by losing the HD. Information regarding the function of ZHD and MIF proteins is scarce. However, different studies have shown that ZHD/MIF proteins play important roles not only in plant growth and development, but also in response to environmental stresses, including drought and pathogen attack. Here we review recent advances relative to ZHD/MIF functions in multiple species, to provide new insights into the diverse roles of these transcription factors in plants. Their mechanism of action in relation to their ability to interact with other proteins and DNA is also discussed. We then propose directions for future studies to understand better their important roles and pinpoint strategies for potential applications in crop improvement.

Homeobox 27, a Homeodomain Transcription Factor, Confers Tolerances to CMV by Associating with Cucumber Mosaic Virus 2b Protein

Transcription factors (TFs) play an important role in plant development; however, their role during viral infection largely remains unknown. The present study was designed to uncover the role transcription factors play in Cucumber mosaic virus (CMV) infection. During the screening of an Arabidopsis thaliana (Col-0) transcription factor library, using the CMV 2b protein as bait in the yeast two-hybrid system, the 2b protein interacted with Homeobox protein 27 (HB27). HB27 belongs to the zinc finger homeodomain family and is known to have a regulatory role in flower development, and responses to biotic and abiotic stress. The interaction between CMV 2b and HB27 proteins was further validated using in planta (bimolecular fluorescence complementation assay) and in vitro far-Western blotting (FWB) methods. In the bimolecular fluorescence complementation assay, these proteins reconstituted YFP fluorescence in the nucleus and the cytoplasmic region as small fluorescent dots. In FWB, positive interaction was detected using bait anti-MYC antibody on the target HB27-HA protein. During CMV infection, upregulation (~3-fold) of the HB27 transcript was observed at 14 days post-infection (dpi) in A. thaliana plants, and expression declined to the same as healthy plants at 21 dpi. To understand the role of the HB27 protein during CMV infection, virus accumulation was determined in HB27-overexpressing (HB27 OE) and knockout mutants. In HB27-overexpressing lines, infected plants developed mild symptoms, accumulating a lower virus titer at 21 dpi compared to wild-type plants. Additionally, knockout HB27 mutants had more severe symptoms and a higher viral accumulation than wild-type plants. These results indicate that HB27 plays an important role in the regulation of plant defense against plant virus infection.

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance

Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.

Genome-wide investigation of the ZF-HD gene family in two varieties of alfalfa (Medicago sativa L.) and its expression pattern under alkaline stress

Background

Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of MsZF-HD genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analysis of the MsZF-HD gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1).

Results

In total, 49 and 11 MsZF-HD genes were identified in the two different varieties respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60 MsZF-HD genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of MsZF-HD genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as ZHD-X1–2, ZHD-X3–2 and ZHD-X4–2) have homologous genes in Arabidopsis thaliana, Medicago truncatula and Glycine max. Through RNA-seq and qRT–PCR verification, it was found that MsZF-HD genes are downregulated to participate in the alkaline stress response.

Conclusion

The results of this study may lay the foundation for the cloning and functional study of MsZF-HD genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08309-x.

Genome-Wide Investigation of the Zinc Finger-Homeodomain Family Genes Reveals Potential Roles in Apple Fruit Ripening

Zinc finger-homeodomain (ZF-HD) transcription factors play an important role in the regulation of plant growth and development, as well as the regulation of stress responses. Studies on the ZF-HD family genes have been conducted in many plants, however, the characteristics of this family in apple (Malus domestica) fruit remains to be poorly understood. In this study, we identified nineteen ZF-HD family genes in apple at the whole-genome scale, which were unevenly located on ten chromosomes. These MdZF-HD genes were phylogenetically divided into two subfamilies: zinc finger-homeodomain (ZHD) and MINI ZINC FINGER (MIF), and the ZHD subfamily was further classified into five groups (ZHDI–ZHDV). Analysis of the gene structures showed that most MdZF-HD genes lack introns. Gene expression analysis indicated that nine selected MdZF-HD genes were differentially responsive to 1-MCP (1-methylcyclopropene) treatment during the postharvest storage of “Qinguan” apple fruit. Moreover, the transcripts of six genes were further validated in “Golden Delicious” apple fruit, and five genes (MdZHD1/2/6/10/11) were significantly repressed and one gene (MdZHD7) was slightly induced by ethylene treatment. These results indicated that these six MdZF-HD genes may involve in the regulation of ethylene induced ripening process of postharvest apple fruit. These findings provide new clues for further functional investigation of ZF-HD genes, such as their roles in the regulation of fruit ripening.

SlZHD17 is involved in the control of chlorophyll and carotenoid metabolism in tomato fruit

Chlorophylls and carotenoids are essential and beneficial substances for both plant and human health. Identifying the regulatory network of these pigments is necessary for improving fruit quality. In a previous study, we identified an R2R3-MYB transcription factor, SlMYB72, that plays an important role in chlorophyll and carotenoid metabolism in tomato fruit. Here, we demonstrated that the SlMYB72-interacting protein SlZHD17, which belongs to the zinc-finger homeodomain transcription factor family, also functions in chlorophyll and carotenoid metabolism. Silencing SlZHD17 in tomato improved multiple beneficial agronomic traits, including dwarfism, accelerated flowering, and earlier fruit harvest. More importantly, downregulating SlZHD17 in fruits resulted in larger chloroplasts and a higher chlorophyll content. Dual-luciferase, yeast one-hybrid and electrophoretic mobility shift assays clarified that SlZHD17 regulates the chlorophyll biosynthesis gene SlPOR-B and chloroplast developmental regulator SlTKN2 in a direct manner. Chlorophyll degradation and plastid transformation were also retarded after suppression of SlZHD17 in fruits, which was caused by the inhibition of SlSGR1, a crucial factor in chlorophyll degradation. On the other hand, the expression of the carotenoid biosynthesis genes SlPSY1 and SlZISO was also suppressed and directly regulated by SlZHD17, which induced uneven pigmentation and decreased the lycopene content in fruits with SlZHD17 suppression at the ripe stage. Furthermore, the protein-protein interactions between SlZHD17 and other pigment regulators, including SlARF4, SlBEL11, and SlTAGL1, were also presented. This study provides new insight into the complex pigment regulatory network and provides new options for breeding strategies aiming to improve fruit quality.

Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis

ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses

Zinc finger-homeodomain transcriptional factors (ZF-HDs), a kind of plant-specific transcription factor, play important roles in plant growth, development and various stress responses. In this study, the genome-wide analysis of the ZF-HD gene family was performed in wheat. A total of 37 TaZF-HD genes were identified in T. aestivum and classified into six groups. The results of a synteny analysis showed that gene replication events contributed to the expansion of the TaZF-HD gene family. The TaZF-HD paralogous gene pairs with similar chromosomal locations in different subgenomes had similar expression patterns. TaZF-HDs were highly induced under PEG (polyethylene glycol), NaCl and cold stress but not induced under heat stress. Gene ontology (GO) annotation and protein-protein interactions suggested that TaZF-HD proteins may participate in various biological processes of plants. These results increase our understanding of ZF-HD genes and provide robust candidate genes for future functional investigations aimed at crop improvement.

Identification and Transcriptional Analysis of Zinc Finger-Homeodomain (ZF-HD) Family Genes in Cucumber

Zinc finger-homeodomain (ZF-HD) proteins encode a family of plant-specific transcription factors that play essential roles in regulating plant growth and development as well as responses to abiotic/biotic stresses by activating or repressing the target genes. In this study, genome-wide characterization and expression profiling of the ZF-HD gene family in cucumber (Cucumis sativus) were performed for the first time. By using bioinformatics approaches, a total of 13 ZF-HD genes (designated as CsMIF1-CsMIF3 and CsZHD1-CsZHD10) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. According to the phylogenetic analysis of cucumber and other species, they were divided into two distinct families, MINI ZINC FINGER (MIF) and zinc finger-homeodomain (ZHD), and the ZHD family was further divided into six subfamilies (ZHDI-ZHDVI). CsZF-HD members were mostly conserved in each subfamily with minor variations in motif distribution, and gene structure analysis showed that the CsZF-HD genes had only one intron or no intron at all. Expression analysis showed that most CsZF-HD genes had tissue-specific expression patterns, and some of them exhibited highly variable expression during fruit development. qRT-PCR results indicated that the selected CsZF-HD genes were responsive to drought stress, and some of them were differentially expressed in response to the inoculation of powdery mildew (PM) and downy mildew (DM) based on publicly available RNA-seq data. The results lay the foundation for further functional analysis of the ZF-HD genes and explore their potential application to the improvement of stress tolerance in cucumber.

Dissecting the Role of Promoters of Pathogen-sensitive Genes in Plant Defense

Plants inherently show resistance to pathogen attack but are susceptible to multiple bacteria, viruses, fungi, and phytoplasmas. Diseases as a result of such infection leads to the deterioration of crop yield. Several pathogen-sensitive gene activities, promoters of such genes, associated transcription factors, and promoter elements responsible for crosstalk between the defense signaling pathways are involved in plant resistance towards a pathogen. Still, only a handful of genes and their promoters related to plant resistance have been identified to date. Such pathogen-sensitive promoters are accountable for elevating the transcriptional activity of certain genes in response to infection. Also, a suitable promoter is a key to devising successful crop improvement strategies as it ensures the optimum expression of the required transgene. The study of the promoters also helps in mining more details about the transcription factors controlling their activities and helps to unveil the involvement of new genes in the pathogen response. Therefore, the only way out to formulate new solutions is by analyzing the molecular aspects of these promoters in detail. In this review, we provided an overview of the promoter motifs and cis-regulatory elements having specific roles in pathogen attack response. To elaborate on the importance and get a vivid picture of the pathogen-sensitive promoter sequences, the key motifs and promoter elements were analyzed with the help of PlantCare and interpreted with available literature. This review intends to provide useful information for reconstructing the gene networks underlying the resistance of plants against pathogens.

Zinc Finger-Homeodomain Genes: Evolution, Functional Differentiation, and Expression Profiling Under Flowering-Related Treatments and Abiotic Stresses in Plants

Zinc finger-homeodomain (ZHD) proteins constitute a plant-specific transcription factor family that play important roles in plant growth, development, and stress responses. In this study, we investigated a total of 10, 17, and 31 ZHD gene members in the peach, Arabidopsis, and apple genome, respectively. The phylogenetic tree divided the identified ZHD genes into 4 subfamilies based on their domain organization, gene structure, and motif distribution with minor variations. The ZHD gene family members were unevenly distributed throughout in apple, peach, and Arabidopsis genomes. Segmental duplication was observed for 14 pairs of genes in apple. Transcript analysis found that ZHD genes mostly expressed in various tissues, particularly in leaves and flowers. Moreover, the transcript of most ZHD genes was significantly affected at different time points in response to various flowering-related exogenous hormones (sugar, gibberellin [GA], and 6-benzylaminopurine [6-BA]), signifying their possible role in the flowering induction in apple. Furthermore, the transcripts of CaZHD6, CaZHD7, CaZHD3, and CaZHD8 have induced in response to abiotic stresses including heat, drought, salt, and cold, indicating their possible involvement in response to abiotic stresses. Our research work systemically presents the different roles of ZHD genes. We believe that this study will provide a platform for future functional characterization of ZHD genes and to deeply unfold their roles in the regulation of flowering induction in plants.

Genome-wide investigation of the ZF-HD gene family in Tartary buckwheat (Fagopyrum tataricum)

BACKGROUND

ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana, florescence advance, the seeds get bigger and the life span of seeds is prolonged, moreover, ZF-HD genes are also participate in responding to adversity stress. The whole genome of the ZF-HD gene family has been studied in several model plants, such as Arabidopsis thaliana and rice. However, there has been little research on the ZF-HD genes in Tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of Tartary buckwheat allows us to study the tissue and expression profiles of the ZF-HD gene family in Tartary buckwheat on a genome-wide basis.

RESULTS

In this study, the whole genome and expression profile of the ZF-HD gene family were analyzed for the first time in Tartary buckwheat. We identified 20 FtZF-HD genes and divided them into MIF and ZHD subfamilies according to phylogeny. The ZHD genes were divided into 5 subfamilies. Twenty FtZF-HD genes were distributed on 7 chromosomes, and almost all the genes had no introns. We detected seven pairs of chromosomes with fragment repeats, but no tandem repeats were detected. In different tissues and at different fruit development stages, the FtZF-HD genes obtained by a real-time quantitative PCR analysis showed obvious expression patterns.

CONCLUSIONS

In this study, 20 FtZF-HD genes were identified in Tartary buckwheat, and the structures, evolution and expression patterns of the proteins were studied. Our findings provide a valuable basis for further analysis of the biological function of the ZF-HD gene family. Our study also laid a foundation for the improvement of Tartary buckwheat crops.

Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut

In previous studies, a sorghum mini core collection was scored over several years for response to Colletotrichum sublineola, Peronosclerospora sorghi, and Sporisorium reilianum, the causal agents of the disease anthracnose, downy mildew, and head smut, respectively. The screening results were combined with over 290,000 Single nucleotide polymorphic (SNP) loci from an updated version of a publicly available genotype by sequencing (GBS) dataset available for the mini core collection. GAPIT (Genome Association and Prediction Integrated Tool) R package was used to identify chromosomal locations that differ in disease response. When the top scoring SNPs were mapped to the most recent version of the published sorghum genome, in each case, a nearby and most often the closest annotated gene has precedence for a role in host defense.

Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development

Zinc finger-homeodomain (ZHD) genes encode a family of plant-specific transcription factors that not only participate in the regulation of plant growth and development but also play an important role in the response to abiotic stress. The ZHD gene family has been studied in several model plants, including Solanum lycopersicum, Zea mays, Oryza sativa, and Arabidopsis thaliana. However, a comprehensive study of the genes of the ZHD family and their roles in fiber development and pigmentation in upland cotton has not been completed. To address this gap, we selected a brown fiber cultivar for our study; brown color in cotton is one of the most desired colors in the textile industry. The natural colored fibers require less processing and little dying, thereby eliminating dye costs and chemical residues. Using bioinformatics approaches, we identified 37 GhZHD genes from Gossypium hirsutum and then divided these genes into seven groups based on their phylogeny. The GhZHD genes were mostly conserved in each subfamily with minor variations in motif distribution and gene structure. These genes were largely distributed on 19 of the 26 upland cotton chromosomes. Among the Gossypium genomes, the paralogs and orthologs of the GhZHD genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in Gossypium genomes (G. hirsutum, G. arboreum, and G. raimondii) were probably derived from segmental duplication or genome-wide duplication (GWD) events. Through a combination of qRT-PCR and proanthocyanidins (PA) accumulation analyses in brown cotton fibers, we concluded that the candidate genes involved in early fiber development and fiber pigment synthesis include the following: GhZHD29, GhZHD35, GhZHD30, GhZHD31, GhZHD11, GhZHD27, GhZHD18, GhZHD15, GhZHD16, GhZHD22, GhZHD6, GhZHD33, GhZHD13, GhZHD5, and GhZHD23. This study delivers insights into the evolution of the GhZHD genes in brown cotton, serves as a valuable resource for further studies, and identifies the conditions necessary for improving the quality of brown cotton fiber.

Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato

Background

Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum).

Results

In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment.

Conclusion

Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4082-y) contains supplementary material, which is available to authorized users.

GmSBH1, a homeobox transcription factor gene, relates to growth and development and involves in response to high temperature and humidity stress in soybean

KEY MESSAGE

GmSBH1 involves in response to high temperature and humidity stress. Homeobox transcription factors are key switches that control plant development processes. Glycine max H1 Sbh1 (GmSBH1) was the first homeobox gene isolated from soybean. In the present study, the full ORF of GmSBH1 was isolated, and the encoded protein was found to be a typical class I KNOX homeobox transcription factor. Subcellular localization and transcriptional activation assays showed that GmSBH1 is a nuclear protein and possesses transcriptional activation activity in the homeodomain. The KNOX1 domain was found to play a clear role in suppressing the transcriptional activation activity of GmSBH1. GmSBH1 showed different expression levels among different soybean tissues and was involved in response to high temperature and humidity (HTH) stress in developing soybean seeds. The overexpression of GmSBH1 in Arabidopsis altered leaf and stoma phenotypes and enhanced seed tolerance to HTH stress. Overall, our results indicated that GmSBH1 is involved in growth, development, and enhances tolerance to pre-harvest seed deterioration caused by HTH stress in soybean.

Genome-wide identification, evolution and expression analysis of the grape (Vitis vinifera L.) zinc finger-homeodomain gene family

Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity.

Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice

Leaf rolling is receiving considerable attention as an important agronomic trait in rice (Oryza sativa L.). However, little has been known on the molecular mechanism of rice leaf rolling, especially the abaxial rolling. We identified a novel abaxially curled and drooping leaf-dominant mutant from a T₁ transgenic rice line. The abaxially curled leaf phenotypes, co-segregating with the inserted transferred DNA, were caused by overexpression of a zinc finger homeodomain class homeobox transcription factor (OsZHD1). OsZHD1 exhibited a constitutive expression pattern in wild-type plants and accumulated in the developing leaves and panicles. Artificial overexpression of OsZHD1 or its closest homolog OsZHD2 induced the abaxial leaf curling. Histological analysis indicated that both the increased number and the abnormal arrangement of bulliform cells in leaf were responsible for the abaxially curled leaves. We herein reported OsZHD1 with key roles in rice morphogenesis, especially in the modulating of leaf rolling, which provided a novel insight into the molecular mechanism of leaf development in rice.

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola

Background

Five-needle pines are important forest species that have been devastated by white pine blister rust (WPBR, caused by Cronartium ribicola) across North America. Currently little transcriptomic and genomic data are available to understand molecular interactions in the WPBR pathosystem.

Results

We report here RNA-seq analysis results using Illumina deep sequencing of primary needles of western white pine (Pinus monticola) infected with WPBR. De novo gene assembly was used to generate the first P. monticola consensus transcriptome, which contained 39,439 unique transcripts with an average length of 1,303 bp and a total length of 51.4 Mb. About 23,000 P. monticola unigenes produced orthologous hits in the Pinus gene index (PGI) database (BLASTn with E values < e-100) and 6,300 genes were expressed actively (at RPKM ≥ 10) in the healthy tissues. Comparison of transcriptomes from WPBR-susceptible and -resistant genotypes revealed a total of 979 differentially expressed genes (DEGs) with a significant fold change > 1.5 during P. monticola- C. ribicola interactions. Three hundred and ten DEGs were regulated similarly in both susceptible and resistant seedlings and 275 DEGs showed regulatory differences between susceptible and resistant seedlings post infection by C. ribicola. The DEGs up-regulated in resistant seedlings included a set of putative signal receptor genes encoding disease resistance protein homologs, calcineurin B-like (CBL)-interacting protein kinases (CIPK), F-box family proteins (FBP), and abscisic acid (ABA) receptor; transcriptional factor (TF) genes of multiple families; genes homologous to apoptosis-inducing factor (AIF), flowering locus T-like protein (FT), and subtilisin-like protease. DEGs up-regulated in resistant seedlings also included a wide diversity of down-stream genes (encoding enzymes involved in different metabolic pathways, pathogenesis-related -PR proteins of multiple families, and anti-microbial proteins). A large proportion of the down-regulated DEGs were related to photosystems, the metabolic pathways of carbon fixation and flavonoid biosynthesis.

Conclusions

The novel P. monticola transcriptome data provide a basis for future studies of genetic resistance in a non-model, coniferous species. Our global gene expression profiling presents a comprehensive view of transcriptomic regulation in the WPBR pathosystem and yields novel insights on molecular and biochemical mechanisms of disease resistance in conifers.

Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics

The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger accumulation of signal molecules, including calcium, H2O2, NO, and sugars, in the resistant than in the susceptible cultivar in response to the infection. Additionally, 31 proteins and 5 phosphoproteins from the pathogen were identified, including metabolic proteins and signaling proteins such as GTP-binding proteins, 14-3-3 proteins, and calcium-binding proteins. Quantitative PCR analysis showed the expression of fungal signaling genes and genes encoding a superoxide dismutase and cell-wall degrading enzymes. These results indicate roles of signaling, antioxidative stress mechanisms, and nutrient acquisition in facilitating the initial symptomless growth. Taken in its entirety, our dataset suggests interplay between the plant and S. tritici through complex signaling networks and downstream molecular events. Resistance is likely related to several rapidly and intensively triggered signal transduction cascades resulting in a multiple-level activation of transcription and translation processes of defense responses. Our sensitive approaches and model provide a comprehensive (phospho)proteomics resource for studying signaling from the point of view of both host and pathogen during a plant-pathogen interaction.

The transcriptional repressor activity of ASYMMETRIC LEAVES1 is inhibited by direct interaction with calmodulin in Arabidopsis

Calmodulin (CaM), a key Ca2+ sensor, regulates diverse cellular processes by modulating the activity of a variety of enzymes and proteins. However, little is known about the biological function of CaM in plant development. In this study, an ASYMMETRIC LEAVES1 (AS1) transcription factor was isolated as a CaM-binding protein. AS1 contains two putative CaM-binding domains (CaMBDs) at the N-terminus. Using domain mapping analysis, both predicted domains were identified as authentic Ca2+ -dependent CaMBDs. We identified three hydrophobic amino acid residues for CaM binding, Trp49 in CaMBDI, and Trp81 and Phe103 in CaMBDII. The interactions of AS1 with CaM were verified in yeast and plant cells. Based on electrophoretic mobility shift assays, CaM inhibited the DNA-binding activity of the AS1/AS2 complex to two cis-regulatory motifs in the KNAT1 promoter. Furthermore, CaM relieved the suppression of KNAT1 transcription by AS1 not only in transient expression assays of protoplasts but also by the overexpression of a CaM-binding negative form of AS1 in as1 mutant plant. Our study suggests that CaM, a calcium sensor, can be involved in the transcriptional control of meristem cell-specific genes by the inhibition of AS1 under the condition of higher levels of Ca2+ in plants.

Activation of camalexin biosynthesis in Arabidopsis thaliana in response to perception of bacterial lipopolysaccharides: a gene-to-metabolite study

Lipopolysaccharides (LPS), as lipoglycan microbe-associated molecular pattern molecules, trigger activation of signal transduction pathways involved in defence that generate an enhanced defensive capacity in plants. The transcriptional regulation of the genes for tryptophan synthase B, TSB1, and the cytochrome P450 monooxygenases CYP79B2 and CYP71B15, involved in the camalexin biosynthetic pathway, were investigated in response to LPS treatment. GUS-reporter assays for CYP71B15 and CYP79B2 gene promoter activation were performed on transgenic plants and showed positive histochemical staining in response to LPS treatment, indicating activation of the promoters. Quantitative PCR revealed that transcripts of TSB1, CYP79B2 and CYP71B15 exhibited differential, transient up-regulation. TSB1 transcript levels were up-regulated between 6 and 9 h after LPS-induction, while CYP71B15 and CYP79B2 both exhibited maxima at 12 h. To obtain information on the gene-to-metabolite network, the effect of the transcriptome changes on the metabolome was correlated to camalexin production. Increases in camalexin concentration were quantified by ultra pressure liquid chromatography-mass spectrometry and both absorbance spectra and elemental composition confirmed its identity. The concentrations increased from 0.03 to 3.7 μg g(-1) fresh weight over a 24-h time period, thus indicating that the up-regulation of the biosynthetic pathway in response to LPS was accompanied by a time-dependent increase in camalexin concentration. Metabolomic analysis through principal component analysis-derived scores plots revealed clusters of sample replicates for 0, 6, 12, 18 and 24 h while loadings plots for LPS data identified camalexin as a biomarker that clearly demonstrated the variability between samples.

Differential expression of miRNAs in response to topping in flue-cured tobacco (Nicotiana tabacum) roots

BACKGROUND

Topping is an important cultivating measure for flue-cured tobacco, and many genes had been found to be differentially expressed in response to topping. But it is still unclear how these genes are regulated. MiRNAs play a critical role in post-transcriptional gene regulation, so we sequenced two sRNA libraries from tobacco roots before and after topping, with a view to exploring transcriptional differences in miRNAs.

METHODOLOGY/PRINCIPAL FINDINGS

Two sRNA libraries were generated from tobacco roots before and after topping. Solexa high-throughput sequencing of tobacco small RNAs revealed a total of 12,104,207 and 11,292,018 reads representing 3,633,398 and 3,084,102 distinct sequences before and after topping. The expressions of 136 conserved miRNAs (belonging to 32 families) and 126 new miRNAs (belonging to 77 families) were determined. There were three major conserved miRNAs families (nta-miR156, nta-miR172 and nta-miR171) and two major new miRNAs families (nta-miRn2 and nta-miRn26). All of these identified miRNAs can be folded into characteristic miRNA stem-loop secondary hairpin structures, and qRT-PCR was adopted to validate and measure the expression of miRNAs. Putative targets were identified for 133 out of 136 conserved miRNAs and 126 new miRNAs. Of these miRNAs whose targets had been identified, the miRNAs which change markedly (>2 folds) belong to 53 families and their targets have different biological functions including development, response to stress, response to hormone, N metabolism, C metabolism, signal transduction, nucleic acid metabolism and other metabolism. Some interesting targets for miRNAs had been determined.

CONCLUSIONS/SIGNIFICANCE

The differential expression profiles of miRNAs were shown in flue-cured tobacco roots before and after topping, which can be expected to regulate transcripts distinctly involved in response to topping. Further identification of these differentially expressed miRNAs and their targets would allow better understanding of the regulatory mechanisms for flue-cured tobacco response to topping.

Competitive inhibition of transcription factors by small interfering peptides

Combinatorial assortment by dynamic dimer formation diversifies gene transcriptional specificities of transcription factors. A similar but biochemically distinct mechanism is competitive inhibition in which small proteins act as negative regulators by competitively forming nonfunctional heterodimers with specific transcription factors. The most extensively studied is the negative regulation of auxin response factors by AUXIN/INDOLE-3-ACETIC ACID repressors. Similarly, Arabidopsis thaliana (Arabidopsis) little zipper and mini finger proteins act as competitive inhibitors of target transcription factors. Competitive inhibitors are also generated by alternative splicing and controlled proteolytic processing. Because they provide a way of attenuating transcription factors we propose to call them small interfering peptides (siPEPs). The siPEP-mediated strategy could be applied to deactivate specific transcription factors in crop plants.

Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability

• Reduced oxygen availability is not only associated with flooding, but occurs also during growth and development. It is largely unknown how hypoxia is perceived and what signaling cascade is involved in activating adaptive responses. • We analysed the expression of over 1900 transcription factors (TFs) and 180 microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots exposed to different hypoxic conditions by means of quantitative PCR. We also analysed the promoters of genes induced by hypoxia with respect to over-represented DNA elements that can act as potential TF binding sites and their in vivo interaction was verified. • We identified various subsets of TFs that responded differentially through time and in an oxygen concentration-dependent manner. The regulatory potential of selected TFs and their predicted DNA binding elements was validated. Although the expression of pri-miRNAs was differentially regulated under hypoxia, only one corresponding mature miRNA changed accordingly. Putative target transcripts of the miRNAs were not significantly affected. • Our results show that the regulation of hypoxia-induced genes is controlled via simultaneous interaction of various combinations of TFs. Under anoxic conditions, an additional set of TFs is induced. Regulation of gene expression via miRNAs appears to play a minor role during hypoxia.

A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution

Transcription factors (TFs) play key roles in the regulation of gene expression by binding in a sequence-specific manner to genomic DNA. In eukaryotes, DNA binding is achieved by a wide range of structural forms and motifs. TFs are typically classified by their DNA-binding domain (DBD) type. In this chapter, we catalogue and survey 91 different TF DBD types in metazoa, plants, fungi, and protists. We briefly discuss well-characterized TF families representing the major DBD superclasses. We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization.

Nuclear import and DNA binding of the ZHD5 transcription factor is modulated by a competitive peptide inhibitor in Arabidopsis

Competitive inhibition of transcription factors by small proteins is an intriguing component of gene regulatory networks in both animals and plants. The small interfering proteins possess limited sequence homologies to specific transcription factors but lack one or more protein motifs required for transcription factor activities. They interfere with the activities of transcription factors, such as DNA binding and transcriptional activation, by forming nonfunctional heterodimers. A potential example is the Arabidopsis MIF1 (mini zinc finger 1) protein consisting of 101 residues. It has a zinc finger domain but lacks other protein motifs normally present in transcription factors. In this work, we show that MIF1 and its functional homologues physically interact with a group of zinc finger homeodomain (ZHD) transcription factors, such as ZHD5, that regulate floral architecture and leaf development. Gel mobility shift assays revealed that MIF1 blocks the DNA binding activity of ZHD5 homodimers by competitively forming MIF1-ZHD5 heterodimers. Accordingly, the transcriptional activation activity of ZHD5 was significantly suppressed by MIF1 coexpressed transiently in Arabidopsis protoplasts. Notably, MIF1 also prevents ZHD5 from nuclear localization. Although ZHD5 was localized exclusively in the nucleus, it was scattered throughout the cytoplasm when MIF1 was coexpressed. Transgenic plants overexpressing the ZHD5 gene (35S:ZHD5) exhibited accelerated growth with larger leaves. Consistent with the negative regulation of ZHD5 by MIF1, the 35S:ZHD5 phenotypes were diminished by MIF1 coexpression. These observations indicate that MIF1 regulates the ZHD5 activities in a dual step manner: nuclear import and DNA binding.

Specificity of DNA sequences recognized by the zinc-finger homeodomain protein, GmZF-HD1 in soybean

Zinc finger-homeodomain proteins (ZF-HDs) have been identified in many plant species. In soybean (Glycine max), GmZF-HD1 functions as a transcription factor that activates the soybean calmodulin isoform-4 (GmCaM-4) gene in response to pathogens. Recently, we reported specific binding of GmZF-HD1 to a 30-nt A/T-rich cis-element which constitutes two repeats of a conserved homeodomain binding site, ATTA, within -1207 to -1128bp of the GmCaM-4 promoter. Herein, homeodomain sequences of the GmZF-HD1 protein were compared to those of other homeodomain proteins and characterized the specificity of DNA sequences in the interaction of the GmCaM-4 promoter with GmZF-HD1 protein. Considering the conservation of homeodomains in plants, the AG sequence within a 30-nt A/T-rich cis-element is required for binding of the GmZF-HD1 protein. Approximately 25-bp of A/T-rich DNA sequences containing an AG sequence is necessary for effective binding to the GmZF-HD1 protein. Taken together, the results support the notion that the GmZF-HD1 protein specifically functions in plant stress signalling by interacting with the promoter of GmCaM-4.

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C₂H₂, C₂C₂, C₃H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.

Functional analysis of the stress-inducible soybean calmodulin isoform-4 (GmCaM-4) promoter in transgenic tobacco plants

The transcription of soybean (Glycine max) calmodulin isoform-4 (GmCaM-4) is dramatically induced within 0.5 h of exposure to pathogen or NaCl. Core cis-acting elements that regulate the expression of the GmCaM-4 gene in response to pathogen and salt stress were previously identified, between -1,207 and -1,128 bp, and between -858 and -728 bp, in the GmCaM-4 promoter. Here, we characterized the properties of the DNA-binding complexes that form at the two core cis-acting elements of the GmCaM-4 promoter in pathogen-treated nuclear extracts. We generated GUS reporter constructs harboring various deletions of approximately 1.3-kb GmCaM-4 promoter, and analyzed GUS expression in tobacco plants transformed with these constructs. The GUS expression analysis suggested that the two previously identified core regions are involved in inducing GmCaM-4 expression in the heterologous system. Finally, a transient expression assay of Arabidopsis protoplasts showed that the GmCaM-4 promoter produced greater levels of GUS activity than did the CaMV35S promoter after pathogen or NaCl treatments, suggesting that the GmCaM-4 promoter may be useful in the production of conditional gene expression systems.

Stress induced and nuclear localized HIPP26 from Arabidopsis thaliana interacts via its heavy metal associated domain with the drought stress related zinc finger transcription factor ATHB29

HIPP26 from Arabidopsis thaliana belongs to a novel class of plant proteins, characterized by a heavy metal associated domain and an additional isoprenylation motif. It is induced during cold, salt and drought stress. The nuclear localization of HIPP26, predicted by a NLS motif, could be confirmed in onion epidermal cells overexpressing GFP-HIPP26. Experiments with modified HIPP26 indicate that the isoprenylation plays a role in the spatial distribution in the nucleus. Using promoter-GUS constructs, a tissue specific expression pattern of HIPP26 could be shown, with high expression in the vascular tissue. By a yeast-two-hybrid approach a strong interaction of HIPP26 with the zinc finger homeodomain transcription factor ATHB29, which is known to play a role in dehydration stress response could be detected. This was confirmed by GST pull-down assays. When using a modified HIPP26 lacking the two central cysteines of the heavy metal associated domain, ATHB29 was not bound in the GST pull-down assay, indicating that this structure is necessary for the interaction. Further yeast-two-hybrid analyses testing interaction of different members of the HIPP family with related zinc finger transcription factors revealed a specific interaction of ATHB29 with several HIPP proteins. A functional relationship between HIPP26 and ATHB29 is also indicated by experiments with mutants of HIPP26 showing altered expression levels of such genes known to be regulated by ATHB29.

Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families

Zinc finger-homeodomain proteins (ZHD) are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER (MIF) genes that possess only the zinc finger. Phylogenetic analyses of ZHD genes from representative land plants suggest that non-seed plant ZHD genes occupy basal positions and angiosperm homologs form seven distinct clades. Several clades contain genes from two or more major angiosperm groups, including eudicots, monocots, magnoliids, and other basal angiosperms, indicating that several duplications occurred before the diversification of flowering plants. In addition, specific lineages have experienced more recent duplications. Unlike the ZHD genes, MIFs are found only from seed plants, possibly derived from ZHDs by loss of the homeodomain before the divergence of seed plants. Moreover, the MIF genes have also undergone relatively recent gene duplications. Finally, genome duplication might have contributed substantially to the expansion of family size in angiosperms and caused a high level of functional redundancy/overlap in these genes.

Modern tools for identification of nucleic acid-binding proteins

Numerous biological mechanisms depend on nucleic acid--protein interactions. The first step to the understanding of these mechanisms is to identify interacting molecules. Knowing one partner, the identification of other associated molecular species can be carried out using affinity-based purification procedures. When the nucleic acid-binding protein is known, the nucleic acid can be isolated and identified by sensitive techniques such as polymerase chain reaction followed by DNA sequencing or hybridization on chips. The reverse identification procedure is less straightforward in part because interesting nucleic acid-binding proteins are generally of low abundance and there are no methods to amplify amino acid sequences. In this article, we will review the strategies that have been developed to identify nucleic acid-binding proteins. We will focus on methods permitting the identification of these proteins without a priori knowledge of protein candidates.