Improved cold tolerance in switchgrass by a novel CCCH-type zinc finger transcription factor gene, PvC3H72, associated with ICE1-CBF-COR regulon and ABA-responsive genes

Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.)

Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.

A LlMYB305-LlC3H18-LlWRKY33 module regulates thermotolerance in lily

The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their roles in thermotolerance are scarce. Here, we identified a heat-inducible CCCH gene LlC3H18 from lily. LlC3H18 was localized in the cytoplasm and nucleus under normal conditions, while it translocated in the cytoplasmic foci and co-located with the markers of two messenger ribonucleoprotein (mRNP) granules, processing bodies (PBs) and stress granules (SGs) under heat stress conditions, and it also exhibited RNA-binding ability. In addition, LlC3H18 exhibited transactivation activity in both yeast and plant cells. In lily and Arabidopsis, overexpression of LlC3H18 damaged their thermotolerances, and silencing of LlC3H18 in lily also impaired its thermotolerance. Similarly, Arabidopsis atc3h18 mutant also showed decreased thermotolerance. These results indicated that the appropriate expression of C3H18 was crucial for establishing thermotolerance. Further analysis found that LlC3H18 directly bound to the promoter of LlWRKY33 and activated its expression. Besides, it was found that LlMYB305 acted as an upstream factor of LlC3H18 and activated its expression. In conclusion, we demonstrated that there may be a LlMYB305-LlC3H18-LlWRKY33 regulatory module in lily that is involved in the establishment of thermotolerance and finely regulates heat stress response.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans

CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans.

Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris

Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.

STRONG STAYGREEN inhibits DNA binding of PvNAP transcription factors during leaf senescence in switchgrass

Fine tuning the progression of leaf senescence is important for plant fitness in nature, while the "staygreen" phenotype with delayed leaf senescence has been considered a valuable agronomic trait in crop genetic improvement. In this study, a switchgrass (Panicum virgatum L.) CCCH-type Zinc finger gene, Strong Staygreen (PvSSG), was characterized as a suppressor of leaf senescence as overexpression or suppression of the gene led to delayed or accelerated leaf senescence, respectively. Transcriptomic analysis marked that chlorophyll (Chl) catabolic pathway genes were involved in the PvSSG-regulated leaf senescence. PvSSG was identified as a nucleus-localized protein with no transcriptional activity. By yeast two-hybrid screening, we identified its interacting proteins, including a pair of paralogous transcription factors, PvNAP1/2 (NAC-LIKE, ACTIVATED BY AP3/PI). Overexpression of PvNAPs led to precocious leaf senescence at least partially by directly targeting and transactivating Chl catabolic genes to promote Chl degradation. PvSSG, through protein-protein interaction, repressed the DNA-binding efficiency of PvNAPs and alleviated its transactivating effect on downstream genes, thereby functioning as a "brake" in the progression of leaf senescence. Moreover, overexpression of PvSSG resulted in up to 47% higher biomass yield and improved biomass feedstock quality, reiterating the importance of leaf senescence regulation in the genetic improvement of switchgrass and other feedstock crops.

Temporal regulation of cold transcriptional response in switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis-regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k-mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k-mers, referred to as putative cis-regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

The NAC factor LpNAL delays leaf senescence by repressing two chlorophyll catabolic genes in perennial ryegrass

Expression of chlorophyll (Chl) catabolic genes during leaf senescence is tightly controlled at the transcriptional level. Here, we identified a NAC family transcription factor, LpNAL, involved in regulating Chl catabolic genes via the yeast one-hybrid system based on truncated promoter analysis of STAYGREEN (LpSGR) in perennial ryegrass (Lolium perenne L.). LpNAL was found to be a transcriptional repressor, directly repressing LpSGR as well as the Chl b reductase gene, NONYELLOWING COLORING1. Perennial ryegrass plants over-expressing LpNAL exhibited delayed leaf senescence or stay-green phenotypes, whereas knocking down LpNAL using RNA interference accelerated leaf senescence. Comparative transcriptome analysis of leaves at 30 d after emergence in wild-type, LpNAL-overexpression, and knock-down transgenic plants revealed that LpNAL-regulated stay-green phenotypes possess altered light reactions of photosynthesis, antioxidant metabolism, ABA and ethylene synthesis and signaling, and Chl catabolism. Collectively, the transcriptional repressor LpNAL targets both Chl a and Chl b catabolic genes and acts as a brake to fine-tune the rate of Chl degradation during leaf senescence in perennial ryegrass.

Identification of the DcHsp20 gene family in carnation (Dianthus caryophyllus) and functional characterization of DcHsp17.8 in heat tolerance

33 heat shock protein 20 (Hsp20) genes were identified from the carnation genome whose expression were altered by abiotic stresses. DcHsp17.8 may function to improve the heat resistance of Arabidopsis. Heat shock proteins 20 (Hsp20s) mainly function as molecular chaperones that play crucial roles in relieving abiotic stresses such as heat stress. In this study, we identified and characterized 33 DcHsp20 genes from the carnation genome that were classified into 9 subfamilies. Gene structure analysis showed that 25 DcHsp20 genes contained 1 intron whilst the remaining 8 DcHsp20 genes did not contain introns. Motif analysis found that DcHsp20 proteins were relatively conserved. Cis-regulatory elements analysis of the Hsp20 promoters revealed a number of cis-regulatory elements that regulate growth and development, hormone and stress responses. Gene expression analysis revealed that DcHsp20 genes had multiple response patterns to heat stress. The largest range of induction occurred in DcHsp17.8 after 1 h of heat stress. Under cold stress, or treatment with saline or abscisic acid, the expression of most DcHsp20 genes was inhibited. To further understand the function of DcHsp20 genes in response to heat stress, we overexpressed DcHsp17.8 in Arabidopis and the plants showed improved heat tolerance, O₂^- and H₂O₂ activities and photosynthetic capacity with reduced relative electrolyte leakage and malondialdehyde content. Gene expression analysis revealed that DcHsp17.8 modulated the expression of genes involved in antioxidant enzyme synthesis. Our data provided a solid foundation for the further detailed study of DcHsp20 genes.

Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple

The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

BACKGROUND

CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley.

RESULTS

In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley.

CONCLUSIONS

Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

Non-TZF Transcriptional Activator AtC3H12 Negatively Affects Seed Germination and Seedling Development in Arabidopsis

CCCH zinc finger proteins are a large protein family and are classified as either tandem CCCH zinc finger (TZF) or non-TZF proteins. The roles of TZF genes in several plants have been well determined, whereas the functions of many non-TZF genes in plants remain uncharacterized. Herein, we describe biological and molecular functions of AtC3H12, an Arabidopsis non-TZF protein containing three CCCH zinc finger motifs. AtC3H12 has orthologs in several plant species but has no paralog in Arabidopsis. AtC3H12-overexpressing transgenic plants (OXs) germinated slower than wild-type (WT) plants, whereas atc3h12 mutants germinated faster than WT plants. The fresh weight (FW) and primary root lengths of AtC3H12 OX seedlings were lighter and shorter than those of WT seedlings, respectively. In contrast, FW and primary root lengths of atc3h12 seedlings were heavier and longer than those of WT seedlings, respectively. AtC3H12 was localized in the nucleus and displayed transactivation activity in both yeast and Arabidopsis. We found that the 97-197 aa region of AtC3H12 is an important part for its transactivation activity. Detection of expression levels and analysis of Arabidopsis transgenic plants harboring a PAtC3H12::GUS construct showed that AtC3H12 expression increases as the Arabidopsis seedlings develop. Taken together, our results demonstrate that AtC3H12 negatively affects seed germination and seedling development as a nuclear transcriptional activator in Arabidopsis. To our knowledge, this is the first report to show that non-TZF proteins negatively affect plant development as nuclear transcriptional activators.

Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress

Drought and heat are two major stresses predicted to increase in the future due to climate change. Plants exposed to multiple stressors elicit unique responses from those observed under individual stresses. A comparative transcriptome analysis of Lolium temulentum exposed to drought plus heat and non-stressed control plants revealed 20,221 unique up-regulated and 17,034 unique down-regulated differentially regulated transcripts. Gene ontology analysis revealed a strong emphasis on transcriptional regulation, protein folding, cell cycle/parts, organelles, binding, transport, signaling, oxidoreductase, and antioxidant activity. Differentially expressed genes (DEGs) encoding for transcriptional control proteins such as basic leucine zipper, APETALA2/Ethylene Responsive Factor, NAC, and WRKY transcription factors, and Zinc Finger (CCCH type and others) proteins were more often up-regulated, while DEGs encoding Basic Helix-Loop-Helix, MYB and GATA transcription factors, and C2H2 type Zinc Finger proteins were more often down-regulated. The DEGs encoding heat shock transcription factors were only up-regulated. Of the hormones, auxin-related DEGs were the most prevalent, encoding for auxin response factors, binding proteins, and efflux/influx carriers. Gibberellin-, cytokinin- and ABA-related DEGs were also prevalent, with fewer DEGs related to jasmonates and brassinosteroids. Knowledge of genes/pathways that grasses use to respond to the combination of heat/drought will be useful in developing multi-stress resistant grasses.

The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance

Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.

HsfA1d promotes hypocotyl elongation under chilling via enhancing expression of ribosomal protein genes in Arabidopsis

How plants maintain growth under nonfreezing low temperatures (chilling) is not well understood. Here we use hypocotyl elongation under dark to investigate the molecular mechanisms for chilling growth in Arabidopsis thaliana. The function of HsfA1d (Heat shock transcription factor A1d) in chilling growth is investigated by physiological and molecular characterization of its mutants. Subcellular localization of HsfA1d under chilling is analyzed. Potential target genes of HsfA1d were identified by transcriptome analysis, chromatin immunoprecipitation, transcriptional activation assay and mutant characterization. HsfA1d is a positive regulator of hypocotyl elongation under chilling. It promotes expression of a large number of ribosome biogenesis genes to a moderate but significant extent under chilling. HsfA1d could bind to the promoter regions of two ribosome protein genes tested and promote their expression. The loss-of-function of one ribosome gene also reduced hypocotyl elongation under chilling. In addition, HsfA1d did not have increased nuclear accumulation under chilling and its basal nuclear accumulation is promoted by a salicylic acid receptor under chilling. This study thus unveils a new HsfA1d-mediated pathway that promotes the expression of cytosolic and plastid cytosolic and plastid ribosomal protein genes which may maintain overall protein translation for plant growth in chilling.

Non-TZF Protein AtC3H59/ZFWD3 Is Involved in Seed Germination, Seedling Development, and Seed Development, Interacting with PPPDE Family Protein Desi1 in Arabidopsis

Despite increasing reports on the function of CCCH zinc finger proteins in plant development and stress response, the functions and molecular aspects of many non-tandem CCCH zinc finger (non-TZF) proteins remain uncharacterized. AtC3H59/ZFWD3 is an Arabidopsis non-TZF protein and belongs to the ZFWD subfamily harboring a CCCH zinc finger motif and a WD40 domain. In this study, we characterized the biological and molecular functions of AtC3H59, which is subcellularly localized in the nucleus. The seeds of AtC3H59-overexpressing transgenic plants (OXs) germinated faster than those of wild type (WT), whereas atc3h59 mutant seeds germinated slower than WT seeds. AtC3H59 OX seedlings were larger and heavier than WT seedlings, whereas atc3h59 mutant seedlings were smaller and lighter than WT seedlings. Moreover, AtC3H59 OX seedlings had longer primary root length than WT seedlings, whereas atc3h59 mutant seedlings had shorter primary root length than WT seedlings, owing to altered cell division activity in the root meristem. During seed development, AtC3H59 OXs formed larger and heavier seeds than WT. Using yeast two-hybrid screening, we isolated Desi1, a PPPDE family protein, as an interacting partner of AtC3H59. AtC3H59 and Desi1 interacted via their WD40 domain and C-terminal region, respectively, in the nucleus. Taken together, our results indicate that AtC3H59 has pleiotropic effects on seed germination, seedling development, and seed development, and interacts with Desi1 in the nucleus via its entire WD40 domain. To our knowledge, this is the first report to describe the biological functions of the ZFWD protein and Desi1 in Arabidopsis.

Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. chow (Orchidaceae)

BACKGROUND

Gastrodia elata Bl. f. glauca S. Chow is a medicinal plant. G. elata f. glauca is unavoidably infected by pathogens in their growth process. In previous work, we have successfully isolated and identified Penicillium oxalicum from fungal diseased tubers of G. elata f. glauca. As a widespread epidemic, this fungal disease seriously affected the yield and quality of G. elata f. glauca. We speculate that the healthy G. elata F. glauca might carry resistance genes, which can resist against fungal disease. In this study, healthy and fungal diseased mature tubers of G. elata f. glauca from Changbai Mountain area were used as experimental materials to help us find potential resistance genes against the fungal disease.

RESULTS

A total of 7540 differentially expressed Unigenes (DEGs) were identified (FDR < 0.01, log2FC > 2). The current study screened 10 potential resistance genes. They were attached to transcription factors (TFs) in plant hormone signal transduction pathway and plant pathogen interaction pathway, including WRKY22, GH3, TIFY/JAZ, ERF1, WRKY33, TGA. In addition, four of these genes were closely related to jasmonic acid signaling pathway.

CONCLUSIONS

The immune response mechanism of fungal disease in G. elata f. glauca is a complex biological process, involving plant hormones such as ethylene, jasmonic acid, salicylic acid and disease-resistant transcription factors such as WRKY, TGA.