Regulation of cold signaling by sumoylation of ICE1

Cold Conditioned: Discovery of Novel Alleles for Low-Temperature Tolerance in the Vavilov Barley Collection

Climate changes leading to higher summer temperatures can adversely affect cool season crops like spring barley. In the Upper Midwest region of the United States, one option for escaping this stress factor is to plant winter or facultative type cultivars in the autumn and then harvest in early summer before the onset of high-temperature stress. However, the major challenge in breeding such cultivars is incorporating sufficient winter hardiness to survive the extremely low temperatures that commonly occur in this production region. To broaden the genetic base for winter hardiness in the University of Minnesota breeding program, 2,214 accessions from the N. I. Vavilov Institute of Plant Industry (VIR) were evaluated for winter survival (WS) in St. Paul, Minnesota. From this field trial, 267 (>12%) accessions survived [designated as the VIR-low-temperature tolerant (LTT) panel] and were subsequently evaluated for WS across six northern and central Great Plains states. The VIR-LTT panel was genotyped with the Illumina 9K SNP chip, and then a genome-wide association study was performed on seven WS datasets. Twelve significant associations for WS were identified, including the previously reported frost resistance gene FR-H2 as well as several novel ones. Multi-allelic haplotype analysis revealed the most favorable alleles for WS in the VIR-LTT panel as well as another recently studied panel (CAP-LTT). Seventy-eight accessions from the VIR-LTT panel exhibited a high and consistent level of WS and select ones are being used in winter barley breeding programs in the United States and in a multiparent population.

SUMOylation: A critical transcription modulator in plant cells

Gene transcription is critical for various cellular processes and is precisely controlled at multiple levels, and posttranslational modification (PTM) is a fast and powerful way to regulate transcription factors (TFs). SUMOylation, which conjugates small ubiquitin-related modifier (SUMO) molecules to protein substrates, is a crucial PTM that modulates the activity, stability, subcellular localization, and partner interactions of TFs in plant cells. Here, we summarize the mechanisms of SUMOylation in the regulation of transcription in plant development and stress responses. We also discuss the crosstalk between SUMOylation and other PTMs, as well as the potential functions of SUMOylation in the regulation of transcription-associated complexes on plant chromatin. This summary and perspective will improve understanding of the molecular mechanism of PTMs in plant transcription regulation.

Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine

Background

Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.).

Result

Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses.

Conclusion

Our study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.

Pyrophosphate modulates plant stress responses via SUMOylation

Pyrophosphate (PPi), a byproduct of macromolecule biosynthesis is maintained at low levels by soluble inorganic pyrophosphatases (sPPase) found in all eukaryotes. In plants, H⁺-pumping pyrophosphatases (H⁺-PPase) convert the substantial energy present in PPi into an electrochemical gradient. We show here, that both cold- and heat stress sensitivity of fugu5 mutants lacking the major H⁺-PPase isoform AVP1 is correlated with reduced SUMOylation. In addition, we show that increased PPi concentrations interfere with SUMOylation in yeast and we provide evidence that SUMO activating E1-enzymes are inhibited by micromolar concentrations of PPi in a non-competitive manner. Taken together, our results do not only provide a mechanistic explanation for the beneficial effects of AVP1 overexpression in plants but they also highlight PPi as an important integrator of metabolism and stress tolerance.

A novel Zea mays ssp. mexicana L. MYC-type ICE-like transcription factor gene ZmmICE1, enhances freezing tolerance in transgenic Arabidopsis thaliana

The annual Zea mays ssp. mexicana L., a member of the teosinte group, is a close wild relative of maize and thus can be effectively used in maize improvement. In this study, an ICE-like gene, ZmmICE1, was isolated from a cDNA library of RNA-Seq from cold-treated seedling tissues of Zea mays ssp. mexicana L. The deduced protein of ZmmICE1 contains a highly conserved basic helix-loop-helix (bHLH) domain and C-terminal region of ICE-like proteins. The ZmmICE1 protein localizes to the nucleus and shows sumoylation when expressed in an Escherichia coli reconstitution system. In addition, yeast one hybrid assays indicated that ZmmICE1 has transactivation activities. Moreover, ectopic expression of ZmmICE1 in the Arabidopsis ice1-2 mutant increased freezing tolerance. The ZmmICE1 overexpressed plants showed lower electrolyte leakage (EL), reduced contents of malondialdehyde (MDA). The expression of downstream cold related genes of Arabidopsis C-repeat-binding factors (AtCBF1, AtCBF2 and AtCBF3), cold-responsive genes (AtCOR15A and AtCOR47), kinesin-1 member gene (AtKIN1) and responsive to desiccation gene (AtRD29A) was significantly induced when compared with wild type under low temperature treatment. Taken together, these results indicated that ZmmICE1 is the homolog of Arabidopsis inducer of CBF expression genes (AtICE1/2) and plays an important role in the regulation of freezing stress response.

Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing

Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (-8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants.

Functional characterization of DnSIZ1, a SIZ/PIAS-type SUMO E3 ligase from Dendrobium

BACKGROUND

SUMOylation is an important post-translational modification of eukaryotic proteins that involves the reversible conjugation of a small ubiquitin-related modifier (SUMO) polypeptide to its specific protein substrates, thereby regulating numerous complex cellular processes. The PIAS (protein inhibitor of activated signal transducers and activators of transcription [STAT]) and SIZ (scaffold attachment factor A/B/acinus/PIAS [SAP] and MIZ) proteins are SUMO E3 ligases that modulate SUMO conjugation. The characteristic features and SUMOylation mechanisms of SIZ1 protein in monocotyledon are poorly understood. Here, we examined the functions of a homolog of Arabidopsis SIZ1, a functional SIZ/PIAS-type SUMO E3 ligase from Dendrobium.

RESULTS

In Dendrobium, the predicted DnSIZ1 protein has domains that are highly conserved among SIZ/PIAS-type proteins. DnSIZ1 is widely expressed in Dendrobium organs and has a up-regulated trend by treatment with cold, high temperature and wounding. The DnSIZ1 protein localizes to the nucleus and shows SUMO E3 ligase activity when expressed in an Escherichia coli reconstitution system. Moreover, ectopic expression of DnSIZ1 in the Arabidopsis siz1-2 mutant partially complements several phenotypes and results in enhanced levels of SUMO conjugates in plants exposed to heat shock conditions. We observed that DnSIZ1 acts as a negative regulator of flowering transition which may be via a vernalization-induced pathway. In addition, ABA-hypersensitivity of siz1-2 seed germination can be partially suppressed by DnSIZ1.

CONCLUSIONS

Our results suggest that DnSIZ1 is a functional homolog of the Arabidopsis SIZ1 with SUMO E3 ligase activity and may play an important role in the regulation of Dendrobium stress responses, flowering and development.

Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress

Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of V. amurensis.

Structure, function and networks of transcription factors involved in abiotic stress responses

Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes and the phytohormone ABA. Although ectopic expression of several TFs has improved abiotic stress tolerance in plants, fine-tuning of TF expression and protein levels remains a challenge to avoid crop yield loss. To further our understanding of TFs in abiotic stress responses, emerging gene regulatory networks based on TFs and their direct targets genes are presented. These revealed components shared between ABA-dependent and independent signaling as well as abiotic and biotic stress signaling. Protein structure analysis suggested that TFs hubs of large interactomes have extended regions with protein intrinsic disorder (ID), referring to their lack of fixed tertiary structures. ID is now an emerging topic in plant science. Furthermore, the importance of the ubiquitin-proteasome protein degradation systems and modification by sumoylation is also apparent from the interactomes. Therefore; TF interaction partners such as E3 ubiquitin ligases and TF regions with ID represent future targets for engineering improved abiotic stress tolerance in crops.

Root architecture remodeling induced by phosphate starvation

Plants have evolved efficient strategies for utilizing nutrients in the soil in order to survive, grow, and reproduce. Inorganic phosphate (Pi) is a major macroelement source for plant growth; however, the availability and distribution of Pi are varying widely across locations. Thus, plants in many areas experience Pi deficiency. To maintain cellular Pi homeostasis, plants have developed a series of adaptive responses to facilitate external Pi acquisition, limit Pi consumption, and adjust Pi recycling internally under Pi starvation conditions. This review focuses on the molecular regulators that modulate Pi starvation-induced root architectural changes.

AtCPL5, a novel Ser-2-specific RNA polymerase II C-terminal domain phosphatase, positively regulates ABA and drought responses in Arabidopsis

Arabidopsis RNA polymerase II (RNAPII) C-terminal domain (CTD) phosphatases regulate stress-responsive gene expression and plant development via the dephosphorylation of serine (Ser) residues of the CTD. Some of these phosphatases (CTD phosphatase-like 1 (CPL1) to CPL3) negatively regulate ABA and stress responses. Here, we isolated AtCPL5, a cDNA encoding a protein containing two CTD phosphatase domains (CPDs). To characterize AtCPL5, we analyzed the gene expression patterns and subcellular protein localization, investigated various phenotypes of AtCPL5-overexpressors and knockout mutants involved in ABA and drought responses, performed microarray and RNA hybridization analyses using AtCPL5-overexpressors, and assessed the CTD phosphatase activities of the purified AtCPL5 and each CPD of the protein. Transcripts of the nucleus-localized AtCPL5 were induced by ABA and drought. AtCPL5-overexpressors exhibited ABA-hypersensitive phenotypes (increased inhibition of seed germination, seedling growth, and stomatal aperture), lower transpiration rates upon dehydration, and enhanced drought tolerance, while the knockout mutants showed weak ABA hyposensitivity. AtCPL5 overexpression changed the expression of numerous genes, including those involved in ABA-mediated responses. In contrast to Ser-5-specific phosphatase activity of the negative stress response regulators, purified AtCPL5 and each CPD of the protein specifically dephosphorylated Ser-2 in RNAPII CTD. We conclude that AtCPL5 is a unique CPL family protein that positively regulates ABA-mediated development and drought responses in Arabidopsis.

Transcription factor AtMYB44 regulates induced expression of the ETHYLENE INSENSITIVE2 gene in Arabidopsis responding to a harpin protein

AtMYB44 is a transcription factor that functions in association with the ethylene-signaling pathway in Arabidopsis thaliana. The pathway depends on ETHYLENE INSENSITIVE2 (EIN2), an essential component of ethylene signaling, to regulate defense responses in the plant following treatment with HrpN(Ea), a harpin protein from a bacterial plant pathogen. Here, we show that AtMYB44 regulates induced expression of the EIN2 gene in HrpN(Ea)-treated Arabidopsis plants. A HrpN(Ea) and ethylene-responsive fragment of the AtMYB44 promoter is sufficient to support coordinate expression of AtMYB44 and EIN2 in specific transgenic Arabidopsis. In the plant, the AtMYB44 protein localizes to nuclei and binds the EIN2 promoter; the HrpN(Ea) treatment promotes AtMYB44 production, binding activity, and transcription of AtMYB44 and EIN2. AtMYB44 overexpression results in increased production of the AtMYB44 protein and the occurrence of AtMYB44-EIN2 interaction under all genetic backgrounds of wild-type Arabidopsis and the etr1-1, ein2-1, ein3-1, and ein5-1 mutants, which have defects in the ethylene receptor ETR1 and the signal regulators EIN2, EIN3, and EIN5. However, AtMYB44 overexpression leads to enhanced EIN2 expression only under backgrounds of wild type, ein3-1, and ein5-1 but not etr1-1 and ein2-1, suggesting that ethylene perception is necessary to the regulation of EIN2 transcription by AtMYB44.

SIZ1 regulation of phosphate starvation-induced root architecture remodeling involves the control of auxin accumulation

Phosphate (Pi) limitation causes plants to modulate the architecture of their root systems to facilitate the acquisition of Pi. Previously, we reported that the Arabidopsis (Arabidopsis thaliana) SUMO E3 ligase SIZ1 regulates root architecture remodeling in response to Pi limitation; namely, the siz1 mutations cause the inhibition of primary root (PR) elongation and the promotion of lateral root (LR) formation. Here, we present evidence that SIZ1 is involved in the negative regulation of auxin patterning to modulate root system architecture in response to Pi starvation. The siz1 mutations caused greater PR growth inhibition and LR development of seedlings in response to Pi limitation. Similar root phenotypes occurred if Pi-deficient wild-type seedlings were supplemented with auxin. N-1-Naphthylphthalamic acid, an inhibitor of auxin efflux activity, reduced the Pi starvation-induced LR root formation of siz1 seedlings to a level equivalent to that seen in the wild type. Monitoring of the auxin-responsive reporter DR5::uidA indicated that auxin accumulates in PR tips at early stages of the Pi starvation response. Subsequently, DR5::uidA expression was observed in the LR primordia, which was associated with LR elongation. The time-sequential patterning of DR5::uidA expression occurred earlier in the roots of siz1 as compared with the wild type. In addition, microarray analysis revealed that several other auxin-responsive genes, including genes involved in cell wall loosening and biosynthesis, were up-regulated in siz1 relative to wild-type seedlings in response to Pi starvation. Together, these results suggest that SIZ1 negatively regulates Pi starvation-induced root architecture remodeling through the control of auxin patterning.

Overexpression of a homopeptide repeat-containing bHLH protein gene (OrbHLH001) from Dongxiang Wild Rice confers freezing and salt tolerance in transgenic Arabidopsis

Dongxiang Wild Rice (Oryza rufipogon) is the northernmost wild rice in the world known to date and has extremely high cold tolerance and many other adversity-resistant properties. To identify the genes responsible for the high stress tolerance, we isolated and characterized a basic helix-loop-helix (bHLH) protein gene OrbHLH001 from Dongxiang Wild Rice. The gene encodes an ICE1-like protein containing multiple homopeptide repeats. Expression of OrbHLH001 is induced by salt stress and is predominant in the shoots of wild rice seedlings. Overexpression of OrbHLH001 enhanced the tolerance to freezing and salt stresses in transgenic Arabidopsis. Examination of the expression of cold-responsive genes in transgenic Arabidopsis showed that the function of OrbHLH001 differs from that of ICE1 and is independent of a CBF/DREB1 cold-response pathway.

Cold-responsive gene regulation during cold acclimation in plants

Regulation of the transcriptome is necessary for plants to acquire cold tolerance, and cold induces several genes via a cold signaling pathway. The transcription factors CBF/DREB1 (C-repeat binding factor/dehydration responsive element binding1) and ICE1 (inducer of CBF expression1) have important roles in the regulation of cold-responsive gene expression. ICE1 is post-translationally regulated by ubiquitylation-mediated proteolysis and sumoylation. This mini-review highlights some recent studies on plant cold signaling. The relationships among cold signaling, salicylic acid accumulation and stomatal development are also discussed.

SIZ1, a small ubiquitin-related modifier ligase, controls cold signaling through regulation of salicylic acid accumulation

Low temperature induces several genes to acquire plant cold tolerance. Here, we demonstrate that accumulation of salicylic acid (SA) is involved in the regulation of the DREB1A/CBF3 regulon and plant tolerance to cold stresses. The SA-accumulating mutant siz1 exhibits sensitivity to chilling and freezing conditions and decreased expression of DREB1A/CBF3 and its regulon genes. Reduction of SA levels in siz1 by nahG restored cold sensitivity and down-regulation of these genes. Database analyses and RT-PCR analysis revealed that the ice1 mutation also increased expression of SA-responsive genes. As well as siz1, another SA-accumulating mutant acd6 exhibited freezing sensitivity and the sensitivity was suppressed in acd6 nahG plants. Taken together, these data indicate that SA is involved in regulation of cold signaling.

SIZ1 controls cell growth and plant development in Arabidopsis through salicylic acid

The post-translational conjugation of small ubiquitin-related modifiers (SUMOs) to other proteins is involved in regulation of many processes in eukaryotic development; although its role in plant development is beginning to be dissected. Previously, we demonstrated that the siz1 mutant, which is impaired in SUMO E3 ligase, showed a dwarf-like shoot phenotype with accumulation of salicylic acid (SA), and the expression of nahG, a bacterial salicylate hydroxylase that catabolizes SA, in siz1 reduced the SA level and suppressed dwarfism. Herein, we provide evidence that the SIZ1 gene controls cell division and elongation through regulation of the SA level. Mature siz1-2 and siz1-3 plants exhibited a dwarf-like shoot phenotype that is attributable to decreased leaf cell volume and number relative to the wild type. Cell division and expansion defects caused by siz1 were also suppressed by the expression of nahG. Expression of XTH8 and XTH31, encoding xyloglucan endotransglycosylase/hydrolase, which are thought to facilitate leaf cell expansion, was down-regulated in siz1 leaves. However, reduced XTH8 and XTH31 expression in siz1 plants was restored in nahG siz1-2 plants. These results indicate that SIZ1 regulates cell growth and plant development with regulation of SA accumulation. Also, XTH8 and XTH31 genes may be responsible for reduced leaf cell expansion.

Sumoylation and abscisic acid signaling

The conjugation of small ubiquitin-related modifier (SUMO) to substrates (sumoylation) is one of posttranslational modification systems in eukaryotes. Sumoylation plays an important role in the regulation of environmental stress response, biotic stress response, and flowering control in plants. Covalent SUMO conjugation requires an E1/E2/E3 enzyme, and SUMO E3 ligase SIZ1 is essential for these regulations. This addendum summarizes our recent study in which it has been established that in Arabidopsis, SUMO E3 ligase SIZ1 negatively controls abscisic acid (ABA) signaling through the sumoylation of ABI5. The conjugation of SUMO to ABI5 represses its activity and also prevents ABI5 from undergoing degradation.