Low temperature promotes intron retention in two e-cor genes of durum wheat

Comparative transcriptomics reveals potential regulators of climate adaptation in Santalum album L. (Indian Sandalwood)

Santalum album L. (Indian Sandalwood), a valued tree species known for its fragrant heartwood and essential oil is facing increasing threat due to severe anthropogenic pressures compounded by climate change which has resulted in depletion of its adaptive gene pool. The present study investigates the transcriptome-level responses of nine sandalwood genotypes sourced from diverse climatic zones to identify adaptive genes in the species. Comparative transcriptomics predicted 727, 1141 and 479 differentially expressed transcripts (DETs) across wet vs. dry; monsoon vs. dry and wet vs. monsoon conditions, respectively, and majority of DETs were up-regulated in samples sourced from high rainfall areas. Transcripts including heat shock proteins, Zinc finger binding protein, ribosomal proteins, transcription factors and protein kinase were identified as probable regulators of climate adaptation in S. album. The expression changes of eight selected transcripts were further validated by real-time quantitative PCR. Protein-protein interaction analysis revealed key hub transcripts involved in climate response, while alternative splicing events in transcripts such as SURP and G-patch domain-containing protein 1-like protein, G-type lectin S-receptor-like serine/threonine protein kinase B120, Tetraspanin-3 and ARM repeat superfamily protein indicated the probable role of alternate splicing in increasing the transcript diversity during adaptation. This study presents the first insight into the molecular mechanisms of climate adaptation in the species and can form the basis for specific interventions such as selective breeding, genetic manipulation, and habitat management for conservation and long-term survival of sandalwood.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04218-4.

Exploitation and Application of a New Genetic Sex Marker Based on Intron Insertion Variation of erc2 Gene in Oplegnathus punctatus

Spotted knifejaw (Oplegnathus punctatus), one of the most valuable mariculture species, grows with significant sexual dimorphism, with males growing significantly faster than females. O. punctatus not only has excellent growth characteristics and high food value, but also shows high economic value in aquaculture, which has become a hotspot in the field of aquaculture. The current insufficiency of sex marker identification in O. punctatus restricts the process of its unisexual breeding. Rapid identification of sex will help to study the mechanisms of sex determination and accelerate the development of sex-controlled breeding. With the completion of the sequencing of the male and female genomes of O. punctatus, the efficient and precise development of genetic sex markers has been made possible. In this study, we used genome-wide information combined with molecular biology techniques from marker sequences to further establish a rapid method for DNA insertion variant detection in the intron of O. punctatus erc2 gene, which can be used to rapidly, accurately, and efficiently identify whether DNA insertion occurs in the intron of O. punctatus erc2 gene to be detected, and to identify the sex of O. punctatus to be detected. It could also be distinguished by agarose gel electrophoresis, which would shorten the time for accurate identification and improves the detection efficiency. Homozygous comparison of male and female individuals showed that the length of the DNA fragment of the erc2 gene was 239 bp on chromosome X1 and 1173 bp on chromosome Y. It can therefore be inferred that a 934 bp insertion fragment exists on the Y chromosome. The PCR amplification results showed that two DNA fragments of 1173 bp and 239 bp could be amplified in male O. punctatus, and the 1173 bp fragment was a marker fragment specific to the variant intron erc2 gene, while only a single DNA fragment of 239 bp was amplified in female O. punctatus. It has important significance and application value in the study of neurotransmitter transmission and environmental adaptability of female and male fish based on erc2 gene, as well as the identification of male and female sex, the preparation of high male fry, and family breeding.

Exonic Circular RNAs Are Involved in Arabidopsis Immune Response Against Bacterial and Fungal Pathogens and Function Synergistically with Corresponding Linear RNAs

Circular RNAs (circRNAs) are a group of covalently closed RNAs, and their biological function is largely unknown. In this study, we focused on circRNAs that are generated from exon back-splicing (exonic circRNAs). The linear RNA counterparts encode functional proteins so that we can compare and investigate the relationship between circular and linear RNAs. We compared circRNA expression profiles between untreated and Pseudomonas syringae-infected Arabidopsis and identified and experimentally validated differentially expressed exonic circRNAs by multiple approaches. We found that exonic circRNAs are preferentially enriched in biological processes that associate with biotic and abiotic stress responses. We discovered that circR194 and circR4022 are involved in plant response against P. syringae infection, whereas circR11208 is involved in response against Botrytis cinerea infection. Intriguingly, our results indicate that these exonic circRNAs function synergistically with their corresponding linear RNAs. Furthermore, circR4022 and circR11208 also play substantial roles in Arabidopsis tolerance to salt stress. This study extends our understanding of the molecular functions of plant circRNAs.

Regulation of alternative splicing in response to temperature variation in plants

Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.

Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches

BACKGROUND

Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. This study leverages genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance.

RESULTS

A GWAS and a GWES were performed using 460 diverse soybean PI lines from 27 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this approach with available RNA-sequencing data identified significant markers, genomic regions, and novel genes associated with or responding to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified across 19 chromosomes via the GWAS, including the major-effect quantitative trait locus (QTL) on chromosome Gm03. Cluster analysis of significant SNPs in this region deconstructed this historically prominent QTL into four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. The complementary GWES identified SNPs in this region interacting with nine other genomic regions, providing the first evidence of epistatic interactions impacting iron deficiency tolerance.

CONCLUSIONS

This study demonstrates that integrating cutting edge genome wide association (GWA), genome wide epistasis (GWE), and gene expression studies is a powerful strategy to identify novel iron tolerance QTL and candidate loci from diverse germplasm. Crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. Leveraging genomics-enabled approaches to study these adaptations is essential for future crop improvement.

Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant

BACKGROUND

Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis).

RESULTS

In this study, the AS transcriptional landscape was characterized in the tea plant genome using high-throughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents.

CONCLUSION

Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.

Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vanname

Alternative splicing (AS) can enhance transcript diversity dramatically and play an important role in stress adaptation. Limited researches of AS have been reported in the Pacific white shrimp (Litopenaeus vannamei), which is an important aquaculture species in the world. Here, we performed a genome-wide identification of AS events in L. vannamei based on eight transcriptomes. We identified 38,781 AS events in the shrimp genome, and some of them were validated by polymerase chain reaction experiments. These AS events correspond to 9,209 genes, accounting for 36% of protein-coding genes in the shrimp genome. The number of AS events increased after virus or bacteria infection and low salinity stress. Type 1 AS genes (AS was initially activated) were mainly enriched in substance and energy metabolism, such as carbon metabolism and amino metabolism. However, type 2 AS genes (AS events changed) displayed specific enrichment under different stress challenges. Specifically, type 2 AS genes under biotic stresses were mainly enriched in the pathogenic pathway and immune network, and the AS genes under low salinity stress were significantly enriched for betalain biosynthesis. In summary, our study indicates that AS events are complex in shrimp and may be related to stress adaptation. These results will provide valuable resource for functional genomic studies on crustaceans.

Transcriptomic response of durum wheat to cold stress at reproductive stage

Understanding the genetic basis of cold tolerance is a key step towards obtaining new and improved crop varieties. Current geographical distribution of durum wheat in Argentina exposes the plants to frost damage when spikes have already emerged. Biochemical pathways involved in cold tolerance are known to be early activated at above freezing temperatures. In this study we reported the transcriptome of CBW0101 spring durum wheat by merging data from untreated control and cold (5 °C) treated plant samples at reproductive stage. A total of 128,804 unigenes were predicted. Near 62% of the unigenes were annotated in at least one database. In total 876 unigenes were differentially expressed (DEGs), 562 were up-regulated and 314 down-regulated in treated samples. DEGs are involved in many critical processes including, photosynthetic activity, lipid and carbohydrate synthesis and accumulation of amino acids and seed proteins. Twenty-eight transcription factors (TFs) belonging to 14 families resulted differentially expressed from which eight families comprised of only TFs induced by cold. We also found 31 differentially expressed Long non-coding RNAs (lncRNAs), most of them up-regulated in treated plants. Two of these lncRNAs could operate via microRNAs (miRNAs) target mimic. Our results suggest a reprogramming of expression patterns in CBW0101 that affects a number of genes that is closer to the number reported in winter genotypes. These observations could partially explain its moderate tolerance (low proportion of frost-damaged spikes) when exposed to freezing days in the field.

Arabidopsis PCaP2 Plays an Important Role in Chilling Tolerance and ABA Response by Activating CBF- and SnRK2-Mediated Transcriptional Regulatory Network

Chilling stress affects plant growth and productivity. However, the multi-underlying mechanisms of chilling tolerance are not well understood. Arabidopsis PCaP2 is involved in regulating the dynamic of microtubules (MTs) and F-actin and Ca²⁺-binding ability. Here, the results showed that the PCaP2 expression was highly induced in roots, cotyledons, true leaves, lateral roots and flowers under cold stress. Compared with the wild type, PCaP2-overexpressing plants displayed the enhanced tolerance, whereas its RNAi and mutant were more sensitive in seed germination, seedling and reproductive growth under chilling stress in Arabidopsis. In addition, PCaP2 was also a positive regulator of ABA signaling pathway by analyzing the expression of PCaP2 and the phenotypes of PCaP2-overexpressing, mutant and RNAi plants under ABA treatment. Interestingly, disruption of PCaP2 inhibited the expression of CBF1, -3 and CBF-target COR genes, while increased the CBF2 expression in response to cold or ABA. Moreover, we found that SnRK2s were involved in cold stress and PCaP2 mutants down-regulated the transcription level of SnRK2.2, -2.3 and SnRK2-mediated downstream genes including ABF2, RD29A, KIN1, KIN2, but up-regulated SnRK2.6, ABF1, -3, -4 in ABA and cold treatments. It is well-accepted that PCaP2 as a Ca²⁺-binding protein triggers the gene expression to enhance plant chilling tolerance. Our further studies showed that MT destabilizing activity of PCaP2, but not F-actin-severing function, may be involved in chilling stress. Taken together, our results highlight that PCaP2 plays an important role in chilling tolerance and ABA response by triggering the CBF- and SnRK2-meditated transcriptional regulatory pathways, providing novel evidences of underlying mechanisms of multi-pathways in chilling stress.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

Conservation of AtTZF1, AtTZF2, and AtTZF3 homolog gene regulation by salt stress in evolutionarily distant plant species

Arginine-rich tandem zinc-finger proteins (RR-TZF) participate in a wide range of plant developmental processes and adaptive responses to abiotic stress, such as cold, salt, and drought. This study investigates the conservation of the genes AtTZF1-5 at the level of their sequences and expression across plant species. The genomic sequences of the two RR-TZF genes TdTZF1-A and TdTZF1-B were isolated in durum wheat and assigned to chromosomes 3A and 3B, respectively. Sequence comparisons revealed that they encode proteins that are highly homologous to AtTZF1, AtTZF2, and AtTZF3. The expression profiles of these RR-TZF durum wheat and Arabidopsis proteins support a common function in the regulation of seed germination and responses to abiotic stress. In particular, analysis of plants with attenuated and overexpressed AtTZF3 indicate that AtTZF3 is a negative regulator of seed germination under conditions of salt stress. Finally, comparative sequence analyses establish that the RR-TZF genes are encoded by lower plants, including the bryophyte Physcomitrella patens and the alga Chlamydomonas reinhardtii. The regulation of the Physcomitrella AtTZF1-2-3-like genes by salt stress strongly suggests that a subgroup of the RR-TZF proteins has a function that has been conserved throughout evolution.

The crucial role of Φ- and K-segments in the in vitro functionality of Vitis vinifera dehydrin DHN1a

Dehydrins (DHNs), group II LEA (Late Embryogenesis Abundant) proteins, are among the most commonly observed proteins which accumulate in plants in response to cold and any other environmental factors, causing the dehydration of cells. In previous studies, we isolated a YSK2-type VvcDHN1a gene from table grapes (Vitis vinifera cv. Cardinal) which presented two spliced variants (the spliced, DHN1a_s and the unspliced, DHN1a_u). Their expression was induced by low temperature storage and CO2, although with different accumulation patterns. DHN1a_u codifies for a truncated YS protein lacking Ф- and K-segments, which might affect its functionality. In this work, we expressed both DHN1a_s and DHN1a_u recombinant proteins in Escherichia coli. We carried out a number of in vitro assays to analyze the implications that Ф- and K-segments have in the protective role of VvcDHN1 against different abiotic stresses and their antifungal activity against the fungal pathogen Botrytis cinerea. Our results showed that unlike DHN1a_u, DHN1a_s has a potent cryoprotective effect on lactate dehydrogenase activity, protects malate dehydrogenase against dehydration and partially inhibits B. cinerea growth. Moreover, the DHN1a promoter presented cis-regulatory elements related to cold and drought, as well as biotic stress-related elements. We also observed that both spliced variants interact weakly with DNA, suggesting that K-segments are not involved in DNA binding. Overall, this work highlights the crucial role of Ф- and K-segments in DHNs function in plant response to abiotic stress showing for the first time, the potential role of the V. vinifera DHN1a_s in the protection against freezing and dehydration as well as inhibiting B. cinerea growth.

Comparative analyses between retained introns and constitutively spliced introns in Arabidopsis thaliana using random forest and support vector machine

One of the important modes of pre-mRNA post-transcriptional modification is alternative splicing. Alternative splicing allows creation of many distinct mature mRNA transcripts from a single gene by utilizing different splice sites. In plants like Arabidopsis thaliana, the most common type of alternative splicing is intron retention. Many studies in the past focus on positional distribution of retained introns (RIs) among different genic regions and their expression regulations, while little systematic classification of RIs from constitutively spliced introns (CSIs) has been conducted using machine learning approaches. We used random forest and support vector machine (SVM) with radial basis kernel function (RBF) to differentiate these two types of introns in Arabidopsis. By comparing coordinates of introns of all annotated mRNAs from TAIR10, we obtained our high-quality experimental data. To distinguish RIs from CSIs, We investigated the unique characteristics of RIs in comparison with CSIs and finally extracted 37 quantitative features: local and global nucleotide sequence features of introns, frequent motifs, the signal strength of splice sites, and the similarity between sequences of introns and their flanking regions. We demonstrated that our proposed feature extraction approach was more accurate in effectively classifying RIs from CSIs in comparison with other four approaches. The optimal penalty parameter C and the RBF kernel parameter in SVM were set based on particle swarm optimization algorithm (PSOSVM). Our classification performance showed F-Measure of 80.8% (random forest) and 77.4% (PSOSVM). Not only the basic sequence features and positional distribution characteristics of RIs were obtained, but also putative regulatory motifs in intron splicing were predicted based on our feature extraction approach. Clearly, our study will facilitate a better understanding of underlying mechanisms involved in intron retention.

Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray

Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

Molecular physiology and breeding at the crossroads of cold hardiness improvement

Alfalfa (Medicago sativa L.) is a major forage legume grown extensively worldwide with important agronomic and environmental attributes. Insufficient cold hardiness is a major impediment to its reliable production in northern climates. Improvement of freezing tolerance using conventional breeding approaches is slowed by the quantitative nature of inheritance and strong interactions with the environment. The development of gene-based markers would facilitate the identification of genotypes with superior stress tolerance. Successive cycles of recurrent selection were applied using an indoor screening method to develop populations with significantly higher tolerance to freezing (TF). Bulk segregant analysis of heterogeneous TF populations identified DNA variations that are progressively enriched in frequency in response to selection. Polymorphisms resulting from intragenic variations within a dehydrin gene were identified and could potentially lead to the development of robust selection tools. Our results illustrate the benefits of feedback interactions between germplasm development programs and molecular physiology for a deeper understanding of the molecular and genetic bases of cold hardiness.

The role of canonical and noncanonical pre-mRNA splicing in plant stress responses

Plants are sessile organisms capable of adapting to various environmental constraints, such as high or low temperatures, drought, soil salinity, or pathogen attack. To survive the unfavorable conditions, plants actively employ pre-mRNA splicing as a mechanism to regulate expression of stress-responsive genes and reprogram intracellular regulatory networks. There is a growing evidence that various stresses strongly affect the frequency and diversity of alternative splicing events in the stress-responsive genes and lead to an increased accumulation of mRNAs containing premature stop codons, which in turn have an impact on plant stress response. A number of studies revealed that some mRNAs involved in plant stress response are spliced counter to the traditional conception of alternative splicing. Such noncanonical mRNA splicing events include trans-splicing, intraexonic deletions, or variations affecting multiple exons and often require short direct repeats to occur. The noncanonical alternative splicing, along with common splicing events, targets the spliced transcripts to degradation through nonsense-mediated mRNA decay or leads to translation of truncated proteins. Investigation of the diversity, biological consequences, and mechanisms of the canonical and noncanonical alternative splicing events will help one to identify those transcripts which are promising for using in genetic engineering and selection of stress-tolerant plants.

Characterization of the variable 3' UTR and expression of the two intron-containing KIN transcripts from Capsella bursa-pastoris

KIN genes are crucial members of the cold-regulated (COR) gene family, and are exclusively involved in normal developmental processes in many organs and respond to a variety of abiotic stresses in plants. Here, we cloned and sequenced not only two completely-spliced KIN transcripts (CbKIN1-S and CbKIN2-S), but also two intron-containing KIN transcripts (CbKIN1-U and CbKIN2-U), from Capsella bursa-pastoris, a widespread plant of the Brassicaceae family. The CbKIN1-U and CbKIN2-U transcripts each contained one additional intron in the coding region compared to the corresponding CbKIN1-S and CbKIN2-S transcripts. In addition, the two intron-containing KIN transcripts were found by rapid amplification of cDNA 3' ends (3' RACE) analysis with specific primers to have variable 3' untranslated regions (3' UTRs). We also analyzed CbKIN1-U and CbKIN2-U levels in different organs and embryonic stages by quantitative polymerase chain reaction (qPCR). They were found to be expressed in middle-stage embryos and flowers. After abscisic acid (ABA) treatment, CbKIN1-U and CbKIN2-U showed strong responses in young leaves and weak responses in flowers. Levels of the two intron-containing KIN transcripts were markedly increased in young leaves when plants were exposed to cold and heat stress. Both of them showed stronger responses to ABA treatment and cold stress than that to heat stress. CbKIN1-U and CbKIN2-U share similar gene expression profiles in development and in response to exposure to different stresses, suggesting that they probably play similar biological roles in C. bursa-pastoris.

Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity

Alternative splicing is a mechanism for the regulation of gene expression that is widespread in higher eukaryotes. Genome-wide approaches, based on comparison of expressed and genomic sequences, on tiling arrays, and on next-generation sequencing, have provided growing knowledge of the extent, distribution and association of alternative splicing with stress-related genes in plants. The functional meaning of alternative splicing in response to stress has been defined for many genes, and in particular for those involved in the regulation of the stress responses, such as protein kinases, transcription factors, splicing regulators and pathogen-resistance genes. The production of proteins with diverse domain rearrangements from the same gene is the main alternative splicing mechanism for pathogen-resistance genes. The plant response to abiotic stress is also characterized by a second mechanism, which consists of the expression of alternative transcripts that are targeted to nonsense-mediated decay. These quantitatively regulate stress-related gene expression. Many alternative splicing events are well conserved among plant species, and also across kingdoms, especially those observed in response to stress, for genes encoding splicing regulators, and other classes of RNA-binding proteins. Nevertheless, non-conserved events indicate that alternative splicing represents an evolutionary strategy that rapidly increases genome plasticity and develops new gene functions, along with other mechanisms such as gene duplication. Finally, the study of the naturally occurring variability of alternative splicing and the identification of genomic regions involved in the regulation of alternative splicing in crops are proposed as strategies for selecting genotypes with superior performance under adverse environmental conditions.

Identification of a protein network interacting with TdRF1, a wheat RING ubiquitin ligase with a protective role against cellular dehydration

Plants exploit ubiquitination to modulate the proteome with the final aim to ensure environmental adaptation and developmental plasticity. Ubiquitination targets are specifically driven to degradation through the action of E3 ubiquitin ligases. Genetic analyses have indicated wide functions of ubiquitination in plant life; nevertheless, despite the large number of predicted E3s, only a few of them have been characterized so far, and only a few ubiquitination targets are known. In this work, we characterized durum wheat (Triticum durum) RING Finger1 (TdRF1) as a durum wheat nuclear ubiquitin ligase. Moreover, its barley (Hordeum vulgare) homolog was shown to protect cells from dehydration stress. A protein network interacting with TdRF1 has been defined. The transcription factor WHEAT BEL1-TYPE HOMEODOMAIN1 (WBLH1) was degraded in a TdRF1-dependent manner through the 26S proteasome in vivo, the mitogen-activated protein kinase TdWNK5 [for Triticum durum WITH NO LYSINE (K)5] was able to phosphorylate TdRF1 in vitro, and the RING-finger protein WHEAT VIVIPAROUS-INTERACTING PROTEIN2 (WVIP2) was shown to have a strong E3 ligase activity. The genes coding for the TdRF1 interactors were all responsive to cold and/or dehydration stress, and a negative regulative function in dehydration tolerance was observed for the barley homolog of WVIP2. A role in the control of plant development was previously known, or predictable based on homology, for wheat BEL1-type homeodomain1(WBLH1). Thus, TdRF1 E3 ligase might act regulating the response to abiotic stress and remodeling plant development in response to environmental constraints.

The e3 ubiquitin ligase gene family in plants: regulation by degradation

The regulation of protein expression and activity has been for long time considered only in terms of transcription/translation efficiency. In the last years, the discovery of post-transcriptional and post-translational regulation mechanisms pointed out that the key factor in determining transcript/protein amount is the synthesis/degradation ratio, together with post-translational modifications of proteins. Polyubiquitinaytion marks target proteins directed to degradation mediated by 26S-proteasome. Recent functional genomics studies pointed out that about 5% of Arabidopsis genome codes for proteins of ubiquitination pathway. The most of them (more than one thousand genes) correspond to E3 ubiquitin ligases that specifically recognise target proteins. The huge size of this gene family, whose members are involved in regulation of a number of biological processes including hormonal control of vegetative growth, plant reproduction, light response, biotic and abiotic stress tolerance and DNA repair, indicates a major role for protein degradation in control of plant life.

A role for SR proteins in plant stress responses

Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress.

Alternative splicing in the coding region of Ppo-A1 directly influences the polyphenol oxidase activity in common wheat (Triticum aestivum L.)

Polyphenol oxidase (PPO) plays a crucial role in browning reactions in fresh and processed fruits and vegetables, as well as products made from cereal grains. Common wheat (Triticum aestivum L.) has a large genome, representing an interesting system to advance our understanding of plant PPO gene expression, regulation and function. In the present study, we characterized the expression of Ppo-A1, a major PPO gene located on wheat chromosome 2A, using DNA sequencing, semi-quantitative RT-PCR, PPO activity assays and whole-grain staining methods during grain development. The results indicated that the expression of the Ppo-A1b allele was regulated by alternative splicing of pre-mRNAs, resulting from a 191-bp insertion in intron 1 and one C/G SNP in exon 2. Eight mRNA isoforms were identified in developing grains based on alignments between cDNA and genomic DNA sequences. Only the constitutively spliced isoform b encodes a putative full-length PPO protein based on its coding sequence whereas the other seven spliced isoforms, a, c, d, e, f, g and h, have premature termination codons resulting in potential nonsense-mediated mRNA decay. The differences in expression of Ppo-A1a and Ppo-A1b were confirmed by PPO activity assays and whole grain staining, providing direct evidence for the influence of alternative splicing in the coding region of Ppo-A1 on polyphenol oxidase activity in common wheat grains.

Gene regulation during cold stress acclimation in plants

Cold stress adversely affects plant growth and development and thus limits crop productivity. Diverse plant species tolerate cold stress to a varying degree, which depends on reprogramming gene expression to modify their physiology, metabolism, and growth. Cold signal in plants is transmitted to activate CBF-dependent (C-repeat/drought-responsive element binding factor-dependent) and CBF-independent transcriptional pathway, of which CBF-dependent pathway activates CBF regulon. CBF transcription factor genes are induced by the constitutively expressed ICE1 (inducer of CBF expression 1) by binding to the CBF promoter. ICE1-CBF cold response pathway is conserved in diverse plant species. Transgenic analysis in different plant species revealed that cold tolerance can be significantly enhanced by genetic engineering CBF pathway. Posttranscriptional regulation at pre-mRNA processing and export from nucleus plays a role in cold acclimation. Small noncoding RNAs, namely micro-RNAs (miRNAs) and small interfering RNAs (siRNAs), are emerging as key players of posttranscriptional gene silencing. Cold stress-regulated miRNAs have been identified in Arabidopsis and rice. In this chapter, recent advances on cold stress signaling and tolerance are highlighted.

A diurnally regulated dehydrin from Avicennia marina that shows nucleo-cytoplasmic localization and is phosphorylated by Casein kinase II in vitro

Dehydrins have a key role in protecting plants from dehydration stress. We report here the isolation of two cDNAs coding for the same dehydrin, AmDHN1 and AmDHN1a from salt stressed leaves of Avicennia marina (Forsk.) Vierh. by EST library screening. AmDHN1 was found to contain a retained intron that was absent in AmDHN1a. AmDHN1 expression in the context of various environmental stresses was investigated. In leaves, AmDHN1 shows a diurnal pattern of regulation and is induced only by mannitol application. In roots, AmDHN1 is rapidly induced by salinity (NaCl) and dehydration stress (PEG and mannitol). A fragment of 795 bp corresponding to the 5' upstream region of AmDHN1 was isolated by TAIL-PCR. In silico analysis of this sequence reveals the presence of putative stress regulatory elements (ABRE, DRE, MYB and MYC binding sequences). Putative phosphorylation sites for Casein kinase II were identified in the AmDHN1a ORF. In vitro phosphorylation of Escherichia coli expressed Trx-AmDHN1a by Casein kinase II was observed that was reversed by Shrimp Alkaline Phosphatase treatment. A putative nuclear targeting domain was identified in the translated AmDHN1a ORF and stably transformed AmDHNIa-GFP was found to show nucleo-cytoplasmic localization in tobacco guard cells. As observed for maize Rab 17, the phosphorylation of AmDHN1a may contribute to its nuclear localization.

Regulation of alternative splicing of pre-mRNAs by stresses

A substantial fraction (approximately 30%) of plant genes is alternatively spliced, but how alternative splicing is regulated remains unknown. Many plant genes undergo alternative splicing in response to a variety of stresses. Large-scale computational analyses and experimental approaches focused on select genes are beginning to reveal that alternative splicing constitutes an integral part of gene regulation in stress responses. Based on the studies discussed in this chapter, it appears that alternative splicing generates transcriptome/proteome complexity that is likely to be important for stress adaptation. However, the signaling pathways that relay stress conditions to splicing machinery and if and how the alternative spliced products confer adaptive advantages to plants are poorly understood.

Post-harvest regulated gene expression and splicing efficiency in storage roots of sugar beet (Beta vulgaris L.)

Sixteen post-harvest upregulated genes from sugar beet comprising five novel sequences were isolated by subtractive cloning. Transcription profiles covering a period of up to 49 days after harvest under controlled storage conditions and in field clamps are reported. Post-harvest induced genes are involved in wound response, pathogen defense, dehydration stress, and detoxification of reactive oxygen species. An early induction of a cationic peroxidase indicates a response to post-harvest damage. Wound response reactions may also involve genes required for cell division such as a regulator of chromatin condensation and a precursor of the growth stimulating peptide phytohormone phytosulfokine-alpha. Surprisingly, also three putative non-protein coding genes were isolated. Two of these genes show intron specific and storage temperature dependent splicing of a precursor mRNA. The temperature dependent splicing of an intron containing sugar beet mRNA is also maintained in transgenic Arabidopsis thaliana. The storage induced genes are integrated into a model that proposes the response to several post-harvest stress conditions. Temperature regulated splicing may be a mechanism to sense seasonal temperature changes.

Integration of metabolomic and proteomic phenotypes: analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana

Statistical mining and integration of complex molecular data including metabolites, proteins, and transcripts is one of the critical goals of systems biology (Ideker, T., Galitski, T., and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343–372). A number of studies have demonstrated the parallel analysis of metabolites and large scale transcript expression. Protein analysis has been ignored in these studies, although a clear correlation between transcript and protein levels is shown only in rare cases, necessitating that actual protein levels have to be determined for protein function analysis. Here, we present an approach to investigate the combined covariance structure of metabolite and protein dynamics in a systemic response to abiotic temperature stress in Arabidopsis thaliana wild-type and a corresponding starch-deficient mutant (phosphoglucomutase-deficient). Independent component analysis revealed phenotype classification resolving genotype-dependent response effects to temperature treatment and genotype-independent general temperature compensation mechanisms. An observation is the stress-induced increase of raffinose-family-oligosaccharide levels in the absence of transitory starch storage/mobilization in temperature-treated phosphoglucomutase plants indicating that sucrose synthesis and storage in these mutant plants is sufficient to bypass the typical starch storage/mobilization pathways under abiotic stress. Eventually, sample pattern recognition and correlation network topology analysis allowed for the detection of specific metabolite-protein co-regulation and assignment of a circadian output regulated RNA-binding protein to these processes. The whole concept of high-dimensional profiling data integration from many replicates, subsequent multivariate statistics for dimensionality reduction, and covariance structure analysis is proposed to be a major strategy for revealing central responses of the biological system under study.

Redox and heavy metal effects on the biochemical activities of an Arabidopsis polyadenylation factor subunit

The Arabidopsis CPSF30 ortholog (AtCPSF30) is an RNA-binding endonuclease that is part of the plant polyadenylation complex. Previous work (B. Addepalli, A.G. Hunt, Nucleic Acids Res. 35 (2007) 4453-4463) demonstrated that different zinc finger motifs in the protein were responsible for RNA-binding and nuclease activity, respectively. In this study, a more detailed functional map of AtCPSF30 is presented, a map that includes descriptions of novel biochemical activities. Elevated temperatures, the specific zinc chelator 1,10-phenanthroline, and the sulfhydryl reagent dithiothreitol all had differential inhibitory effects on the RNA-binding and nuclease activities. The endonuclease activity of AtCPSF30 was inhibited by relatively high (>100muM) concentrations of zinc, and this inhibition required a plant-specific N-terminal domain apart from the zinc finger core of the protein. ATP stimulated the nuclease activity in the presence of zinc, and this stimulation required a plant-specific C-terminal domain, again apart from the zinc finger core. These studies reveal a subtle and unexpected complexity to AtCPSF30, and raise the possibility that multiple avenues of regulation may impinge on this protein through different functional domains.

Cold stress regulation of gene expression in plants

Cold stress adversely affects plant growth and development. Most temperate plants acquire freezing tolerance by a process called cold acclimation. Here, we focus on recent progress in transcriptional, post-transcriptional and post-translational regulation of gene expression that is critical for cold acclimation. Transcriptional regulation is mediated by the inducer of C-repeat binding factor (CBF) expression 1 (ICE1), the CBF transcriptional cascade and CBF-independent regulons during cold acclimation. ICE1 is negatively regulated by ubiquitination-mediated proteolysis and positively regulated by SUMO (small ubiquitin-related modifier) E3 ligase-catalyzed sumoylation. Post-transcriptional regulatory mechanisms, such as pre-mRNA splicing, mRNA export and small RNA-directed mRNA degradation, also play important roles in cold stress responses.

The transcript levels of two plant mitochondrial uncoupling protein (pUCP)-related genes are not affected by hyperosmotic stress in durum wheat seedlings showing an increased level of pUCP activity

Etiolated early seedlings of durum wheat submitted to moderate and severe salt (NaCl) and osmotic (mannitol) stress showed no relevant increase of both transcript levels of two plant uncoupling protein (pUCP)-related genes and maximal pUCP activity in purified mitochondria (which estimates protein level); contrarily, pUCP functioning due to endogenous free fatty acids strongly increased. These results show that pUCP activation under hyperosmotic stress may be due to modulation of pUCP reaction rather than to an increased protein synthesis. Finally, a properly developed method, based on a single membrane potential measurement, to evaluate both pUCP maximal activity and functioning, is reported.

Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses

Precursor mRNAs with introns can undergo alternative splicing (AS) to produce structurally and functionally different proteins from the same gene. Here, we show that the pre-mRNAs of Arabidopsis genes that encode serine/arginine-rich (SR) proteins, a conserved family of splicing regulators in eukaryotes, are extensively alternatively spliced. Remarkably about 95 transcripts are produced from only 15 genes, thereby increasing the complexity of the SR gene family transcriptome by six-fold. The AS of some SR genes is controlled in a developmental and tissue-specific manner. Interestingly, among the various hormones and abiotic stresses tested, temperature stress (cold and heat) dramatically altered the AS of pre-mRNAs of several SR genes, whereas hormones altered the splicing of only three SR genes. These results indicate that abiotic stresses regulate the AS of the pre-mRNAs of SR genes to produce different isoforms of SR proteins that are likely to have altered function(s) in pre-mRNA splicing. Sequence analysis of splice variants revealed that predicted proteins from a majority of these variants either lack one or more modular domains or contain truncated domains. Because of the modular nature of the various domains in SR proteins, the proteins produced from splice variants are likely to have distinct functions. Together our results indicate that Arabidopsis SR genes generate surprisingly large transcriptome complexity, which is altered by stresses and hormones.

Regulation of the beta-hydroxyacyl ACP dehydratase gene of Picea mariana by alternative splicing

The gene for beta-hydroxyacyl ACP dehydratase, a de novo fatty acid biosynthetic enzyme, was cloned from Picea mariana (black spruce) and consists of five exons and four introns. The first intron of the beta-hydroxyacyl ACP dehydratase mRNA is alternatively spliced. Retention of intron 1 in splice variants results in truncation of the beta-hydroxyacyl ACP dehydratase ORF at a premature termination codon. In addition, splicing of intron 1 was found to be associated with cold temperature. mRNAs retaining intron 1 increase with seed imbibition at 22 degrees C but not 4 degrees C, whereas, splicing of intron 1 increases in winter weeks with temperatures below freezing. These results provide evidence that alternative splicing may also contribute to regulation of lipid biosynthesis in Picea mariana.