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Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 26074

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Special Issue Editors

Dr. Bei Gao

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Guest Editor

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Interests: evolutionary genomics; bioinformatics; early land plants; desiccation tolerance
Special Issues, Collections and Topics in MDPI journals

Dr. Moxian Chen

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Guest Editor

State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China
Interests: proteogenomics; abiotic stress; post-transcriptional regulation; genetic engineering
Special Issues, Collections and Topics in MDPI journals

Dr. Melvin J. Oliver

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Guest Editor

College of Agriculture, Food & Natural Resources, University of Missouri, Columbia, MO 65211, USA
Interests: abiotic stress; desiccation tolerance; plant physiology; phylogenetics; genomics; transcriptomics; metabolomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Post-transcriptional regulations, especially alternative splicing (AS) events, substantially contribute to the complexity of eukaryotic transcriptomes. With the advent of 3rd generation Iso-Seq technology, full-length transcripts could be obtained accurately and efficiently, with or without a reference genome. Investigating alternative splicing events comes to their golden age as high fidelity of Pacbio reads were achieved and the costs became more affordable. We consider that investigating and comparing AS events of genes across lineages or within phylogenetically related species would also be a very interesting topic.

Agricultural productivity has been threatened by the growing climate change problems, so investigating the molecular mechanisms underlying the various kinds of environmental stresses has become an urgent task for crop improvement. A lot of literature has revealed a linkage between AS events and plant stress tolerance. Furthermore, AS mutation has direct effect on animals and approximately 15-35% of human diseases are related to missense mutation of human genes. Thus, AS plays an important role in Kingdom Eukarya.

This Special Issue will focus on the alternative splicing events of genes and their regulation in response to abiotic stress or disease, and their evolution in different genomes. Notwithstanding, contributions on related topics aimed at understanding the biological functions of alternative splicing in plants are also welcomed, including reviews and original research articles.

Dr. Bei Gao
Dr. Moxian Chen
Dr. Melvin J. Oliver
Guest Editors

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Keywords

alternative splicing
Iso-Seq
PacBio
exon skipping
intron retention
abiotic stress
water deficit
desiccation tolerance

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

4 pages, 183 KiB

Open AccessEditorial

Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics

by Bei Gao, Moxian Chen and Melvin J. Oliver

Int. J. Mol. Sci. 2023, 24(7), 6708; https://doi.org/10.3390/ijms24076708 - 4 Apr 2023

Cited by 3 | Viewed by 1455

Abstract

The post-transcriptional regulation of gene expression, in particular alternative splicing (AS) events, substantially contributes to the complexity of eukaryotic transcriptomes and proteomes [...] Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

Research

Jump to: Editorial, Review

16 pages, 3198 KiB

Open AccessArticle

SWATH-MS-Based Proteomics Reveals the Regulatory Metabolism of Amaryllidaceae Alkaloids in Three Lycoris Species

by Meng Tang, Chaohan Li, Cheng Zhang, Youming Cai, Yongchun Zhang, Liuyan Yang, Moxian Chen, Fuyuan Zhu, Qingzhu Li and Kehu Li

Int. J. Mol. Sci. 2023, 24(5), 4495; https://doi.org/10.3390/ijms24054495 - 24 Feb 2023

Cited by 5 | Viewed by 1766

Abstract

Alkaloids are a class of nitrogen-containing alkaline organic compounds found in nature, with significant biological activity, and are also important active ingredients in Chinese herbal medicine. Amaryllidaceae plants are rich in alkaloids, among which galanthamine, lycorine, and lycoramine are representative. Since the difficulty and high cost of synthesizing alkaloids have been the major obstacles in industrial production, particularly the molecular mechanism underlying alkaloid biosynthesis is largely unknown. Here, we determined the alkaloid content in Lycoris longituba, Lycoris incarnata, and Lycoris sprengeri, and performed a SWATH-MS (sequential window acquisition of all theoretical mass spectra)-based quantitative approach to detect proteome changes in the three Lycoris. A total of 2193 proteins were quantified, of which 720 proteins showed a difference in abundance between Ll and Ls, and 463 proteins showed a difference in abundance between Li and Ls. KEGG enrichment analysis revealed that differentially expressed proteins are distributed in specific biological processes including amino acid metabolism, starch, and sucrose metabolism, implicating a supportive role for Amaryllidaceae alkaloids metabolism in Lycoris. Furthermore, several key genes collectively known as OMT and NMT were identified, which are probably responsible for galanthamine biosynthesis. Interestingly, RNA processing-related proteins were also abundantly detected in alkaloid-rich Ll, suggesting that posttranscriptional regulation such as alternative splicing may contribute to the biosynthesis of Amaryllidaceae alkaloids. Taken together, our SWATH-MS-based proteomic investigation may reveal the differences in alkaloid contents at the protein levels, providing a comprehensive proteome reference for the regulatory metabolism of Amaryllidaceae alkaloids. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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27 pages, 8564 KiB

Open AccessArticle

Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed

by Ying-Peng Hua, Peng-Jia Wu, Tian-Yu Zhang, Hai-Li Song, Yi-Fan Zhang, Jun-Fan Chen, Cai-Peng Yue, Jin-Yong Huang, Tao Sun and Ting Zhou

Int. J. Mol. Sci. 2022, 23(22), 14484; https://doi.org/10.3390/ijms232214484 - 21 Nov 2022

Cited by 4 | Viewed by 2023

Abstract

The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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14 pages, 2460 KiB

Open AccessArticle

Regulation of Heat Stress in Physcomitrium (Physcomitrella) patens Provides Novel Insight into the Functions of Plant RNase H1s

by Zhuo Yang, Liu Duan, Hongyu Li, Ting Tang, Liuzhu Chen, Keming Hu, Hong Yang and Li Liu

Int. J. Mol. Sci. 2022, 23(16), 9270; https://doi.org/10.3390/ijms23169270 - 17 Aug 2022

Cited by 3 | Viewed by 1815

Abstract

RNase H1s are associated with growth and development in both plants and animals, while the roles of RNase H1s in bryophytes have been rarely reported. Our previous data found that PpRNH1A, a member of the RNase H1 family, could regulate the development of Physcomitrium (Physcomitrella) patens by regulating the auxin. In this study, we further investigated the biological functions of PpRNH1A and found PpRNH1A may participate in response to heat stress by affecting the numbers and the mobilization of lipid droplets and regulating the expression of heat-related genes. The expression level of PpRNH1A was induced by heat stress (HS), and we found that the PpRNH1A overexpression plants (A-OE) were more sensitive to HS. At the same time, A-OE plants have a higher number of lipid droplets but with less mobility in cells. Consistent with the HS sensitivity phenotype in A-OE plants, transcriptomic analysis results indicated that PpRNH1A is involved in the regulation of expression of heat-related genes such as DNAJ and DNAJC. Taken together, these results provide novel insight into the functions of RNase H1s. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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18 pages, 2741 KiB

Open AccessArticle

Overexpression of the Arabidopsis MACPF Protein AtMACP2 Promotes Pathogen Resistance by Activating SA Signaling

by Xue Zhang, Yang-Shuo Dai, Yu-Xin Wang, Ze-Zhuo Su, Lu-Jun Yu, Zhen-Fei Zhang, Shi Xiao and Qin-Fang Chen

Int. J. Mol. Sci. 2022, 23(15), 8784; https://doi.org/10.3390/ijms23158784 - 7 Aug 2022

Cited by 9 | Viewed by 2330

Abstract

Immune response in plants is tightly regulated by the coordination of the cell surface and intracellular receptors. In animals, the membrane attack complex/perforin-like (MACPF) protein superfamily creates oligomeric pore structures on the cell surface during pathogen infection. However, the function and molecular mechanism of MACPF proteins in plant pathogen responses remain largely unclear. In this study, we identified an Arabidopsis MACP2 and investigated the responsiveness of this protein during both bacterial and fungal pathogens. We suggest that MACP2 induces programmed cell death, bacterial pathogen resistance, and necrotrophic fungal pathogen sensitivity by activating the biosynthesis of tryptophan-derived indole glucosinolates and the salicylic acid signaling pathway dependent on the activity of enhanced disease susceptibility 1 (EDS1). Moreover, the response of MACP2 mRNA isoforms upon pathogen attack is differentially regulated by a posttranscriptional mechanism: alternative splicing. In comparison to previously reported MACPFs in Arabidopsis, MACP2 shares a redundant but nonoverlapping role in plant immunity. Thus, our findings provide novel insights and genetic tools for the MACPF family in maintaining SA accumulation in response to pathogens in Arabidopsis. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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13 pages, 2609 KiB

Open AccessArticle

Moderate Soil Drying-Induced Alternative Splicing Provides a Potential Novel Approach for the Regulation of Grain Filling in Rice Inferior Spikelets

by Zhenning Teng, Qin Zheng, Bohan Liu, Shuan Meng, Jianhua Zhang and Nenghui Ye

Int. J. Mol. Sci. 2022, 23(14), 7770; https://doi.org/10.3390/ijms23147770 - 14 Jul 2022

Cited by 5 | Viewed by 1772

Abstract

Poor grain filling of inferior spikelets, especially in some large-panicle rice varieties, is becoming a major limitation in breaking the ceiling of rice production. In our previous studies, we proved that post-anthesis moderate soil drying (MD) was an effective way to promote starch synthesis and inferior grain filling. As one of the most important regulatory processes in response to environmental cues and at different developmental stages, the function of alternative splicing (AS) has not yet been revealed in regulating grain filling under MD conditions. In this study, AS events at the most active grain-filling stage were identified in inferior spikelets under well-watered control (CK) and MD treatments. Of 16,089 AS events, 1840 AS events involving 1392 genes occurred differentially between the CK and MD treatments, many of which function on spliceosome, ncRNA metabolic process, starch, and sucrose metabolism, and other functions. Some of the splicing factors and starch synthesis-related genes, such as SR protein, hnRNP protein, OsAGPL2, OsAPS2, OsSSIVa, OsSSIVb, OsGBSSII, and OsISA1 showed differential AS changes under MD treatment. The expression of miR439f and miR444b was reduced due to an AS event which occurred in the intron where miRNAs were located in the MD-treated inferior spikelets. On the contrary, OsAGPL2, an AGPase encoding gene, was alternatively spliced, resulting in different transcripts with or without the miR393b binding site, suggesting a potential mechanism for miRNA-mediated gene regulation on grain filling of inferior spikelets in response to MD treatment. This study provides some new insights into the function of AS on the MD-promoted grain filling of inferior spikelets, and potential application in agriculture to increase rice yields by genetic approaches. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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21 pages, 5214 KiB

Open AccessArticle

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

by Yukang Hou, Qi Lu, Jianxun Su, Xing Jin, Changfu Jia, Lizhe An, Yongke Tian and Yuan Song

Int. J. Mol. Sci. 2022, 23(14), 7622; https://doi.org/10.3390/ijms23147622 - 10 Jul 2022

Cited by 7 | Viewed by 2179

Abstract

Histone deacetylases (HDACs), widely found in various types of eukaryotic cells, play crucial roles in biological process, including the biotic and abiotic stress responses in plants. However, no research on the HDACs of Fagopyrum tataricum has been reported. Here, 14 putative FtHDAC genes were identified and annotated in Fagopyrum tataricum. Their gene structure, motif composition, cis-acting elements, phylogenetic relationships, protein structure, alternative splicing events, subcellular localization and gene expression pattern were investigated. The gene structure showed FtHDACs were classified into three subfamilies. The promoter analysis revealed the presence of various cis-acting elements responsible for hormone, abiotic stress and developmental regulation for the specific induction of FtHDACs. Two duplication events were identified in FtHDA6-1, FtHDA6-2, and FtHDA19. The expression patterns of FtHDACs showed their correlation with the flavonoid synthesis pathway genes. In addition, alternative splicing, mRNA enrichment profiles and transgenic analysis showed the potential role of FtHDACs in cold responses. Our study characterized FtHDACs, providing a candidate gene family for agricultural breeding and crop improvement. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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14 pages, 5712 KiB

Open AccessArticle

Identifying QTLs for Grain Size in a Colossal Grain Rice (Oryza sativa L.) Line, and Analysis of Additive Effects of QTLs

by Xuanxuan Hou, Moxian Chen, Yinke Chen, Xin Hou, Zichang Jia, Xue Yang, Jianhua Zhang, Yinggao Liu and Nenghui Ye

Int. J. Mol. Sci. 2022, 23(7), 3526; https://doi.org/10.3390/ijms23073526 - 24 Mar 2022

Cited by 2 | Viewed by 2353

Abstract

Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F₂ intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on Os03g0841800 (qGL3.3), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, qTGW2.1 and qGW2.3 were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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Review

Jump to: Editorial, Research

20 pages, 3116 KiB

Open AccessReview

Alternative Splicing and Its Roles in Plant Metabolism

by Pui Ying Lam, Lanxiang Wang, Clive Lo and Fu-Yuan Zhu

Int. J. Mol. Sci. 2022, 23(13), 7355; https://doi.org/10.3390/ijms23137355 - 1 Jul 2022

Cited by 28 | Viewed by 3561

Abstract

Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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16 pages, 1082 KiB

Open AccessReview

Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome

by Yue-Han Li, Yuan-You Yang, Zhi-Gang Wang and Zhuo Chen

Int. J. Mol. Sci. 2022, 23(9), 4860; https://doi.org/10.3390/ijms23094860 - 27 Apr 2022

Cited by 4 | Viewed by 2604

Abstract

In recent years, host–microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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13 pages, 1330 KiB

Open AccessReview

The Importance of a Genome-Wide Association Analysis in the Study of Alternative Splicing Mutations in Plants with a Special Focus on Maize

by Zi-Chang Jia, Xue Yang, Xuan-Xuan Hou, Yong-Xin Nie and Jian Wu

Int. J. Mol. Sci. 2022, 23(8), 4201; https://doi.org/10.3390/ijms23084201 - 11 Apr 2022

Cited by 4 | Viewed by 2397

Abstract

Alternative splicing is an important mechanism for regulating gene expressions at the post-transcriptional level. In eukaryotes, the genes are transcribed in the nucleus to produce pre-mRNAs and alternative splicing can splice a pre-mRNA to eventually form multiple different mature mRNAs, greatly increasing the number of genes and protein diversity. Alternative splicing is involved in the regulation of various plant life activities, especially the response of plants to abiotic stresses and is also an important process of plant growth and development. This review aims to clarify the usefulness of a genome-wide association analysis in the study of alternatively spliced variants by summarizing the application of alternative splicing, genome-wide association analyses and genome-wide association analyses in alternative splicing, as well as summarizing the related research progress. Full article

(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics)

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