scholarly journals Circadian Regulation of Alternative Splicing of Drought-Associated CIPK Genes in Dendrobium catenatum (Orchidaceae)

2019 ◽  
Vol 20 (3) ◽  
pp. 688 ◽  
Author(s):  
Xiao Wan ◽  
Long-Hai Zou ◽  
Bao-Qiang Zheng ◽  
Yan Wang
Keyword(s):  
Signal Transduction ◽  
Abiotic Stress ◽  
Alternative Splicing ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Biological Clock ◽  
Pcr Analysis ◽  
Gene Transcript ◽  
Drought Treatment ◽  
Protein Motifs

Dendrobium catenatum, an epiphytic and lithophytic species, suffers frequently from perennial shortage of water in the wild. The molecular mechanisms of this orchid’s tolerance to abiotic stress, especially drought, remain largely unknown. It is well-known that CBL-interacting protein kinase (CIPKs) proteins play important roles in plant developmental processes, signal transduction, and responses to abiotic stress. To study the CIPKs’ functions for D. catenatum, we first identified 24 CIPK genes from it. We divided them into three subgroups, with varying intron numbers and protein motifs, based on phylogeny analysis. Expression patterns of CIPK family genes in different tissues and in response to either drought or cold stresses suggested DcaCIPK11 may be associated with signal transduction and energy metabolism. DcaCIPK9, -14, and -16 are predicted to play critical roles during drought treatment specifically. Furthermore, transcript expression abundances of DcaCIPK16 showed polar opposites during day and night. Whether under drought treatment or not, DcaCIPK16 tended to emphatically express transcript1 during the day and transcript3 at night. This implied that expression of the transcripts might be regulated by circadian rhythm. qRT-PCR analysis also indicated that DcaCIPK3, -8, and -20 were strongly influenced by circadian rhythmicity. In contrast with previous studies, for the first time to our knowledge, our study revealed that the major CIPK gene transcript expressed was not always the same and was affected by the biological clock, providing a different perspective on alternative splicing preference.

scholarly journals Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Vânia Gonçalves ◽  
Peter Jordan
Keyword(s):  
Alternative Splicing ◽  
Cancer Cell ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Current Knowledge ◽  
Expression Patterns ◽  
Regulatory Protein ◽  
Gene Transcript

Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

scholarly journals Preliminary Classification of the ABC Transporter Family in Betula halophila and Expression Patterns in Response to Exogenous Phytohormones and Abiotic Stresses

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 722
Author(s):  
An ◽  
Ma ◽  
Du ◽  
Yu ◽  
Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Abc Transporters ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Structural Domain ◽  
Transcriptional Responses ◽  
Hormone Transport ◽  
Transporter Family

ATP-binding cassette (ABC) transporters comprise a transport system superfamily which is ubiquitous in eukaryotic and prokaryotic cells. In plants, ABC transporters play important roles in hormone transport and stress tolerance. In this study, 15 BhABC transporters encoded by genes identified from the transcriptome of Betula halophila were categorized into four subfamilies (ABCB, ABCF, ABCG, and ABCI) using structural domain and phylogenetic analyses. Upon B. halophila exposure to exogenous phytohormones and abiotic stressors, gene expression patterns and transcriptional responses for each subfamily of genes were obtained using semi-quantitative RT-PCR analysis. The results demonstrated that expression of most genes belonging to ABCB and ABCG subfamilies changed in response to exogenous phytohormone exposures and abiotic stress. These results suggest that BhABC genes may participate in hormone transport and that their expression may be influenced by ABA-dependent signaling pathways involved in abiotic stress responses to various stressors.

scholarly journals Identification, Characterization and Expression Analysis Reveal the Potential Function of Annexin Genes in Response to Abiotic stress, Calcium and Hormones in Cassava (Manihot esculeta Crantz)

2019 ◽  
Author(s):  
Ruimei Li ◽  
Yuqing Wang ◽  
Yangjiao Zhou ◽  
Tingting Qiu ◽  
Yu Song ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Expression Patterns ◽  
Membrane Lipid ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Promoter Regions ◽  
Manihot Esculenta Crantz ◽  
Diverse Range ◽  
Drought And Salt Stress

Abstract Background The calcium (Ca2+)-dependent phospholipid binding protein annexin gene family, which is known to be related to membrane lipid and cytoskeletal components, is involved in a diverse range of biological functions. However, in cassava (Manihot esculenta Crantz), no studies focusing on the roles of annexin genes in response to abiotic stresses, calcium, and hormones have been informed. Results 12 annexin genes were found and assigned to eight chromosomes in the cassava genome. All of the MeAnns contain a typical annexin domain with four 70-amino acid repeats. The MeAnns are classified into six groups in the phylogenetic tree. In their promoter regions, MeAnns possess at least 3 hormone response-related cis-elements and 1 abiotic stress response-related cis-acting element. MeAnn1, MeAnn2 and MeAnn5 exhibit very high levels of expression in each tested organs or tissues. By contrast, MeAnn12 exhibits very low levels in all the tested organs or tissues. qRT-PCR analysis indicates that both MeAnn5 and MeAnn9 have significantly high expression in leaves after cold, drought, and salt treatments and are highly responsive to CaCl2, GA and JA treatments. MeAnn2 and MeAnn10 are significantly downregulated in leaves by cold, drought and salt stress and negatively respond to CaCl2, GA and JA. The expression patterns of MeAnns under cold, drought, and salt stress are irregular in shoots. In roots, MeAnn1 and MeAnn9 are downregulated by cold, CaCl2 and JA treatments, while their other gene expression patterns are irregular. Conclutions In this study, we identified annexin genes in cassava and our expression profiling analysis demonstrated that cassava annexin genes responded to multiple stresses. Our results laid the foundation for further study of the function of cassava anesxin genes and provided an entry point for understanding the response mechanism of cassava to abiotic stress.

scholarly journals Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

2020 ◽  
Author(s):  
Wei Wang ◽  
Lei Wang ◽  
Ling Wang ◽  
Meilian Tan ◽  
Collins O. Ogutu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Single Molecule ◽  
Linum Usitatissimum ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Resistant Variety ◽  
Drought Treatment ◽  
Oil Crops ◽  
Drought Resistant

Abstract Background Oil flax (Linum usitatissimum L.) also as known as linseed is one of the most important oil crops in the world. Although linseed was reported to show better tolerance to abiotic stress conditions compared to other oil crops, the molecular mechanisms underlying linseed tolerance to drought stress are largely unknown. Moreover, as a result of climate change, drought dramatically reduces linseed yield and quality, but so far very little is known about how linseed coordinates the drought-resistant genes expression of response to different level of drought stress on the genome-wide level. Results To explore the transcriptional response of linseed to drought stress (DS) and repeated drought stress (RD), we first determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) using single-molecule real-time sequencing and RNA-sequencing under drought stress (DS) and repeated drought stress (RD) at the seedling stage. Gene Ontology (GO) enrichment analysis showed that compared with NY-17, the up-regulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance under drought stress. In addition, the number of up-regulated genes in linseed under RD was more 30% than it under DS. In addition, a total of, 4,436 linseed transcription factors were identified, of these, 1,190 genes were responsive to stress treatments. Finally, the expression patterns of proline biosynthesis and DNA repair structural genes were verified by RT- PCR. Conclusions Drought tolerance of Z141 may be related to its specifically up-regulated drought tolerance genes under drought stress. Several variable physiological responses occurred in repeated than in sustained drought treatment. Sum up, this study provides a new perspective to understand the drought adaptability of linseed.

scholarly journals Comparative Transcriptome Analysis of a Fan-shaped Inflorescence in Pineapple Using RNA-seq

2020 ◽  
Author(s):  
Tao Xie ◽  
Zhiquan Cai ◽  
Aiping Luan ◽  
Wei Zhang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Soluble Sugar ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Stem Apex ◽  
Inflorescence Axis ◽  
Flower Stem

Abstract Background: Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was evolved in an exceptional material, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between a fan-shaped inflorescence (FI) and a capitulum inflorescence (CI) pineapples were analyzed in the three tissues, i.e., the flower stem apex (FIs and CIs), the base of the inflorescence (FIb and CIb), and the inflorescence axis (FIa and CIa).Results: Except for a clear differentiation of inflorescence morphology, no significant differences in the structure of inflorescence organs and the main nutritional components (soluble solids, soluble sugar, titratable acid, and VC) in fruits were found between the two pineapples. Between the fan- and capitulum-shaped inflorescences, a total of 5370 differentially expressed genes (DEGs) were identified across the three tissues; and 3142, 2526 and 2255 DEGs were found in the flower stem apex, the base of the inflorescence, and the inflorescence axis, respectively. Of these genes, there were 489 overlapping DEGs in all three tissue comparisons. In addition, 5769 DEGs were identified between different tissues within each pineapple. Functional analysis indicated between the two pineapples that 444 transcription factors (TFs) and 206 inflorescence development related genes (IDGs) were differentially expressed in at least one tissue comparison, while 45 TFs and 21 IDGs were overlapped across the 3 tissues. Among the 489 overlapping DEGs in the 3 tissue comparisons between the two pineapples, excluding the IDGs and TFs, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the same gene expression patterns in the three tissues. Conclusions: Our result provided novel cues for understanding the molecular mechanisms of the formation of fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of the pineapples.

scholarly journals Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10963 ◽  
Author(s):  
Yaqian Li ◽  
Jinghan Song ◽  
Guang Zhu ◽  
Zehao Hou ◽  
Lin Wang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Intracellular Transport ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Specific Expression ◽  
Wheat Varieties

The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.

scholarly journals Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 215 ◽  
Author(s):  
Qingnan Hao ◽  
Ling Zhang ◽  
Yanyan Yang ◽  
Zhihui Shan ◽  
Xin-an Zhou
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Regeneration Ability ◽  
Functional Identification ◽  
Phylogenetic Tree Analysis ◽  
Wox Genes

WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide. In this study, based on the available genome data of soybean, the WOX gene family was identified by bioinformatics analysis. The chromosome distribution, gene and protein structures, phylogenetic relationship and gene expression patterns of this family were comprehensively compared. The results showed that a total of 33 putative WOX genes in the soybean genome were found and then designated as GmWOX1- GmWOX33, which were distributed across 19 chromosomes except chromosome 16. Multiple sequence analysis of the GmWOX gene family revealed a highly conserved homeodomain. Phylogenetic tree analysis showed that 33 WOX genes could be divided into three major clades (modern/WUS, intermediate and ancient) in soybean. Of these 33 WOX genes, some showed differential expression patterns in the tested tissues (leaves, pods, unopen and open flowers, nodules, seed, roots, root hairs, stems, shoot apical meristems and shoot tips). In addition, the expression profile and qRT-PCR analysis showed that most of the GmWOX genes responded to different abiotic stress treatments (cold and drought). According to the expression pattern of GmWOX genes in the high regeneration capacity soybean material P3, overexpression of GmWOX18 was selected for function analysis. The overexpression of GmWOX18 increased the regeneration ability of clustered buds. The results will provide valuable information for further studies on the roles of WOX genes in regulating soybean growth, development and responses to abiotic stress, as well as a basis for the functional identification and analysis of WOX genes in soybean.

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