scholarly journals Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in Brassica rapa

2018 ◽  
Vol 2018 ◽  
pp. 1-18 ◽  
Author(s):  
Nadeem Khan ◽  
Chun-mei Hu ◽  
Waleed Amjad Khan ◽  
Emal Naseri ◽  
Han Ke ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Network Analyses ◽  
Heat And Cold Stress ◽  
Ubiquitin Conjugating Enzymes

To understand ubiquitination mechanism, E2s (ubiquitin conjugating enzymes) have crucial part as they play a major role in regulating many biological processes in plants. Meanwhile, Brassica rapa is an important leafy vegetable crop and therefore its characterization along with the expression pattern of E2s under various stresses is imperative. In this study, a total of 83 genes were identified in B. rapa and were classified into four different classes based on domain information. Here, we analyzed phylogenetic relationships, collinear correlation, gene duplication, interacting network, and expression patterns of E2 genes in B. rapa. Furthermore, RT-PCR analysis for 8 multiple abiotic and hormone treatments (namely, ABA, GA, JA, BR, PEG, NaCl, and heat and cold stress) illustrated striking expression pattern under one or more treatments, speculating that these might be stress-responsive genes. The cis-elements and interaction network analyses implicate valuable clues of important function of E2 genes in development and multiple stress responses in B. rapa. This study will further facilitate functional analysis of E2s for improving stress resistance mechanism in B. rapa.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 315
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Xuemei Xu ◽  
Chenghao Li
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Element Analysis ◽  
Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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 Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1412
Author(s):  
Ruchi Bansal ◽  
Nitika Rana ◽  
Akshay Singh ◽  
Pallavi Dhiman ◽  
Rushil Mandlik ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Rice ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
North East ◽  
Wild Rice Species

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

scholarly journals Characterization of Brassica rapa RAP2.4-Related Proteins in Stress Response and as CUL3-Dependent E3 Ligase Substrates

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 336 ◽  
Author(s):  
Sutton Mooney ◽  
Raed Al-Saharin ◽  
Christina M. Choi ◽  
Kyle Tucker ◽  
Chase Beathard ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Stress Responses ◽  
Expression Patterns ◽  
Economic Value ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Dependent Manner ◽  
E3 Ligases ◽  
Subsequent Degradation ◽  
Stress Dependent

The turnip Brassica rapa has important economic value and represents a good model system to study gene function in crop plants. ERF/AP2 transcription factors are a major group of proteins that are often involved in regulating stress-responses and developmental programs. Some ERF/AP2 proteins are targets of CULLIN3-based E3 ligases that use BTB/POZ-MATH proteins as substrate receptors. These receptors bind the transcription factor and facilitate their ubiquitylation and subsequent degradation via the 26S proteasome. Here, we show tissue and stress-dependent expression patterns for three Brassica rapa ERF/AP2 proteins that are closely related to Arabidopsis thaliana AtRAP2.4. Cloning of the Brassica genes showed that the corresponding proteins can assemble with a BPM protein and CULLIN3, and that they are instable in a 26S proteasome dependent manner. This work demonstrates the conserved nature of the ERF/AP2-CULLIN3-based E3 ligase interplay, and represents a first step to analyze their function in a commercially relevant crop plant.

scholarly journals Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa

Plants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 526 ◽  
Author(s):  
Gaofeng Liu ◽  
Nadeem Khan ◽  
Xiaoqing Ma ◽  
Xilin Hou
Keyword(s):  
Network Analysis ◽  
Brassica Rapa ◽  
Regulatory Network ◽  
Sequence Data ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Composition Analysis ◽  
Lysine Methylation ◽  
Histone Lysine ◽  
Heat And Cold Stress

Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics of histone lysine methyltransferases and histone demethylase in Brassica rapa. We identified 60 SET (HKMTases), 53 JmjC, and 4 LSD (HDMases) genes in B. rapa. The domain composition analysis subcategorized them into seven and nine subgroups, respectively. Duplication analysis for paralogous pairs of SET and JmjC (eight and nine pairs, respectively) exhibited variation. Interestingly, three pairs of SET exhibited Ka/Ks > 1.00 values, signifying positive selection, whereas the remaining underwent purifying selection with values less than 1.00. Furthermore, RT-PCR validation analysis and RNA-sequence data acquired on six different tissues (i.e., leaf, stem, callus, silique, flower, and root) revealed dynamic expression patterns. This comprehensive study on the abundance, classification, co-regulatory network analysis, gene duplication, and responses to heat and cold stress of SET and JmjC provides insights into the structure and diversification of these family members in B. rapa. This study will be helpful to reveal functions of these putative SET and JmjC genes in B. rapa.

scholarly journals Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.)

2019 ◽  
Vol 20 (2) ◽  
pp. 251 ◽  
Author(s):  
Jiaming Li ◽  
Minghui Zhang ◽  
Jian Sun ◽  
Xinrui Mao ◽  
Jing Wang ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Developmental Stages ◽  
Oryza Sativa L ◽  
Expression Patterns ◽  
Rice Genome ◽  
High Salt ◽  
Pcr Analysis ◽  
Signal Molecule

Trihelix transcription factors play a role in plant growth, development and various stress responses. Here, we identified 41 trihelix family genes in the rice genome. These OsMSLs (Myb/SANT-LIKE) were located on twelve chromosomes. Synteny analysis indicated only six duplicated gene pairs in the rice trihelix family. Phylogenetic analysis of these OsMSLs and the trihelix genes from other species divided them into five clusters. OsMSLs from different groups significantly diverged in terms of gene structure and conserved functional domains. However, all OsMSLs contained the same five cis-elements. Some of these were responsive to light and dehydration stress. All OsMSLs expressed in four tissues and six developmental stages of rice but with different expression patterns. Quantitative real-time PCR analysis revealed that the OsMSLs responded to abiotic stresses including drought and high salt stress and stress signal molecule including ABA (abscisic acid), hydrogen peroxide. OsMSL39 were simultaneously expressed under all treatments, while OsMSL28 showed high expression under hydrogen peroxide, drought, and high salt treatments. Moreover, OsMSL16/27/33 displayed significant expression under ABA and drought treatments. Nevertheless, their responses were regulated by light. The expression levels of the 12 chosen OsMSLs differed between light and dark conditions. In conclusion, our results helped elucidate the biological functions of rice trihelix genes and provided a theoretical basis for further characterizing their biological roles in responding to abiotic stresses.

scholarly journals Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 294 ◽  
Author(s):  
Zhengwu Fang ◽  
Wenqiang Jiang ◽  
Yiqin He ◽  
Dongfang Ma ◽  
Yike Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Growth And Development ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Structure Characterization ◽  
Sequence Length ◽  
Pcr Analysis ◽  
Segmental Duplications ◽  
Biotic And Abiotic Stress

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

scholarly journals MicroRNA Microarray Expression Profiling in Human Myocardial Infarction

2009 ◽  
Vol 27 (6) ◽  
pp. 255-268 ◽  
Author(s):  
Emanuela Boštjančič ◽  
Nina Zidar ◽  
Damjan Glavač
Keyword(s):  
Myocardial Infarction ◽  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Expression Pattern ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Pcr Analysis ◽  
Rna Molecules ◽  
Mirna Expression Pattern

MicroRNAs (miRNAs), small non-coding RNA molecules, are negative regulators of gene expression. Recent studies have indicated their role in various forms of cardiovascular disease. In spite of the number of miRNA microarray analyses performed, little is known about the genome-wide miRNA expression pattern in human myocardial infarction (MI). Using miRNA microarrays and bioinformatic analysis, miRNA expression was analyzed on human MI and foetal hearts compared to healthy adult hearts, to determine whether there is any similar expression pattern between MI and foetal hearts, and to identified miRNAs that have not previously been described as dysregulated in cardiovascular diseases. Of 719 miRNAs analyzed, ∼ 50% were expressed in human hearts, 77 miRNAs were absent from all tested tissues and 57 were confidently dysregulated in at least one tested group. Some expression patterns appeared to be similar in MI and foetal hearts. Bioinformatic analysis revealed 10 miRNAs as dysregulated in MI not yet related to cardiovascular disease, and 5 miRNAs previously described only in animal models of cardiovascular diseases. Finally, qRT-PCR analysis confirmed dysregulation of 7 miRNAs,miR-150, miR-186, miR-210, miR-451, and muscle-specific, miR-1 and miR-133a/b; all of these are believed to be involved in various physiological and pathological processes.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background: Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). Results: In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion: This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLKs might play in the life cycle of cucumber.

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