Multidimensional analysis of actin depolymerising factor family in pigeon pea under different environmental stress revealed specific response genes in each subgroup

2021 ◽  
Vol 48 (2) ◽  
pp. 180
Author(s):  
Hongyan Cao ◽  
Rohul Amin ◽  
Lili Niu ◽  
Zhihua Song ◽  
Biying Dong ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Expression ◽  
Pigeon Pea ◽  
Multidimensional Analysis ◽  
Actin Binding ◽  
Structure Evolution ◽  
Aluminium Tolerance ◽  
Specific Response ◽  
Biotic And Abiotic Stress ◽  
Specific Expression

Actin depolymerising factor (ADF) is an actin binding protein that is ubiquitous in animal and plant cells. It plays an important role in plant growth and development, as well as resistance to biotic and abiotic stress. The research of plant ADF family has been restricted to Arabidopsis thaliana (L.) Heynh. and some herb crops, but no woody cash crops have been reported to date. All members of the Cajanus cajan (L.) Millsp. ADF (CcADF) family were identified from the pigeon pea genome, and distributed among the four subfamilies by phylogenetic analysis. CcADFs were relatively conservative in gene structure evolution, protein structure and functional expression, and different CcADFs showed specific expression patterns under different treatments. The expression characteristics of several key CcADFs were revealed by analysing the stress response pattern of CcADFs and the time series RNA-seq of aluminium stress. Among them, CcADF9 in the first subgroup specifically responded to aluminium stress in the roots; CcADF3 in the second subgroup intensively responded to fungal infection in the leaves; and CcADF2 in the fourth subgroup positively responded to various stress treatments in different tissues. This study extended the relationship between plant ADF family and aluminium tolerance, as well as adding to the understanding of CcADF family in woody crops.

scholarly journals Myogenin and MEF2 function synergistically to activate the MRF4 promoter during myogenesis.

1995 ◽  
Vol 15 (5) ◽  
pp. 2707-2718 ◽  
Author(s):  
P S Naidu ◽  
D C Ludolph ◽  
R Q To ◽  
T J Hinterberger ◽  
S F Konieczny
Keyword(s):  
Molecular Mechanisms ◽  
Muscle Development ◽  
Expression Patterns ◽  
Proximal Promoter ◽  
Sufficient Information ◽  
Specific Response ◽  
Specific Expression ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
E Box

The basic helix-loop-helix muscle regulatory factor (MRF) gene family encodes four distinct muscle-specific transcription factors known as MyoD, myogenin, Myf-5, and MRF4. These proteins represent key regulatory factors that control many aspects of skeletal myogenesis. Although the MRFs often exhibit overlapping functional activities, their distinct expression patterns during embryogenesis suggest that each protein plays a unique role in controlling aspects of muscle development. As a first step in determining how MRF4 gene expression is developmentally regulated, we examined the ability of the MRF4 gene to be expressed in a muscle-specific fashion in vitro. Our studies show that the proximal MRF4 promoter contains sufficient information to direct muscle-specific expression. Located within the proximal promoter are a single MEF2 site and E box that are required for maximum MRF4 expression. Mutation of the MEF2 site or E box severely impairs the ability of this promoter to produce a muscle-specific response. In addition, the MEF2 site and E box function in concert to synergistically activate the MRF4 gene in nonmuscle cells coexpressing MEF2 and myogenin proteins. Thus, the MRF4 promoter is regulated by the MEF2 and basic helix-loop-helix MRF protein family through a cross-regulatory circuitry. Surprisingly, the MRF4 promoter itself is not transactivated by MRF4, suggesting that this MRF gene is not subject to an autoregulatory pathway as previously implied by other studies. Understanding the molecular mechanisms regulating expression of each MRF gene is central to fully understanding how these factors control developmental events.

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 Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)

2019 ◽  
Vol 20 (13) ◽  
pp. 3180 ◽  
Author(s):  
Nadeem Khan ◽  
Fizza Fatima ◽  
Muhammad Salman Haider ◽  
Hamna Shazadee ◽  
Zhongjie Liu ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Vitis Vinifera L ◽  
Specific Response ◽  
Gene Duplications ◽  
Crop Species ◽  
Specific Expression ◽  
Tissue Specific

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.

Reporter Gene Expression Patterns Regulated by an Ara h 2 Promoter Differ in Homologous Versus Heterologous Systems1

2012 ◽  
Vol 39 (1) ◽  
pp. 43-52 ◽  
Author(s):  
A Bhattacharya ◽  
M. L. Ramos ◽  
P. Faustinelli ◽  
P. Ozias-Akins
Keyword(s):  
Fluorescent Protein ◽  
Expression Patterns ◽  
Initiation Site ◽  
Gus Expression ◽  
Translation Initiation Site ◽  
Specific Response ◽  
Specific Expression ◽  
Ara H 2 ◽  
B Genome ◽  
Green Fluorescent

Abstract Peanut (Arachis hypogaea L.) is a globally important crop whose seeds are widely used in food products. Peanut seeds contain proteins that serve a nutrient reservoir function and that also are major allergens. As part of an investigation to determine the effect of reducing/eliminating the peanut allergen Ara h 2 from seeds, gene sequence including upstream regulatory regions was characterized. The ability of regions upstream of the translation initiation site to regulate seed-specific expression of reporter genes was tested in peanut and Arabidopsis. Two independent transgenic peanut lines biolistically transformed with 1kb of DNA upstream of the Ara h 2.02 (B-genome) coding sequence controlling a Green Fluorescent Protein – β-glucuronidase (Gfp-Gus) fusion were obtained. All T1, T2 and T3 generations of transgenic plants showed the expression of GFP and GUS restricted to seeds and near background levels in vegetative tissues. However, constitutive GUS expression was observed in Arabidopsis transgenic lines, a heterologous system. It is possible that trans-acting factors regulating seed specificity in peanut are too divergent in Arabidopsis to enable the seed specific response. Thus, the promoter described in this paper may have potential use for expression of transgenes in peanut where seed-specificity is desired, but expression patterns should be tested in heterologous systems prior to off-the-shelf adoption.

scholarly journals Genome-Wide Identification and Characterization of Actin-Depolymerizing Factor (ADF) Family Genes and Expression Analysis of Responses to Various Stresses in Zea Mays L.

2020 ◽  
Vol 21 (5) ◽  
pp. 1751
Author(s):  
Jun Huang ◽  
Wei Sun ◽  
Jiaxin Ren ◽  
Ruichun Yang ◽  
Jingsheng Fan ◽  
...  
Keyword(s):  
Zea Mays ◽  
Expression Analysis ◽  
Physcomitrella Patens ◽  
Zea Mays L ◽  
Expression Patterns ◽  
Actin Binding ◽  
Actin Depolymerizing Factor ◽  
Specific Expression ◽  
Group V ◽  
Growth Development

Actin-depolymerizing factor (ADF) is a small class of actin-binding proteins that regulates the dynamics of actin in cells. Moreover, it is well known that the plant ADF family plays key roles in growth, development and defense-related functions. Results: Thirteen maize (Zea mays L., ZmADFs) ADF genes were identified using Hidden Markov Model. Phylogenetic analysis indicated that the 36 identified ADF genes in Physcomitrella patens, Arabidopsis thaliana, Oryza sativa japonica, and Zea mays were clustered into five groups. Four pairs of segmental genes were found in the maize ADF gene family. The tissue-specific expression of ZmADFs and OsADFs was analyzed using microarray data obtained from the Maize and Rice eFP Browsers. Five ZmADFs (ZmADF1/2/7/12/13) from group V exhibited specifically high expression in tassel, pollen, and anther. The expression patterns of 13 ZmADFs in seedlings under five abiotic stresses were analyzed using qRT-PCR, and we found that the ADFs mainly responded to heat, salt, drought, and ABA. Conclusions: In our study, we identified ADF genes in maize and analyzed the gene structure and phylogenetic relationships. The results of expression analysis demonstrated that the expression level of ADF genes was diverse in various tissues and different stimuli, including abiotic and phytohormone stresses, indicating their different roles in plant growth, development, and response to external stimulus. This report extends our knowledge to understand the function of ADF genes in maize.

scholarly journals Genome-Wide Identification and Characterization of HSP90-RAR1-SGT1-Complex Members From Arachis Genomes and Their Responses to Biotic and Abiotic Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Cuiling Yuan ◽  
Chunjuan Li ◽  
Xiaobo Zhao ◽  
Caixia Yan ◽  
Juan Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Chromosomal Location ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Biotic And Abiotic Stress ◽  
Specific Expression ◽  
Systematic Analysis ◽  
In The Wild ◽  
Wild Peanut

The molecular chaperone complex HSP90-RAR1-SGT1 (HRS) plays important roles in both biotic and abiotic stress responses in plants. A previous study showed that wild peanut Arachis diogoi SGT1 (AdSGT1) could enhance disease resistance in transgenic tobacco and peanut. However, no systematic analysis of the HRS complex in Arachis has been conducted to date. In this study, a comprehensive analysis of the HRS complex were performed in Arachis. Nineteen HSP90, two RAR1 and six SGT1 genes were identified from the allotetraploid peanut Arachis hypogaea, a number close to the sum of those from the two wild diploid peanut species Arachis duranensis and Arachis ipaensis. According to phylogenetic and chromosomal location analyses, thirteen orthologous gene pairs from Arachis were identified, all of which except AhHSP90-A8, AhHSP90-B9, AdHSP90-9, and AiHSP90-9 were localized on the syntenic locus, and they shared similar exon-intron structures, conserved motifs and expression patterns. Phylogenetic analysis showed that HSP90 and RAR1 from dicot and monocot plants diverged into different clusters throughout their evolution. Chromosomal location analysis indicated that AdSGT1 (the orthologous gene of AhSGT1-B3 in this study) might provide resistance to leaf late spot disease dependent on the orthologous genes of AhHSP90-B10 and AhRAR1-B in the wild peanut A. diogoi. Several HRS genes exhibited tissue-specific expression patterns, which may reflect the sites where they perform functions. By exploring published RNA-seq data, we found that several HSP90 genes play major roles in both biotic and abiotic stress responses, especially salt and drought responses. Autoactivation assays showed that AhSGT1-B1 could not be used as bait for yeast two-hybrid (Y2H) library screening. AhRAR1 and AhSGT1 could strongly interact with each other and interact with AhHSP90-B8. The present study represents the first systematic analysis of HRS complex genes in Arachis and provides valuable information for functional analyses of HRS complex genes. This study also offers potential stress-resistant genes for peanut improvement.

Tissue-specific expression patterns of nuclear receptors

2013 ◽  
Author(s):  
AL Bookout ◽  
Y Jeong ◽  
M Downes ◽  
RT Yu ◽  
RM Evans ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Overexpression of the Oral Mucosa-Specific microRNA-31 Promotes Skin Wound Closure

2019 ◽  
Vol 20 (15) ◽  
pp. 3679 ◽  
Author(s):  
Lin Chen ◽  
Alyne Simões ◽  
Zujian Chen ◽  
Yan Zhao ◽  
Xinming Wu ◽  
...  
Keyword(s):  
Wound Healing ◽  
Oral Mucosa ◽  
Wound Closure ◽  
Expression Patterns ◽  
Skin Wound ◽  
Skin Wound Healing ◽  
Specific Expression ◽  
Keratinocyte Proliferation

Wounds within the oral mucosa are known to heal more rapidly than skin wounds. Recent studies suggest that differences in the microRNAome profiles may underlie the exceptional healing that occurs in oral mucosa. Here, we test whether skin wound-healing can be accelerating by increasing the levels of oral mucosa-specific microRNAs. A panel of 57 differentially expressed high expresser microRNAs were identified based on our previously published miR-seq dataset of paired skin and oral mucosal wound-healing [Sci. Rep. (2019) 9:7160]. These microRNAs were further grouped into 5 clusters based on their expression patterns, and their differential expression was confirmed by TaqMan-based quantification of LCM-captured epithelial cells from the wound edges. Of these 5 clusters, Cluster IV (consisting of 8 microRNAs, including miR-31) is most intriguing due to its tissue-specific expression pattern and temporal changes during wound-healing. The in vitro functional assays show that ectopic transfection of miR-31 consistently enhanced keratinocyte proliferation and migration. In vivo, miR-31 mimic treatment led to a statistically significant acceleration of wound closure. Our results demonstrate that wound-healing can be enhanced in skin through the overexpression of microRNAs that are highly expressed in the privileged healing response of the oral mucosa.

scholarly journals Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 776
Author(s):  
Shipra Kumari ◽  
Bashistha Kumar Kanth ◽  
Ju young Ahn ◽  
Jong Hwa Kim ◽  
Geung-Joo Lee
Keyword(s):  
Abiotic Stress ◽  
Biotic Stress ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Lilium Longiflorum ◽  
Biotic And Abiotic Stress ◽  
Biotic Stresses ◽  
Genome Wide

Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes—LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12—were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.

scholarly journals Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leyla A. Erozenci ◽  
Sander R. Piersma ◽  
Thang V. Pham ◽  
Irene V. Bijnsdorp ◽  
Connie R. Jimenez
Keyword(s):  
Expression Patterns ◽  
Interaction Network ◽  
Extracellular Vesicle ◽  
Protein Signaling ◽  
Protein Patterns ◽  
Specific Expression ◽  
Non Invasive ◽  
Data Independent Acquisition ◽  
Time Period ◽  
Using Data

AbstractThe protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.

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