scholarly journals Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengyun Chen ◽  
Hongliang Jian ◽  
Fei Wei ◽  
Lijiao Gu ◽  
Tingli Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Cold Stress ◽  
Membrane Attack Complex ◽  
Functional Differentiation ◽  
Functional Verification ◽  
Virus Induced Gene Silencing ◽  
Phylogenetic Groups ◽  
Cotton Species ◽  
Evolutionary View ◽  
Macpf Domain

The membrane attack complex/perforin (MACPF) domain-containing proteins are involved in the various developmental processes and in responding to diverse abiotic stress. The function and regulatory network of the MACPF genes are rarely reported in Gossypium spp. We study the detailed identification and partial functional verification of the members of the MACPF family. Totally, 100 putative MACPF proteins containing complete MACPF domain were identified from the four cotton species. They were classified into three phylogenetic groups and underwent multifold pressure indicating that selection produced new functional differentiation. Cotton MACPF gene family members expanded mainly through the whole-genome duplication (WGD)/segmental followed by the dispersed. Expression and cis-acting elements analysis revealed that MACPFs play a role in resistance to abiotic stresses, and some selected GhMACPFs were able to respond to the PEG and cold stresses. Co-expression analysis showed that GhMACPFs might interact with valine-glutamine (VQ), WRKY, and Apetala 2 (AP2)/ethylene responsive factor (ERF) domain-containing genes under cold stress. In addition, silencing endogenous GhMACPF26 in cotton by the virus-induced gene silencing (VIGS) method indicated that GhMACPF26 negatively regulates cold tolerance. Our data provided a comprehensive phylogenetic evolutionary view of Gossypium MACPFs. The MACPFs may work together with multiple transcriptional factors and play roles in acclimation to abiotic stress, especially cold stress in cotton.

scholarly journals Functional examination of lncRNAs in allotetraploid Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luyao Wang ◽  
Jin Han ◽  
Kening Lu ◽  
Menglin Li ◽  
Mengtao Gao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Patterns ◽  
Leaf Tissue ◽  
Evolutionary Model ◽  
Cotton Leaf ◽  
Functional Screening ◽  
Virus Induced Gene Silencing ◽  
Individual Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Abstract Background An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. Results We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. Conclusions Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

ATP hydrolysis determines cold tolerance by regulating available energy for glutathione synthesis in rice seedling plants

2020 ◽  
Author(s):  
Pinghui Yu ◽  
Ning Jiang ◽  
Weimeng Fu ◽  
Guangjie Zheng ◽  
Guangyan Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Recombinant Inbred ◽  
Atp Hydrolysis ◽  
Rice Seedling ◽  
Energy Deficit ◽  
Energy Status ◽  
Available Energy ◽  
Pure Lines

Abstract Background: Glutathione (GSH) is important for plants to resist abiotic stress, and a large amount of energy is required in the process. However, it is not clear how the energy status affects the accumulation of GSH in plants under cold stress. Results: Two rice pure lines, Zhongzao39 (ZZ39) and its recombinant inbred line 82 (RIL82) were subjected to cold stress for 48 h. Under cold stress, RIL82 suffered more damages than ZZ39 plants, in which higher increases in APX activity and GSH content were showed in the latter than the former compared with their respective controls. This indicated that GSH was mainly responsible for the different cold tolerance between these two rice plants. Interestingly, under cold stress, greater increases in contents of carbohydrate, NAD(H), NADP(H) and ATP as well as the expression levels of GSH1 and GSH2 were showed in RIL82 than ZZ39 plants. In contrast, ATPase content in RIL82 plants was adversely inhibited by cold stress while it increased significantly in ZZ39 plants. This indicated that cold stress reduced the accumulation of GSH in RIL82 plants mainly due to the inhibition on ATP hydrolysis rather than energy deficit. Conclusion: We inferred that the energy status determined by ATP hydrolysis involved in regulating the cold tolerance of plants by controlling GSH synthesis.

scholarly journals Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1617
Author(s):  
Jie Zhang ◽  
Junping Feng ◽  
Wei Liu ◽  
Zhongying Ren ◽  
Junjie Zhao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Function Analysis ◽  
Histone Demethylase ◽  
Abiotic Stress Response ◽  
Cotton Species ◽  
Jmjc Domain ◽  
Allotetraploid Cotton

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

Control of growth factor signalling by MACPF proteins

2019 ◽  
Vol 47 (3) ◽  
pp. 801-810
Author(s):  
Daniel Bakopoulos ◽  
James C. Whisstock ◽  
Travis K. Johnson
Keyword(s):  
Cell Death ◽  
Growth Factor ◽  
Membrane Attack Complex ◽  
Fruit Fly ◽  
Mechanisms Of Action ◽  
Signalling Pathways ◽  
Growth Factor Signalling ◽  
Macpf Domain ◽  
Apoptotic Factors ◽  
Unique Ability

AbstractMembers of the membrane attack complex/perforin-like (MACPF) protein superfamily have long captured interest because of their unique ability to assemble into large oligomeric pores on the surfaces of cells. The best characterised of these act in vertebrate immunity where they function to deliver pro-apoptotic factors or induce the cytolysis and death of targeted cells. Less appreciated, however, is that rather than causing cell death, MACPF proteins have also evolved to control cellular signalling pathways and influence developmental programmes such as pattern formation and neurogenesis. Torso-like (Tsl) from the fruit fly Drosophila, for example, functions to localise the activity of a growth factor for patterning its embryonic termini. It remains unclear whether these developmental proteins employ an attenuated form of the classical MACPF lytic pore, or if they have evolved to function via alternative mechanisms of action. In this minireview, we examine the evidence that links pore-forming MACPF proteins to the control of growth factor and cytokine signalling. We will then attempt to reconcile how the MACPF domain may have been repurposed during evolution for developmental events rather than cell killing.

scholarly journals Functional Analysis of Aux/IAAs and SAURs on Shoot Growth of Lagerstroemia indica through Virus-Induced Gene Silencing (VIGS)

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1288
Author(s):  
Lu Feng ◽  
Xiaohan Liang ◽  
Yang Zhou ◽  
Ye Zhang ◽  
Jieru Liu ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Gene Silencing ◽  
Shoot Growth ◽  
Expression Patterns ◽  
Functional Verification ◽  
Regulation Mechanism ◽  
Virus Induced Gene Silencing ◽  
Short Shoot ◽  
Indole 3 Acetic Acid ◽  
Six Genes

The plant hormone auxin plays an important role in cell division and the elongation of shoots to affect the plant architecture, which has a great impact on the plant yield, fruit quality and ornamental value; however, the regulatory mechanism of auxin controlling shoot growth is unclear in crape myrtle. In this study, two auxin/indole-3-acetic acid (Aux/IAA) genes and four small auxin upregulated RNA (SAUR) genes of auxin response gene families were isolated from dwarf and non-dwarf progenies of Lagerstroemia indica and then functionally characterized. Sequence alignment revealed that the six genes contain typical conserved domains. Different expression patterns of the six genes at three different tissue stages of two types of progenies showed that the regulation mechanism of these genes may be different. Functional verification of the six genes upon shoot growth of crape myrtle was performed via virus-induced gene silencing. When the LfiAUX22 gene was silenced, a short shoot phenotype was observed in non-dwarf progenies, accompanied by decreased auxin content. Therefore, we preliminarily speculated that LfiAUX22 plays an important role in the shoot growth of crape myrtle, which regulates the accumulation of indole-3-acetic acid (IAA) and the elongation of cells to eventually control shoot length.

scholarly journals ATP hydrolysis determines cold tolerance in rice by regulating available energy for glutathione synthesis

2020 ◽  
Author(s):  
Pinghui Yu ◽  
Ning Jiang ◽  
Weimeng Fu ◽  
Guangjie Zheng ◽  
Guangyan Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Atpase Activity ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Recombinant Inbred ◽  
Atp Hydrolysis ◽  
Energy Deficit ◽  
Energy Status ◽  
Available Energy ◽  
Rice Genotypes

Abstract Background Glutathione (GSH) is important for plants to resist against abiotic stress, and a large amount of energy is required in the process. However, it is not clear how the energy status affects the accumulation of GSH in plants under cold stress. Results Two rice genotypes, Zhongzao39 (ZZ39) and its recombinant inbred line 82 (RIL82) were subjected to cold stress for 48 h. Under cold stress, RIL82 suffered more damages than ZZ39 plants, in which the latter had higher increases in APX activity and GSH content than the former compared with their respective controls. This indicated that GSH was mainly responsible for the different cold tolerance between these two rice plants. Interestingly, under cold stress, greater increases in contents of carbohydrate, NAD(H), NADP(H) and ATP as well as the expression levels of GSH1 and GSH2 were showed in RIL82 than ZZ39 plants. In contrast, ATPase activity in RIL82 plants was adversely inhibited by cold stress while it significantly increased in ZZ39 plants. This indicated that cold stress reduced the accumulation of GSH in RIL82 plants mainly due to the inhibition on ATP hydrolysis rather than energy deficit. Conclusion We inferred that the energy status determined by ATP hydrolysis involved in regulating the cold tolerance of plants by controlling GSH synthesis.

scholarly journals QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jingjing Zhang ◽  
Xiaoyun Jia ◽  
Xiaohao Guo ◽  
Hengling Wei ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fiber Quality ◽  
Functional Verification ◽  
Virus Induced Gene Silencing ◽  
Flower Bud ◽  
Early Maturity ◽  
Polymorphic Snps ◽  
Fruiting Branch ◽  
Early Maturing ◽  
Nucleotide Data

Abstract Background The node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber quality and yield, but there has been little attention to traits related to early maturity, especially the NFFB, in cotton. Results To identify the QTL associated with the NFFB in cotton, a BC4F2 population comprising 278 individual plants was constructed. The parents and two DNA bulks for high and low NFFB were whole genome sequenced, and 243.8 Gb of clean nucleotide data were generated. A total of 449,302 polymorphic SNPs and 135,353 Indels between two bulks were identified for QTL-seq. Seventeen QTLs were detected and localized on 11 chromosomes in the cotton genome, among which two QTLs (qNFFB-Dt2–1 and qNFFB-Dt3–3) were located in hotspots. Two candidate genes (GhAPL and GhHDA5) related to the NFFB were identified using quantitative real-time PCR (qRT-PCR) and virus-induced gene silencing (VIGS) experiments in this study. Both genes exhibited higher expression levels in the early-maturing cotton material RIL182 during flower bud differentiation, and the silencing of GhAPL and GhHDA5 delayed the flowering time and increased the NFFB compared to those of VA plants in cotton. Conclusions Our study preliminarily found that GhAPL and GhHDA5 are related to the early maturity in cotton. The findings provide a basis for the further functional verification of candidate genes related to the NFFB and contribute to the study of early maturity in cotton.

scholarly journals Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean

2021 ◽  
Vol 22 (20) ◽  
pp. 11032
Author(s):  
Jamie A. O’Rourke ◽  
Michael J. Morrisey ◽  
Ryan Merry ◽  
Mary Jane Espina ◽  
Aaron J. Lorenz ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Iron Deficiency ◽  
Gene Silencing ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Yield Loss ◽  
Abiotic Stress Tolerance ◽  
Iron Stress ◽  
Rna Seq ◽  
Virus Induced Gene Silencing

The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.

scholarly journals Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean

2020 ◽  
Vol 21 (5) ◽  
pp. 1810
Author(s):  
Shu-Ping Zhao ◽  
Xin-Yuan Song ◽  
Lin-Lin Guo ◽  
Xiang-Zhan Zhang ◽  
Wei-Jun Zheng
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Functional Verification ◽  
Marker Genes ◽  
Functional Identification ◽  
Related Sequence ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide

The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.

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