Proteomic analyses on xylem sap provides insights into the defense response of Gossypium hirsutum against Verticillium dahliae

Comparative proteomic analysis of resistant and susceptible cotton genotypes in response to leaf hopper infestation

The cotton leaf hopper is a major pest in cotton, causing a hopper burn in leaves. In this study, a comparative proteomic analysis of NDLH2010 (Resistant) and LRA5166 (Susceptible), infected with leaf hopper, was employed using a nano LC-MS/MS approach. A total of 1402 proteins varied significantly between leaf hopper-infected and control plants. The resistant and susceptible genotypes had differentially expressed proteins (DEPs) of 743 and 659, respectively. Functional annotation of DEPs revealed that the DEPs were primarily associated with stress response, hormone synthesis, photosynthesis, cell wall, and secondary metabolites. Notably, DEPs such as polyphenol oxidase, carboxypeptidase, heat shock proteins, protein BTR1-like isoform X2, chaperone protein ClpB1, and β glucosidase factors associated with environmental stress response were also detected. Quantitative real-time PCR (qRT-PCR) analysis confirmed a positive correlation between protein abundances and transcripts for all genes. Collectively, this study provides the molecular mechanisms associated with cotton defense responses against leaf hopper. SIGNIFICANCE STATEMENT: Cotton, a natural fiber, assumes a pivotal role as a raw material for textile industries, thereby bearing significant importance in the global economy. The cotton production sector is considerably affected by both biotic and abiotic stresses. The cotton leaf hopper (Amrasca biguttula biguttula (Ishida)) stands as a polyphagous insect, emerging as a dominant sap-feeding pest of the cotton crop. The continuous onslaught of sap-feeding insects on cotton plants has a detrimental impact, with leaf hoppers potentially causing yield reductions of up to 50%. Therefore, comprehending the molecular interplay between cotton and leaf hopper, elucidated at the proteome level, holds promise for more effective pest management strategies. This approach holds the potential to offer insights that contribute to the development of leaf hopper-resistant cotton varieties.

Identification and characterization of the Bicupin domain family and functional analysis of GhBCD11 in response to verticillium wilt in cotton

Bicupin domain protein (BCD) family, an important component of Cupin domain superfamily, plays important roles in oxalic acid (OA) degradation and stress responses in high plants. However, no studies have been reported on the Cupin domain family in cotton up till now. In our study, a total 110 proteins including Cupin domain were identified from the upland cotton (Gossypium hirsutum). Among them, 17 proteins contained Bicupin domain. Subsequently, we found that V. dahliae produces OA leading to cotton leaf wilting. RT-qPCR analysis of GhBCDs revealed that OA and V. dahliae Vd080 significantly enhanced the expression of GhBCD11. The Virus-induced gene silencing and overexpression analysis showed that GhBCD11 positively regulates plant resistance to V. dahliae. Subcellular localization showed GhBCD11 located on the plasma membrane. The analysis of expression pattern showed that GhBCD11 can be induced via hormone-mediated signal pathway including salicylic acid (SA), ethephon (ET), methyl jasmonate (JA) and abscisic acid (ABA). In addition, we identified an interaction between 60 S ribosomal protein GhRPL12-3 and GhBCD11 by yeast double hybridization. Overall, this is the first study, where we identified Cupin domain family in cotton, clarified the role of GhBCD11 in cotton for resistance to V. dahliae and found an interaction between GhRPL12-3 and GhBCD11.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Galactosyltransferase GhRFS6 interacting with GhOPR9 involved in defense against Verticillium wilt in cotton

The soil-borne fungus Verticillium dahliae causes Verticillium wilt (VW), one of the most devastating diseases of cotton. In a previous study showed that GhOPR9 played a positive role in resistance of cotton to VW through the regulation of the Jasmonic acid (JA) pathway. Furtherly, we also found that GhOPR9 interacted with a sucrose galactosyltransferase GhRFS6. Raffinose synthase (RFS) plays a key role in plant innate immunity, including the abiotic stress of drought, darkness. However, there were few reports on the effects of RFS on biotic stress. In this study, we verified the function of GhRFS6 to VW. The expression analysis showed that the GhRFS6 may be regulated by various stresses, and it was upregulated under Vd076 and Vd991 pressures. Inhibition of GhRFS6 expression, hydrogen peroxide (H₂O₂) content, lignin content, cell wall thickness and a series of defense responses were decreased, and the resistance of cotton to V. dahliae was decreased. In addition, this study showed that GhRFS6 has glycosyltransferase activity and can participate in the regulation of α-galactosidase activity and raffinose and inositol synthesis. And that galactose was accumulated in cotton roots after GhRFS6 silencing, which is beneficial for the colonization and growth of V. dahliae. Furthermore, overexpression of GhRFS6 in Arabidopsis thaliana enhanced plant resistance to V. dahliae. In GUS staining, the promoter expression position of GhRFS6 was also altered after V. dahliae infection. Meanwhile, GhRFS6 has also been shown to resist VW through the regulation of the JA pathway. These results suggest that GhRFS6 is a potential molecular target for improving cotton resistance to VW.

New insights into defense responses against Verticillium dahliae infection revealed by a quantitative proteomic analysis in Arabidopsis thaliana

Verticillium wilt is a highly destructive fungal disease that attacks a broad range of plants, including many major crops. However, the mechanism underlying plant immunity toward Verticillium dahliae is very complex and requires further study. By combining bioinformatics analysis and experimental validation, we investigated plant defence responses against V. dahliae infection in the model plant Arabidopsis thaliana L. A total of 301 increased and 214 decreased differentially abundant proteins (DAPs) between mock and infected wild type (WT) plants were acquired and bioinformatics analyses were then conducted and compared (increased vs decreased) in detail. In addition to the currently known mechanisms, several new clues about plant immunity against V. dahliae infection were found in this study: (1) exosome formation was dramatically induced by V. dahliae attack; (2) tryptophan-derived camalexin and cyanogenic biosynthesis were durably promoted in response to infection; and (3) various newly identified components were activated for hub immunity responses. These new clues provide valuable information that extends the current knowledge about the molecular basis of plant immunity against V. dahliae infection.

Multi-omics analysis of xylem sap uncovers dynamic modulation of poplar defenses by ammonium and nitrate

Xylem sap is the major transport route for nutrients from roots to shoots. In the present study, we investigated how variations in nitrogen (N) nutrition affected the metabolome and proteome of xylem sap and the growth of the xylem endophyte Brennaria salicis, and we also report transcriptional re-wiring of leaf defenses in poplar (Populus × canescens). We supplied poplars with high, intermediate or low concentrations of ammonium or nitrate. We identified 288 unique proteins in xylem sap. Approximately 85% of the xylem sap proteins were shared among ammonium- and nitrate-supplied plants. The number of proteins increased with increasing N supply but the major functional categories (catabolic processes, cell wall-related enzymes, defense) were unaffected. Ammonium nutrition caused higher abundances of amino acids and carbohydrates, whereas nitrate caused higher malate levels in xylem sap. Pipecolic acid and N-hydroxy-pipecolic acid increased, whereas salicylic acid and jasmonoyl-isoleucine decreased, with increasing N nutrition. Untargeted metabolome analyses revealed 2179 features in xylem sap, of which 863 were differentially affected by N treatments. We identified 124 metabolites, mainly from specialized metabolism of the groups of salicinoids, phenylpropanoids, phenolics, flavonoids, and benzoates. Their abundances increased with decreasing N, except coumarins. Brennaria salicis growth was reduced in nutrient-supplemented xylem sap of low- and high- NO₃^- -fed plants compared to that of NH₄⁺ -fed plants. The drastic changes in xylem sap composition caused massive changes in the transcriptional landscape of leaves and recruited defenses related to systemic acquired and induced systemic resistance. Our study uncovers unexpected complexity and variability of xylem composition with consequences for plant defenses.

Comparative Proteomic Analysis Reveals the Ascorbate Peroxidase-Mediated Plant Resistance to Verticillium dahliae in Gossypium barbadense

In previous research on the resistance of cotton to Verticillium wilt (VW), Gossypium hirsutum and G. barbadense were usually used as the susceptible and resistant cotton species, despite their different genetic backgrounds. Herein, we present data independent acquisition (DIA)-based comparative proteomic analysis of two G. barbadense cultivars differing in VW tolerance, susceptible XH7 and resistant XH21. A total of 4,118 proteins were identified, and 885 of them were differentially abundant proteins (DAPs). Eight co-expressed modules were identified through weighted gene co-expression network analysis. GO enrichment analysis of the module that significantly correlated with V. dahliae infection time revealed that oxidoreductase and peroxidase were the most significantly enriched GO terms. The last-step rate-limiting enzyme for ascorbate acid (AsA) biosynthesis was further uncovered in the significantly enriched GO terms of the 184 XH21-specific DAPs. Additionally, the expression of ascorbate peroxidase (APX) members showed quick accumulation after inoculation. Compared to XH7, XH21 contained consistently higher AsA contents and rapidly increased levels of APX expression, suggesting their potential importance for the resistance to V. dahliae. Silencing GbAPX1/12 in both XH7 and XH 21 resulted in a dramatic reduction in VW resistance. Our data indicate that APX-mediated oxidoreductive metabolism is important for VW resistance in cotton.

XSP10 and SlSAMT, Fusarium wilt disease responsive genes of tomato (Solanum lycopersicum L.) express tissue specifically and interact with each other at cytoplasm in vivo

Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) is a major fungal disease of tomato (Solanum lycopersicum L.). Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) have been identified as putative negative regulatory genes associated with Fusarium wilt of tomato. Despite their importance as potential genes for developing Fusarium wilt disease tolerance, very little knowledge is available about their expression, cell biology, and functional genomics. Semi-quantitative and quantitative real-time PCR expression analysis of XSP10 and SlSAMT, in this study, revealed higher expression in root and flower tissue respectively in different tomato cultivars viz. Micro-Tom (MT), Arka Vikas (AV), and Arka Abhed (AA). Therefore, the highly up-regulated expression of XSP10 and SlSAMT in biotic stress susceptible tomato cultivar (AV) than a multiple disease resistant cultivar (AA) suggested the disease susceptibility nature of these genes for Fusarium wilt. Sub-cellular localization analysis through the expression of gateway cloning constructs in tomato protoplasts and seedlings showed the predominant localization of XSP10 in the nucleus and SlSAMT at the cytoplasm. A strong in vivo protein-protein interaction of XSP10 with SlSAMT at cytoplasm from bi-molecular fluorescent complementation study suggested that these two proteins function together in regulating responses to Fusarium wilt tolerance in tomato.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01025-y.

Genome-Wide Analysis of Ribosomal Protein GhRPS6 and Its Role in Cotton Verticillium Wilt Resistance

Verticillium wilt is threatening the world’s cotton production. The pathogenic fungus Verticillium dahliae can survive in the soil in the form of microsclerotia for a long time, colonize through the root of cotton, and invade into vascular bundles, causing yellowing and wilting of cotton leaves, and in serious cases, leading to plant death. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. In previous studies, proteomic analysis was carried out on different cotton varieties inoculated with V. dahliae strain Vd080. It was found that GhRPS6 was phosphorylated after inoculation, and the phosphorylation level in resistant cultivars was 1.5 times than that in susceptible cultivars. In this study, knockdown of GhRPS6 expression results in the reduction of SA and JA content, and suppresses a series of defensive response, enhancing cotton plants susceptibility to V. dahliae. Overexpression in Arabidopsis thaliana transgenic plants was found to be more resistant to V. dahliae. Further, serines at 237 and 240 were mutated to phenylalanine, respectively and jointly. The transgenic Arabidopsis plants demonstrated that seri-237 compromised the plant resistance to V. dahliae. Subcellular localization in Nicotiana benthamiana showed that GhRPS6 was localized in the nucleus. Additionally, the pathogen inoculation and phosphorylation site mutation did not change its localization. These results indicate that GhRPS6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.

Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

BACKGROUND

Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear.

RESULTS

Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA.

CONCLUSION

This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

Calcium-Dependent Protein Kinase GhCDPK28 Was Dentified and Involved in Verticillium Wilt Resistance in Cotton

Verticillium dahliae is a soil-borne fungus that causes vascular wilt through the roots of plants. Verticillium wilt caused by V. dahliae is one of the main diseases in cotton producing areas of the world, resulting in huge economic losses. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. Calcium-dependent protein kinases (CDPKs) play a pivotal role in plant innate immunity, including regulation of oxidative burst, gene expression as well as hormone signal transduction. However, the function of cotton CDPKs in response to V. dahliae stress remains unexplored. In this study, 96, 44 and 57 CDPKs were identified from Gossypium hirsutum, Gossypium raimondii and Gossypium arboretum, respectively. Phylogenetic analysis showed that these CDPKs could be divided into four branches. All GhCDPKs of the same clade are generally similar in gene structure and conserved domain arrangement. Cis-acting elements related to hormones, stress response, cell cycle and development were predicted in the promoter region. The expression of GhCDPKs could be regulated by various stresses. Gh_D11G188500.1 and Gh_A11G186100.1 was up-regulated under Vd0738 and Vd991 stress. Further phosphoproteomics analysis showed that Gh_A11G186100.1 (named as GhCDPK28-6) was phosphorylated under the stress of V. dahliae. Knockdown of GhCDPK28-6 expression, the content of reactive oxygen species was increased, a series of defense responses were enhanced, and the sensitivity of cotton to V. dahliae was reduced. Moreover, overexpression of GhCDPK28-6 in Arabidopsis thaliana weakened the resistance of plants to this pathogen. Subcellular localization revealed that GhCDPK28-6 was localized in the cell membrane. We also found that GhPBL9 and GhRPL12C may interact with GhCDPK28-6. These results indicate that GhCDPK28-6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.