scholarly journals Genome-Wide Identification and Expression of Chitinase Class I Genes in Garlic (Allium sativum L.) Cultivars Resistant and Susceptible to Fusarium proliferatum

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 720
Author(s):  
Mikhail A. Filyushin ◽  
Olga K. Anisimova ◽  
Elena Z. Kochieva ◽  
Anna V. Shchennikova
Keyword(s):  
Allium Sativum ◽  
Early Stage ◽  
Fungal Growth ◽  
Fusarium Proliferatum ◽  
Class I ◽  
Mrna Levels ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Chitinase Genes ◽  
Related Proteins

Vegetables of the Allium genus are prone to infection by Fusarium fungi. Chitinases of the GH19 family are pathogenesis-related proteins inhibiting fungal growth through the hydrolysis of cell wall chitin; however, the information on garlic (Allium sativum L.) chitinases is limited. In the present study, we identified seven class I chitinase genes, AsCHI1–7, in the A. sativum cv. Ershuizao genome, which may have a conserved function in the garlic defense against Fusarium attack. The AsCHI1–7 promoters contained jasmonic acid-, salicylic acid-, gibberellins-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with defense against pathogens. The expression of AsCHI2, AsCHI3, and AsCHI7 genes was constitutive in Fusarium-resistant and -susceptible garlic cultivars and was mostly induced at the early stage of F. proliferatum infection. In roots, AsCHI2 and AsCHI3 mRNA levels were increased in the susceptible and decreased in the resistant cultivar, whereas in cloves, AsCHI7 and AsCHI5 expression was decreased in the susceptible but increased in the resistant plants, suggesting that these genes are involved in the garlic response to Fusarium proliferatum attack. Our results provide insights into the role of chitinases in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.

scholarly journals Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana

2022 ◽  
Vol 23 (1) ◽  
pp. 511
Author(s):  
Yanjie Zhang ◽  
Yu Ma ◽  
Ruiqi Liu ◽  
Guanglin Li
Keyword(s):  
Arabidopsis Thaliana ◽  
Seed Germination ◽  
Nucleic Acid Binding ◽  
Phylogenetic Tree Analysis ◽  
Genome Wide ◽  
Binding Factor ◽  
Pathogenesis Related ◽  
Kh Domain ◽  
Family Based ◽  
Related Proteins

K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.

scholarly journals Genome-wide identification and expression analysis of chitin-binding gene family in Brassica oleracea L. reveals its role in different disease resistance

2020 ◽  
Author(s):  
Mingzhao Zhu ◽  
Congcong Kong ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Black Spot ◽  
Chitinase Gene ◽  
Chitinase A ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Chitinase Genes ◽  
Related Proteins

Abstract Background Chitinase, a category of pathogenesis-related proteins, is thought to play an important role in defending external stress in plants. However, comprehensive analysis of chitin-binding gene family has not yet been reported in cabbage (Brassica oleracea L.), especially their roles in response to different diseases. Result in this study, A total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into two groups. They were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of colinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) found in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. In addition, under four different stresses of Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression, respectively. Conclusions Our results provide insights for further understanding the role of chitinase in host plants response to different diseases.

scholarly journals Genome-Wide Identification of the Thaumatin-like Protein Family Genes in Gossypium barbadense and Analysis of Their Responses to Verticillium dahliae Infection

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2647
Author(s):  
Yilin Zhang ◽  
Wei Chen ◽  
Xiaohui Sang ◽  
Ting Wang ◽  
Haiyan Gong ◽  
...  
Keyword(s):  
Gene Family ◽  
Verticillium Dahliae ◽  
Gene Family Evolution ◽  
Disease Response ◽  
Genome Wide ◽  
Pathogen Challenge ◽  
Pathogenesis Related ◽  
Related Proteins ◽  
Encoding Genes

(1) Background: Plants respond to pathogen challenge by activating a defense system involving pathogenesis-related (PR) proteins. The PR-5 family includes thaumatin, thaumatin-like proteins (TLPs), and other related proteins. TLPs play an important role in response to biotic and abiotic stresses. Many TLP-encoding genes have been identified and functionally characterized in the model plant species. (2) Results: We identified a total of 90 TLP genes in the G. barbadense genome. They were phylogenetically classified into 10 subfamilies and distributed across 19 chromosomes and nine scaffolds. The genes were characterized by examining their exon–intron structures, promoter cis-elements, conserved domains, synteny and collinearity, gene family evolution, and gene duplications. Several TLP genes were predicted to be targets of miRNAs. Investigation of expression changes of 21 GbTLPs in a G. barbadense cultivar (Hai7124) resistance to Verticillium dahliae revealed 13 GbTLPs being upregulated in response to V. dahliae infection, suggesting a potential role of these GbTLP genes in disease response. (3) Conclusions: The results of this study allow insight into the GbTLP gene family, identify GbTLP genes responsive to V. dahliae infection, and provide candidate genes for future studies of their roles in disease resistance.

scholarly journals OsExo70B1 Positively Regulates Disease Resistance to Magnaporthe oryzae in Rice

2020 ◽  
Vol 21 (19) ◽  
pp. 7049
Author(s):  
Hongna Hou ◽  
Jianbo Fang ◽  
Jiahui Liang ◽  
Zhijuan Diao ◽  
Wei Wang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Early Stage ◽  
Plant Immunity ◽  
Fungal Growth ◽  
Defense Responses ◽  
Pr Genes ◽  
Pathogenesis Related ◽  
Important Regulator ◽  
A Subunit ◽  
Molecular Patterns

The exocyst, an evolutionarily conserved octameric protein complex, mediates tethering of vesicles to the plasma membrane in the early stage of exocytosis. Arabidopsis Exo70, a subunit of the exocyst complex, has been found to be involved in plant immunity. Here, we characterize the function of OsExo70B1 in rice. OsExo70B1 mainly expresses in leaf and shoot and its expression is induced by pathogen-associated molecular patterns (PAMPs) and rice blast fungus Magnaporthe oryzae (M. oryzae). Knocking out OsExo70B1 results in significantly decreased resistance and defense responses to M. oryzae compared to the wild type, including more disease lesions and enhanced fungal growth, downregulated expression of pathogenesis-related (PR) genes, and decreased reactive oxygen species accumulation. In contrast, the exo70B1 mutant does not show any defects in growth and development. Furthermore, OsExo70B1 can interact with the receptor-like kinase OsCERK1, an essential component for chitin reception in rice. Taken together, our data demonstrate that OsExo70B1 functions as an important regulator in rice immunity.

scholarly journals Indole-3-Acetaldoxime-Derived Compounds Restrict Root Colonization in the Beneficial Interaction Between Arabidopsis Roots and the Endophyte Piriformospora indica

2012 ◽  
Vol 25 (9) ◽  
pp. 1186-1197 ◽  
Author(s):  
Pyniarlang L. Nongbri ◽  
Joy Michal Johnson ◽  
Irena Sherameti ◽  
Erich Glawischnig ◽  
Barbara Ann Halkier ◽  
...  
Keyword(s):  
Root Colonization ◽  
Growth Promotion ◽  
Fungal Growth ◽  
Piriformospora Indica ◽  
Mitogen Activated Protein Kinase ◽  
Mrna Levels ◽  
Wild Type ◽  
Defense Genes ◽  
Pathogenesis Related ◽  
Mitogen Activated Protein

The growth-promoting and root-colonizing endophyte Piriformospora indica induces camalexin and the expression of CYP79B2, CYP79B3, CYP71A13, PAD3, and WRKY33 required for the synthesis of indole-3-acetaldoxime (IAOx)-derived compounds in the roots of Arabidopsis seedlings. Upregulation of the mRNA levels by P. indica requires cytoplasmic calcium elevation and mitogen-activated protein kinase 3 but not root-hair-deficient 2, radical oxygen production, or the 3-phosphoinositide-dependent kinase 1/oxidative signal-inducible 1 pathway. Because P. indica–mediated growth promotion is impaired in cyp79B2 cyp79B3 seedlings, while pad3 seedlings—which do not accumulate camalexin—still respond to the fungus, IAOx-derived compounds other than camalexin (e.g., indole glucosinolates) are required during early phases of the beneficial interaction. The roots of cyp79B2 cyp79B3 seedlings are more colonized than wild-type roots, and upregulation of the defense genes pathogenesis-related (PR)-1, PR-3, PDF1.2, phenylalanine ammonia lyase, and germin indicates that the mutant responds to the lack of IAOx-derived compounds by activating other defense processes. After 6 weeks on soil, defense genes are no longer upregulated in wild-type, cyp79B2 cyp79B3, and pad3 roots. This results in uncontrolled fungal growth in the mutant roots and reduced performance of the mutants. We propose that a long-term harmony between the two symbionts requires restriction of root colonization by IAOx-derived compounds.

scholarly journals Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

2021 ◽  
Vol 22 (8) ◽  
pp. 4266
Author(s):  
Yan Liu ◽  
Dalong Li ◽  
Na Yang ◽  
Xiaolong Zhu ◽  
Kexin Han ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Chinese Cabbage ◽  
Plant Disease Resistance ◽  
Expression Profiles ◽  
Black Rot ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Effector Triggered Immunity ◽  
Gene Structures ◽  
Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

scholarly journals A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1007
Author(s):  
Divya Kattupalli ◽  
Asha Sreenivasan ◽  
Eppurathu Vasudevan Soniya
Keyword(s):  
Phytophthora Capsici ◽  
Regulatory Elements ◽  
Piper Nigrum ◽  
Binding Motif ◽  
Altered Expression ◽  
Genome Wide ◽  
A Genome ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

scholarly journals A Yes-Associated Protein (YAP) and Insulin-Like Growth Factor 1 Receptor (IGF-1R) Signaling Loop Is Involved in Sorafenib Resistance in Hepatocellular Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3812
Author(s):  
Mai-Huong T. Ngo ◽  
Sue-Wei Peng ◽  
Yung-Che Kuo ◽  
Chun-Yen Lin ◽  
Ming-Heng Wu ◽  
...  
Keyword(s):  
Nuclear Translocation ◽  
Combination Index ◽  
Specific Inhibitor ◽  
In Vivo Model ◽  
Mrna Levels ◽  
Margin Distribution ◽  
Related Proteins ◽  
Emt Markers

The role of a YAP-IGF-1R signaling loop in HCC resistance to sorafenib remains unknown. Method: Sorafenib-resistant cells were generated by treating naïve cells (HepG2215 and Hep3B) with sorafenib. Different cancer cell lines from databases were analyzed through the ONCOMINE web server. BIOSTORM–LIHC patient tissues (46 nonresponders and 21 responders to sorafenib) were used to compare YAP mRNA levels. The HepG2215_R-derived xenograft in SCID mice was used as an in vivo model. HCC tissues from a patient with sorafenib failure were used to examine differences in YAP and IGF-R signaling. Results: Positive associations exist among the levels of YAP, IGF-1R, and EMT markers in HCC tissues and the levels of these proteins increased with sorafenib failure, with a trend of tumor-margin distribution in vivo. Blocking YAP downregulated IGF-1R signaling-related proteins, while IGF-1/2 treatment enhanced the nuclear translocation of YAP in HCC cells through PI3K-mTOR regulation. The combination of YAP-specific inhibitor verteporfin (VP) and sorafenib effectively decreased cell viability in a synergistic manner, evidenced by the combination index (CI). Conclusion: A YAP-IGF-1R signaling loop may play a role in HCC sorafenib resistance and could provide novel potential targets for combination therapy with sorafenib to overcome drug resistance in HCC.

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