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Vasquez YMSC, Cueva-Yesquen LG, Duarte AWF, Rosa LH, Valladão R, Lopes AR, Costa Bonugli-Santos R, de Oliveira VM. Genomics, Proteomics, and Antifungal Activity of Chitinase from the Antarctic Marine Bacterium Curtobacterium sp. CBMAI 2942. Int J Mol Sci 2024; 25:9250. [PMID: 39273199 PMCID: PMC11395076 DOI: 10.3390/ijms25179250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024] Open
Abstract
This study aimed to evaluate the genomic profile of the Antarctic marine Curtobacterium sp. CBMAI 2942, as well as to optimize the conditions for chitinase production and antifungal potential for biological control. Assembly and annotation of the genome confirmed the genomic potential for chitinase synthesis, revealing two ChBDs of chitin binding (Chi C). The optimization enzyme production using an experimental design resulted in a 3.7-fold increase in chitinase production. The chitinase enzyme was identified by SDS-PAGE and confirmed through mass spectrometry analysis. The enzymatic extract obtained using acetone showed antifungal activity against the phytopathogenic fungus Aspergillus sp. series Nigri CBMAI 1846. The genetic capability of Curtobacterium sp. CBMAI 2942 for chitin degradation was confirmed through genomic analysis. The basal culture medium was adjusted, and the chitinase produced by this isolate from Antarctica showed significant inhibition against Aspergillus sp. Nigri series CBMAI 1846, which is a tomato phytopathogenic fungus. This suggests that this marine bacterium could potentially be used as a biological control of agricultural pests.
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Affiliation(s)
- Yesenia Melissa Santa-Cruz Vasquez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia 13148-218, SP, Brazil; (Y.M.S.-C.V.); (L.G.C.-Y.)
- Institute of Biology, Campinas State University (UNICAMP), Campinas 13083-970, SP, Brazil
| | - Luis Gabriel Cueva-Yesquen
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia 13148-218, SP, Brazil; (Y.M.S.-C.V.); (L.G.C.-Y.)
- Institute of Biology, Campinas State University (UNICAMP), Campinas 13083-970, SP, Brazil
| | - Alysson Wagner Fernandes Duarte
- Complexo de Ciências Médicas e de Enfermagem, Universidade Federal de Alagoas, Campus Arapiraca, Arapiraca 57309-005, AL, Brazil
| | - Luiz Henrique Rosa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Rodrigo Valladão
- Laboratory of Biochemistry, Instituto Butantan, São Paulo 05585-000, SP, Brazil; (R.V.); (A.R.L.)
| | - Adriana Rios Lopes
- Laboratory of Biochemistry, Instituto Butantan, São Paulo 05585-000, SP, Brazil; (R.V.); (A.R.L.)
| | - Rafaella Costa Bonugli-Santos
- Instituto Latino Americano de Ciências da Vida e da Natureza (ILACVN), Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu 85870-650, PR, Brazil;
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia 13148-218, SP, Brazil; (Y.M.S.-C.V.); (L.G.C.-Y.)
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Cazares-Álvarez JE, Báez-Astorga PA, Arroyo-Becerra A, Maldonado-Mendoza IE. Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection. Genes (Basel) 2024; 15:1087. [PMID: 39202446 PMCID: PMC11353892 DOI: 10.3390/genes15081087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.
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Affiliation(s)
- Jesús Eduardo Cazares-Álvarez
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Paúl Alán Báez-Astorga
- CONAHCYT—Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico;
| | - Ignacio Eduardo Maldonado-Mendoza
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
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Xuan C, Feng M, Li X, Hou Y, Wei C, Zhang X. Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection. Int J Mol Sci 2024; 25:638. [PMID: 38203810 PMCID: PMC10779513 DOI: 10.3390/ijms25010638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses.
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Affiliation(s)
- Changqing Xuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Mengjiao Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Nye DG, Irigoyen ML, Perez-Fons L, Bohorquez-Chaux A, Hur M, Medina-Yerena D, Lopez-Lavalle LAB, Fraser PD, Walling LL. Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance. BMC PLANT BIOLOGY 2023; 23:657. [PMID: 38124051 PMCID: PMC10731783 DOI: 10.1186/s12870-023-04607-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Whiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated. RESULTS Whitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246's response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava's hormone-responsive genes showed striking divergence in expression. CONCLUSIONS This study provides the first characterization of cassava's global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.
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Affiliation(s)
- Danielle G Nye
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Maria L Irigoyen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Laura Perez-Fons
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Adriana Bohorquez-Chaux
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Manhoi Hur
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Diana Medina-Yerena
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Luis Augusto Becerra Lopez-Lavalle
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present Address: International Center of Biosaline Agriculture, Dubai, United Arab Emirates
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Nazari L, Aslan MF, Sabanci K, Ropelewska E. Integrated transcriptomic meta-analysis and comparative artificial intelligence models in maize under biotic stress. Sci Rep 2023; 13:15899. [PMID: 37741865 PMCID: PMC10517993 DOI: 10.1038/s41598-023-42984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/17/2023] [Indexed: 09/25/2023] Open
Abstract
Biotic stress imposed by pathogens, including fungal, bacterial, and viral, can cause heavy damage leading to yield reduction in maize. Therefore, the identification of resistant genes paves the way to the development of disease-resistant cultivars and is essential for reliable production in maize. Identifying different gene expression patterns can deepen our perception of maize resistance to disease. This study includes machine learning and deep learning-based application for classifying genes expressed under normal and biotic stress in maize. Machine learning algorithms used are Naive Bayes (NB), K-Nearest Neighbor (KNN), Ensemble, Support Vector Machine (SVM), and Decision Tree (DT). A Bidirectional Long Short Term Memory (BiLSTM) based network with Recurrent Neural Network (RNN) architecture is proposed for gene classification with deep learning. To increase the performance of these algorithms, feature selection is made from the raw gene features through the Relief feature selection algorithm. The obtained finding indicated the efficacy of BiLSTM over other machine learning algorithms. Some top genes ((S)-beta-macrocarpene synthase, zealexin A1 synthase, polyphenol oxidase I, chloroplastic, pathogenesis-related protein 10, CHY1, chitinase chem 5, barwin, and uncharacterized LOC100273479 were proved to be differentially upregulated under biotic stress condition.
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Affiliation(s)
- Leyla Nazari
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | - Muhammet Fatih Aslan
- Electrical and Electronics Engineering, Karamanoglu Mehmetbey University, Karaman, Turkey
| | - Kadir Sabanci
- Electrical and Electronics Engineering, Karamanoglu Mehmetbey University, Karaman, Turkey
| | - Ewa Ropelewska
- Fruit and Vegetable Storage and Processing Department, The National Institute of Horticultural Research, Skierniewice, Poland
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Di Giacomo M, Vega TA, Cambiaso V, Picardi LA, Rodríguez GR, Pereira da Costa JH. An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life. PLANTS (BASEL, SWITZERLAND) 2023; 12:2812. [PMID: 37570966 PMCID: PMC10421356 DOI: 10.3390/plants12152812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.
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Affiliation(s)
- Melisa Di Giacomo
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Tatiana Alejandra Vega
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Liliana Amelia Picardi
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Javier Hernán Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
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He T, Fan J, Jiao G, Liu Y, Zhang Q, Luo N, Ahmad B, Chen Q, Wen Z. Bioinformatics and Expression Analysis of the Chitinase Genes in Strawberry ( Fragaria vesca) and Functional Study of FvChi-14. PLANTS (BASEL, SWITZERLAND) 2023; 12:1543. [PMID: 37050169 PMCID: PMC10097121 DOI: 10.3390/plants12071543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Plant chitinases (EC 3.2.1.14) are pathogenesis-related (PR) proteins and are well studied in many plant species. However, little is known about the genomic organization and expression of chitinase genes in strawberries (Fragaria vesca). Here, 23 FvChi genes were identified in the genome of strawberry (F. vesca) and divided into GH18 and GH19 subfamilies based on phylogenetic relationships. A detailed bioinformatics analysis of the FvChi genes was performed, including gene physicochemical properties, chromosomal location, exon-intron distribution, domain arrangement, and subcellular localization. Twenty-two FvChi genes showed upregulation after Colletotrichum gloeosporioides infection. Following the exogenous application of SA, FvChi-3, 4, and 5 showed significant changes in expression. The ectopic expression of FvChi-14 in Arabidopsis thaliana increased resistance to C. higginsianum via controlling the SA and JA signaling pathway genes (AtPR1, AtICS1, AtPDF1.2, and AtLOX3). The FvChi-14 protein location was predicted in the cell wall or extracellular matrix. We speculate that FvChi-14 is involved in disease resistance by regulating the SA and JA signaling pathways. The findings of this study provide a theoretical reference for the functional studies of FvChi genes and new candidates for strawberry stress resistance breeding programs.
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Affiliation(s)
- Tiannan He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianshuai Fan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Gaozhen Jiao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuhan Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qimeng Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ning Luo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bilal Ahmad
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qingxi Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhifeng Wen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Haxim Y, Kahar G, Zhang X, Si Y, Waheed A, Liu X, Wen X, Li X, Zhang D. Genome-wide characterization of the chitinase gene family in wild apple ( Malus sieversii) and domesticated apple ( Malus domestica) reveals its role in resistance to Valsa mali. FRONTIERS IN PLANT SCIENCE 2022; 13:1007936. [PMID: 36420026 PMCID: PMC9676469 DOI: 10.3389/fpls.2022.1007936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Chitinases are responsible for catalyzing the hydrolysis of chitin and contribute to plant defense against fungal pathogens by degrading fungal chitin. In this study, genome-wide identification of the chitinase gene family of wild apple (Malus sieversii) and domesticated apple (Malus domestica) was conducted, and the expression profile was analyzed in response to Valsa mali infection. A total of 36 and 47 chitinase genes belonging to the glycosyl hydrolase 18 (GH18) and 19 (GH19) families were identified in the genomes of M. sieversii and M. domestica, respectively. These genes were classified into five classes based on their phylogenetic relationships and conserved catalytic domains. The genes were randomly distributed on the chromosomes and exhibited expansion by tandem and segmental duplication. Eight of the 36 MsChi genes and 17 of the 47 MdChi genes were differentially expressed in response to V. mali inoculation. In particular, MsChi35 and its ortholog MdChi41, a class IV chitinase, were constitutively expressed at high levels in M. sieversii and domesticated apple, respectively, and may play a crucial role in the defense response against V. mali. These results improve knowledge of the chitinase gene family in apple species and provide a foundation for further studies of fungal disease prevention in apple.
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Affiliation(s)
- Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- University of Chinese Academy of Sciences, College of Resources and Environment, Beijing, China
| | - Xuechun Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- School of Life Sciences, Xinjiang Normal University, Ürümqi, China
| | - Yu Si
- University of Chinese Academy of Sciences, College of Resources and Environment, Beijing, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Xiaoshuang Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
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Lv P, Zhang C, Xie P, Yang X, El-Sheikh MA, Hefft DI, Ahmad P, Zhao T, Bhat JA. Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max). Life (Basel) 2022; 12:life12091340. [PMID: 36143377 PMCID: PMC9504482 DOI: 10.3390/life12091340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I–V. From a broader view, the I–V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Xie
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Yang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- School of Chemical Engineering, Edgbaston Campus, University of Birmingham, Birmingham B15 2TT, UK
| | - Parvaiz Ahmad
- Department of Botany, GDC, Pulwama 192301, Jammu and Kashmir, India
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
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10
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Karimi-Jashni M, Maeda K, Yazdanpanah F, de Wit PJGM, Iida Y. An Integrated Omics Approach Uncovers the Novel Effector Ecp20-2 Required for Full Virulence of Cladosporium fulvum on Tomato. Front Microbiol 2022; 13:919809. [PMID: 35865936 PMCID: PMC9294515 DOI: 10.3389/fmicb.2022.919809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022] Open
Abstract
The fungus Cladosporium fulvum causes the leaf mould in tomatoes. During the colonization of the host, it secretes plenty of effector proteins into the plant apoplast to suppress the plant’s immune system. Here, we characterized and functionally analyzed the Ecp20-2 gene of C. fulvum using combined omics approaches. RNA-sequencing of susceptible tomato plants inoculated with C. fulvum race 0WU showed strongly induced expression of the Ecp20-2 gene. Strong upregulation of expression of the Ecp20-2 gene was confirmed by qPCR, and levels were comparable to those of other known effectors of C. fulvum. The Ecp20-2 gene encodes a small secreted protein of 149 amino acids with a predicted signal peptide of 17 amino acids. Mass spectrometry of apoplastic fluids from infected tomato leaves revealed the presence of several peptides originating from the Ecp20-2 protein, indicating that the protein is secreted and likely functions in the apoplast. In the genome of C. fulvum, Ecp20-2 is surrounded by various repetitive elements, but no allelic variation was detected in the coding region of Ecp20-2 among 120 C. fulvum isolates collected in Japan. Δecp20-2 deletion mutants of strain 0WU of C. fulvum showed decreased virulence, supporting that Ecp20-2 is an effector required for full virulence of the fungus. Virulence assays confirmed a significant reduction of fungal biomass in plants inoculated with Δecp20-2 mutants compared to those inoculated with wild-type, Δecp20-2-complemented mutants, and ectopic transformants. Sequence similarity analysis showed the presence of Ecp20-2 homologs in the genomes of several Dothideomycete fungi. The Ecp20-2 protein shows the best 3D homology with the PevD1 effector of Verticillium dahliae, which interacts with and inhibits the activity of the pathogenesis-related protein PR5, which is involved in the immunity of several host plants.
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Affiliation(s)
- Mansoor Karimi-Jashni
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
- *Correspondence: Mansoor Karimi-Jashni,
| | - Kazuya Maeda
- Laboratory of Plant Pathology, Setsunan University, Hirakata, Japan
| | - Farzaneh Yazdanpanah
- Department of Cell and Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | | | - Yuichiro Iida
- Laboratory of Plant Pathology, Setsunan University, Hirakata, Japan
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11
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Liu Z, Yu W, Zhang X, Huang J, Wang W, Miao M, Hu L, Wan C, Yuan Y, Wu B, Lyu M. Genome-Wide Identification and Expression Analysis of Chitinase-like Genes in Petunia axillaris. PLANTS (BASEL, SWITZERLAND) 2022; 11:1269. [PMID: 35567270 PMCID: PMC9100346 DOI: 10.3390/plants11091269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Chitinase (EC 3.2.1.14) is a kind of chitin-degrading glycosidase, which plays important roles in the abiotic and biotic defense of plants. In this study, we conducted whole-genome annotation, molecular evolution, and gene expression analyses on the chitinase-like (CTL) gene family members of Petunia axillaris. Thirty-three Petunia axillarischitinase-like genes (PaCTLs) were identified from the latest Petunia genome database. According to the phylogenetic analyses, these genes were divided into GH18 and GH19 subgroups and further subdivided into five classes (Class I to Class V). Conserved motif arrangements indicated their functional relevance within each group. The expansion and homeology analyses showed that gene replication events played an important role in the evolution of PaCTLs and the increase of the GH18 subgroup members was the main reason for the expansion of the PaCTL gene family in the evolution progress. By qRT-PCR analysis, we found that most of the PaCTLs showed a very low expression level in the normal growing plants. But lots of PaCTLs showed upregulated expression profiles when the plants suffered different abiotic stress conditions. Among them, five PaCTLs responded to high temperature and exhibited significantly upregulate expression level. Correspondingly, many hormone responses, as well as biotic and abiotic stress elements were found in the promoters of PaCTLs by using cis-acting element analysis. These results provide a foundation for the exploration of PaCTLs' function and enrich the evolutionary process of the CTL gene family.
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Affiliation(s)
- Zhuoyi Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
- College of Horticulture, South China Agriculture University, Guangzhou 510642, China
| | - Wenfei Yu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Xiaowen Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Jinfeng Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Wei Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Miao Miao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Li Hu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Chao Wan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Yuan Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Binghua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Meiling Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
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12
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Shi L, Liu Q, Qiao Q, Zhu Y, Huang W, Wang X, Ren Z. Exploring the effects of pectate and pectate lyase on the fruit softening and transcription profiling of Solanum lycopersicum. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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13
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Poria V, Rana A, Kumari A, Grewal J, Pranaw K, Singh S. Current Perspectives on Chitinolytic Enzymes and Their Agro-Industrial Applications. BIOLOGY 2021; 10:1319. [PMID: 34943233 PMCID: PMC8698876 DOI: 10.3390/biology10121319] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022]
Abstract
Chitinases are a large and diversified category of enzymes that break down chitin, the world's second most prevalent polymer after cellulose. GH18 is the most studied family of chitinases, even though chitinolytic enzymes come from a variety of glycosyl hydrolase (GH) families. Most of the distinct GH families, as well as the unique structural and catalytic features of various chitinolytic enzymes, have been thoroughly explored to demonstrate their use in the development of tailor-made chitinases by protein engineering. Although chitin-degrading enzymes may be found in plants and other organisms, such as arthropods, mollusks, protozoans, and nematodes, microbial chitinases are a promising and sustainable option for industrial production. Despite this, the inducible nature, low titer, high production expenses, and susceptibility to severe environments are barriers to upscaling microbial chitinase production. The goal of this study is to address all of the elements that influence microbial fermentation for chitinase production, as well as the purifying procedures for attaining high-quality yield and purity.
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Affiliation(s)
- Vikram Poria
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
| | - Anuj Rana
- Department of Microbiology (COBS & H), CCS Haryana Agricultural University, Hisar 125004, India;
| | - Arti Kumari
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
| | - Jasneet Grewal
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa, 102-096 Warsaw, Poland; (J.G.); (K.P.)
| | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa, 102-096 Warsaw, Poland; (J.G.); (K.P.)
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
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14
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Abady SM, M Ghanem K, Ghanem NB, Embaby AM. Molecular cloning, heterologous expression, and in silico sequence analysis of Enterobacter GH19 class I chitinase (chiRAM gene). Mol Biol Rep 2021; 49:951-969. [PMID: 34773550 DOI: 10.1007/s11033-021-06914-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/30/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Using in silico sequence analyses, the present study aims to clone and express the gene-encoding sequence of a GH19 chitinase from Enterobacter sp. in Escherichia coli. METHODS AND RESULTS The putative open reading frame of a GH19 chitinase from Enterobacter sp. strain EGY1 was cloned and expressed into pGEM®-T and pET-28a (+) vectors, respectively using a degenerate primer. The isolated nucleotide sequence (1821 bp, GenBank accession no.: MK533791.2) was translated to a chiRAM protein (606 amino acids, UniProt accession no.: A0A4D6J2L9). The in silico protein sequence analysis of chiRAM revealed a class I GH19 chitinase: an N-terminus signal peptide (Met1-Ala23), a catalytic domain (Val83-Glu347 and the catalytic triad Glu149, Glu171, and Ser218), a proline-rich hinge region (Pro414 -Pro450), a polycystic kidney disease protein motif (Gly 465-Ser 533), a C-terminus chitin-binding domain (Ala553- Glu593), and conserved class I motifs (NYNY and AQETGG). A three-dimensional model was constructed by LOMETS MODELLER of PDB template: 2dkvA (class I chitinase of Oryza sativa L. japonica). Recombinant chiRAM was overexpressed as inclusion bodies (IBs) (~ 72 kDa; SDS-PAGE) in 1.0 mM IPTG induced E. coli BL21 (DE3) Rosetta strain at room temperature 18 h after induction. Optimized expression yielded active chiRAM with 1.974 ± 0.0002 U/mL, on shrimp colloidal chitin (SCC), in induced E. coli BL21 (DE3) Rosetta cells growing in SB medium. LC-MS/MS identified a band of 72 kDa in the soluble fraction with a 52.3% coverage sequence exclusive to the GH19 chitinase of Enterobacter cloacae (WP_063869339.1). CONCLUSIONS Although chiRAM of Enterobacter sp. was successfully cloned and expressed in E. coli with appreciable chitinase activity, future studies should focus on minimizing IBs to facilitate chiRAM purification and characterization.
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Affiliation(s)
- Shahinaz M Abady
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Khaled M Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Nevine B Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, P.O.Box 832, 163 Horreya Avenue, Chatby, Alexandria, 21526, Egypt.
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15
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Cheng H, Shao Z, Lu C, Duan D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC PLANT BIOLOGY 2021; 21:87. [PMID: 33568068 PMCID: PMC7874618 DOI: 10.1186/s12870-021-02849-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. RESULTS Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. CONCLUSIONS Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.
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Affiliation(s)
- Haomiao Cheng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
| | - Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400, P. R. China.
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16
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Bordoloi KS, Krishnatreya DB, Baruah PM, Borah AK, Mondal TK, Agarwala N. Genome-wide identification and expression profiling of chitinase genes in tea ( Camellia sinensis (L.) O. Kuntze) under biotic stress conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:369-385. [PMID: 33707875 PMCID: PMC7907415 DOI: 10.1007/s12298-021-00947-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 05/05/2023]
Abstract
Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant's defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.
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Affiliation(s)
| | | | - Pooja Moni Baruah
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
| | - Anuj Kumar Borah
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028 India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa, IARI, New Delhi, 110012 India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
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17
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Komárková M, Chromý J, Pokorná E, Soudek P, Máchová P. Physiological and Transcriptomic Response of Grey Poplar ( Populus ×canescens Aiton Sm.) to Cadmium Stress. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1485. [PMID: 33158073 PMCID: PMC7694188 DOI: 10.3390/plants9111485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
(1) Background: Populus ×canescens (Aiton) Sm. is a fast-growing woody plant belonging to the family Salicaceae. Two poplar genotypes characterized by unique phenotypic traits (TP11 and TP20) were chosen to be characterized and tested for a physiological and transcriptomic response to Cd stress. (2) Methods: A comparative analysis of the effects of exposure to high cadmium (Cd) concentrations (10 µM and 100 µM) of TP11 and TP20 was performed. (3) Results: Neither of the tested Cd concentration negatively affected plant growth; however, the chlorophyll content significantly decreased. The potassium (K) content was higher in the shoots than in the roots. The magnesium concentrations were only slightly affected by Cd treatment. The zinc content in the shoots of TP20 was lower than that in the shoots of TP11. Cd accumulation was higher in the roots than in the shoots. After 10 days of exposure, 10 µM Cd resulted in comparable amounts of Cd in the roots and shoots of TP20. The most significant change in transcript amount was observed in endochitinase 2, 12-oxophytodienoate reductase 1 and phi classglutathione S-transferase. (4) Conclusions: Our study provided new insights for effective assessing the ability of different poplar genotypes to tolerate Cd stress and underlying Cd tolerance.
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Affiliation(s)
- Martina Komárková
- Forestry and Game Management Research Institute, Strnady, 25202 Jiloviste, Czech Republic; (J.C.); (E.P.); (P.M.)
| | - Jakub Chromý
- Forestry and Game Management Research Institute, Strnady, 25202 Jiloviste, Czech Republic; (J.C.); (E.P.); (P.M.)
| | - Eva Pokorná
- Forestry and Game Management Research Institute, Strnady, 25202 Jiloviste, Czech Republic; (J.C.); (E.P.); (P.M.)
| | - Petr Soudek
- The Czech Academy of Sciences, Institute of Experimental Botany, 16502 Prague, Czech Republic;
| | - Pavlína Máchová
- Forestry and Game Management Research Institute, Strnady, 25202 Jiloviste, Czech Republic; (J.C.); (E.P.); (P.M.)
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18
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Boba A, Kostyn K, Kozak B, Wojtasik W, Preisner M, Prescha A, Gola EM, Lysh D, Dudek B, Szopa J, Kulma A. Fusarium oxysporum infection activates the plastidial branch of the terpenoid biosynthesis pathway in flax, leading to increased ABA synthesis. PLANTA 2020; 251:50. [PMID: 31950395 DOI: 10.1007/s00425-020-03339-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/07/2020] [Indexed: 05/07/2023]
Abstract
Upregulation of the terpenoid pathway and increased ABA content in flax upon Fusarium infection leads to activation of the early plant's response (PR genes, cell wall remodeling, and redox status). Plants have developed a number of defense strategies against the adverse effects of fungi such as Fusarium oxysporum. One such defense is the production of antioxidant secondary metabolites, which fall into two main groups: the phenylpropanoids and the terpenoids. While functions and biosynthesis of phenylpropanoids have been extensively studied, very little is known about the genes controlling the terpenoid synthesis pathway in flax. They can serve as antioxidants, but are also substrates for a plethora of different compounds, including those of regulatory functions, like ABA. ABA's function during pathogen attack remains obscure and often depends on the specific plant-pathogen interactions. In our study we showed that in flax the non-mevalonate pathway is strongly activated in the early hours of pathogen infection and that there is a redirection of metabolites towards ABA synthesis. The elevated synthesis of ABA correlates with flax resistance to F. oxysporum, thus we suggest ABA to be a positive regulator of the plant's early response to the infection.
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Affiliation(s)
- Aleksandra Boba
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.
| | - Kamil Kostyn
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, Plac Grunwaldzki 24A, 53-363, Wrocław, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, Plac Grunwaldzki 24A, 53-363, Wrocław, Poland
| | - Wioleta Wojtasik
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Marta Preisner
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, Plac Grunwaldzki 24A, 53-363, Wrocław, Poland
| | - Anna Prescha
- Department of Food Science and Nutrition, Wroclaw Medical University, ul. Borowska 211, 50-556, Wrocław, Poland
| | - Edyta M Gola
- Deptartment of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wrocław, Kanonia 6/8, 50-328, Wrocław, Poland
| | - Dzmitry Lysh
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Barbara Dudek
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Jan Szopa
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, Plac Grunwaldzki 24A, 53-363, Wrocław, Poland
| | - Anna Kulma
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.
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Bioactive Polyphenols Modulate Enzymes Involved in Grapevine Pathogenesis and Chitinase Activity at Increasing Complexity Levels. Int J Mol Sci 2019; 20:ijms20246357. [PMID: 31861147 PMCID: PMC6940873 DOI: 10.3390/ijms20246357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 11/25/2022] Open
Abstract
The reduction of synthetic chemistry use in modern viticulture relies on either the biological control of microorganisms or the induction of pathogenesis-related proteins. In the present study, the effects of hydro-alcoholic plant extracts (PEs) (i.e., by-products of Vitis vinifera L., leaves of Olea europaea L. and Ailanthus altissima (Mill.) Swingle) were tested on purified enzymes activity involved in plant-pathogen interactions. The polyphenolic composition was assayed and analyzed to characterize the extract profiles. In addition, suspension cell cultures of grapevine were treated with PEs to study their modulation of chitinase activity. Application of grape marc’s PE enhanced chitinase activity at 4 g L−1. Additionally, foliar treatment of grape marc’s PE at two doses (4 g L−1 and 800 g L−1) on grapevine cuttings induced a concentration-dependent stimulation of chitinase activity. The obtained results showed that the application of bioactive compounds based on PEs, rich in phenolic compounds, was effective both at in vitro and ex/in vivo level. The overall effects of PEs on plant-pathogen interaction were further discussed by applying a multi-criteria decision analysis, showing that grape marc was the most effective extract.
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Patel P, Yadav K, Srivastava AK, Suprasanna P, Ganapathi TR. Overexpression of native Musa-miR397 enhances plant biomass without compromising abiotic stress tolerance in banana. Sci Rep 2019; 9:16434. [PMID: 31712582 PMCID: PMC6848093 DOI: 10.1038/s41598-019-52858-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Plant micro RNAs (miRNAs) control growth, development and stress tolerance but are comparatively unexplored in banana, whose cultivation is threatened by abiotic stress and nutrient deficiencies. In this study, a native Musa-miR397 precursor harboring 11 copper-responsive GTAC motifs in its promoter element was identified from banana genome. Musa-miR397 was significantly upregulated (8-10) fold in banana roots and leaves under copper deficiency, correlating with expression of root copper deficiency marker genes such as Musa-COPT and Musa-FRO2. Correspondingly, target laccases were significantly downregulated (>-2 fold), indicating miRNA-mediated silencing for Cu salvaging. No significant expression changes in the miR397-laccase module were observed under iron stress. Musa-miR397 was also significantly upregulated (>2 fold) under ABA, MV and heat treatments but downregulated under NaCl stress, indicating universal stress-responsiveness. Further, Musa-miR397 overexpression in banana significantly increased plant growth by 2-3 fold compared with wild-type but did not compromise tolerance towards Cu deficiency and NaCl stress. RNA-seq of transgenic and wild type plants revealed modulation in expression of 71 genes related to diverse aspects of growth and development, collectively promoting enhanced biomass. Summing up, our results not only portray Musa-miR397 as a candidate for enhancing plant biomass but also highlight it at the crossroads of growth-defense trade-offs.
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Affiliation(s)
- Prashanti Patel
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Karuna Yadav
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Ashish Kumar Srivastava
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Thumballi Ramabhatta Ganapathi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
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Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback ( Pungitius sinensis). Animals (Basel) 2019; 9:ani9110873. [PMID: 31661806 PMCID: PMC6912322 DOI: 10.3390/ani9110873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450s (CYPs) are a family of membrane-bound mono-oxygenase proteins, which are involved in cell metabolism and detoxification of various xenobiotic substances. In this study, we identified 58 putative CYP genes in Amur stickleback (Pungitius sinensis) based on the transcriptome sequencing. Conserved motif distribution suggested their functional relevance within each group. Some present recombination events have accelerated the evolution of this gene family. Moreover, a few positive selection sites were identified, which may have accelerated the functional divergence of this family of proteins. Expression patterns of these CYP genes were investigated and indicated that most were affected by dimethoate treatment, suggesting that CYPs were involved in the detoxication of dimethoate. This study will provide a foundation for the further functional investigation of CYP genes in fishes.
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22
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Cao S, Wang Y, Li Z, Shi W, Gao F, Zhou Y, Zhang G, Feng J. Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic stress in Ammopiptanthus nanus. Genes (Basel) 2019; 10:genes10060472. [PMID: 31234426 PMCID: PMC6627877 DOI: 10.3390/genes10060472] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/15/2023] Open
Abstract
Chitinase is a kind of hydrolase with chitin as a substrate and is proposed to play an essential role in plant defense system by functioning against fungal pathogens through degrading chitin. Recent studies indicated chitinase is also involved in abiotic stress response in plants, helping plants to survive in stressful environments. A. nanus, a rare evergreen broad-leaved shrub distrusted in deserts in Central Asia, exhibits a high level of tolerance to drought and low temperature stresses. To identify the chitinase gene involved in drought and low temperature responses in A. nanus, we performed genome-wide identification, classification, sequence alignment, and spatio-temporal gene expression analysis of the chitinases in A. nanus under osmotic and low temperature stress. A total of 32 chitinase genes belonging to glycosyl hydrolase 18 (GH18) and GH19 families were identified from A. nanus. Class III chitinases appear to be amplified quantitatively in A. nanus, and their genes carry less introns, indicating their involvement in stress response in A. nanus. The expression level of the majority of chitinases varied in leaves, stems, and roots, and regulated under environmental stress. Some chitinases, such as EVM0022783, EVM0020238, and EVM0003645, are strongly induced by low temperature and osmotic stress, and the MYC/ICE1 (inducer of CBF expression 1) binding sites in promoter regions may mediate the induction of these chitinases under stress. These chitinases might play key roles in the tolerance to these abiotic stress in A. nanus and have potential for biotechnological applications. This study provided important data for understanding the biological functions of chitinases in A. nanus.
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Affiliation(s)
- Shilin Cao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Ying Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Zhiqiang Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Wei Shi
- Key Laboratory of Biogeography and Bioresource in Arid Land, Institute of Ecology and Geography in Xinjiang, The Chinese Academy of Sciences, Urumqi, Xinjiang, China.
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Genfa Zhang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Jinchao Feng
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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