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Piombo E, Vetukuri RR, Konakalla NC, Kalyandurg PB, Sundararajan P, Jensen DF, Karlsson M, Dubey M. RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. BMC Biol 2024; 22:219. [PMID: 39343898 PMCID: PMC11441109 DOI: 10.1186/s12915-024-02014-9] [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: 11/10/2023] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Small RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions. RESULTS C. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs. CONCLUSIONS We provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Naga Charan Konakalla
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Pruthvi B Kalyandurg
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Poorva Sundararajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Piombo E, Tzelepis G, Ruus AG, Rafiei V, Jensen DF, Karlsson M, Dubey M. Sterol regulatory element-binding proteins mediate intrinsic fungicide tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea IK726. Microbiol Res 2024; 289:127922. [PMID: 39368255 DOI: 10.1016/j.micres.2024.127922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/10/2024] [Accepted: 09/25/2024] [Indexed: 10/07/2024]
Abstract
Sterol regulatory element-binding proteins (SREBPs) are transcription factors governing various biological processes in fungi, including virulence and fungicide tolerance, by regulating ergosterol biosynthesis and homeostasis. While studied in model fungal species, their role in fungal species used for biocontrol remains elusive. This study delves into the biological and regulatory function of SREBPs in the fungal biocontrol agent (BCA) Clonostachys rosea IK726, with a specific focus on fungicide tolerance and antagonism. Clonostachys rosea genome contains two SREBP coding genes (sre1 and sre2) with distinct characteristics. Deletion of sre1 resulted in mutant strains with pleiotropic phenotypes, including reduced C. rosea growth on medium supplemented with prothioconazole and boscalid fungicides, hypoxia mimicking agent CoCl2 and cell wall stressor SDS, and altered antagonistic abilities against Botrytis cinerea and Rhizoctonia solani. However, Δsre2 strains showed no significant effect. Consistent with the gene deletion results, overexpression of sre1 in Saccharomyces cerevisiae enhanced tolerance to prothioconazole. The functional differentiation between SRE1 and SRE2 was elucidated by the yeast-two-hybridization assay, which showed an interaction between SREBP cleavage-activating protein (SCAP) and SRE1 but not between SRE2 and SCAP. Transcriptome analysis of the Δsre1 strain unveiled SRE1-mediated expression regulation of genes involved in lipid metabolism, respiration, and xenobiotic tolerance. Notably, genes coding for antimicrobial compounds chitinases and polyketide synthases were downregulated, aligning with the altered antagonism phenotype. This study uncovers the role of SREBPs in fungal BCAs, providing insights for C. rosea IK726 application into integrated pest management strategies.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Georgios Tzelepis
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alma Gustavsson Ruus
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Vahideh Rafiei
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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3
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Kim WJ, Yang B, Kim DG, Kim SH, Lee YJ, Kim J, Baek SH, Kang SY, Ahn JW, Choi YJ, Bae CH, Iwar K, Kim SH, Ryu J. Genotyping-by-Sequencing Analysis Reveals Associations between Agronomic and Oil Traits in Gamma Ray-Derived Mutant Rapeseed ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1576. [PMID: 38891384 PMCID: PMC11174930 DOI: 10.3390/plants13111576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Rapeseed (Brassica napus L.) holds significant commercial value as one of the leading oil crops, with its agronomic features and oil quality being crucial determinants. In this investigation, 73,226 single nucleotide polymorphisms (SNPs) across 95 rapeseed mutant lines induced by gamma rays, alongside the original cultivar ('Tamra'), using genotyping-by-sequencing (GBS) analysis were examined. This study encompassed gene ontology (GO) analysis and a genomewide association study (GWAS), thereby concentrating on agronomic traits (e.g., plant height, ear length, thousand-seed weight, and seed yield) and oil traits (including fatty acid composition and crude fat content). The GO analysis unveiled a multitude of genes with SNP variations associated with cellular processes, intracellular anatomical structures, and organic cyclic compound binding. Through GWAS, we detected 320 significant SNPs linked to both agronomic (104 SNPs) and oil traits (216 SNPs). Notably, two novel candidate genes, Bna.A05p02350D (SFGH) and Bna.C02p22490D (MDN1), are implicated in thousand-seed weight regulation. Additionally, Bna.C03p14350D (EXO70) and Bna.A09p05630D (PI4Kα1) emerged as novel candidate genes associated with erucic acid and crude fat content, respectively. These findings carry implications for identifying superior genotypes for the development of new cultivars. Association studies offer a cost-effective means of screening mutants and selecting elite rapeseed breeding lines, thereby enhancing the commercial viability of this pivotal oil crop.
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Affiliation(s)
- Woon Ji Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - Baul Yang
- Imsil Cheese & Food Research Institute, Imsil-gun 55918, Republic of Korea; (B.Y.); (Y.-J.C.)
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - Ye-Jin Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - Juyoung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - So Hyeon Baek
- Department of Plant Production Sciences, Graduate School, Sunchon National University, Suncheon 57922, Republic of Korea; (S.H.B.); (C.-H.B.)
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea;
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
| | - Yu-Jin Choi
- Imsil Cheese & Food Research Institute, Imsil-gun 55918, Republic of Korea; (B.Y.); (Y.-J.C.)
| | - Chang-Hyu Bae
- Department of Plant Production Sciences, Graduate School, Sunchon National University, Suncheon 57922, Republic of Korea; (S.H.B.); (C.-H.B.)
| | - Kanivalan Iwar
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.I.); (S.-H.K.)
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.I.); (S.-H.K.)
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; (W.J.K.); (D.-G.K.); (S.H.K.); (Y.-J.L.); (J.K.); (J.-W.A.)
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Zheng H, Zhao H, Xiong H, Awais MM, Zeng S, Sun J. Impact of the Transboundary Interference Inhibitor on RNAi and the Baculovirus Expression System in Insect Cells. INSECTS 2024; 15:375. [PMID: 38921090 PMCID: PMC11203448 DOI: 10.3390/insects15060375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/27/2024]
Abstract
RNA interference inhibitors were initially discovered in plant viruses, representing a unique mechanism employed by these viruses to counteract host RNA interference. This mechanism has found extensive applications in plant disease resistance breeding and other fields; however, the impact of such interference inhibitors on insect cell RNA interference remains largely unknown. In this study, we screened three distinct interference inhibitors from plant and mammal viruses that act through different mechanisms and systematically investigated their effects on the insect cell cycle and baculovirus infection period at various time intervals. Our findings demonstrated that the viral suppressors of RNA silencing (VSRs) derived from plant and mammal viruses significantly attenuated the RNA interference effect in insect cells, as evidenced by reduced apoptosis rates, altered gene regulation patterns in cells, enhanced expression of exogenous proteins, and improved production efficiency of recombinant virus progeny. Further investigations revealed that the early expression of VSRs yielded superior results compared with late expression during RNA interference processes. Additionally, our results indicated that dsRNA-binding inhibition exhibited more pronounced effects than other modes of action employed by these interference inhibitors. The outcomes presented herein provide novel insights into enhancing defense mechanisms within insect cells using plant and mammal single-stranded RNA virus-derived interference inhibitors and have potential implications for expanding the scope of transformation within insect cell expression systems.
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Affiliation(s)
- Hao Zheng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding & Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (H.Z.); (H.X.); (M.M.A.)
| | - Hengfeng Zhao
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding & Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (H.Z.); (H.X.); (M.M.A.)
| | - Haifan Xiong
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding & Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (H.Z.); (H.X.); (M.M.A.)
| | - Mian Muhammad Awais
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding & Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (H.Z.); (H.X.); (M.M.A.)
| | - Songrong Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China;
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding & Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (H.Z.); (H.X.); (M.M.A.)
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Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024; 12:e0316523. [PMID: 38441469 PMCID: PMC10986496 DOI: 10.1128/spectrum.03165-23] [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: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host's cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride-RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2, and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (het) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.IMPORTANCEThere is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride.
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Affiliation(s)
- Eli Efrain Enriquez-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - Camilo Pérez-Salazar
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - José Guillermo Rico-Ruiz
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | | | - Pablo Cruz-Morales
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
- Plant and Microbial Biology Department, University of California, Berkeley, Carlifornia, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, Carlifornia, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
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6
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Qu Q, Liu N, Su Q, Liu X, Jia H, Liu Y, Sun M, Cao Z, Dong J. MicroRNAs involved in the trans-kingdom gene regulation in the interaction of maize kernels and Fusarium verticillioides. Int J Biol Macromol 2023:125046. [PMID: 37245767 DOI: 10.1016/j.ijbiomac.2023.125046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Maize ear rot is a widespread disease and the main pathogen is Fusarium verticillioides. Plant microRNAs (miRNAs) have great effects on disease resistance and it has been reported that maize miRNA participates in defense responses in maize ear rot. However, the trans-kingdom regulation of miRNAs between maize and F. verticillioides remains uncharacterized. In this study, the relationship between miRNA-like RNAs (milRNAs) of F. verticillioides and pathogenicity was investigated, followed by sRNA analysis and degradome sequencing of miRNA profiles and the target genes of maize and F. verticillioides after inoculation. It was found that the milRNA biogenesis positively regulated the pathogenicity of F. verticillioides by knocking out the gene FvDicer2-encoded Dicer-like protein in F. verticillioides. Following inoculation with F. verticillioides, 284 known and 6571 novel miRNAs were obtained in maize, including 28 miRNAs differentially expressed at multiple time points. The target genes of maize differentially expressed miRNAs in F. verticillioides mediated multiple pathways, including autophagy and MAPK signaling pathway. Fifty-one novel F. verticillioides milRNAs were predicted to target 333 genes in maize involved in MAPK signaling pathways, plant hormone signaling transduction and plant-pathogen interaction pathways. Additionally, the miR528b-5p in maize targeted the mRNA of FvTTP which encoded a twice transmembrane protein in F. verticillioides. The FvTTP-knockout mutants displayed decreased pathogenicity and reduced synthesis of fumonisins. Thus, by interfering with the translation of FvTTP, the miR528b-5p inhibited F. verticillioides infection. These findings suggested a novel function of miR528 in resisting F. verticillioides infection. The miRNAs identified in this research and their putative target genes can be used to further elucidate the trans-kingdom functions of microRNAs in plant pathogen interaction.
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Affiliation(s)
- Qing Qu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Ning Liu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Qianfu Su
- Jilin Academy of Agricultural Sciences, Jilin 130033, China
| | - Xinfang Liu
- Corn Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Hui Jia
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Yuwei Liu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China
| | - Manli Sun
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Zhiyan Cao
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China.
| | - Jingao Dong
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China.
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7
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Cai X, Dou R, Guo C, Tang J, Li X, Chen J, Zhang J. Cationic Polymers as Transfection Reagents for Nucleic Acid Delivery. Pharmaceutics 2023; 15:pharmaceutics15051502. [PMID: 37242744 DOI: 10.3390/pharmaceutics15051502] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/09/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Nucleic acid therapy can achieve lasting and even curative effects through gene augmentation, gene suppression, and genome editing. However, it is difficult for naked nucleic acid molecules to enter cells. As a result, the key to nucleic acid therapy is the introduction of nucleic acid molecules into cells. Cationic polymers are non-viral nucleic acid delivery systems with positively charged groups on their molecules that concentrate nucleic acid molecules to form nanoparticles, which help nucleic acids cross barriers to express proteins in cells or inhibit target gene expression. Cationic polymers are easy to synthesize, modify, and structurally control, making them a promising class of nucleic acid delivery systems. In this manuscript, we describe several representative cationic polymers, especially biodegradable cationic polymers, and provide an outlook on cationic polymers as nucleic acid delivery vehicles.
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Affiliation(s)
- Xiaomeng Cai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Rui Dou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Chen Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jiaruo Tang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xiajuan Li
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China National Center for Bioinformation, Beijing 100101, China
| | - Jun Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jiayu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-Disciplinary Research Division, Institute of High Energy Physics and University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS), Beijing 100049, China
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8
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Hirpara DG, Gajera HP, Savaliya DD, Parakhia MV. Exploring conserved and novel MicroRNA-like small RNAs from stress tolerant Trichoderma fusants and parental strains during interaction with fungal phytopathogen Sclerotium rolfsii Sacc. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105368. [PMID: 36963937 DOI: 10.1016/j.pestbp.2023.105368] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The study investigated potential microRNA-like small RNAs (milRNAs) from multi-stress-tolerant Tricho-fusants and parental strains (P1- Trichoderma virens NBAIITvs12 and P2- Trichoderma koningii MTCC796) for antagonistic activity during interaction with phytopathogen Sclerotium rolfsii. The Trichoderma was cultured in-vitro, with and without antagonism, against the pathogen and total RNA was extracted followed by small RNA library construction and sequencing. The milRNAs were identified by mapping high-quality unique reads against a reference genome. The milRNAs were recognized higher in antagonist Trichoderma during interaction with test pathogen compared to normal growth. The novel milRNAs candidates were found to vary during interaction with the pathogen and normal growth. The gene ontology and functional analysis illustrated that a total of 5828 potential targeted genes were recognized for 93 milRNAs of potent Fu21_IB and 3053 genes for 62 milRNAs of least fusant Fu28_IL. Functional annotation of milRNA-predicted genes integrating KEGG pathways indicates new insights into regulatory mechanisms, by interfering with milRNAs, associated with signal transduction, amino sugar metabolism, benzoate degradation, amino acid metabolism, and steroid and alkaloid metabolism for potential biocontrol of stress-tolerant Tricho-fusant FU21 during interaction with S. rolfsii. The present investigation is the first report of conserved and novel milRNAs from Tricho-fusants and parental strains interacting with S. rolfsii.
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Affiliation(s)
- Darshna G Hirpara
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - H P Gajera
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India.
| | - Disha D Savaliya
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - M V Parakhia
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
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Piombo E, Kelbessa BG, Sundararajan P, Whisson SC, Vetukuri RR, Dubey M. RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents. Front Microbiol 2023; 14:1076522. [PMID: 37032886 PMCID: PMC10080066 DOI: 10.3389/fmicb.2023.1076522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Oomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors. Methods To gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species. Results and discussion Each of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bekele Gelena Kelbessa
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Poorva Sundararajan
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Stephen C. Whisson
- Department of Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- *Correspondence: Ramesh Raju Vetukuri, ; Mukesh Dubey,
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Ramesh Raju Vetukuri, ; Mukesh Dubey,
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Piombo E, Guaschino M, Jensen DF, Karlsson M, Dubey M. Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes. Front Microbiol 2023; 14:1112673. [PMID: 36876087 PMCID: PMC9978495 DOI: 10.3389/fmicb.2023.1112673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction The fungal secretome comprise diverse proteins that are involved in various aspects of fungal lifestyles, including adaptation to ecological niches and environmental interactions. The aim of this study was to investigate the composition and activity of fungal secretomes in mycoparasitic and beneficial fungal-plant interactions. Methods We used six Clonostachys spp. that exhibit saprotrophic, mycotrophic and plant endophytic lifestyles. Genome-wide analyses was performed to investigate the composition, diversity, evolution and gene expression of Clonostachys secretomes in relation to their potential role in mycoparasitic and endophytic lifestyles. Results and discussion Our analyses showed that the predicted secretomes of the analyzed species comprised between 7 and 8% of the respective proteomes. Mining of transcriptome data collected during previous studies showed that 18% of the genes encoding predicted secreted proteins were upregulated during the interactions with the mycohosts Fusarium graminearum and Helminthosporium solani. Functional annotation of the predicted secretomes revealed that the most represented protease family was subclass S8A (11-14% of the total), which include members that are shown to be involved in the response to nematodes and mycohosts. Conversely, the most numerous lipases and carbohydrate-active enzyme (CAZyme) groups appeared to be potentially involved in eliciting defense responses in the plants. For example, analysis of gene family evolution identified nine CAZyme orthogroups evolving for gene gains (p ≤ 0.05), predicted to be involved in hemicellulose degradation, potentially producing plant defense-inducing oligomers. Moreover, 8-10% of the secretomes was composed of cysteine-enriched proteins, including hydrophobins, important for root colonization. Effectors were more numerous, comprising 35-37% of the secretomes, where certain members belonged to seven orthogroups evolving for gene gains and were induced during the C. rosea response to F. graminearum or H. solani. Furthermore, the considered Clonostachys spp. possessed high numbers of proteins containing Common in Fungal Extracellular Membranes (CFEM) modules, known for their role in fungal virulence. Overall, this study improves our understanding of Clonostachys spp. adaptation to diverse ecological niches and establishes a basis for future investigation aiming at sustainable biocontrol of plant diseases.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Micol Guaschino
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea. Appl Environ Microbiol 2022; 88:e0064322. [PMID: 35695572 PMCID: PMC9275246 DOI: 10.1128/aem.00643-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact, and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small RNAs (sRNAs) are vital components of posttranscriptional gene regulation, although their role in gene expression regulation during mycoparasitisms remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tag sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were downregulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing desuppression (upregulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated potential gene targets for 282 differentially expressed sRNAs. Analysis of sRNA potential gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. The regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum, highlighting common and mycohost-specific gene regulation of C. rosea. By combining these results with transcriptome data collected during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism. IMPORTANCE Small RNAs (sRNAs) are emerging as key players in pathogenic and mutualistic fungus-plant interactions; however, their role in fungus-fungus interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions. The combined approach of sRNA and degradome tag sequencing identified 201 sRNA-mediated putative gene targets for 282 differentially expressed sRNAs, highlighting the role of sRNA-mediated regulation of mycoparasitism in C. rosea. We also identified 36 known and 13 novel microRNAs (miRNAs) and their potential gene targets at the endogenous level and at a cross-species level in B. cinerea and F. graminearum, indicating a role of cross-species RNA interference (RNAi) in mycoparasitism, representing a novel mechanism in biocontrol interactions. Furthermore, we showed that C. rosea adapts its transcriptional response, and thereby its interaction mechanisms, based on the interaction stages and identity of the mycohost.
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