Profiling of BABA-induced differentially expressed genes of Zea mays using suppression subtractive hybridization

Shaw, Arun K.; Bhardwaj, Pardeep Kumar; Ghosh, Supriya; Azahar, Ikbal; Adhikari, Sinchan; Adhikari, Ayan; Sherpa, Ang Rinzing; Saha, Samir K.; Hossain, Zahed

doi:10.1039/c7ra06220f

Cited by 3 publications

(2 citation statements)

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“…Many other DCL-responsive genes are related to resistance to various types of abiotic stresses. We could detect seven DHN dehydrins, involved in the response to dehydration and cold (Shakirova et al 2016), one H-type thioredoxin, mediating responses to oxidative stresses (Wu et al 2017; Shaw et al 2017) and one aldose reductase, whose overexpression improves drought resistance in transgenic plants (Fehér-Juhász et al 2014). Other detected genes were involved in resistance to pathogens, such as one Bowman-Birk type trypsin inhibitor-like isoform X2, which can inhibit in vitro growth of F. graminearum , Fusarium culmorum and Fusarium tritici (Chilosi et al 2000), and one premnaspirodiene oxygenase-like protein, involved in resistance to Phytophthora capsici in black pepper (Paul et al 2019).…”

Section: Resultsmentioning

confidence: 99%

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions

Piombo,

Vetukuri,

Jensen

et al. 2023

Preprint

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The intricate molecular interplay between beneficial fungi and plants is vital to plant growth promotion and induced defense response. This study explored the role of DCL-mediated RNA silencing in the interaction between the biocontrol fungus Clonostachys rosea and wheat roots. We investigated the impact of DCL (Dicer-like) gene deletions in C. rosea on its root colonization ability. Our results revealed that the deletion of dcl2 significantly enhanced C. rosea biomass on wheat roots, indicating a pivotal role of DCL2 in root colonization. Transcriptome sequencing of C. rosea and wheat during their interactions unveiled extensive gene expression changes. In wheat, genes related to stress responses were upregulated during C. rosea interactions, while genes associated with plant cell wall modification and metabolic processes were downregulated, suggesting complex regulatory responses and a trade-off between defense mechanisms and growth promotion. Deletion of C. rosea dcl1 and dcl2 altered the transcriptomic responses of wheat roots during interactions. Wheat genes associated with stress responses were downregulated during interactions with DCL deletion strains. In contrast, genes involved in metabolic processes and growth were upregulated, emphasizing the cross-kingdom regulatory role of C. rosea small RNAs (sRNAs). We identified 18 wheat miRNAs responsive to C. rosea interactions. Furthermore, we identified 24 endogenous and six cross-kingdom potential gene targets for seven and five differentially expressed miRNAs, supported by their inverse gene expression pattern. In C. rosea, we found a large transcriptional reprogramming of genes during interaction with wheat roots. The upregulated genes were associated with carbohydrate and polysaccharide catabolic processes, membrane transporters and effectors. Conversely, downregulated genes were mainly associated with transition metal ion transport and homeostasis processes. The deletion of dcl1 and dcl2 had significant effects on gene expression. A higher number of genes upregulated in WT during the interaction were restored in DCL deletion mutants, suggesting DCL-mediated gene expression regulation. Furthermore, we identified 21 differentially expressed micro-RNA-like RNAs (milRNAs) in C. rosea; nine were DCL-dependent. They had putative gene targets in C. rosea, including transcription factors, effectors, transporters, and enzymes involved in specialized metabolite production. Cross-kingdom RNA silencing was also observed, with seven DCL-dependent C. rosea milRNAs potentially targeting 29 genes in wheat. These findings provide valuable insights into the molecular mechanisms underlying the beneficial interaction between fungi and plant roots. In addition, the study shed light on the role of sRNA-mediated gene regulation in the C. rosea-wheat interaction, with potential implications for sustainable agriculture and biocontrol strategies.

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Section: Resultsmentioning

confidence: 99%

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions

Piombo,

Vetukuri,

Jensen

et al. 2023

Preprint

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“…mRNA was purified from total RNA using an Oligotex dT30 mRNA kit (TaKaRa, Japan) according to the manufacturer's instructions. SSH was performed using the PCR-select cDNA SSH kit (Clontech, USA); the detailed protocol was previously reported (47). The resulting PCR products enriched for differentially expressed cDNAs were separately cloned into the TA cloning system (Invitrogen, USA) to construct forward and reverse libraries.…”

Section: Methodsmentioning

confidence: 99%

Microbial Communities in Different Developmental Stages of the Oriental Fruit Fly, Bactrocera dorsalis, Are Associated with Differentially Expressed Peptidoglycan Recognition Protein-Encoding Genes

Huang

Ren

Cheng

2019

Appl Environ Microbiol

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The insect microbiota can change dramatically to enable adaptation of the host in different developmental stages and environments; however, little is known about how the host maintains its microbiota to achieve such adaptations. In this study, 16S rRNA sequencing revealed that the microorganisms in larvae and adults of the Oriental fruit fly, Bactrocera dorsalis, are primarily Gram-negative bacteria but that the major components in pupae are Gram-positive bacteria. Using suppression subtractive hybridization (SSH) and transcriptome analysis, we screened two specifically expressed genes encoding peptidoglycan recognition proteins (PGRP-LB and PGRP-SB1) and analyzed their relationship to B. dorsalis microbial communities. Knockdown of the PGRP-LB gene in larvae and adults led to increased ratios of Gram-positive bacteria; knockdown of the PGRP-SB1 gene in pupae led to increased ratios of Gram-negative bacteria. Our results suggest that maintenance of the microbiota in different developmental stages of B. dorsalis may be associated with the PGRP-LB and PGRP-SB1 genes. IMPORTANCE Microorganisms are ubiquitous in insects and have widespread impacts on multiple aspects of insect biology. However, the microorganisms present in insects can change dramatically in different developmental stages, and it is critical to maintain the appropriate microorganisms in specific host developmental stages. Therefore, analysis of the factors associated with the microbiota in specific development stages of the host is needed. In this study, we applied suppression subtractive hybridization (SSH) combined with transcriptome analysis to investigate whether the microbiota in development stages of the Oriental fruit fly, Bactrocera dorsalis, is associated with expression of PGRP genes. We found that two different PGRP genes were specifically expressed during development and that these genes may be associated with changes in microbial communities in different developmental stages of B. dorsalis.

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RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

Piombo,

Vetukuri,

Konakalla

et al. 2024

BMC Biol

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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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Profiling of BABA-induced differentially expressed genes of Zea mays using suppression subtractive hybridization

Abstract: This study aims to identify differentially expressed transcripts in BABA-primed maize leaves using suppression subtractive hybridization (SSH) strategy. Findings shed new light on the BABA potentiated defense mechanisms in plants.

Cited by 3 publications

References 89 publications

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions

Microbial Communities in Different Developmental Stages of the Oriental Fruit Fly, Bactrocera dorsalis, Are Associated with Differentially Expressed Peptidoglycan Recognition Protein-Encoding Genes

RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

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