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Yang Q, Mao Z, Hao Y, Zheng S, Zhao J, Li Y, Yang Y, Xie B, Ling J, Li Y. Genome-wide transcriptome profiling reveals molecular response pathways of Trichoderma harzianum in response to salt stress. Front Microbiol 2024; 15:1342584. [PMID: 38362502 PMCID: PMC10867199 DOI: 10.3389/fmicb.2024.1342584] [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: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Trichoderma harzianum exhibits a strong biological control effect on many important plant pathogens, such as Fusarium oxysporum, Botrytis cinerea, and Meloidogyne. However, its biocontrol effectiveness is weakened or reduced under salt stress. The aim of this study was to investigate the molecular response of T. harzianum to salt stress at the whole-genome level. Here, we present a 44.47 Mb near-complete genome assembly of the T. harzianum qt40003 strain for the first time, which was assembled de novo with 7.59 Gb Nanopore sequencing long reads (~170-fold) and 5.2 Gb Illumina short reads (~116-fold). The assembled qt40003 genome contains 12 contigs, with a contig N50 of 4.81 Mb, in which four of the 12 contigs were entirely reconstructed in a single chromosome from telomere to telomere. The qt40003 genome contains 4.27 Mb of repeat sequences and 12,238 protein-coding genes with a BUSCO completeness of 97.5%, indicating the high accuracy and completeness of our gene annotations. Genome-wide transcriptomic analysis was used to investigate gene expression changes related to salt stress in qt40003 at 0, 2% (T2), and 4% (T4) sodium chloride concentrations. A total of 2,937 and 3,527 differentially expressed genes (DEGs) were obtained under T2 and T4 conditions, respectively. GO enrichment analysis showed that the T2-treatment DEGs were highly enriched in detoxification (p < 0.001), while the T4 DEGs were mainly enriched in cell components, mostly in cellular detoxification, cell surface, and cell wall. KEGG metabolic pathway analysis showed that 91 and 173 DEGs were significantly enriched in the T2 and T4 treatments, respectively (p < 0.01), mainly in the glutathione metabolism pathway. We further experimentally analyzed the differentially expressed glutathione transferase genes in the glutathione metabolic pathway, most of which were downregulated (13/15). In addition, we screened 13 genes related to active oxygen clearance, including six upregulated and seven downregulated genes, alongside five fungal hydrophobic proteins, of which two genes were highly expressed. Our study provides high-quality genome information for the use of T. harzianum for biological control and offers significant insights into the molecular responses of T. harzianum under salt-stress conditions.
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Affiliation(s)
- Qihong Yang
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yali Hao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shijie Zheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingyan Xie
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanlin Li
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha, China
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Marchal C, Defossez PA, Miotto B. Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38. Epigenetics 2022; 17:2122-2143. [PMID: 36000449 DOI: 10.1080/15592294.2022.2111135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.
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Affiliation(s)
- Claire Marchal
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | | | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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Nishio M, Matsuura T, Hibi S, Ohta S, Oka C, Sasai N, Ishida Y, Matsuda E. Heterozygous loss of Zbtb38 leads to early embryonic lethality via the suppression of Nanog and Sox2 expression. Cell Prolif 2022; 55:e13215. [PMID: 35297517 PMCID: PMC9055898 DOI: 10.1111/cpr.13215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/27/2023] Open
Abstract
Objectives Mammalian DNA methyltransferases are essential to re‐establish global DNA methylation patterns during implantation, which is critical for transmitting epigenetic information to the next generation. In contrast, the significance of methyl‐CpG binding proteins (MBPs) that bind methylated CpG remains almost unknown at this stage. We previously demonstrated that Zbtb38 (also known as CIBZ)—a zinc finger type of MBP—is required for mouse embryonic stem (ES) cell proliferation by positively regulating Nanog expression. However, the physiological function of Zbtb38 in vivo remains unclear. Materials and Methods This study used the Cre‐loxP system to generate conditional Zbtb38 knockout mice. Cell proliferation and apoptosis were studied by immunofluorescence staining. Quantitative real‐time PCR, immunoblotting and immunofluorescence were performed to investigate the molecular mechanisms. Results Germline loss of the Zbtb38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. Heterozygous loss of Zbtb38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Although this early lethal phenotype, Zbtb38 is dispensable for ES cell establishment and identity. Conclusions These findings indicate that Zbtb38 is essential for early embryonic development via the suppression of Nanog and Sox2 expression.
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Affiliation(s)
- Miki Nishio
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan.,Cosmo Bio Co., Ltd., Tokyo, Japan
| | - Takuya Matsuura
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shunya Hibi
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shiomi Ohta
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Chio Oka
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Noriaki Sasai
- Development Biomedical Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yasumasa Ishida
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Eishou Matsuda
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
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Wong R, Bhattacharya D. ZBTB38 is dispensable for antibody responses. PLoS One 2020; 15:e0235183. [PMID: 32956421 PMCID: PMC7505459 DOI: 10.1371/journal.pone.0235183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/07/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the broad complex, tram track, bric-a-brac and zinc finger (BTB-ZF) family of transcription factors, such as BCL-6, ZBTB20, and ZBTB32, regulate antigen-specific B cell differentiation, plasma cell longevity, and the duration of antibody production. We found that ZBTB38, a different member of the BTB-ZF family that binds methylated DNA at CpG motifs, is highly expressed by germinal center B cells and plasma cells. To define the functional role of ZBTB38 in B cell responses, we generated mice conditionally deficient in this transcription factor. Germinal center B cells lacking ZBTB38 dysregulated very few genes relative to wild-type and heterozygous littermate controls. Accordingly, mice with hematopoietic-specific deletion of Zbtb38 showed normal germinal center B cell numbers and antibody responses following immunization with hapten-protein conjugates. Memory B cells from these animals functioned normally in secondary recall responses. Despite expression of ZBTB38 in hematopoietic stem cells, progenitors and mature myeloid and lymphoid lineages were also present in normal numbers in mutant mice. These data demonstrate that ZBTB38 is dispensable for hematopoiesis and antibody responses. These conditional knockout mice may instead be useful in defining the functional importance of ZBTB38 in other cell types and contexts.
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Affiliation(s)
- Rachel Wong
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, United States of America
- Department of Immunobiology, University of Arizona, Tucson, AZ, United States of America
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona, Tucson, AZ, United States of America
- * E-mail:
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Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer. Cancers (Basel) 2020; 12:cancers12051106. [PMID: 32365491 PMCID: PMC7281456 DOI: 10.3390/cancers12051106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/12/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men. A number of genomic and clinical studies have led to a better understanding of prostate cancer biology. Still, the care of patients as well as the prediction of disease aggressiveness, recurrence and outcome remain challenging. Here, we showed that expression of the gene ZBTB38 is associated with poor prognosis in localised prostate cancer and could help discriminate aggressive localised prostate tumours from those who can benefit only from observation. Analysis of different prostate cancer cohorts indicates that low expression levels of ZBTB38 associate with increased levels of chromosomal abnormalities and more aggressive pathological features, including higher rate of biochemical recurrence of the disease. Importantly, gene expression profiling of these tumours, complemented with cellular assays on prostate cancer cell lines, unveiled that tumours with low levels of ZBTB38 expression might be targeted by doxorubicin, a compound generating reactive oxygen species. Our study shows that ZBTB38 is involved in prostate cancer pathogenesis and may represent a useful marker to identify high risk and highly rearranged localised prostate cancer susceptible to doxorubicin.
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