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Zuo D, Lei S, Qian F, Gu L, Wang H, Du X, Zeng T, Zhu B. Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata. BMC PLANT BIOLOGY 2024; 24:296. [PMID: 38632529 PMCID: PMC11022436 DOI: 10.1186/s12870-024-05004-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca2+ signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods. RESULTS Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress. CONCLUSION This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.
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Affiliation(s)
- Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Shaolin Lei
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550009, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
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202
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Justice JL, Reed TJ, Phelan B, Greco TM, Hutton JE, Cristea IM. DNA-PK and ATM drive phosphorylation signatures that antagonistically regulate cytokine responses to herpesvirus infection or DNA damage. Cell Syst 2024; 15:339-361.e8. [PMID: 38593799 PMCID: PMC11098675 DOI: 10.1016/j.cels.2024.03.003] [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: 08/17/2023] [Revised: 01/09/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
The DNA-dependent protein kinase, DNA-PK, is an essential regulator of DNA damage repair. DNA-PK-driven phosphorylation events and the activated DNA damage response (DDR) pathways are also components of antiviral intrinsic and innate immune responses. Yet, it is not clear whether and how the DNA-PK response differs between these two forms of nucleic acid stress-DNA damage and DNA virus infection. Here, we define DNA-PK substrates and the signature cellular phosphoproteome response to DNA damage or infection with the nuclear-replicating DNA herpesvirus, HSV-1. We establish that DNA-PK negatively regulates the ataxia-telangiectasia-mutated (ATM) DDR kinase during viral infection. In turn, ATM blocks the binding of DNA-PK and the nuclear DNA sensor IFI16 to viral DNA, thereby inhibiting cytokine responses. However, following DNA damage, DNA-PK enhances ATM activity, which is required for IFN-β expression. These findings demonstrate that the DDR autoregulates cytokine expression through the opposing modulation of DDR kinases.
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Affiliation(s)
- Joshua L Justice
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Tavis J Reed
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Brett Phelan
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Josiah E Hutton
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA.
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203
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Jun SE, Cho KH, Schaffrath R, Kim GT. Evolutionary Conservation in Protein-Protein Interactions and Structures of the Elongator Sub-Complex ELP456 from Arabidopsis and Yeast. Int J Mol Sci 2024; 25:4370. [PMID: 38673955 PMCID: PMC11050213 DOI: 10.3390/ijms25084370] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the precise details of the evolutionary conservation of the holo-Elongator complex and its individual sub-complexes (i.e., ELP123; ELP456) in plants remain limited. In this study, we conducted an in vivo analysis of protein-protein interactions among Arabidopsis ELP4, ELP5, and ELP6 proteins. Additionally, we predicted their structural configurations and performed a comparative analysis with the structure of the yeast Elp456 sub-complex. Protein-protein interaction analysis revealed that AtELP4 interacts with AtELP6 but not directly with AtELP5. Furthermore, we found that the Arabidopsis Elongator-associated protein, Deformed Roots and Leaves 1 (DRL1), did not directly bind to AtELP proteins. The structural comparison of the ELP456 sub-complex between Arabidopsis and yeast demonstrated high similarity, encompassing the RecA-ATPase fold and the positions of hydrogen bonds, despite their relatively low sequence homology. Our findings suggest that Arabidopsis ELP4, ELP5, and ELP6 proteins form a heterotrimer, with ELP6 serving as a bridge, indicating high structural conservation between the ELP456 sub-complexes from Arabidopsis and yeast.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Gyeongbuk Institute for Bioindustry, Andong 36618, Republic of Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany;
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Graduate School of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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204
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Gorityala N, Baidya AS, Sagurthi SR. Genome mining of Mycobacterium tuberculosis: targeting SufD as a novel drug candidate through in silico characterization and inhibitor screening. Front Microbiol 2024; 15:1369645. [PMID: 38686111 PMCID: PMC11057465 DOI: 10.3389/fmicb.2024.1369645] [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: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease globally, causing 1.3 million deaths in 2022. The resurgence of TB and the alarming rise of antibiotic resistance demand urgent call to develop novel antituberculosis drugs. Despite concerted efforts to control TB, the disease persists and spreads rapidly on a global scale. Targeting stress response pathways in Mycobacterium tuberculosis (Mtb) has become imperative to achieve complete eradication. This study employs subtractive genomics to identify and prioritize potential drug targets among the hypothetical proteins of Mtb, focusing on indispensable pathways. Amongst 177 essential hypothetical proteins, 152 were nonhomologous to human. These proteins participated in 34 pathways, and a 20-fold enrichment of SUF pathway genes led to its selection as a target pathway. Fe-S clusters are fundamental, widely distributed protein cofactors involved in vital cellular processes. The survival of Mtb in a hypoxic environment relies on the iron-sulfur (Fe-S) cluster biogenesis pathway for the repair of damaged Fe-S clusters. It also protects pathogen against drugs, ensuring controlled iron utilization and contributing to drug resistance. In Mtb, six proteins of Fe-S cluster assembly pathway are encoded by the suf operon. The present study was focused on SufD because of its role in iron acquisition and prevention of Fenton reaction. The research further delves into the in silico characterization of SufD, utilizing bioinformatics tools for sequence and structure based analysis. The protein's structural features, including the identification of conserved regions, motifs, and 3D structure prediction enhanced functional annotation. Target based virtual screening of compounds from the ChEMBL database resulted in 12 inhibitors with best binding affinities. Drug likeness and ADMET profiling of potential inhibitors identified promising compounds with favorable drug-like properties. The study also involved cloning in SUMO-pRSF-Duet1 expression vector, overexpression, and purification of recombinant SufD from E. coli BL21 (DE3) cells. Optimization of expression conditions resulted in soluble production, and subsequent purification highlighting the efficacy of the SUMO fusion system for challenging Mtb proteins in E. coli. These findings provide valuable insights into pharmacological targets for future experimental studies, holding promise for the development of targeted therapy against Mtb.
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Affiliation(s)
- Neelima Gorityala
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Anthony Samit Baidya
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar R Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
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205
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Kumawat G, Cao D, Park C, Xu D. C-terminally encoded peptide-like genes are associated with the development of primary root at qRL16.1 in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1387954. [PMID: 38685962 PMCID: PMC11056954 DOI: 10.3389/fpls.2024.1387954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Root architecture traits are belowground traits that harness moisture and nutrients from the soil and are equally important to above-ground traits in crop improvement. In soybean, the root length locus qRL16.1 was previously mapped on chromosome 16. The qRL16.1 has been characterized by transcriptome analysis of roots in near-isogenic lines (NILs), gene expression analysis in a pair of lines contrasting with alleles of qRL16.1, and differential gene expression analysis in germplasm accessions contrasting with root length. Two candidate genes, Glyma.16g108500 and Glyma.16g108700, have shown relatively higher expression in longer root accessions than in shorter rooting accessions. The C-terminal domain of Glyma.16g108500 and Glyma.16g108700 is similar to the conserved domain of C-terminally encoded peptides (CEPs) that regulate root length and nutrient response in Arabidopsis. Two polymorphisms upstream of Glyma.16g108500 showed a significant association with primary root length and total root length traits in a germplasm set. Synthetic peptide assay with predicted CEP variants of Glyma.16g108500 and Glyma.16g108700 demonstrated their positive effect on primary root length. The two genes are root-specific in the early stage of soybean growth and showed differential expression only in the primary root. These genes will be useful for improving soybean to develop a deep and robust root system to withstand low moisture and nutrient regimes.
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Affiliation(s)
- Giriraj Kumawat
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Crop Improvement Section, ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
| | - Dong Cao
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Cheolwoo Park
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
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206
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He W, Belsham DD. RNA-Binding Protein Motifs Predict microRNA Secretion and Cellular Retention in Hypothalamic and Other Cell Types. Biomedicines 2024; 12:857. [PMID: 38672211 PMCID: PMC11048351 DOI: 10.3390/biomedicines12040857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cellular microRNAs (miRNAs) can be selectively secreted or retained, adding another layer to their critical role in regulating human health and disease. To date, select RNA-binding proteins (RBPs) have been proposed to be a mechanism underlying miRNA localization, but the overall relevance of RBPs in systematic miRNA sorting remains unclear. This study profiles intracellular and small extracellular vesicles' (sEVs) miRNAs in NPY-expressing hypothalamic neurons. These findings were corroborated by the publicly available sEV and intracellular miRNA profiles of white and brown adipocytes, endothelium, liver, and muscle from various databases. Using experimentally determined binding motifs of 93 RBPs, our enrichment analysis revealed that sEV-originating miRNAs contained significantly different RBP motifs than those of intracellularly retained miRNAs. Multiple RBP motifs were shared across cell types; for instance, RBM4 and SAMD4 are significantly enriched in neurons, hepatocytes, skeletal muscle, and endothelial cells. Homologs of both proteins physically interact with Argonaute1/2 proteins, suggesting that they play a role in miRNA sorting. Machine learning modelling also demonstrates that significantly enriched RBP motifs could predict cell-specific preferential miRNA sorting. Non-optimized machine learning modeling of the motifs using Random Forest and Naive Bayes in all cell types except WAT achieved an area under the receiver operating characteristic (ROC) curve of 0.77-0.84, indicating a high predictive accuracy. Given that the RBP motifs have a significant predictive power, these results underscore the critical role that RBPs play in miRNA sorting within mammalian cells and reinforce the importance of miRNA sequencing in preferential localization. For the future development of small RNA therapeutics, considering these RBP-RNA interactions could be crucial to maximize delivery effectiveness and minimize off-target effects.
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Affiliation(s)
- Wenyuan He
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Denise D. Belsham
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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207
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Sun S, Bakkeren G. A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1369299. [PMID: 38681221 PMCID: PMC11046709 DOI: 10.3389/fpls.2024.1369299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.
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Affiliation(s)
- Sherry Sun
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Center, Summerland, BC, Canada
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208
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Liu C, Fan E, Liu Y, Wang M, Wang Q, Wang S, Chen S, Yang C, You X, Qu G. Genome-Wide Identification and Analysis of the EIN3/EIL Transcription Factor Gene Family in Doubled Haploid (DH) Poplar. Int J Mol Sci 2024; 25:4116. [PMID: 38612925 PMCID: PMC11012330 DOI: 10.3390/ijms25074116] [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: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Ethylene (ET) is an important phytohormone that regulates plant growth, development and stress responses. The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor family, as a key regulator of the ET signal transduction pathway, plays an important role in regulating the expression of ET-responsive genes. Although studies of EIN3/EIL family members have been completed in many species, their role in doubled haploid (DH) poplar derived from another culture of diploid Populus simonii × P. nigra (donor tree, DT) remains ambiguous. In this study, a total of seven EIN3/EIL gene family members in the DH poplar genome were identified. Basic physical and chemical property analyses of these genes were performed, and these proteins were predicted to be localized to the nucleus. According to the phylogenetic relationship, EIN3/EIL genes were divided into two groups, and the genes in the same group had a similar gene structure and conserved motifs. The expression patterns of EIN3/EIL genes in the apical buds of different DH poplar plants were analyzed based on transcriptome data. At the same time, the expression patterns of PsnEIL1, PsnEIN3, PsnEIL4 and PsnEIL5 genes in different tissues of different DH plants were detected via RT-qPCR, including the apical buds, young leaves, functional leaves, xylem, cambium and roots. The findings presented above indicate notable variations in the expression levels of PsnEIL genes across various tissues of distinct DH plants. Finally, the PsnEIL1 gene was overexpressed in DT, and the transgenic plants showed a dwarf phenotype, indicating that the PsnEIL1 gene was involved in regulating the growth and development of poplar. In this study, the EIN3/EIL gene family of DH poplar was analyzed and functionally characterized, which provides a theoretical basis for the future exploration of the EIN3/EIL gene function.
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Affiliation(s)
- Caixia Liu
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (C.L.); (X.Y.)
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa Bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuhang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Meng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Qiuyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Sui Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China;
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
| | - Xiangling You
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (C.L.); (X.Y.)
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (Y.L.); (M.W.); (Q.W.); (S.C.); (C.Y.)
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209
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Zhu T, Wei C, Yu Y, Zhang Z, Zhu J, Liang Z, Song X, Fu W, Cui Y, Wang ZY, Li C. The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis. Dev Cell 2024; 59:924-939.e6. [PMID: 38359831 PMCID: PMC11003849 DOI: 10.1016/j.devcel.2024.01.021] [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: 08/02/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.
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Affiliation(s)
- Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chuangqi Wei
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenzhen Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiameng Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-food Canada, London, ON N5V 4T3, Canada
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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210
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Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
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Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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211
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Li C, Zou Q, Jia C, Zheng J. AMPpred-MFA: An Interpretable Antimicrobial Peptide Predictor with a Stacking Architecture, Multiple Features, and Multihead Attention. J Chem Inf Model 2024; 64:2393-2404. [PMID: 37799091 DOI: 10.1021/acs.jcim.3c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Antimicrobial peptides (AMPs) are small molecular polypeptides that can be widely used in the prevention and treatment of microbial infections. Although many computational models have been proposed to help identify AMPs, a high-performance and interpretable model is still lacking. In this study, new benchmark data sets are collected and processed, and a stacking deep architecture named AMPpred-MFA is carefully designed to discover and identify AMPs. Multiple features and a multihead attention mechanism are utilized on the basis of a bidirectional long short-term memory (LSTM) network and a convolutional neural network (CNN). The effectiveness of AMPpred-MFA is verified through five independent tests conducted in batches. Experimental results show that AMPpred-MFA achieves a state-of-the-art performance. The visualization interpretability analyses and ablation experiments offer a further understanding of the model behavior and performance, validating the importance of our feature representation and stacking architecture, especially the multihead attention mechanism. Therefore, AMPpred-MFA can be considered a reliable and efficient approach to understanding and predicting AMPs.
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Affiliation(s)
- Changjiang Li
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Cangzhi Jia
- School of Science, Dalian Maritime University, Dalian 116026, China
| | - Jia Zheng
- School of Science, Dalian Maritime University, Dalian 116026, China
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212
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Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588333. [PMID: 38617258 PMCID: PMC11014505 DOI: 10.1101/2024.04.05.588333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- MM Inge
- Department of Biology, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - R Miller
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - H Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - D Bray
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - JL Keenan
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - R Zhao
- Department of Biology, Boston University, Boston, MA, USA
| | - TD Gilmore
- Department of Biology, Boston University, Boston, MA, USA
| | - T Siggers
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
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213
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Augustijn HE, Karapliafis D, Joosten KMM, Rigali S, van Wezel GP, Medema MH. LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria. J Mol Biol 2024:168558. [PMID: 38580076 DOI: 10.1016/j.jmb.2024.168558] [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: 02/06/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Actinobacteria undergo a complex multicellular life cycle and produce a wide range of specialized metabolites, including the majority of the antibiotics. These biological processes are controlled by intricate regulatory pathways, and to better understand how they are controlled we need to augment our insights into the transcription factor binding sites. Here, we present LogoMotif (https://logomotif.bioinformatics.nl), an open-source database for characterized and predicted transcription factor binding sites in Actinobacteria, along with their cognate position weight matrices and hidden Markov models. Genome-wide predictions of binding site locations in Streptomyces model organisms are supplied and visualized in interactive regulatory networks. In the web interface, users can freely access, download and investigate the underlying data. With this curated collection of actinobacterial regulatory interactions, LogoMotif serves as a basis for binding site predictions, thus providing users with clues on how to elicit the expression of genes of interest and guide genome mining efforts.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Kristy M M Joosten
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Sébastien Rigali
- InBioS - Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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214
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Chen Q, Zhu C, Guo L, Bu X, Yang W, Cheng S, Cong X, Xu F. Genome-wide identification of HMT gene family explores BpHMT2 enhancing selenium accumulation and tolerance in Broussonetia papyrifera. TREE PHYSIOLOGY 2024; 44:tpae030. [PMID: 38498335 DOI: 10.1093/treephys/tpae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
Broussonetia papyrifera, a valuable feed resource, is known for its fast growth, wide adaptability, high protein content and strong selenium enrichment capacity. Selenomethionine (SeMet), the main selenium form in selenium fortification B. papyrifera, is safe for animals and this enhances its nutritional value as a feed resource. However, the molecular mechanisms underlying SeMet synthesis remain unclear. This study identified three homocysteine S-methyltransferase genes from the B. papyrifera genome. The phylogenetic tree demonstrated that BpHMTs were divided into two classes, and BpHMT2 in the Class 2-D subfamily evolved earlier and possesses more fundamental functions. On the basis of the correlation between gene expression levels and selenium content, BpHMT2 was identified as a key candidate gene associated with selenium tolerance. Subcellular localization experiments confirmed the targeting of BpHMT2 in nucleus, cell membrane and chloroplasts. Moreover, three BpHMT2 overexpression Arabidopsis thaliana lines were confirmed to enhance plant selenium tolerance and SeMet accumulation. Overall, our finding provides insights into the molecular mechanisms of selenium metabolism in B. papyrifera, highlighting the potential role of BpHMT2 in SeMet synthesis. This research contributes to our understanding of selenium-enriched feed resources, with increased SeMet content contributing to the improved nutritional value of B. papyrifera as a feed resource.
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Affiliation(s)
- Qiangwen Chen
- Enshi Se-Run Material Engineering Technology Co., Ltd, Enshi, Hubei 445000, China
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Changye Zhu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Longfei Guo
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Xianchen Bu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Wei Yang
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
- Hubei National Se-rich Technology Development Co., Ltd, Enshi 445000, China
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, Hubei 445000, China
| | - Xin Cong
- Enshi Se-Run Material Engineering Technology Co., Ltd, Enshi, Hubei 445000, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
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215
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Sami A, Haider MZ, Shafiq M, Sadiq S, Ahmad F. Genome-wide identification and in-silico expression analysis of CCO gene family in sunflower (Helianthus annnus) against abiotic stress. PLANT MOLECULAR BIOLOGY 2024; 114:34. [PMID: 38568355 PMCID: PMC10991017 DOI: 10.1007/s11103-024-01433-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
Carotenoid cleavage oxygenases (CCOs) enzymes play an important role in plant growth and development by producing a wide array of apocarotenoids and their derivatives. These compounds are vital for colouring flowers and fruits and synthesizing plant hormones such as abscisic acid and strigolactones. Despite their importance, the gene family responsible for CCO enzymes in sunflowers has not been identified. In this study, we identify the CCO genes of the sunflower plant to fill this knowledge gap. Phylogenetic and synteny analysis indicated that the Helianthus annnus CCO (HaCCO) genes were conserved in different plant species and they could be divided into three subgroups based on their conserved domains. Analysis using MEME tool and multiple sequence alignment identified conserved motifs in the HaCCO gene sequence. Cis-regulatory elements (CREs) analysis of the HaCCO genes indicated the presence of various responsive elements related to plant hormones, development, and responses to both biotic and abiotic stresses. This implies that these genes may respond to plant hormones, developmental cues, and drought stress, offering potential applications in the development of more resistant crops. Genes belonging to the 9-cis-epoxy carotenoid dioxygenases (NCED) subgroups predominantly exhibited chloroplast localization, whereas the genes found in other groups are primarily localized in the cytoplasm. These 21 identified HaCCOs were regulated by 60 miRNAs, indicating the crucial role of microRNAs in gene regulation in sunflowers. Gene expression analysis under drought stress revealed significant up-regulation of HaNCED16 and HaNCED19, genes that are pivotal in ABA hormone biosynthesis. During organ-specific gene expression analysis, HaCCD12 and HaCCD20 genes exhibit higher activity in leaves, indicating a potential role in leaf pigmentation. This study provides a foundation for future research on the regulation and functions of the CCO gene family in sunflower and beyond. There is potential for developing molecular markers that could be employed in breeding programs to create new sunflower lines resistant to biotic and abiotic stresses.
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Affiliation(s)
- Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Muhammad Zeeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Saleh Sadiq
- Institute of Biochemistry, Biotechnology, and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Farooq Ahmad
- Sustainable Forest Management Research Institute (iuFOR), University of Valladolid and INIA, Avenida de Madrid, Palencia, 34004, Spain.
- Department of Vegetable Production and Forest Resources, University of Valladolid, Avda. de Madrid, Palencia, 34004, Spain.
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216
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Wu T, Liu Z, Yu T, Zhou R, Yang Q, Cao R, Nie F, Ma X, Bai Y, Song X. Flowering genes identification, network analysis, and database construction for 837 plants. HORTICULTURE RESEARCH 2024; 11:uhae013. [PMID: 38585015 PMCID: PMC10995624 DOI: 10.1093/hr/uhae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/02/2024] [Indexed: 04/09/2024]
Abstract
Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183 720 genes across eight pathways, along with 10 155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the Plant Flowering-time Gene Database (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.
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Affiliation(s)
- Tong Wu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Yu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus 8200, Denmark
| | - Qihang Yang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei 066600, China
| | - Yun Bai
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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217
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Zhou D, Ding M, Wen S, Tian Q, Zhang X, Fang Y, Xue D. Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1010. [PMID: 38611539 PMCID: PMC11013768 DOI: 10.3390/plants13071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/30/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024]
Abstract
Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs.
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Affiliation(s)
- Danni Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Mingyu Ding
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Shuting Wen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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218
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Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol 2024; 121:742-766. [PMID: 38204420 PMCID: PMC11023807 DOI: 10.1111/mmi.15225] [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: 06/09/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
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Affiliation(s)
- Rylee K. Hackley
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Sungmin Hwang
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Jake T. Herb
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Preeti Bhanap
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Katie Lam
- Biology Department, Duke University, Durham, North Carolina, USA
| | | | | | | | - Johnathan H. Martin
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Amy K. Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
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219
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Gagliano T, Kerschbamer E, Baccarani U, Minisini M, Di Giorgio E, Dalla E, Weichenberger CX, Cherchi V, Terrosu G, Brancolini C. Changes in chromatin accessibility and transcriptional landscape induced by HDAC inhibitors in TP53 mutated patient-derived colon cancer organoids. Biomed Pharmacother 2024; 173:116374. [PMID: 38447451 DOI: 10.1016/j.biopha.2024.116374] [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: 01/08/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Here we present the generation and characterization of patient-derived organoids (PDOs) from colorectal cancer patients. PDOs derived from two patients with TP53 mutations were tested with two different HDAC inhibitors (SAHA and NKL54). Cell death induction, transcriptome, and chromatin accessibility changes were analyzed. HDACIs promote the upregulation of low expressed genes and the downregulation of highly expressed genes. A similar differential effect is observed at the level of chromatin accessibility. Only SAHA is a potent inducer of cell death, which is characterized by the upregulation of BH3-only genes BIK and BMF. Up-regulation of BIK is associated with increased accessibility in an intronic region that has enhancer properties. SAHA, but not NKL54, also causes downregulation of BCL2L1 and decreases chromatin accessibility in three distinct regions of the BCL2L1 locus. Both inhibitors upregulate the expression of innate immunity genes and members of the MHC family. In summary, our exploratory study indicates a mechanism of action for SAHA and demonstrate the low efficacy of NKL54 as a single agent for apoptosis induction, using two PDOs. These observations need to be validated in a larger cohort of PDOs.
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Affiliation(s)
- Teresa Gagliano
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Emanuela Kerschbamer
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Umberto Baccarani
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | | | - Vittorio Cherchi
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine, Italy
| | - Giovanni Terrosu
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy.
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220
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Waheed A, Chen Y, Rizwan HM, Adnan M, Ma X, Liu G. Genomic characterization and expression profiling of the lytic polysaccharide monooxygenases AA9 family in thermophilic fungi Thermothelomyces fergusii in response to carbon source media. Int J Biol Macromol 2024; 265:130740. [PMID: 38462117 DOI: 10.1016/j.ijbiomac.2024.130740] [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: 12/04/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Enhancing enzyme activity and stability in biomass degradation can improve substrate saccharification and, increases biorefinery efficiency. For the first time, we identified 20 lytic polysaccharide monooxygenases (LPMOs) AA9 genes in the genome of Thermothelomyces fergusii. Our results showed that TfAA9 was categorized into LPMOs1, LPMOs2, and LPMOs3 subgroups based on protein diversity. Protein- 3D structure analysis showed strong interactions between Myceliophthora thermophila AA9 proteins and 17 TfAA9 proteins. Gene ontology analysis indicated a high enrichment of cellulase activity in TfAA9 genes. KEGG pathways analysis revealed the role of TfAA9 proteins in the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. Numerous TfAA9s gene transcripts were up-regulated on avicel, cellobiose, and glucose, with a higher proportion on avicel. Protein concentration, endoglucanase, and cellulase activity were also boosted on avicel. However, limited fungal biomass was observed on avicel, despite the abundance of AA9 LPMOs in the T. fergusii genome. These findings expand our understanding of fungal AA9 genes and their role in lignocellulolytic degradation. The disparity between biomass and enzymatic activity suggests screening TfAA9 genes for highly active enzymes and redundant genes via heterologous expression. In short, functional characterization of these genes could contribute to improving the saccharification process of industrial raw materials.
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Affiliation(s)
- Abdul Waheed
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yi Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hafiz Muhammad Rizwan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Food Nutrition and Health, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuekun Ma
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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Li G, Zhu W, Tian M, Liu R, Ruan Y, Liu C. Genome-Wide Identification of the SPP/SPPL Gene Family and BnaSPPL4 Regulating Male Fertility in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:3936. [PMID: 38612746 PMCID: PMC11012144 DOI: 10.3390/ijms25073936] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, the functions of SPP/SPPL in rapeseed (Brassica napus L.) have not been reported. In this study, 26 SPP/SPPLs were identified in rapeseed and categorized into three groups: SPP, SPPL2, and SPPL3. These members mainly contained the Peptidase_A22 and PA domains, which were distributed on 17 out of 19 chromosomes. Evolutionary analyses indicated that BnaSPP/SPPLs evolved with a large number of whole-genome duplication (WGD) events and strong purifying selection. Members are widely expressed and play a key role in the growth and development of rapeseed. The regulation of rapeseed pollen fertility by the BnaSPPL4 gene was further validated through experiments based on bioinformatics analysis, concluding that BnaSPPL4 silencing causes male sterility. Cytological observation showed that male infertility caused by loss of BnaSPPL4 gene function occurs late in the mononucleate stage due to microspore dysplasia.
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Affiliation(s)
- Guangze Li
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Wenjun Zhu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Minyu Tian
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Rong Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Ying Ruan
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
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Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587306. [PMID: 38617318 PMCID: PMC11014486 DOI: 10.1101/2024.03.29.587306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
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Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- The James Hutton Institute, Dundee, Scotland DD2 5DA, UK
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Li G, Manzoor MA, Chen R, Zhang Y, Song C. Genome-wide identification and expression analysis of TIFY genes under MeJA, cold and PEG-induced drought stress treatment in Dendrobium huoshanense. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:527-542. [PMID: 38737319 PMCID: PMC11087441 DOI: 10.1007/s12298-024-01442-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
The TIFY family consists of plant-specific genes that regulates multiple plant functions, including developmental and defense responses. Here, we performed a comprehensive genomic analysis of TIFY genes in Dendrobium huoshanense. Our analysis encompassed their phylogenetic relationships, gene structures, chromosomal distributions, promoter regions, and patterns of collinearity. A total of 16 DhTIFY genes were identified, and classified into distinct clusters named JAZ, PPD, ZIM, and TIFY based on their phylogenetic relationship. These DhTIFYs exhibited an uneven distribution across 7 chromosomes. The expansion of the DhTIFY gene family appears to have been significantly influenced by whole-genome and segmental duplication events. The ratio of non-synonymous to synonymous substitutions (Ka/Ks) implies that the purifying selection has been predominant, maintaining a constrained functional diversification after duplication events. Gene structure analysis indicated that DhTIFYs exhibited significant structural variation, particularly in terms of gene organization and intron numbers. Moreover, numerous cis-acting elements related to hormone signaling, developmental processes, and stress responses were identified within the promoter regions. Subsequently, qRT-PCR experiments demonstrated that the expression of DhTIFYs is modulated in response to MeJA (Methyl jasmonate), cold, and drought treatment. Collectively, these results enhance our understanding of the functional dynamics of TIFY genes in D. huoshanense and may pinpoint potential candidates for detailed examination of the biological roles of TIFY genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01442-9.
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Affiliation(s)
- Guohui Li
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Chen
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003 China
| | - Cheng Song
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012 China
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224
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Fang Y, Bansal K, Mostafavi S, Benoist C, Mathis D. AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization. Nature 2024; 628:400-407. [PMID: 38480882 PMCID: PMC11091860 DOI: 10.1038/s41586-024-07169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells1-4. The biological logic of AIRE's target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE's cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice5. Both approaches nominated Z-DNA and NFE2-MAF as putative positive influences on AIRE's target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene's promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.
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Affiliation(s)
- Yuan Fang
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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Shi K, Liu J, Liang H, Dong H, Zhang J, Wei Y, Zhou L, Wang S, Zhu J, Cao M, Jones CS, Ma D, Wang Z. An alfalfa MYB-like transcriptional factor MsMYBH positively regulates alfalfa seedling drought resistance and undergoes MsWAV3-mediated degradation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:683-699. [PMID: 38358036 DOI: 10.1111/jipb.13626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Drought is a major threat to alfalfa (Medicago sativa L.) production. The discovery of important alfalfa genes regulating drought response will facilitate breeding for drought-resistant alfalfa cultivars. Here, we report a genome-wide association study of drought resistance in alfalfa. We identified and functionally characterized an MYB-like transcription factor gene (MsMYBH), which increases the drought resistance in alfalfa. Compared with the wild-types, the biomass and forage quality were enhanced in MsMYBH overexpressed plants. Combined RNA-seq, proteomics and chromatin immunoprecipitation analysis showed that MsMYBH can directly bind to the promoters of MsMCP1, MsMCP2, MsPRX1A and MsCARCAB to improve their expression. The outcomes of such interactions include better water balance, high photosynthetic efficiency and scavenge excess H2O2 in response to drought. Furthermore, an E3 ubiquitin ligase (MsWAV3) was found to induce MsMYBH degradation under long-term drought, via the 26S proteasome pathway. Furthermore, variable-number tandem repeats in MsMYBH promoter were characterized among a collection of germplasms, and the variation is associated with promoter activity. Collectively, our findings shed light on the functions of MsMYBH and provide a pivotal gene that could be leveraged for breeding drought-resistant alfalfa. This discovery also offers new insights into the mechanisms of drought resistance in alfalfa.
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Affiliation(s)
- Kun Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huan Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongbin Dong
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinli Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuanhong Wei
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Le Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shaopeng Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiahao Zhu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingshu Cao
- AgResearch Grasslands Research Centre, Palmerston North, 4442, New Zealand
| | - Chris S Jones
- International Livestock Research Institute, Nairobi, 00100, Kenya
| | - Dongmei Ma
- School of Ecology and Environment, Ningxia University, Yinchuan, 750021, China
| | - Zan Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
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Atanasov V, Schumacher J, Muiño JM, Larasati C, Wang L, Kaufmann K, Leister D, Kleine T. Arabidopsis BBX14 is involved in high light acclimation and seedling development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:141-158. [PMID: 38128030 DOI: 10.1111/tpj.16597] [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: 07/15/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
The development of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways and receives input from the biogenic signal integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light (HL) levels and biogenic signals, which was studied by using inhibitors of chloroplast development. Our chromatin immunoprecipitation-Seq experiments revealed that BBX14 is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 may function as a regulator of the circadian clock. In addition, BBX14 plays a role in chlorophyll biosynthesis during early onset of light. Knockout of BBX14 results in a long hypocotyl phenotype dependent on a retrograde signal. Furthermore, the expression of BBX14 and BBX15 during biogenic signaling requires GUN1. Investigation of the role of BBX14 and BBX15 in GUN-type biogenic (gun) signaling showed that the overexpression of BBX14 or BBX15 caused de-repression of CA1 mRNA levels, when seedlings were grown on norflurazon. Notably, transcripts of the LHCB1.2 marker are not de-repressed. Furthermore, BBX14 is required to acclimate plants to HL stress. We propose that BBX14 is an integrator of biogenic signals and that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module. However, we do not classify BBX14 or BBX15 overexpressors as gun mutants based on a critical evaluation of our results and those reported in the literature. Finally, we discuss a classification system necessary for the declaration of new gun mutants.
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Affiliation(s)
- Vasil Atanasov
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Julia Schumacher
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M Muiño
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Catharina Larasati
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Liangsheng Wang
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Kerstin Kaufmann
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
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Xiang KL, Wu SD, Lian L, He WC, Peng D, Peng HW, Zhang XN, Li HL, Xue JY, Shan HY, Xu GX, Liu Y, Wu ZQ, Wang W. Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae. SCIENCE CHINA. LIFE SCIENCES 2024; 67:803-816. [PMID: 38087029 DOI: 10.1007/s11427-023-2448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 04/06/2024]
Abstract
Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- China National Botanical Garden, Beijing, 100093, China
| | - Sheng-Dan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lian Lian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Yan Shan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Gui-Xia Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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228
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Tadesse D, Yee EF, Wolabu TW, Wang H, Yun J, Grosjean N, Kumaran D, Santiago K, Kong W, Sharma A, Chen J, Paterson AH, Xie M, Tadege M. Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation. THE NEW PHYTOLOGIST 2024; 242:786-796. [PMID: 38451101 DOI: 10.1111/nph.19591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7 overexpression (OE) completely prevented sorghum flowering. Additionally, we show that SbGhd7 is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10 (SbFT10) and floral activators EARLY HEADING DATE (SbEhd1), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (SbFKF1) and EARLY FLOWERING 3 (SbELF3). Reinforcing the direct effect of SbGhd7, SbEhd1 OE activated the promoters of three functional florigens (SbFT1, SbFT8 and SbFT10), dramatically accelerating flowering. Our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.
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Affiliation(s)
- Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Estella F Yee
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Tezera W Wolabu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Hui Wang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianfei Yun
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Nicolas Grosjean
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Kassandra Santiago
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wenqian Kong
- Department of Soil and Crop Science, University of Georgia, Athens, GA, 30602, USA
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jianghua Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
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Lorenzi A, Legeai F, Jouan V, Girard PA, Strand MR, Ravallec M, Eychenne M, Bretaudeau A, Robin S, Rochefort J, Villegas M, Burke GR, Rebollo R, Nègre N, Volkoff AN. Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps. PLoS Pathog 2024; 20:e1011980. [PMID: 38662774 DOI: 10.1371/journal.ppat.1011980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/07/2024] [Accepted: 03/22/2024] [Indexed: 05/08/2024] Open
Abstract
Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs). Large quantities of DNA-containing IV virions are produced in ovary calyx cells during the pupal and adult stages of female wasps. Females parasitize host insects by injecting eggs and virions into the body cavity. After injection, virions rapidly infect host cells which is followed by expression of IV genes that promote the successful development of wasp offspring. IV genomes consist of two components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus that produce virions. In this study, we generated a chromosome-scale genome assembly for Hyposoter didymator that harbors H. didymator ichnovirus (HdIV). We identified a total of 67 HdIV loci that are amplified in calyx cells during the wasp pupal stage. We then focused on an HdIV gene, U16, which is transcribed in calyx cells during the initial stages of replication. Sequence analysis indicated that U16 contains a conserved domain in primases from select other viruses. Knockdown of U16 by RNA interference inhibited virion morphogenesis in calyx cells. Genome-wide analysis indicated U16 knockdown also inhibited amplification of HdIV loci in calyx cells. Altogether, our results identified several previously unknown HdIV loci, demonstrated that all HdIV loci are amplified in calyx cells during the pupal stage, and showed that U16 is required for amplification and virion morphogenesis.
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Affiliation(s)
- Ange Lorenzi
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Fabrice Legeai
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Anthony Bretaudeau
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - Stéphanie Robin
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Rita Rebollo
- INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, France
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Marqués-Gálvez JE, Pandharikar G, Basso V, Kohler A, Lackus ND, Barry K, Keymanesh K, Johnson J, Singan V, Grigoriev IV, Vilgalys R, Martin F, Veneault-Fourrey C. Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. THE NEW PHYTOLOGIST 2024; 242:658-674. [PMID: 38375883 DOI: 10.1111/nph.19609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024]
Abstract
The jasmonic acid (JA) signalling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis. The Laccaria bicolor effector MiSSP7 stabilizes JA corepressor JAZ6, thereby inhibiting the activity of Populus MYC2 transcription factors. Although the role of MYC2 in orchestrating plant defences against pathogens is well established, its exact contribution to ECM symbiosis remains unclear. This information is crucial for understanding the balance between plant immunity and symbiotic relationships. Transgenic poplars overexpressing or silencing for the two paralogues of MYC2 transcription factor (MYC2s) were produced, and their ability to establish ectomycorrhiza was assessed. Transcriptomics and DNA affinity purification sequencing were performed. MYC2s overexpression led to a decrease in fungal colonization, whereas its silencing increased it. The enrichment of terpene synthase genes in the MYC2-regulated gene set suggests a complex interplay between the host monoterpenes and fungal growth. Several root monoterpenes have been identified as inhibitors of fungal growth and ECM symbiosis. Our results highlight the significance of poplar MYC2s and terpenes in mutualistic symbiosis by controlling root fungal colonization. We identified poplar genes which direct or indirect control by MYC2 is required for ECM establishment. These findings deepen our understanding of the molecular mechanisms underlying ECM symbiosis.
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Affiliation(s)
- José Eduardo Marqués-Gálvez
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Gaurav Pandharikar
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Veronica Basso
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Nathalie D Lackus
- Lehrstuhl für Pharmazeutische Biologie, Julius-von-Sachs-Institut für Biowissenschaften, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs-Platz 2, Würzburg, 97082, Deutschland
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
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231
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Maghraby A, Alzalaty M. Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress. Sci Rep 2024; 14:7610. [PMID: 38556556 PMCID: PMC10982304 DOI: 10.1038/s41598-024-57376-5] [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: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
AP2 (APETALA2)/EREBP (ethylene-responsive element-binding protein), cytochrome c oxidase (COX) and nonspecific lipid transfer proteins (LTP) play important roles in the response to drought stress. This is the first study to identify the COX gene in Zea mays L. via genome-wide analysis. The qRT‒PCR results indicated that AP2/EREBP, COX and LTP were downregulated, with fold changes of 0.84, 0.53 and 0.31, respectively, after 12 h of drought stress. Genome-wide analysis identified 78 AP2/EREBP, 6 COX and 10 LTP genes in Z. mays L. Domain analysis confirmed the presence of the AP2 domain, Cyt_c_Oxidase_Vb domain and nsLTP1 in the AP2/EREBP, COX and LTP proteins, respectively. The AP2/EREBP protein family (AP2) includes five different domain types: the AP2/ERF domain, the EREBP-like factor (EREBP), the ethylene responsive factor (ERF), the dehydration responsive element binding protein (DREB) and the SHN SHINE. Synteny analysis of the AP2/EREBP, COX and LTP genes revealed collinearity orthologous relationships in O. sativa, H. vulgare and A. thaliana. AP2/EREBP genes were found on the 10 chromosomes of Z. mays L. COX genes were found on chromosomes 1, 3, 4, 5, 7 and 8. LTP genes were found on chromosomes 1, 3, 6, 8, 9 and 10. In the present study, the Ka/Ks ratios of the AP2/EREBP paralogous pairs indicated that the AP2/EREBP genes were influenced primarily by purifying selection, which indicated that the AP2/EREBP genes received strong environmental pressure during evolution. The Ka/Ks ratios of the COX-3/COX-4 paralogous pairs indicate that the COX-3/COX-4 genes were influenced primarily by Darwinian selection (driving change). For the LTP genes, the Ka/Ks ratios of the LTP-1/LTP-10, LTP-5/LTP-3 and LTP-4/LTP-8 paralogous pairs indicate that these genes were influenced primarily by purifying selection, while the Ka/Ks ratios of the LTP-2/LTP-6 paralogous pairs indicate that these genes were influenced primarily by Darwinian selection. The duplication time of the AP2/EREBP paralogous gene pairs in Z. mays L. ranged from approximately 9.364 to 100.935 Mya. The duplication time of the COX-3/COX-4 paralogous gene pair was approximately 5.217 Mya. The duplication time of the LTP paralogous gene pairs ranged from approximately 19.064 to 96.477 Mya. The major focus of research is to identify the genes that are responsible for drought stress tolerance to improve maize for drought stress tolerance. The results of the present study will improve the understanding of the functions of the AP2/EREBP, COX and LTP genes in response to drought stress.
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Affiliation(s)
- Amaal Maghraby
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Mohamed Alzalaty
- Department of Plant Genetic Transformation, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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232
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Chen L, Chen K, Xi X, Du X, Zou X, Ma Y, Song Y, Luo C, Weining S. The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome. Int J Mol Sci 2024; 25:3883. [PMID: 38612691 PMCID: PMC11011394 DOI: 10.3390/ijms25073883] [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: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.
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Affiliation(s)
- Liqin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Kunxiang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xi Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xianghong Du
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Xinyi Zou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Yujia Ma
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China;
| | - Yingying Song
- College of Plant Protection, Northwest A&F University, Xianyang 712100, China;
| | - Changquan Luo
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China;
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
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233
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Parolia A, Eyunni S, Verma BK, Young E, Liu L, George J, Aras S, Das CK, Mannan R, Rasool RU, Luo J, Carson SE, Mitchell-Velasquez E, Liu Y, Xiao L, Gajjala PR, Jaber M, Wang X, He T, Qiao Y, Pang M, Zhang Y, Alhusayan M, Cao X, Tavana O, Hou C, Wang Z, Ding K, Chinnaiyan AM, Asangani IA. NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581560. [PMID: 38464251 PMCID: PMC10925163 DOI: 10.1101/2024.02.22.581560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The androgen receptor (AR) is a ligand-responsive transcription factor that binds at enhancers to drive terminal differentiation of the prostatic luminal epithelia. By contrast, in tumors originating from these cells, AR chromatin occupancy is extensively reprogrammed to drive hyper-proliferative, metastatic, or therapy-resistant phenotypes, the molecular mechanisms of which remain poorly understood. Here, we show that the tumor-specific enhancer circuitry of AR is critically reliant on the activity of Nuclear Receptor Binding SET Domain Protein 2 (NSD2), a histone 3 lysine 36 di-methyltransferase. NSD2 expression is abnormally gained in prostate cancer cells and its functional inhibition impairs AR trans-activation potential through partial off-loading from over 40,000 genomic sites, which is greater than 65% of the AR tumor cistrome. The NSD2-dependent AR sites distinctly harbor a chimeric AR-half motif juxtaposed to a FOXA1 element. Similar chimeric motifs of AR are absent at the NSD2-independent AR enhancers and instead contain the canonical palindromic motifs. Meta-analyses of AR cistromes from patient tumors uncovered chimeric AR motifs to exclusively participate in tumor-specific enhancer circuitries, with a minimal role in the physiological activity of AR. Accordingly, NSD2 inactivation attenuated hallmark cancer phenotypes that were fully reinstated upon exogenous NSD2 re-expression. Inactivation of NSD2 also engendered increased dependency on its paralog NSD1, which independently maintained AR and MYC hyper-transcriptional programs in cancer cells. Concordantly, a dual NSD1/2 PROTAC degrader, called LLC0150, was preferentially cytotoxic in AR-dependent prostate cancer as well as NSD2-altered hematologic malignancies. Altogether, we identify NSD2 as a novel subunit of the AR neo-enhanceosome that wires prostate cancer gene expression programs, positioning NSD1/2 as viable paralog co-targets in advanced prostate cancer.
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Affiliation(s)
- Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Brijesh Kumar Verma
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- These authors contributed equally
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lianchao Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - James George
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shweta Aras
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chandan Kanta Das
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Reyaz ur Rasool
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Luo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sandra E. Carson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Erick Mitchell-Velasquez
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yihan Liu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Cancer Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Prathibha R. Gajjala
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mustapha Jaber
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Pang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mohammed Alhusayan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Omid Tavana
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Caiyun Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Ke Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irfan A. Asangani
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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234
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Ling Z, Li J, Jiang T, Zhang Z, Zhu Y, Zhou Z, Yang J, Tong X, Yang B, Huang L. Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits. Commun Biol 2024; 7:381. [PMID: 38553586 PMCID: PMC10980749 DOI: 10.1038/s42003-024-06050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers. Combined with genome resequencing and RNA-seq data, we identify 28,425 H3K27ac quantitative trait loci (acQTLs) and 12,250 expression quantitative trait loci (eQTLs). Through the allelic imbalance analysis, we validate two causative acQTL variants in independent datasets. We observe substantial sharing of genetic controls between gene expression and H3K27ac, particularly within promoters. We infer that 46% of H3K27ac exhibit a concomitant rather than causative relationship with gene expression. By integrating GWAS, eQTLs, acQTLs, and transcription factor binding prediction, we further demonstrate their application, through metabolites dulcitol, phosphatidylcholine (PC) (16:0/16:0) and published phenotypes, in identifying likely causal variants and genes, and discovering sub-threshold GWAS loci. We provide insight into the relationship between regulatory elements and gene expression, and the genetic foundation for dissecting the molecular mechanism of phenotypes.
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Affiliation(s)
- Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Jing Li
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Tao Jiang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhen Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Yaling Zhu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhimin Zhou
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Jiawen Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Bin Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
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235
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Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [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: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
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Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Gil Rosas M, Centola C, Torres M, Mouguelar VS, David AP, Piga EJ, Gomez D, Calcaterra NB, Armas P, Coux G. The transcription of the main gene associated with Treacher-Collins syndrome (TCOF1) is regulated by G-quadruplexes and cellular nucleic acid binding protein (CNBP). Sci Rep 2024; 14:7472. [PMID: 38553547 PMCID: PMC10980799 DOI: 10.1038/s41598-024-58255-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
Treacle ribosome biogenesis factor 1 (TCOF1) is responsible for about 80% of mandibular dysostosis (MD) cases. We have formerly identified a correlation between TCOF1 and CNBP (CCHC-type zinc finger nucleic acid binding protein) expression in human mesenchymal cells. Given the established role of CNBP in gene regulation during rostral development, we explored the potential for CNBP to modulate TCOF1 transcription. Computational analysis for CNBP binding sites (CNBP-BSs) in the TCOF1 promoter revealed several putative binding sites, two of which (Hs791 and Hs2160) overlap with putative G-quadruplex (G4) sequences (PQSs). We validated the folding of these PQSs measuring circular dichroism and fluorescence of appropriate synthetic oligonucleotides. In vitro studies confirmed binding of purified CNBP to the target PQSs (both folded as G4 and unfolded) with Kd values in the nM range. ChIP assays conducted in HeLa cells chromatin detected the CNBP binding to TCOF1 promoter. Transient transfections of HEK293 cells revealed that Hs2160 cloned upstream SV40 promoter increased transcription of downstream firefly luciferase reporter gene. We also detected a CNBP-BS and PQS (Dr2393) in the zebrafish TCOF1 orthologue promoter (nolc1). Disrupting this G4 in zebrafish embryos by microinjecting DNA antisense oligonucleotides complementary to Dr2393 reduced the transcription of nolc1 and recapitulated the craniofacial anomalies characteristic of Treacher Collins Syndrome. Both cnbp overexpression and Morpholino-mediated knockdown in zebrafish induced nolc1 transcription. These results suggest that CNBP modulates the transcriptional expression of TCOF1 through a mechanism involving G-quadruplex folding/unfolding, and that this regulation is active in vertebrates as distantly related as bony fish and humans. These findings may have implications for understanding and treating MD.
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Affiliation(s)
- Mauco Gil Rosas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Cielo Centola
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Mercedes Torres
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Valeria S Mouguelar
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Aldana P David
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS-Universite de Toulouse, Equipe Labellisée Ligue Nationale contre le Cancer 2018, 31077, Toulouse, France
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina
| | - Gabriela Coux
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (S2000EZP), Rosario, Argentina.
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Shen H, Hou Y, Wang X, Li Y, Wu J, Lou H. Genome-Wide Identification, Expression Analysis under Abiotic Stress and Co-Expression Analysis of MATE Gene Family in Torreya grandis. Int J Mol Sci 2024; 25:3859. [PMID: 38612669 PMCID: PMC11012001 DOI: 10.3390/ijms25073859] [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: 02/03/2024] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis.
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Affiliation(s)
| | | | | | | | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
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238
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Xing L, Zhang Y, Ge M, Zhao L, Huo X. Identification of WRKY gene family in Dioscorea opposita Thunb. reveals that DoWRKY71 enhanced the tolerance to cold and ABA stress. PeerJ 2024; 12:e17016. [PMID: 38560473 PMCID: PMC10981886 DOI: 10.7717/peerj.17016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
WRKY transcription factors constitute one of the largest plant-specific gene families, regulating various aspects of plant growth, development, physiological processes, and responses to abiotic stresses. This study aimed to comprehensively analyze the WRKY gene family of yam (Dioscorea opposita Thunb.), to understand their expression patterns during the growth and development process and their response to different treatments of yam and analyze the function of DoWRKY71 in detail. A total of 25 DoWRKY genes were identified from the transcriptome of yam, which were divided into six clades (I, IIa, IIc, IId, IIe, III) based on phylogenetic analysis. The analysis of conserved motifs revealed 10 motifs, varying in length from 16 to 50 amino acids. Based on real-time quantitative PCR (qRT-PCR) analysis, DoWRKY genes were expressed at different stages of growth and development and responded differentially to various abiotic stresses. The expression level of DoWRKY71 genes was up-regulated in the early stage and then down-regulated in tuber enlargement. This gene showed responsiveness to cold and abiotic stresses, such as abscisic acid (ABA) and methyl jasmonate (MeJA). Therefore, further study was conducted on this gene. Subcellular localization analysis revealed that the DoWRKY71 protein was localized in the nucleus. Moreover, the overexpression of DoWRKY71 enhanced the cold tolerance of transgenic tobacco and promoted ABA mediated stomatal closure. This study presents the first systematic analysis of the WRKY gene family in yam, offering new insights for studying WRKY transcription factors in yam. The functional study of DoWRKY71 lays theoretical foundation for further exploring the regulatory function of the DoWRKY71 gene in the growth and development related signaling pathway of yam.
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Affiliation(s)
- Linan Xing
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhehaote, Inner Mongolia, China
| | - Yanfang Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhehaote, Inner Mongolia, China
| | - Mingran Ge
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhehaote, Inner Mongolia, China
| | - Lingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhehaote, Inner Mongolia, China
| | - Xiuwen Huo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhehaote, Inner Mongolia, China
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239
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Cheng G, Pratto F, Brick K, Li X, Alleva B, Huang M, Lam G, Camerini-Otero RD. High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586627. [PMID: 38903112 PMCID: PMC11188084 DOI: 10.1101/2024.03.25.586627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.
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Affiliation(s)
- Gang Cheng
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Florencia Pratto
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brick
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xin Li
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Alleva
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Mini Huang
- Present address: Sun Yat-Sen University, School of Medicine, Shen Zhen, China
| | - Gabriel Lam
- Present address: RNA Regulation Section, NIA, National Institutes of Health, Baltimore, MD, USA
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240
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Candia AA, Lean SC, Zhang CXW, McKeating DR, Cochrane A, Gulacsi E, Herrera EA, Krause BJ, Sferruzzi-Perri AN. Obesogenic Diet in Mice Leads to Inflammation and Oxidative Stress in the Mother in Association with Sex-Specific Changes in Fetal Development, Inflammatory Markers and Placental Transcriptome. Antioxidants (Basel) 2024; 13:411. [PMID: 38671859 PMCID: PMC11047652 DOI: 10.3390/antiox13040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Obesity during pregnancy is related to adverse maternal and neonatal outcomes. Factors involved in these outcomes may include increased maternal insulin resistance, inflammation, oxidative stress, and nutrient mishandling. The placenta is the primary determinant of fetal outcomes, and its function can be impacted by maternal obesity. The aim of this study on mice was to determine the effect of obesity on maternal lipid handling, inflammatory and redox state, and placental oxidative stress, inflammatory signaling, and gene expression relative to female and male fetal growth. METHODS Female mice were fed control or obesogenic high-fat/high-sugar diet (HFHS) from 9 weeks prior to, and during, pregnancy. On day 18.5 of pregnancy, maternal plasma, and liver, placenta, and fetal serum were collected to examine the immune and redox states. The placental labyrinth zone (Lz) was dissected for RNA-sequencing analysis of gene expression changes. RESULTS the HFHS diet induced, in the dams, hepatic steatosis, oxidative stress (reduced catalase, elevated protein oxidation) and the activation of pro-inflammatory pathways (p38-MAPK), along with imbalanced circulating cytokine concentrations (increased IL-6 and decreased IL-5 and IL-17A). HFHS fetuses were asymmetrically growth-restricted, showing sex-specific changes in circulating cytokines (GM-CSF, TNF-α, IL-6 and IFN-γ). The morphology of the placenta Lz was modified by an HFHS diet, in association with sex-specific alterations in the expression of genes and proteins implicated in oxidative stress, inflammation, and stress signaling. Placental gene expression changes were comparable to that seen in models of intrauterine inflammation and were related to a transcriptional network involving transcription factors, LYL1 and PLAG1. CONCLUSION This study shows that fetal growth restriction with maternal obesity is related to elevated oxidative stress, inflammatory pathways, and sex-specific placental changes. Our data are important, given the marked consequences and the rising rates of obesity worldwide.
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Affiliation(s)
- Alejandro A. Candia
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
- Institute of Health Sciences, University of O’Higgins, Rancagua 2841959, Chile;
- Pathophysiology Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago 7500922, Chile;
- Department for the Woman and Newborn Health Promotion, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Samantha C. Lean
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
| | - Cindy X. W. Zhang
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
| | - Daniel R. McKeating
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
| | - Anna Cochrane
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
| | - Edina Gulacsi
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
| | - Emilio A. Herrera
- Pathophysiology Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago 7500922, Chile;
| | - Bernardo J. Krause
- Institute of Health Sciences, University of O’Higgins, Rancagua 2841959, Chile;
| | - Amanda N. Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; (A.A.C.); (C.X.W.Z.); (D.R.M.); (A.C.); (E.G.)
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241
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Segura M, García A, Gamarra G, Benítez Á, Iglesias-Moya J, Martínez C, Jamilena M. An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1948-1966. [PMID: 38066672 DOI: 10.1093/jxb/erad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/08/2023] [Indexed: 03/28/2024]
Abstract
The sex determination process in cucurbits involves the control of stamen or carpel development during the specification of male or female flowers from a bisexual floral meristem, a function coordinated by ethylene. A gain-of-function mutation in the miR164-binding site of CpCUC2B, ortholog of the Arabidopsis transcription factor gene CUC2, not only produced ectopic floral meristems and organs, but also suppressed the development of carpels and promoted the development of stamens. The cuc2b mutation induced the transcription of CpCUC2B in the apical shoots of plants after female flowering but repressed other CUC genes regulated by miR164, suggesting a conserved functional redundancy of these genes in the development of squash flowers. The synergistic androecious phenotype of the double mutant between cuc2b and etr2b, an ethylene-insensitive mutation that enhances the production of male flowers, demonstrated that CpCUC2B arrests the development of carpels independently of ethylene and CpWIP1B. The transcriptional regulation of CpCUC1, CpCUC2, and ethylene genes in cuc2b and ethylene mutants also confirms this conclusion. However, the epistasis of cuc2b over aco1a, a mutation that suppresses stamen arrest in female flowers, and the down-regulation of CpACS27A in cuc2b female apical shoots, indicated that CpCUC2B promotes stamen development by suppressing the late ethylene production.
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Affiliation(s)
- María Segura
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Alicia García
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Germán Gamarra
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Álvaro Benítez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Cecilia Martínez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
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Huang G, Hu Y, Li F, Zuo X, Wang X, Li F, Li R. Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing. FRONTIERS IN PLANT SCIENCE 2024; 15:1369883. [PMID: 38601304 PMCID: PMC11004388 DOI: 10.3389/fpls.2024.1369883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Introduction Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined. Methods and results In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria. Discussion Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.
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Affiliation(s)
- Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fengyao Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
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243
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Pereira Dos Santos M, Zotta Mota AP, Coiti Togawa R, Florencio Martins N, Fabricio de Melo Bellard do Nascimento E, Lucena VS, Castellani MA, Saliba Albuquerque EV, Hilliou F. The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily. Sci Rep 2024; 14:7119. [PMID: 38531918 DOI: 10.1038/s41598-024-57869-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.
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Affiliation(s)
- Mateus Pereira Dos Santos
- Department of Crop Science and Animal Science, State University of Southwestern Bahia, Vitória da Conquista, 45083-300, Brazil
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France
| | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France
| | | | | | | | | | - Maria Aparecida Castellani
- Department of Crop Science and Animal Science, State University of Southwestern Bahia, Vitória da Conquista, 45083-300, Brazil
| | | | - Frédérique Hilliou
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France.
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Ortañez J, Degnan PH. Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis. Front Microbiol 2024; 15:1241582. [PMID: 38601936 PMCID: PMC11005914 DOI: 10.3389/fmicb.2024.1241582] [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: 06/19/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.
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Affiliation(s)
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Jiao Y, Tan J, Guo H, Huang B, Ying Y, Ramakrishnan M, Zhang Z. Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth. BMC PLANT BIOLOGY 2024; 24:213. [PMID: 38528453 DOI: 10.1186/s12870-024-04883-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown. RESULTS The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data. The KNOX gene promoters were found to contain several light and stress-related cis-acting elements. Synteny analysis revealed stronger similarity with rice KNOX genes than with Arabidopsis KNOX genes. Additionally, several conserved structural domains and motifs were identified in the KNOX proteins. The expansion of the KNOX gene family was primarily regulated by tandem duplications. Furthermore, the KNOX genes were responsive to naphthaleneacetic acid (NAA) and gibberellin (GA) hormones, exhibiting distinct temporal expression patterns in four different organs of Moso bamboo. Short Time-series Expression Miner (STEM) analysis and quantitative real-time PCR (qRT-PCR) assays demonstrated that PeKNOX genes may play a role in promoting rapid shoot growth. Additionally, Gene Ontology (GO) and Protein-Protein Interaction (PPI) network enrichment analyses revealed several functional annotations for PeKNOXs. By regulating downstream target genes, PeKNOXs are involved in the synthesis of AUX /IAA, ultimately affecting cell division and elongation. CONCLUSIONS In the present study, we identified and characterized a total of 24 KNOX genes in Moso bamboo and investigated their physiological properties and conserved structural domains. To understand their functional roles, we conducted an analysis of gene expression profiles using STEM and RNA-seq data. This analysis successfully revealed regulatory networks of the KNOX genes, involving both upstream and downstream genes. Furthermore, the KNOX genes are involved in the AUX/IAA metabolic pathway, which accelerates shoot growth by influencing downstream target genes. These results provide a theoretical foundation for studying the molecular mechanisms underlying the rapid growth and establish the groundwork for future research into the functions and transcriptional regulatory networks of the KNOX gene family.
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Affiliation(s)
- Yang Jiao
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Hui Guo
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Bin Huang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yeqing Ying
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Qian F, Zuo D, Zeng T, Gu L, Wang H, Du X, Zhu B, Ou J. Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus. PLANTS (BASEL, SWITZERLAND) 2024; 13:950. [PMID: 38611479 PMCID: PMC11013218 DOI: 10.3390/plants13070950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.
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Affiliation(s)
- Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Jing Ou
- College of Forestry, Guizhou University, Guiyang 550025, China
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247
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Zhang X, Peng W, Chen H, Xing H. BnAP2-12 overexpression delays ramie flowering: evidence from AP2/ERF gene expression. FRONTIERS IN PLANT SCIENCE 2024; 15:1367837. [PMID: 38590749 PMCID: PMC10999622 DOI: 10.3389/fpls.2024.1367837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Introduction The APETALA2/ethylene response factor (AP2/ERF) superfamily plays a significant role in regulating plant gene expression in response to growth and development. To date, there have been no studies into whether the ramie AP2/ERF genes are involved in the regulation of flower development. Methods Here, 84 BnAP2/ERF members were identified from the ramie genome database, and various bioinformatics data on the AP2/ERF gene family, structure, replication, promoters and regulatory networks were analysed. BnAP2-12 was transferred into Arabidopsis through the flower-dipping method. Results Phylogenetic analysis classified the 84 BnAP2/ERF members into four subfamilies: AP2 (18), RAV (3), ERF (42), and DREB (21). The functional domain analysis of genes revealed 10 conserved motifs. Genetic mapping localised the 84 members on 14 chromosomes, among which chromosomes 1, 3, 5, and 8 had more members. Collinearity analysis revealed that 43.37% possibly resulted from replication events during the evolution of the ramie genome. Promoter sequence analysis identified classified cis-acting elements associated with plant growth and development, and responses to stress, hormones, and light. Transcriptomic comparison identified 3,635 differentially expressed genes (DEGs) between male and female flowers (1,803 and 1,832 upregulated and downregulated genes, respectively). Kyoto Encyclopaedia of Genes and Genomes pathway analysis categorised DEGs involved in metabolic pathways and biosynthesis of secondary metabolites. Gene Ontology enrichment analysis further identified enriched genes associated with pollen and female gamete formations. Of the 84 BnAP2/ERFs genes, 22 and 8 upregulated and downregulated genes, respectively, were present in female flowers. Co-expression network analysis identified AP2/ERF members associated with flower development, including BnAP2-12. Subcellular localisation analysis showed that the BnAP2-12 protein is localised in the nucleus and cell membrane. Overexpression BnAP2-12 delayed the flowering time of Arabidopsis thaliana. Conclusion These findings provide insights into the mechanism of ramie flower development.
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Affiliation(s)
- Xiaoyang Zhang
- Agricultural College of Hunan Agricultural University, Changsha, China
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
| | - Wenxian Peng
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
- Changsha Tobacco Company, Ningxiang, China
| | - Hao Chen
- Agricultural College of Hunan Agricultural University, Changsha, China
| | - Hucheng Xing
- Agricultural College of Hunan Agricultural University, Changsha, China
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
- Hunan Key Laboratory of Germplasm Resources Innovation and Resource Utilization Crop Breeding Center, Changsha, China
- Hunan Provincial Engineering Technology Research Center of Grass Crop Germplasm Innovation and Utilization, Changsha, China
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248
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Liu X, Chen H, Li Z, Yang X, Jin W, Wang Y, Zheng J, Li L, Xuan C, Yuan J, Yang Y. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nat Commun 2024; 15:2583. [PMID: 38519498 PMCID: PMC10960005 DOI: 10.1038/s41467-024-46875-8] [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: 06/12/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Alternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has been implicated in diverse biological processes and diseases, as it can produce noncoding transcripts or transcripts with truncated coding regions. However, a reliable method is required to accurately characterize IPA. Here, we propose a computational method called InPACT, which allows for the precise characterization of IPA from conventional RNA-seq data. InPACT successfully identifies numerous previously unannotated IPA transcripts in human cells, many of which are translated, as evidenced by ribosome profiling data. We have demonstrated that InPACT outperforms other methods in terms of IPA identification and quantification. Moreover, InPACT applied to monocyte activation reveals temporally coordinated IPA events. Further application on single-cell RNA-seq data of human fetal bone marrow reveals the expression of several IPA isoforms in a context-specific manner. Therefore, InPACT represents a powerful tool for the accurate characterization of IPA from RNA-seq data.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Hao Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jian Zheng
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Long Li
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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Ramirez CFA, Taranto D, Ando-Kuri M, de Groot MHP, Tsouri E, Huang Z, de Groot D, Kluin RJC, Kloosterman DJ, Verheij J, Xu J, Vegna S, Akkari L. Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma. Nat Commun 2024; 15:2581. [PMID: 38519484 PMCID: PMC10959959 DOI: 10.1038/s41467-024-46835-2] [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: 11/02/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Myeloid cells are abundant and plastic immune cell subsets in the liver, to which pro-tumorigenic, inflammatory and immunosuppressive roles have been assigned in the course of tumorigenesis. Yet several aspects underlying their dynamic alterations in hepatocellular carcinoma (HCC) progression remain elusive, including the impact of distinct genetic mutations in shaping a cancer-permissive tumor microenvironment (TME). Here, in newly generated, clinically-relevant somatic female HCC mouse models, we identify cancer genetics' specific and stage-dependent alterations of the liver TME associated with distinct histopathological and malignant HCC features. Mitogen-activated protein kinase (MAPK)-activated, NrasG12D-driven tumors exhibit a mixed phenotype of prominent inflammation and immunosuppression in a T cell-excluded TME. Mechanistically, we report a NrasG12D cancer cell-driven, MEK-ERK1/2-SP1-dependent GM-CSF secretion enabling the accumulation of immunosuppressive and proinflammatory monocyte-derived Ly6Clow cells. GM-CSF blockade curbs the accumulation of these cells, reduces inflammation, induces cancer cell death and prolongs animal survival. Furthermore, GM-CSF neutralization synergizes with a vascular endothelial growth factor (VEGF) inhibitor to restrain HCC outgrowth. These findings underscore the profound alterations of the myeloid TME consequential to MAPK pathway activation intensity and the potential of GM-CSF inhibition as a myeloid-centric therapy tailored to subsets of HCC patients.
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Affiliation(s)
- Christel F A Ramirez
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Taranto
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Masami Ando-Kuri
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H P de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Efi Tsouri
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Zhijie Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roelof J C Kluin
- Genomics Core facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan J Kloosterman
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jing Xu
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Serena Vegna
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Leila Akkari
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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250
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Xie X, Pei M, Liu S, Wang X, Gong S, Chen J, Zhang Y, Wang Z, Lu G, Li Y. Comprehensive Analysis of Autophagy-Related Genes in Rice Immunity against Magnaporthe oryzae. PLANTS (BASEL, SWITZERLAND) 2024; 13:927. [PMID: 38611457 PMCID: PMC11013097 DOI: 10.3390/plants13070927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Rice blast disease, caused by the fungus Magnaporthe oryzae, is a significant threat to rice production. Resistant cultivars can effectively resist the invasion of M. oryzae. Thus, the identification of disease-resistant genes is of utmost importance for improving rice production. Autophagy, a cellular process that recycles damaged components, plays a vital role in plant growth, development, senescence, stress response, and immunity. To understand the involvement of autophagy-related genes (ATGs) in rice immune response against M. oryzae, we conducted a comprehensive analysis of 37 OsATGs, including bioinformatic analysis, transcriptome analysis, disease resistance analysis, and protein interaction analysis. Bioinformatic analysis revealed that the promoter regions of 33 OsATGs contained cis-acting elements responsive to salicylic acid (SA) or jasmonic acid (JA), two key hormones involved in plant defense responses. Transcriptome data showed that 21 OsATGs were upregulated during M. oryzae infection. Loss-of-function experiments demonstrated that OsATG6c, OsATG8a, OsATG9b, and OsATG13a contribute to rice blast resistance. Additionally, through protein interaction analysis, we identified five proteins that may interact with OsATG13a and potentially contribute to plant immunity. Our study highlights the important role of autophagy in rice immunity and suggests that OsATGs may enhance resistance to rice blast fungus through the involvement of SA, JA, or immune-related proteins. These findings provide valuable insights for future efforts in improving rice production through the identification and utilization of autophagy-related genes.
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Affiliation(s)
- Xuze Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Mengtian Pei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Shan Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Xinxiao Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Shanshan Gong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Ye Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
- Fujian Provincial Quality Safety Inspection and Test Center for Agricultural Products, Fuzhou 350003, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Minjiang University, Fuzhou 350108, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
| | - Ya Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (M.P.); (S.L.); (X.W.); (S.G.); (J.C.); (Y.Z.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou 350013, China
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