151
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Jung JM, Rahman A, Schiffer AM, Weisberg AJ. Beav: a bacterial genome and mobile element annotation pipeline. mSphere 2024; 9:e0020924. [PMID: 39037262 PMCID: PMC11351099 DOI: 10.1128/msphere.00209-24] [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: 03/12/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024] Open
Abstract
Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav. IMPORTANCE Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
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Affiliation(s)
- Jewell M. Jung
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Arafat Rahman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Andrea M. Schiffer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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152
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Dhatterwal P, Sharma N, Prasad M. Decoding the functionality of plant transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4745-4759. [PMID: 38761104 DOI: 10.1093/jxb/erae231] [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: 03/08/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
Transcription factors (TFs) intricately govern cellular processes and responses to external stimuli by modulating gene expression. TFs help plants to balance the trade-off between stress tolerance and growth, thus ensuring their long-term survival in challenging environments. Understanding the factors and mechanisms that define the functionality of plant TFs is of paramount importance for unravelling the intricate regulatory networks governing development, growth, and responses to environmental stimuli in plants. This review provides a comprehensive understanding of these factors and mechanisms defining the activity of TFs. Understanding the dynamic nature of TFs has practical implications for modern molecular breeding programmes, as it provides insights into how to manipulate gene expression to optimize desired traits in crops. Moreover, recent studies also report the functional duality of TFs, highlighting their ability to switch between activation and repression modes; this represents an important mechanism for attuning gene expression. Here we discuss what the possible reasons for the dual nature of TFs are and how this duality instructs the cell fate decision during development, and fine-tunes stress responses in plants, enabling them to adapt to various environmental challenges.
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Affiliation(s)
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
- Department of Genetics, University of Delhi South Campus, New Delhi, India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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153
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Stocks J, Gilbert N. Nuclear RNA: a transcription-dependent regulator of chromatin structure. Biochem Soc Trans 2024; 52:1605-1615. [PMID: 39082979 DOI: 10.1042/bst20230787] [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: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/29/2024]
Abstract
Although the majority of RNAs are retained in the nucleus, their significance is often overlooked. However, it is now becoming clear that nuclear RNA forms a dynamic structure through interacting with various proteins that can influence the three-dimensional structure of chromatin. We review the emerging evidence for a nuclear RNA mesh or gel, highlighting the interplay between DNA, RNA and RNA-binding proteins (RBPs), and assessing the critical role of protein and RNA in governing chromatin architecture. We also discuss a proposed role for the formation and regulation of the nuclear gel in transcriptional control. We suggest that it may concentrate the transcriptional machinery either by direct binding or inducing RBPs to form microphase condensates, nanometre sized membraneless structures with distinct properties to the surrounding medium and an enrichment of particular macromolecules.
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Affiliation(s)
- Jon Stocks
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
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154
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Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with cancer survival and gene expression in multiple cancer types. Int J Cancer 2024. [PMID: 39194330 DOI: 10.1002/ijc.35148] [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: 03/21/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024]
Abstract
Different endogenous and exogenous mutational processes cause specific patterns of somatic mutations and mutational signatures. Although their biological research has been intensive, there are only rare studies assessing the possible prognostic role of mutational signatures. We used data from The Cancer Genome Atlas to study the associations between the activity of the mutational signatures and four survival endpoints in 18 types of malignancies. We further explored the prognostic differences according to, for example, the HPV status in head and neck squamous cell carcinomas and smoking status in lung cancers. The predictive power of the signatures over time was evaluated with a dynamic area under the curve model, and the links between mutational signature activities and differences in gene expression patterns were analyzed. In 12 of 18 studied cancer types, we identified at least one mutational signature whose activity predicted survival outcomes after adjusting for the established prognostic factors. For example, overall survival was associated with the activity of mutational signatures in nine cancer types and disease-specific survival in seven cancer types. The clock-like signatures SBS5 and SBS40 were most commonly associated with survival endpoints. The genes of the myosin binding protein and melanoma antigen families were among the most substantially dysregulated genes between the signatures of low and high activity. The differences in gene expression also revealed various enriched pathways. Based on these data, specific mutational signatures associate with the gene expression and have the potential to serve as strong prognostic factors in several cancer types.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki, Finland
- Department of Oncology and Radiotherapy, Oulu University Hospital, Oulu, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- K. Albin Johansson Cancer Research Fellow, Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
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155
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Wondimagegnhu B, Ma W, Paul T, Liao TW, Lee CY, Sanford S, Opresko PL, Myong S. The molecular mechanism for TERRA recruitment and annealing to telomeres. Nucleic Acids Res 2024:gkae732. [PMID: 39189448 DOI: 10.1093/nar/gkae732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024] Open
Abstract
Telomeric repeat containing RNA (TERRA) is a noncoding RNA that is transcribed from telomeres. Previous study showed that TERRA trans anneals by invading into the telomeric duplex to form an R-loop in mammalian cells. Here, we elucidate the molecular mechanism underlying TERRA recruitment and invasion into telomeres in the context of shelterin proteins, RAD51 and RNase H using single molecule (sm) assays. We demonstrate that TERRA trans annealing into telomeric DNA exhibits dynamic movement that is stabilized by TRF2. TERRA annealing to the telomeric duplex results in the formation of a stable triplex structure which differs from a conventional R-loop. We identified that the presence of a sub-telomeric DNA and a telomeric overhang in the form of a G-quadruplex significantly enhances TERRA annealing to telomeric duplex. We also demonstrate that RAD51-TERRA complex invades telomere duplex more efficiently than TERRA alone. Additionally, TRF2 increases TERRA affinity to telomeric duplex and protects it from RNase H digestion. In contrast, TRF1 represses TERRA annealing to telomeric duplex and fails to provide protection against RNase H digestion. Our findings provide an in-depth molecular mechanism underpinning TERRA recruitment and annealing to the telomere.
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Affiliation(s)
- Bersabel Wondimagegnhu
- Program in Cell, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wen Ma
- Department of Physics, The University of Vermont, Burlington, VT 05405, USA
| | - Tapas Paul
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ting-Wei Liao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chun Ying Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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156
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Márquez EJ, Gómez-Chavarría DA, Alzate JF. Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes). PLoS One 2024; 19:e0300830. [PMID: 39190628 PMCID: PMC11349099 DOI: 10.1371/journal.pone.0300830] [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: 03/05/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.
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Affiliation(s)
- Edna Judith Márquez
- Laboratorio de Biología Molecular y Celular, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | - Daniel Alfredo Gómez-Chavarría
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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157
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Estrem B, Davis R, Wang J. End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination. Nucleic Acids Res 2024; 52:8913-8929. [PMID: 38953168 PMCID: PMC11347171 DOI: 10.1093/nar/gkae579] [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: 03/15/2024] [Revised: 05/24/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the human and pig parasitic nematode Ascaris to characterize the DSBs. Using END-seq, we demonstrate that DSBs are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3'-overhangs before the addition of neotelomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB ends may be due to the sequestration of the eliminated DNA into micronuclei, preventing neotelomere formation at their ends. Additional DNA breaks occur within the eliminated DNA in both Ascaris and Parascaris, ensuring chromosomal breakage and providing a fail-safe mechanism for PDE. Overall, our data indicate that telomere healing of DSBs is specific to the break sites responsible for nematode PDE.
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Affiliation(s)
- Brandon Estrem
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jianbin Wang
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
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158
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Zhang H, Zhu JK. Epigenetic gene regulation in plants and its potential applications in crop improvement. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00769-1. [PMID: 39192154 DOI: 10.1038/s41580-024-00769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.
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Affiliation(s)
- Heng Zhang
- Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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159
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Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani A, Gilski M, Xu SY, Bochtler M. Structural analysis of the BisI family of modification dependent restriction endonucleases. Nucleic Acids Res 2024; 52:9103-9118. [PMID: 39041409 PMCID: PMC11347163 DOI: 10.1093/nar/gkae634] [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: 01/18/2024] [Revised: 06/22/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
The BisI family of restriction endonucleases is unique in requiring multiple methylated or hydroxymethylated cytosine residues within a short recognition sequence (GCNGC), and in cleaving directly within this sequence, rather than at a distance. Here, we report that the number of modified cytosines that are required for cleavage can be tuned by the salt concentration. We present crystal structures of two members of the BisI family, NhoI and Eco15I_Ntd (N-terminal domain of Eco15I), in the absence of DNA and in specific complexes with tetra-methylated GCNGC target DNA. The structures show that NhoI and Eco15I_Ntd sense modified cytosine bases in the context of double-stranded DNA (dsDNA) without base flipping. In the co-crystal structures of NhoI and Eco15I_Ntd with DNA, the internal methyl groups (G5mCNGC) interact with the side chains of an (H/R)(V/I/T/M) di-amino acid motif near the C-terminus of the distal enzyme subunit and arginine residue from the proximal subunit. The external methyl groups (GCNG5mC) interact with the proximal enzyme subunit, mostly through main chain contacts. Surface plasmon resonance analysis for Eco15I_Ntd shows that the internal and external methyl binding pockets contribute about equally to sensing of cytosine methyl groups.
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Affiliation(s)
- Katarzyna Szafran
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | - Mirosław Gilski
- Faculty of Chemistry, Adam Mickiewicz University, Poznan
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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160
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Dong J, Zhu XN, Zeng PM, Cao DD, Yang Y, Hu J, Luo ZG. A hominoid-specific signaling axis regulating the tempo of synaptic maturation. Cell Rep 2024; 43:114548. [PMID: 39052482 DOI: 10.1016/j.celrep.2024.114548] [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: 11/13/2023] [Revised: 04/15/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Human cortical neurons (hCNs) exhibit high dendritic complexity and synaptic density, and the maturation process is greatly protracted. However, the molecular mechanism governing these specific features remains unclear. Here, we report that the hominoid-specific gene TBC1D3 promotes dendritic arborization and protracts the pace of synaptogenesis. Ablation of TBC1D3 in induced hCNs causes reduction of dendritic growth and precocious synaptic maturation. Forced expression of TBC1D3 in the mouse cortex protracts synaptic maturation while increasing dendritic growth. Mechanistically, TBC1D3 functions via interaction with MICAL1, a monooxygenase that mediates oxidation of actin filament. At the early stage of differentiation, the TBC1D3/MICAL1 interaction in the cytosol promotes dendritic growth via F-actin oxidation and enhanced actin dynamics. At late stages, TBC1D3 escorts MICAL1 into the nucleus and downregulates the expression of genes related with synaptic maturation through interaction with the chromatin remodeling factor ATRX. Thus, this study delineates the molecular mechanisms underlying human neuron development.
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Affiliation(s)
- Jian Dong
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Na Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Peng-Ming Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Dong-Dong Cao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Yang Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Ji Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China.
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161
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Busetto V, Pshanichnaya L, Lichtenberger R, Hann S, Ketting R, Falk S. MUT-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Res 2024; 52:9076-9091. [PMID: 39188014 PMCID: PMC11347159 DOI: 10.1093/nar/gkae610] [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: 01/09/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 08/28/2024] Open
Abstract
The MUT-7 family of 3'-5' exoribonucleases is evolutionarily conserved across the animal kingdom and plays essential roles in small RNA production in the germline. Most MUT-7 homologues carry a C-terminal domain of unknown function named MUT7-C appended to the exoribonuclease domain. Our analysis shows that the MUT7-C is evolutionary ancient, as a minimal version of the domain exists as an individual protein in prokaryotes. In animals, MUT7-C has acquired an insertion that diverged during evolution, expanding its functions. Caenorhabditis elegans MUT-7 contains a specific insertion within MUT7-C, which allows binding to MUT-8 and, consequently, MUT-7 recruitment to germ granules. In addition, in C. elegans and human MUT-7, the MUT7-C domain contributes to RNA binding and is thereby crucial for ribonuclease activity. This RNA-binding function most likely represents the ancestral function of the MUT7-C domain. Overall, this study sheds light on MUT7-C and assigns two functions to this previously uncharacterized domain.
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Affiliation(s)
- Virginia Busetto
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Lizaveta Pshanichnaya
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - Raffael Lichtenberger
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099Mainz, Germany
| | - Sebastian Falk
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
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162
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Bandyra KJ, Fröhlich KS, Vogel J, Rodnina M, Goyal A, Luisi B. Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance. Nucleic Acids Res 2024; 52:9161-9173. [PMID: 38842944 PMCID: PMC11347162 DOI: 10.1093/nar/gkae455] [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: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 08/28/2024] Open
Abstract
The ompD transcript, encoding an outer membrane porin in Salmonella, harbors a controlling element in its coding region that base-pairs imperfectly with a 'seed' region of the small regulatory RNA (sRNA) MicC. When tagged with the sRNA, the ompD mRNA is cleaved downstream of the pairing site by the conserved endoribonuclease RNase E, leading to transcript destruction. We observe that the sRNA-induced cleavage site is accessible to RNase E in vitro upon recruitment of ompD into the 30S translation pre-initiation complex (PIC) in the presence of the degradosome components. Evaluation of substrate accessibility suggests that the paused 30S PIC presents the mRNA for targeted recognition and degradation. Ribonuclease activity on PIC-bound ompD is critically dependent on the recruitment of RNase E into the multi-enzyme RNA degradosome, and our data suggest a process of substrate capture and handover to catalytic sites within the degradosome, in which sequential steps of seed matching and duplex remodelling contribute to cleavage efficiency. Our findings support a putative mechanism of surveillance at translation that potentially terminates gene expression efficiently and rapidly in response to signals provided by regulatory RNA.
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Affiliation(s)
- Katarzyna J Bandyra
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kathrin S Fröhlich
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Akanksha Goyal
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ben F Luisi
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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163
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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024; 53:8713-8763. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [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: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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164
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Lipońska A, Lee H, Yap MN. Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor. Nucleic Acids Res 2024; 52:8998-9013. [PMID: 38979572 PMCID: PMC11347170 DOI: 10.1093/nar/gkae596] [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: 02/27/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
The hibernation-promoting factor (Hpf) in Staphylococcus aureus binds to 70S ribosomes and induces the formation of the 100S complex (70S dimer), leading to translational avoidance and occlusion of ribosomes from RNase R-mediated degradation. Here, we show that the 3'-5' exoribonuclease YhaM plays a previously unrecognized role in modulating ribosome stability. Unlike RNase R, which directly degrades the 16S rRNA of ribosomes in S. aureus cells lacking Hpf, YhaM destabilizes ribosomes by indirectly degrading the 3'-hpf mRNA that carries an intrinsic terminator. YhaM adopts an active hexameric assembly and robustly cleaves ssRNA in a manganese-dependent manner. In vivo, YhaM appears to be a low-processive enzyme, trimming the hpf mRNA by only 1 nucleotide. Deletion of yhaM delays cell growth. These findings substantiate the physiological significance of this cryptic enzyme and the protective role of Hpf in ribosome integrity, providing a mechanistic understanding of bacterial ribosome turnover.
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Affiliation(s)
- Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core in Research Resources Center, University of Illinois at Chicago (UIC), 1100 S Ashland Ave, Chicago, IL 60607, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
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165
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Maiti A, Erimban S, Daschakraborty S. Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments. Chem Commun (Camb) 2024. [PMID: 39190300 DOI: 10.1039/d4cc03114h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India.
| | - Shakkira Erimban
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India.
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166
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Liu X, Xie H, Liu W, Zuo J, Li S, Tian Y, Zhao J, Bai M, Li J, Bao L, Han J, Zhang ZC. Dynamic regulation of alternative polyadenylation by PQBP1 during neurogenesis. Cell Rep 2024; 43:114525. [PMID: 39037895 DOI: 10.1016/j.celrep.2024.114525] [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: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Alternative polyadenylation (APA) is a critical post-transcriptional process that generates mRNA isoforms with distinct 3' untranslated regions (3' UTRs), thereby regulating mRNA localization, stability, and translational efficiency. Cell-type-specific APA extensively shapes the diversity of the cellular transcriptome, particularly during cell fate transition. Despite its recognized significance, the precise regulatory mechanisms governing cell-type-specific APA remain unclear. In this study, we uncover PQBP1 as an emerging APA regulator that actively maintains cell-specific APA profiles in neural progenitor cells (NPCs) and delicately manages the equilibrium between NPC proliferation and differentiation. Multi-omics analysis shows that PQBP1 directly interacts with the upstream UGUA elements, impeding the recruitment of the CFIm complex and influencing polyadenylation site selection within genes associated with the cell cycle. Our findings elucidate the molecular mechanism by which PQBP1 orchestrates dynamic APA changes during neurogenesis, providing valuable insights into the precise regulation of cell-type-specific APA and the underlying pathogenic mechanisms in neurodevelopmental disorders.
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Affiliation(s)
- Xian Liu
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Hao Xie
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Wenhua Liu
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Jian Zuo
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Song Li
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Yao Tian
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China
| | | | - Meizhu Bai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junhai Han
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China.
| | - Zi Chao Zhang
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 210096, China.
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167
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Tabara M, Uraguchi S, Kiyono M, Watanabe I, Takeda A, Takahashi H, Fukuhara T. A resilient mutualistic interaction between cucumber mosaic virus and its natural host to adapt to an excess zinc environment and drought stress. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01573-w. [PMID: 39190237 DOI: 10.1007/s10265-024-01573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024]
Abstract
A perennial pseudometallophyte Arabidopsis halleri is frequently infected with cucumber mosaic virus (CMV) in its natural habitat. The purpose of this study was to characterize the effect of CMV infection on the environmental adaptation of its natural host A. halleri. The CMV(Ho) strain isolated from A. halleri was inoculated into clonal virus-free A. halleri plants, and a unique plant-virus system consisting of CMV(Ho) and its natural wild plant host was established. In a control environment with ambient zinc supplementation, CMV(Ho) infection retarded growth in the above-ground part of host plants but conferred strong drought tolerance. On the other hand, in an excess zinc environment, simulating a natural edaphic environment of A halleri, host plants hyperaccumulated zinc and CMV(Ho) infection did not cause any symptoms to host plants while conferring mild drought tolerance. We also demonstrated in Nicotiana benthamiana as another host that similar effects were induced by the combination of excess zinc and CMV(Ho) infection. Transcriptomic analysis indicated that the host plant recognized CMV(Ho) as a mutualistic symbiont rather than a parasitic pathogen. These results suggest a resilient mutualistic interaction between CMV(Ho) and its natural host A. halleri in its natural habitat.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Shimpei Uraguchi
- Department of Public Health, School of Pharmacy, Kitasato University, Tokyo, 108-8641, Japan
| | - Masako Kiyono
- Department of Public Health, School of Pharmacy, Kitasato University, Tokyo, 108-8641, Japan
| | - Izumi Watanabe
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Atsushi Takeda
- College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, Aramaki-Aza-Aoba, 468-1, Sendai, 980-0845, Japan
| | - Toshiyuki Fukuhara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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168
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Nguyen TBH, Foulongne-Oriol M, Jany JL, le Floch G, Picot A. New insights into mycotoxin risk management through fungal population genetics and genomics. Crit Rev Microbiol 2024:1-22. [PMID: 39188135 DOI: 10.1080/1040841x.2024.2392179] [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: 02/09/2024] [Revised: 05/08/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]
Abstract
Mycotoxin contamination of food and feed is a major global concern. Chronic or acute dietary exposure to contaminated food and feed can negatively affect both human and animal health. Contamination occurs through plant infection by toxigenic fungi, primarily Aspergillus and Fusarium spp., either before or after harvest. Despite the application of various management strategies, controlling these pathogens remains a major challenge primarily because of their ability to adapt to environmental changes and selection pressures. Understanding the genetic structure of plant pathogen populations is pivotal for gaining new insights into their biology and epidemiology, as well as for understanding the mechanisms behind their adaptability. Such deeper understanding is crucial for developing effective and preemptive management strategies tailored to the evolving nature of pathogenic populations. This review focuses on the population-level variations within the two most economically significant toxigenic fungal genera according to space, host, and pathogenicity. Outcomes in terms of migration patterns, gene flow within populations, mating abilities, and the potential for host jumps are examined. We also discuss effective yet often underutilized applications of population genetics and genomics to address practical challenges in the epidemiology and disease control of toxigenic fungi.
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Affiliation(s)
- Toan Bao Hung Nguyen
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | | | - Jean-Luc Jany
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Gaétan le Floch
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
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169
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Liu Y, Xiao W, Liao L, Zheng B, Cao Y, Zhao Y, Zhang RX, Han Y. A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39185667 DOI: 10.1111/jipb.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024]
Abstract
WRKY transcription factors play key roles in plant resistance to various stresses, but their roles in fruit ripening remain largely unknown. Here, we report a WRKY gene PpWRKY14 involved in the regulation of fruit ripening in peach. The expression of PpWRKY14 showed an increasing trend throughout fruit development. PpWRKY14 was a target gene of PpNAC1, a master regulator of peach fruit ripening. PpWRKY14 could directly bind to the promoters of PpACS1 and PpACO1 to induce their expression, and this induction was greatly enhanced when PpWRKY14 formed a dimer with PpNAC1. However, the transcription of PpNAC1 could be directly suppressed by two EIN3/EIL1 genes, PpEIL2 and PpEIL3. The PpEIL2/3 genes were highly expressed at the early stages of fruit development, but their expression was programmed to decrease significantly during the ripening stage, thus derepressing the expression of PpNAC1. These results suggested a PpEIL2/3-PpNAC1-PpWRKY14 module that regulates fruit ripening by modulating ethylene production in peach. Our results provided an insight into the regulatory roles of EIN3/EIL1 and WRKY genes in fruit ripening.
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Affiliation(s)
- Yudi Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Xiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liao Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Beibei Zheng
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yunpeng Cao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yun Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ruo-Xi Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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170
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Day CC, Alò D, Simmons RK, Cotey SR, Zarn KE, Gazeley IF, Small M, Fortin MJ, Bearlin AR, Smith SR, Landguth EL. Disentangling effects of dispersal, environment and anthropogenic barriers on functional connectivity in aquatic systems. Mol Ecol 2024:e17500. [PMID: 39188095 DOI: 10.1111/mec.17500] [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: 11/20/2023] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
Disentangling the roles of structural landscape factors and animal movement behaviour can present challenges for practitioners managing landscapes to maintain functional connectivity and achieve conservation goals. We used a landscape genetics approach to combine robust demographic, behavioural and genetic datasets with spatially explicit simulations to evaluate the effects of anthropogenic barriers (dams, culverts) and natural landscape resistance (gradient, elevation) affecting dispersal behaviour, genetic connectivity and genetic structure in a resident population of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi). Analyses based on 10 years of sampling effort revealed a pattern of restricted dispersal, and population genetics identified discrete population clusters between distal tributaries and the mainstem stream and no structure within the mainstem stream. Demogenetic simulations demonstrated that, for this population, the effects of existing anthropogenic barriers on population structure are redundant with effects of restricted dispersal associated with the underlying environmental resistance. Our approach provides an example of how extensive field sampling combined with landscape genetics can be incorporated into spatially explicit simulation modelling to explore how, together, movement ecology and landscape resistance can be used to inform decisions around restoration and connectivity.
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Affiliation(s)
- Casey C Day
- Computational Ecology Lab, University of Montana, Missoula, Montana, USA
| | - Dominique Alò
- Departamento de Sistemas Acuáticos. Facultad de Ciencias Ambientales y Centro de Ciencias Ambientales EULA-Chile, Universidad de Concepción, Concepción, Chile
| | - Ryan K Simmons
- Environment, Land, and Licensing, Seattle City Light, Seattle, Washington, USA
| | - Stacy R Cotey
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Katherine E Zarn
- National Technology and Development Program, USDA Forest Service, Flagstaff, Arizona, USA
| | - Ian F Gazeley
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Maureen Small
- Washington Department of Fish and Wildlife, Olympia, Washington, USA
| | - Marie-Josee Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew R Bearlin
- Environment, Land, and Licensing, Seattle City Light, Seattle, Washington, USA
| | - Seth R Smith
- Washington Department of Fish and Wildlife, Olympia, Washington, USA
| | - Erin L Landguth
- Computational Ecology Lab, University of Montana, Missoula, Montana, USA
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171
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Li J, Lam LCW, Lu H. Decoding MRI-informed brain age using mutual information. Insights Imaging 2024; 15:216. [PMID: 39186199 PMCID: PMC11347523 DOI: 10.1186/s13244-024-01791-9] [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: 04/12/2024] [Accepted: 07/31/2024] [Indexed: 08/27/2024] Open
Abstract
OBJECTIVE We aimed to develop a standardized method to investigate the relationship between estimated brain age and regional morphometric features, meeting the criteria for simplicity, generalization, and intuitive interpretability. METHODS We utilized T1-weighted magnetic resonance imaging (MRI) data from the Cambridge Centre for Ageing and Neuroscience project (N = 609) and employed a support vector regression method to train a brain age model. The pre-trained brain age model was applied to the dataset of the brain development project (N = 547). Kraskov (KSG) estimator was used to compute the mutual information (MI) value between brain age and regional morphometric features, including gray matter volume (GMV), white matter volume (WMV), cerebrospinal fluid (CSF) volume, and cortical thickness (CT). RESULTS Among four types of brain features, GMV had the highest MI value (8.71), peaking in the pre-central gyrus (0.69). CSF volume was ranked second (7.76), with the highest MI value in the cingulate (0.87). CT was ranked third (6.22), with the highest MI value in superior temporal gyrus (0.53). WMV had the lowest MI value (4.59), with the insula showing the highest MI value (0.53). For brain parenchyma, the volume of the superior frontal gyrus exhibited the highest MI value (0.80). CONCLUSION This is the first demonstration that MI value between estimated brain age and morphometric features may serve as a benchmark for assessing the regional contributions to estimated brain age. Our findings highlighted that both GMV and CSF are the key features that determined the estimated brain age, which may add value to existing computational models of brain age. CRITICAL RELEVANCE STATEMENT Mutual information (MI) analysis reveals gray matter volume (GMV) and cerebrospinal fluid (CSF) volume as pivotal in computing individuals' brain age. KEY POINTS Mutual information (MI) interprets estimated brain age with morphometric features. Gray matter volume in the pre-central gyrus has the highest MI value for estimated brain age. Cerebrospinal fluid volume in the cingulate has the highest MI value. Regarding brain parenchymal volume, the superior frontal gyrus has the highest MI value. The value of mutual information underscores the key brain regions related to brain age.
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Affiliation(s)
- Jing Li
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Linda Chiu Wa Lam
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hanna Lu
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China.
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China.
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172
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Haussmann AJ, McMahan ZH, Volkmann ER. Understanding the gastrointestinal microbiome in systemic sclerosis: methodological advancements and emerging research. Curr Opin Rheumatol 2024:00002281-990000000-00138. [PMID: 39189041 DOI: 10.1097/bor.0000000000001048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
PURPOSE OF REVIEW This review highlights the role of the gastrointestinal (GI) microbiome in systemic sclerosis (SSc). We describe techniques for evaluating the GI microbiome in humans, and emerging research linking GI microbiome alterations (i.e., dysbiosis) and distinct SSc clinical manifestations. We also address the evolving treatment landscape targeting dysbiosis in SSc. RECENT FINDINGS Recent literature brings into focus the complex relationship between the GI microbiome and SSc pathogenesis. Advanced techniques (e.g., shotgun metagenomics, meta-transcriptomics) provide deeper insights into microbial taxonomy and active gene expression, exposing dysbiosis as a potential driver of SSc. New studies demonstrate that SSc patients who possess specific SSc clinical features, (e.g., interstitial lung disease), have unique GI microbiome profiles. SUMMARY Dysbiosis is associated with specific clinical features in patients with SSc. New tools for studying the GI microbiome have furthered our understanding of the relationship between dysbiosis and SSc complications. Therapeutic avenues such as dietary adjustments, probiotics, antibiotics, mindfulness practices, and fecal transplants offer potential for managing SSc and preventing its progression through GI microbiome modulation. By clarifying what is known about the relationship between the GI dysbiosis, GI dysfunction, and SSc, this review enhances our understanding of SSc pathogenesis and proposes targeted interventions.
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Affiliation(s)
- Alana J Haussmann
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine
| | - Zsuzsanna H McMahan
- Department of Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Elizabeth R Volkmann
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine
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173
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Ferveur JF, Cortot J, Moussian B, Everaerts C. Population Density Affects Drosophila Male Pheromones in Laboratory-Acclimated and Natural Lines. J Chem Ecol 2024:10.1007/s10886-024-01540-8. [PMID: 39186176 DOI: 10.1007/s10886-024-01540-8] [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: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
In large groups of vertebrates and invertebrates, aggregation can affect biological characters such as gene expression, physiological, immunological and behavioral responses. The insect cuticle is covered with hydrocarbons (cuticular hydrocarbons; CHCs) which reduce dehydration and increase protection against xenobiotics. Drosophila melanogaster and D. simulans flies also use some of their CHCs as contact pheromones. In these two sibling species, males also produce the volatile pheromone 11-cis-Vaccenyl acetate (cVa). To investigate the effect of insect density on the production of CHCs and cVa we compared the level of these male pheromones in groups of different sizes. These compounds were measured in six lines acclimated for many generations in our laboratory - four wild-type and one CHC mutant D. melanogaster lines plus one D. simulans line. Increasing the group size substantially changed pheromone amounts only in the four D. melanogaster wild-type lines. To evaluate the role of laboratory acclimation in this effect, we measured density-dependent pheromonal production in 21 lines caught in nature after 1, 12 and 25 generations in the laboratory. These lines showed varied effects which rarely persisted across generations. Although increasing group size often affected pheromone production in laboratory-established and freshly-caught D. melanogaster lines, this effect was not linear, suggesting complex determinants.
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Affiliation(s)
- Jean-François Ferveur
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Université de Bourgogne Franche-Comté, 6, Bd Gabriel, Dijon, 21000, France.
| | - Jérôme Cortot
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Université de Bourgogne Franche-Comté, 6, Bd Gabriel, Dijon, 21000, France
| | - Bernard Moussian
- Interfaculty Institute for Cell Biology, Animal Genetics, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Claude Everaerts
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Université de Bourgogne Franche-Comté, 6, Bd Gabriel, Dijon, 21000, France
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174
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Wang Y, Allen SL, Reddiex AJ, Chenoweth SF. The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach. Mol Ecol 2024:e17499. [PMID: 39188068 DOI: 10.1111/mec.17499] [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: 03/20/2024] [Revised: 07/22/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.
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Affiliation(s)
- Yiguan Wang
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Scott L Allen
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Adam J Reddiex
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Biological Data Science Institute, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen F Chenoweth
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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175
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Fang Z, Pan N, Liu S, Li H, Pan M, Zhang J, Li Z, Liu M, Ge X. Comparative Analysis of Brain Age Prediction Using Structural and Diffusion MRIs in Neonates. Neuroimage 2024:120815. [PMID: 39191358 DOI: 10.1016/j.neuroimage.2024.120815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/02/2024] [Accepted: 08/24/2024] [Indexed: 08/29/2024] Open
Abstract
Using machine learning techniques to predict brain age from multimodal data has become a crucial biomarker for assessing brain development. Among various types of brain imaging data, structural magnetic resonance imaging (sMRI) and diffusion magnetic resonance imaging (dMRI) are the most commonly used modalities. sMRI focuses on depicting macrostructural features of the brain, while dMRI reveals the orientation of major white matter fibers and changes in tissue microstructure. However, their differential capabilities in reflecting newborn age and clinical implications have not been systematically studied. This study aims to explore the impact of sMRI and dMRI on brain age prediction. Comparing predictions based on T2-weighted(T2w) and fractional anisotropy (FA) images, we found their mean absolute errors (MAE) in predicting infant age to be similar. Exploratory analysis revealed for T2w images, areas such as the cerebral cortex and ventricles contribute most significantly to age prediction, whereas FA images highlight the cerebral cortex and regions of the main white matter tracts. Despite both modalities focusing on the cerebral cortex, they exhibit significant region-wise differences, reflecting developmental disparities in macro- and microstructural aspects of the cortex. Additionally, we examined the effects of prematurity, gender, and hemispherical asymmetry of the brain on age prediction for both modalities. Results showed significant differences (p<0.05) in age prediction biases based on FA images across gender and hemispherical asymmetry, whereas no significant differences were observed with T2w images. This study underscores the differences between T2w and FA images in predicting infant brain age, offering new perspectives for studying infant brain development and aiding more effective assessment and tracking of infant development.
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Affiliation(s)
- Zhicong Fang
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Ningning Pan
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Shujuan Liu
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Hongzhuang Li
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Minmin Pan
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Jiong Zhang
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China
| | - Zhuoshuo Li
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, China
| | - Mengting Liu
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, China.
| | - Xinting Ge
- School of Information Science and Engineering, Shandong Normal University, Shandong, China.
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176
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Basit A, Lim KB. Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024:112236. [PMID: 39186951 DOI: 10.1016/j.plantsci.2024.112236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/15/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Polyploidy is thought to be an evolutionary and systematic mechanism for gene flow and phenotypic advancement in flowering plants. It is a natural phenomenon that promotes diversity by creating new permutations enhancing the prime potentials as compared to progenitors. Two different pathways have been recognized in studying polyploidy in nature; mitotic or somatic chromosome doubling and cytogenetics variation. Secondly, the vital influence of being polyploid is its heritable property (unreduced reproductive cells) formed during first and second-division restitution (FDR & SDR). Different approaches either chemical (Colchicine, Oryzalin, Caffeine, Trifuralin, or phosphoric amides) or gaseous i.e. Nitrous oxide have been deliberated as strong polyploidy causing agents. A wide range of cytogenetic practices like chromosomes study, ploidy, genome analysis, and plant morphology and anatomy have been studied in different plant species. Flow cytometry for ploidy and chromosome analysis through fluorescence and genomic in situ hybridization (FISH & GISH) are the basic methods to evaluate heredity substances sampled from leaves and roots. Many horticultural crops have been developed successfully and released commercially for consumption. Moreover, some deep detailed studies are needed to check the strong relationship between unique morphological features and genetic makeup concerning genes and hormonal expression in a strong approach.
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Affiliation(s)
- Abdul Basit
- Department of Horticultural Science, Kyungpook National University, 41566, Daegu, South Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, 41566, Daegu, South Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, Republic of Korea.
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177
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Colicino-Murbach E, Hathaway C, Dungrawala H. Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair. Nucleic Acids Res 2024:gkae721. [PMID: 39180395 DOI: 10.1093/nar/gkae721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 07/03/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024] Open
Abstract
Eukaryotic chromosomal replication occurs in a segmented, temporal manner wherein open euchromatin and compact heterochromatin replicate during early and late S-phase respectively. Using single molecule DNA fiber analyses coupled with cell synchronization, we find that newly synthesized strands remain stable at perturbed forks in early S-phase. Unexpectedly, stalled forks are susceptible to nucleolytic digestion during late replication resulting in defective fork restart. This inherent vulnerability to nascent strand degradation is dependent on fork reversal enzymes and resection nucleases MRE11, DNA2 and EXO1. Inducing chromatin compaction elicits digestion of nascent DNA in response to fork stalling due to reduced association of RAD51 with nascent DNA. Furthermore, RAD51 occupancy at stalled forks in late S-phase is diminished indicating that densely packed chromatin limits RAD51 accessibility to mediate replication fork protection. Genetic analyses reveal that susceptibility of late replicating forks to nascent DNA digestion is dependent on EXO1 via DNA mismatch repair (MMR) and that the BRCA2-mediated replication fork protection blocks MMR from degrading nascent DNA. Overall, our findings illustrate differential regulation of fork protection between early and late replication and demonstrate nascent strand degradation as a critical determinant of heterochromatin instability in response to replication stress.
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Affiliation(s)
| | - Caitlin Hathaway
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Huzefa Dungrawala
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
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178
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Wang Z, Qi J, Yang Y, Li C. Insufficient and excessive Ca 2+ intake negatively impact the life history performance and disrupt the hemolymph metabolism of Spodoptera litura. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116921. [PMID: 39182284 DOI: 10.1016/j.ecoenv.2024.116921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/17/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Calcium ions (Ca2+), essential as second messengers in all cells, play a pivotal role as micronutrients in insects. However, few studies have explored the effects of both insufficient and excessive Ca2+ intake on life history performance and population parameters. This study examines the impact of varying Ca2+ intake levels-insufficient (0 mg/kg), appropriate (100 mg/kg), and excessive (250 mg/kg)-on the life history performance and population parameters of Spodoptera litura using two-sex life tables. Insufficient and excessive Ca2+ intakes significantly extended the preadult development period and decreased the preadult survival rates of S. litura, compared to those on an appropriate Ca2+ intake. The population parameters (Intrinsic rate of increase (r), Finite rate of increase (λ), and Net reproductive rate (R0)) of S. litura on a 100 mg/kg diet (r = 0.1364, λ = 1.1462, R0 = 390) were significantly higher than those on a 0 mg/kg diet (r = 0.1091, λ = 1.1153, R0 = 130.52). Additionally, untargeted metabolomics analysis revealed that inappropriate Ca2+ levels (either insufficient or excessive) triggered significant up-regulation of 71.1 % and 92.8 % of the metabolites in the hemolymph, respectively, compared to the appropriate Ca2+ intake. Notably, disruptions in metabolite balance affected critical components such as melatonin and melanin within the tryptophan and tyrosine metabolism pathways. These findings underscore that both insufficient and excessive Ca2+ intakes adversely affect the life history performance and disrupt hemolymph metabolic balance in S. litura.
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Affiliation(s)
- Zailing Wang
- Hubei Engineering Research Center for Pest Forewarning and Management; Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China.
| | - Jingwei Qi
- Hubei Engineering Research Center for Pest Forewarning and Management; Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yang Yang
- Hubei Engineering Research Center for Pest Forewarning and Management; Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Chuanren Li
- Hubei Engineering Research Center for Pest Forewarning and Management; Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China.
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179
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Wu R, Ingle S, Barnes SA, Dahlin HR, Khamrui S, Xiang Y, Shi Y, Bechhofer DH, Lazarus MB. Structural insights into RNA cleavage by a novel family of bacterial RNases. Nucleic Acids Res 2024:gkae717. [PMID: 39180400 DOI: 10.1093/nar/gkae717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024] Open
Abstract
Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.
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Affiliation(s)
- Ruoxi Wu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shakti Ingle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah A Barnes
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Heather R Dahlin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susmita Khamrui
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yufei Xiang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yi Shi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David H Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Lazarus
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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180
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Fang L, Cosgriff C, Alonzo F. Determinants of maturation of the Staphylococcus aureus autoinducing peptide. J Bacteriol 2024:e0019524. [PMID: 39177535 DOI: 10.1128/jb.00195-24] [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: 05/03/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
The accessory gene regulatory (Agr) system is required for virulence factor gene expression and pathogenesis of Staphylococcus aureus. The Agr system is activated in response to the accumulation of a cyclic autoinducing peptide (AIP), which is matured and secreted by the bacterium. The precursor of AIP, AgrD, consists of the AIP flanked by an N-terminal [Formula: see text]-helical Leader and a charged C-terminal tail. AgrD is matured to AIP by the action of two proteases, AgrB and MroQ. AgrB cleaves the C-terminal tail and promotes the formation of a thiolactone ring, whereas MroQ cleaves the N-terminal Leader in a manner that depends on the four-amino acid linker immediately following a conserved IG helix breaker motif. However, the attributes of AgrD that dictate the sequence of events in peptide maturation are not fully defined. Here, we used engineered AgrD peptide intermediates to ascertain the sufficiency of MroQ for N-terminal peptide cleavage, peptide export, and generation of mature AIP. We found that MroQ promotes the removal of the N-terminal Leader peptide from both linear and cyclic peptide intermediates, while peptide cyclization remained essential for signaling. The expression of the Leader peptide in isolation was sufficient for MroQ-dependent cleavage proximal to the four-amino-acid linker. In addition, active site mutations within AgrB destabilized full-length AgrD and thiolactone-containing intermediates and prevented the release of the Leader peptide. Altogether, our data support a tandem peptide maturation event involving both MroQ and AgrB that appears to couple protease activity and export of bioactive AIP.IMPORTANCEThe accessory gene regulatory (Agr) system is important for S. aureus pathogenesis. Activation of the Agr system requires recognition of a cyclic peptide pheromone, which must be fully matured to exert its biological activity. The complete events in cyclic peptide maturation and export from the bacterial cell remain to be fully defined. We and others recently discovered that the membrane peptidase MroQ is required for pheromone maturation. This study builds off the identification of MroQ and considers the attributes of the pheromone pro-peptide that are required for MroQ-mediated processing as well as uncovers features important for peptide stability and export. Overall, the findings in this study have implications for understanding bacterial pheromone maturation and virulence.
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Affiliation(s)
- Liwei Fang
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois, USA
| | - Chance Cosgriff
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois, USA
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181
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Kwon SG, Bae GH, Hong JH, Choi JW, Choi JH, Lim NS, Jeon C, Mali NM, Jun MS, Shin J, Kim J, Cho ES, Han MH, Oh JW. Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 2024:10.1007/s00335-024-10058-z. [PMID: 39177814 DOI: 10.1007/s00335-024-10058-z] [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: 06/14/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
Abstract
Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research.
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Affiliation(s)
- Seong Gyu Kwon
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Geon Hue Bae
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joo Hee Hong
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Woo Choi
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - June Hyug Choi
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nam Seop Lim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - CheolMin Jeon
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nanda Maya Mali
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mee Sook Jun
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - JaeEun Shin
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - JinSoo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun-Seok Cho
- Department of Livestock Resource Development, National Institute of Animal Science, Jeonbuk, Republic of Korea
| | - Man-Hoon Han
- Department of Pathology, Kyungpook National University Hospital, Daegu, Republic of Korea.
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Absolute DNA, Inc., Daegu, Republic of Korea.
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182
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Fedl AS, Tagoh H, Gruenbacher S, Sun Q, Schenk RL, Froussios K, Jaritz M, Busslinger M, Schwickert TA. Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development. Nat Immunol 2024:10.1038/s41590-024-01933-7. [PMID: 39179932 DOI: 10.1038/s41590-024-01933-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
Early B cell lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. In the present study, we used acute protein degradation in mice to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and are essential for early B cell maintenance. Ikaros and Aiolos act as dedicated repressors to cooperatively control early B cell development. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Similar to Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B cell lymphopoiesis by five transcription factors.
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Affiliation(s)
- Anna S Fedl
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Sarah Gruenbacher
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Qiong Sun
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Robyn L Schenk
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Kimon Froussios
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| | - Tanja A Schwickert
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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183
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Sun W, Zhong J, Gao B, Feng J, Ye Z, Lin Y, Zhang K, Su W, Zhu S, Li Y, Jia W. In vitro/In vivo Evaluations of Hydroxyapatite Nanoparticles with Different Geometry. Int J Nanomedicine 2024; 19:8661-8679. [PMID: 39193530 PMCID: PMC11348988 DOI: 10.2147/ijn.s469687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024] Open
Abstract
Purpose Hydroxyapatite-based nanoparticles have found diverse applications in drug delivery, gene carriers, diagnostics, bioimaging and tissue engineering, owing to their ability to easily enter the bloodstream and target specific sites. However, there is limited understanding of the potential adverse effects and molecular mechanisms of these nanoparticles with varying geometries upon their entry into the bloodstream. Here, we used two commercially available hydroxyapatite nanoparticles (HANPs) with different geometries (less than 100 nm in size each) to investigate this issue. Methods First, the particle size, Zeta potential, and surface morphology of nano-hydroxyapatite were characterized. Subsequently, the effects of 2~2000 μM nano-hydroxyapatite on the proliferation, migration, cell cycle distribution, and apoptosis levels of umbilical vein endothelial cells were evaluated. Additionally, the impact of nanoparticles of various shapes on the differential expression of genes was investigated using transcriptome sequencing. Additionally, we investigated the in vivo biocompatibility of HANPs through gavage administration of nanohydroxyapatite in mice. Results Our results demonstrate that while rod-shaped HANPs promote proliferation in Human Umbilical Vein Endothelial Cell (HUVEC) monolayers at 200 μM, sphere-shaped HANPs exhibit significant toxicity to these monolayers at the same concentration, inducing apoptosis/necrosis and S-phase cell cycle arrest through inflammation. Additionally, sphere-shaped HANPs enhance SULT1A3 levels relative to rod-shaped HANPs, facilitating chemical carcinogenesis-DNA adduct signaling pathways in HUVEC monolayers. In vivo experiments have shown that while HANPs can influence the number of blood cells and comprehensive metabolic indicators in blood, they do not exhibit significant toxicity. Conclusion In conclusion, this study has demonstrated that the geometry and surface area of HANPs significantly affect VEC survival status and proliferation. These findings hold significant implications for the optimization of biomaterials in cell engineering applications.
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Affiliation(s)
- Weitang Sun
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jingbin Zhong
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Buyun Gao
- School of Pharmacy, Fudan University, Shanghai, People’s Republic of China
| | - Jieling Feng
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zijie Ye
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yueling Lin
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Kelan Zhang
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenqi Su
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Shibo Zhu
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yinghua Li
- Center Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wei Jia
- Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
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184
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aChIP for comprehensive chromatin profiling in economically important plant organs. NATURE PLANTS 2024:10.1038/s41477-024-01744-6. [PMID: 39179702 DOI: 10.1038/s41477-024-01744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
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185
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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [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: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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186
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Glaser-Schmitt A, Lemoine M, Kaltenpoth M, Parsch J. Pervasive tissue-, genetic background-, and allele-specific gene expression effects in Drosophila melanogaster. PLoS Genet 2024; 20:e1011257. [PMID: 39178312 DOI: 10.1371/journal.pgen.1011257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/30/2024] [Indexed: 08/25/2024] Open
Abstract
The pervasiveness of gene expression variation and its contribution to phenotypic variation and evolution is well known. This gene expression variation is context dependent, with differences in regulatory architecture often associated with intrinsic and environmental factors, and is modulated by regulatory elements that can act in cis (linked) or in trans (unlinked) relative to the genes they affect. So far, little is known about how this genetic variation affects the evolution of regulatory architecture among closely related tissues during population divergence. To address this question, we analyzed gene expression in the midgut, hindgut, and Malpighian tubule as well as microbiome composition in the two gut tissues in four Drosophila melanogaster strains and their F1 hybrids from two divergent populations: one from the derived, European range and one from the ancestral, African range. In both the transcriptome and microbiome data, we detected extensive tissue- and genetic background-specific effects, including effects of genetic background on overall tissue specificity. Tissue-specific effects were typically stronger than genetic background-specific effects, although the two gut tissues were not more similar to each other than to the Malpighian tubules. An examination of allele specific expression revealed that, while both cis and trans effects were more tissue-specific in genes expressed differentially between populations than genes with conserved expression, trans effects were more tissue-specific than cis effects. Despite there being highly variable regulatory architecture, this observation was robust across tissues and genetic backgrounds, suggesting that the expression of trans variation can be spatially fine-tuned as well as or better than cis variation during population divergence and yielding new insights into cis and trans regulatory evolution.
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Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marion Lemoine
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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187
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Onwongá AA, Oyola SO, Juma J, Konongoi S, Nyamota R, Mwangi R, Muli C, Dobi P, Bett BB, Ongus JR. Genome characterization of Rift Valley fever virus isolated from cattle, goats and sheep during interepidemic periods in Kenya. BMC Vet Res 2024; 20:376. [PMID: 39180076 PMCID: PMC11342565 DOI: 10.1186/s12917-024-04161-1] [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: 11/27/2023] [Accepted: 06/26/2024] [Indexed: 08/26/2024] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne RNA virus of the Phlebovirus genus in the phenuviridae family. Its genome is trisegmented with small (S), medium (M) and large (L) fragments. In nature, the virus exists as a single serotype that is responsible for outbreaks of Rift Valley fever (RVF), a zoonotic disease that often occurs in Africa and the Middle East. RVFV genomes are thought to undergo both recombination and reassortment and investigations of these events is important for monitoring the emergence of virulent strains and understanding the evolutionary characteristics of this virus. The aim of this study was to characterize the genomes of RVFV isolates from cattle, sheep, and goats collected during an interepidemic period in Kenya between June 2016 and November 2021. A total of 691 serum samples from cattle (n = 144), goats (n = 185) and sheep (n = 362) were analysed at the Central Veterinary Laboratories. The competitive IgM-capture ELISA, was used to screen the samples; 205 samples (29.67%) tested positive for RVFV. Of the 205 positive samples, 42 (20.5%) were from cattle, 57 (27.8%) from goats, and 106 (51.7%) from sheep. All the IgM-positive samples were further analyzed by qPCR, and 24 (11.71%) tested positive with Ct values ranging from 14.788 to 38.286. Two samples, 201808HABDVS from sheep and 201810CML3DVS from cattle, had Ct values of less than 20.0 and yielded whole genome sequences with 96.8 and 96.4 coverage, respectively. There was no statistically significant evidence of recombination in any of the three segments and also phylogenetic analysis showed no evidence of reassortment in the two isolated RVFV segments when compared with other isolates of different lineages from previous outbreaks whose genomes are deposited in the GenBank. No evidence of reassortment leaves room for other factors to be the most probable contributors of change in virulence, pathogenicity and emergence of highly virulent strains of the RVFV.
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Affiliation(s)
- Amos A Onwongá
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya.
- Department of Veterinary Services, Ministry of Agriculture Livestock and Fisheries, Nairobi, Kenya.
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | | | - Richard Nyamota
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Reuben Mwangi
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Collins Muli
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Paul Dobi
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Bernard B Bett
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Juliette R Ongus
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
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188
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Wang Q, Wang L, Song S, Zhao YN, Gu HH, Zhu Z, Wang J, Lu S. ORANGE interplays with TCP7 to regulate endoreduplication and leaf size. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39176434 DOI: 10.1111/tpj.16994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024]
Abstract
Leaf size is a crucial agronomic trait directly affecting crop yield, which is mainly determined by coordinated cell proliferation, growth, and differentiation. Although endoreduplication is known to be correlated with the onset of cell differentiation and leaf size, the underlying molecular mechanisms are largely unclear. The DnaJ-like zinc finger domain-containing protein ORANGE (OR) was initially demonstrated to confer the massive accumulation of carotenoids in cauliflower curds. However, the cauliflower or mutant also possesses other phenotypes such as smaller curds, smaller leaves with elongated petioles, and delayed flowering. Here, we demonstrated that OR physically interacts with the transcription factor TCP7, which promotes endoreduplication by inducing the expression of the cell cycle gene CYCLIN D 1;1 (CYCD1;1). Overexpression of OR resulted in smaller rosette leaves, whereas the OR-silencing plants had larger rosette leaves than wild-type plants. Our microscopic observations and flow cytometry analysis revealed that the variation in leaf size was a result of different endoreduplication levels. Genetic analyses showed that OR functions antagonistically with TCP7 in regulating the endoreduplication levels in leaf cells. While the expression of OR is induced by TCP7, OR represses the transactivation activity of TCP7 by affecting its binding capability to the TCP-binding motif in the promoter region of CYCD1;1. Through this interaction, OR negatively regulates the expression of CYCD1;1 and reduces the nuclear ploidy level in rosette leaf cells. Our findings provide new insights into the regulatory network of leaf size and also reveal a regulatory circuit controlling endoreduplication in leaf cells.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Linjuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shuyuan Song
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ya-Nan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Hong-Hui Gu
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China
| | - Ziqiang Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiansheng Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Vegetables, Hangzhou, 310021, China
| | - Shan Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
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189
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Zhang Q, Zhong W, Zhu G, Cheng L, Yin C, Deng L, Yang Y, Zhang Z, Shen J, Fu T, Zhu JK, Zhao L. aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs. NATURE PLANTS 2024:10.1038/s41477-024-01743-7. [PMID: 39179701 DOI: 10.1038/s41477-024-01743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 06/19/2024] [Indexed: 08/26/2024]
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs.
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Affiliation(s)
- Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenying Zhong
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guangfeng Zhu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lulu Cheng
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Caijun Yin
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yang Yang
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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190
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Tamai T, Reginato G, Ojiri R, Morita I, Avrutis A, Cejka P, Shinohara M, Sugimoto K. Sae2 controls Mre11 endo- and exonuclease activities by different mechanisms. Nat Commun 2024; 15:7221. [PMID: 39174552 PMCID: PMC11341764 DOI: 10.1038/s41467-024-51493-5] [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: 10/12/2023] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
DNA double-strand breaks (DSBs) must be repaired to ensure cell survival and genomic integrity. In yeast, the Mre11-Rad50-Xrs2 complex (MRX) collaborates with Sae2 to initiate DSB repair. Sae2 stimulates two MRX nuclease activities, endonuclease and 3'-5' exonuclease. However, how Sae2 controls the two nuclease activities remains enigmatic. Using a combined genetic and biochemical approach, we identified a separation-of-function rad50 mutation, rad50-C47, that causes a defect in Sae2-dependent MRX 3'-5' exonuclease activity, but not endonuclease activity. We found that both the endo- and 3'-5' exonuclease activities are essential to release Spo11 from DNA ends, whereas only the endonuclease activity is required for hairpin removal. We also uncovered that MRX-Sae2 endonuclease introduces a cleavage at defined distances from the Spo11-blocked end with gradually decreasing efficiency. Our findings demonstrate that Sae2 stimulates the MRX endo- and exonuclease activities via Rad50 by different mechanisms, ensuring diverse actions of MRX-Sae2 nuclease at DNA ends.
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Affiliation(s)
- Tomoki Tamai
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Giordano Reginato
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ryusei Ojiri
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Issei Morita
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Alexandra Avrutis
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA
| | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
| | - Miki Shinohara
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara City, Nara, 631-8505, Japan.
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA.
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191
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Zhang Q, Zhang Y, Guo S, Wang X, Wang H. Hydrogen sulfide plays an important role by regulating microRNA in different ischemia-reperfusion injury. Biochem Pharmacol 2024; 229:116503. [PMID: 39179120 DOI: 10.1016/j.bcp.2024.116503] [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: 04/25/2024] [Revised: 07/28/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
MicroRNAs (miRNAs) are the short endogenous non-coding RNAs that regulate the expression of the target gene at posttranscriptional level through degrading or inhibiting the specific target messenger RNAs (mRNAs). MiRNAs regulate the expression of approximately one-third of protein coding genes, and in most cases inhibit gene expression. MiRNAs have been reported to regulate various biological processes, such as cell proliferation, apoptosis and differentiation. Therefore, miRNAs participate in multiple diseases, including ischemia-reperfusion (I/R) injury. Hydrogen sulfide (H2S) was once considered as a colorless, toxic and harmful gas with foul smelling. However, in recent years, it has been discovered that it is the third gas signaling molecule after carbon monoxide (CO) and nitric oxide (NO), with multiple important biological functions. Increasing evidence indicates that H2S plays a vital role in I/R injury through regulating miRNA, however, the mechanism has not been fully understood. In this review, we summarized the current knowledge about the role of H2S in I/R injury by regulating miRNAs, and analyzed its mechanism in detail.
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Affiliation(s)
- Qi Zhang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Yanting Zhang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shiyun Guo
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiao Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Honggang Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China.
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192
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Bai G, Endres T, Kühbacher U, Mengoli V, Greer BH, Peacock EM, Newton MD, Stanage T, Dello Stritto MR, Lungu R, Crossley MP, Sathirachinda A, Cortez D, Boulton SJ, Cejka P, Eichman BF, Cimprich KA. HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability. Mol Cell 2024; 84:3044-3060.e11. [PMID: 39142279 DOI: 10.1016/j.molcel.2024.07.018] [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: 11/29/2023] [Revised: 05/29/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes. Their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected role for the double-stranded DNA (dsDNA) translocase helicase-like transcription factor (HLTF) in responding to G4s. We show that HLTF, which is enriched at G4s in the human genome, can directly unfold G4s in vitro and uses this ATP-dependent translocase function to suppress G4 accumulation throughout the cell cycle. Additionally, MSH2 (a component of MutS heterodimers that bind G4s) and HLTF act synergistically to suppress G4 accumulation, restrict alternative lengthening of telomeres, and promote resistance to G4-stabilizing drugs. In a discrete but complementary role, HLTF restrains DNA synthesis when G4s are stabilized by suppressing primase-polymerase (PrimPol)-dependent repriming. Together, the distinct roles of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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Affiliation(s)
- Gongshi Bai
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Theresa Endres
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ulrike Kühbacher
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Valentina Mengoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Briana H Greer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Emma M Peacock
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Matthew D Newton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Roxana Lungu
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Magdalena P Crossley
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ataya Sathirachinda
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Karlene A Cimprich
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA.
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193
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Low GW, Pavlova A, Gan HM, Ko MC, Sadanandan KR, Lee YP, Amos JN, Austin L, Falk S, Dowling DK, Sunnucks P. Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes. Heredity (Edinb) 2024:10.1038/s41437-024-00718-w. [PMID: 39174672 DOI: 10.1038/s41437-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
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Affiliation(s)
- Gabriel Weijie Low
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany.
- National Parks Board, 1 Cluny Road, Singapore Botanical Gardens, Singapore, 259569, Singapore.
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- Patriot Biotech Sdn Bhd, 47500, Subang Jaya, Selangor, Malaysia
| | - Meng-Ching Ko
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Yin Peng Lee
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
| | - Lana Austin
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
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194
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Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T, de Vries J. Phylogeny and evolution of streptophyte algae. ANNALS OF BOTANY 2024; 134:385-400. [PMID: 38832756 PMCID: PMC11341676 DOI: 10.1093/aob/mcae091] [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: 03/02/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors.
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Affiliation(s)
- Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Thomas Pröschold
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Research Department for Limnology, University of Innsbruck, Mondseestr. 9, 5310 Mondsee, Austria
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- Section of Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Department of Experimental Phycology and Culture Collection of Algae, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstraße 1, 37077 Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
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195
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Zhang C, Liu Z, Shu S, Li X, Li Y, Liu L, Liu L, Wang X, Li F, Qanmber G, Yang Z. GhEXL3 participates in brassinosteroids regulation of fiber elongation in Gossypium hirsutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39172024 DOI: 10.1111/tpj.16995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
Cotton fiber (Gossypium hirsutum) serves as an ideal model for investigating the molecular mechanisms of plant cell elongation at the single-cell level. Brassinosteroids (BRs) play a crucial role in regulating plant growth and development. However, the mechanism by which BR influences cotton fiber elongation remains incompletely understood. In this study, we identified EXORDIUM-like (GhEXL3) through transcriptome analysis of fibers from BR-deficient cotton mutant pagoda 1 (pag1) and BRI1-EMS-SUPPRESSOR 1 (GhBES1.4, encoding a central transcription factor of BR signaling) overexpression cotton lines. Knockout of GhEXL3 using CRISPR/Cas9 was found to impede cotton fiber elongation, while its overexpression promoted fiber elongation, suggesting a positive regulatory function for GhEXL3 in fiber elongation. Furthermore, in vitro ovule culture experiments revealed that the overexpression of GhEXL3 partially counteracted the inhibitory effects of brassinazole (BRZ) on cotton fiber elongation, providing additional evidence of GhEXL3 involvement in BR signaling pathways. Moreover, our findings demonstrate that GhBES1.4 directly binds to the E-box (CACGTG) motif in the GhEXL3 promoter region and enhances its transcription. RNA-seq analysis revealed that overexpression of GhEXL3 upregulated the expression of EXPs, XTHs, and other genes associated with fiber cell elongation. Overall, our study contributes to understanding the mechanism by which BR regulates the elongation of cotton fibers through the direct modulation of GhEXL3 expression by GhBES1.4.
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Affiliation(s)
- Changsheng Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
| | - Sheng Shu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinyang Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yujun Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Le Liu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Liu
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi, China
| | - Xuwen Wang
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
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196
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Chen Y, Luo S, Hu Y, Mao B, Wang X, Lu Z, Shan Q, Zhang J, Wang S, Feng G, Wang C, Liang C, Tang N, Niu R, Wang J, Han J, Yang N, Wang H, Zhou Q, Li W. All-RNA-mediated targeted gene integration in mammalian cells with rationally engineered R2 retrotransposons. Cell 2024; 187:4674-4689.e18. [PMID: 38981481 DOI: 10.1016/j.cell.2024.06.020] [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: 11/15/2023] [Revised: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
All-RNA-mediated targeted gene integration methods, rendering reduced immunogenicity, effective deliverability with non-viral vehicles, and a low risk of random mutagenesis, are urgently needed for next-generation gene addition technologies. Naturally occurring R2 retrotransposons hold promise in this context due to their site-specific integration profile. Here, we systematically analyzed the biodiversity of R2 elements and screened several R2 orthologs capable of full-length gene insertion in mammalian cells. Robust R2 system gene integration efficiency was attained using combined donor RNA and protein engineering. Importantly, the all-RNA-delivered engineered R2 system showed effective integration activity, with efficiency over 60% in mouse embryos. Unbiased high-throughput sequencing demonstrated that the engineered R2 system exhibited high on-target integration specificity (99%). In conclusion, our study provides engineered R2 tools for applications based on hit-and-run targeted DNA integration and insights for further optimization of retrotransposon systems.
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Affiliation(s)
- Yangcan Chen
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shengqiu Luo
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Bangwei Mao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinge Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongbao Lu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingtong Shan
- Northeast Agricultural University, Harbin 150030, China
| | - Jin Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Guihai Feng
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxin Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chen Liang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Tang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Rui Niu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqiang Wang
- Northeast Agricultural University, Harbin 150030, China
| | - Jiabao Han
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qi Zhou
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Wei Li
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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197
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Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V. RAD51 protects abasic sites to prevent replication fork breakage. Mol Cell 2024; 84:3026-3043.e11. [PMID: 39178838 DOI: 10.1016/j.molcel.2024.07.004] [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: 03/20/2024] [Revised: 06/03/2024] [Accepted: 07/08/2024] [Indexed: 08/26/2024]
Abstract
Abasic sites are DNA lesions repaired by base excision repair. Cleavage of unrepaired abasic sites in single-stranded DNA (ssDNA) can lead to chromosomal breakage during DNA replication. How rupture of abasic DNA is prevented remains poorly understood. Here, using cryoelectron microscopy (cryo-EM), Xenopus laevis egg extracts, and human cells, we show that RAD51 nucleofilaments specifically recognize and protect abasic sites, which increase RAD51 association rate to DNA. In the absence of BRCA2 or RAD51, abasic sites accumulate as a result of DNA base methylation, oxidation, and deamination, inducing abasic ssDNA gaps that make replicating DNA fibers sensitive to APE1. RAD51 assembled on abasic DNA prevents abasic site cleavage by the MRE11-RAD50 complex, suppressing replication fork breakage triggered by an excess of abasic sites or POLθ polymerase inhibition. Our study highlights the critical role of BRCA2 and RAD51 in safeguarding against unrepaired abasic sites in DNA templates stemming from base alterations, ensuring genomic stability.
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Affiliation(s)
| | | | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Anna De Antoni
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Luay Joudeh
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Salli Waked
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Viviana Barra
- Institute Curie, PSL Research University, CNRS, UMR 144, 26 Rue d'Ulm, 75005 Paris, France
| | - Daniele Fachinetti
- Institute Curie, PSL Research University, CNRS, UMR 144, 26 Rue d'Ulm, 75005 Paris, France
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Vincenzo Costanzo
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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198
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Zhang X, Xiao Y, You X, Sun S, Sui SF. In situ structural determination of cyanobacterial phycobilisome-PSII supercomplex by STAgSPA strategy. Nat Commun 2024; 15:7201. [PMID: 39169020 PMCID: PMC11339077 DOI: 10.1038/s41467-024-51460-0] [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: 11/29/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) and transferred to photosynthetic reaction centers of photosystem II (PSII) and photosystem I (PSI). While most of the protein complexes involved in photosynthesis have been characterized by in vitro structural analyses, how these protein complexes function together in vivo is not well understood. Here we implemented STAgSPA, an in situ structural analysis strategy, to solve the native structure of PBS-PSII supercomplex from the cyanobacteria Arthrospira sp. FACHB439 at resolution of ~3.5 Å. The structure reveals coupling details among adjacent PBSs and PSII dimers, and the collaborative energy transfer mechanism mediated by multiple super-PBS in cyanobacteria. Our results provide insights into the diversity of photosynthesis-related systems between prokaryotic cyanobacteria and eukaryotic red algae but are also a methodological demonstration for high-resolution structural analysis in cellular or tissue samples.
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Affiliation(s)
- Xing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yanan Xiao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xin You
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sen-Fang Sui
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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199
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Cairo LV, Hong X, Müller MBD, Yuste-Checa P, Jagadeesan C, Bracher A, Park SH, Hayer-Hartl M, Hartl FU. Stress-dependent condensate formation regulated by the ubiquitin-related modifier Urm1. Cell 2024; 187:4656-4673.e28. [PMID: 38942013 DOI: 10.1016/j.cell.2024.06.009] [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: 08/27/2023] [Revised: 04/12/2024] [Accepted: 06/08/2024] [Indexed: 06/30/2024]
Abstract
The ability of proteins and RNA to coalesce into phase-separated assemblies, such as the nucleolus and stress granules, is a basic principle in organizing membraneless cellular compartments. While the constituents of biomolecular condensates are generally well documented, the mechanisms underlying their formation under stress are only partially understood. Here, we show in yeast that covalent modification with the ubiquitin-like modifier Urm1 promotes the phase separation of a wide range of proteins. We find that the drop in cellular pH induced by stress triggers Urm1 self-association and its interaction with both target proteins and the Urm1-conjugating enzyme Uba4. Urmylation of stress-sensitive proteins promotes their deposition into stress granules and nuclear condensates. Yeast cells lacking Urm1 exhibit condensate defects that manifest in reduced stress resilience. We propose that Urm1 acts as a reversible molecular "adhesive" to drive protective phase separation of functionally critical proteins under cellular stress.
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Affiliation(s)
- Lucas V Cairo
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xiaoyu Hong
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martin B D Müller
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Patricia Yuste-Checa
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Chandhuru Jagadeesan
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sae-Hun Park
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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200
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Qiao L, Han X, Ding R, Shang X, Xiao L, Gao G, Zhang C, Kang J, Su X, Liu Y, Luo J, Yan X, Lin J. Npc1 deficiency impairs microglia function via TREM2-mTOR signaling in Niemann-Pick disease type C. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167478. [PMID: 39173891 DOI: 10.1016/j.bbadis.2024.167478] [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: 03/13/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
Niemann-Pick disease Type C (NPC) is a neurodegenerative disease mainly caused by the mutation in NPC1 gene, leading to massive accumulation of unesterified cholesterol in the late endosome/lysosome of cells. Impaired phenotype of microglia is a hallmark in Npc1 mutant mice (Npc1-/- mice). However, the mechanism of Npc1 in regulating microglial function is still unclear. Here, we showed that the reactive microglia in the neonatal Npc1-/- mice indicated by the increased lysosome protein CD68 and phagocytic activity were associated with disrupted TREM2-mTOR signaling in microglia. Furthermore, in Npc1-deficient BV2 cells, genetic deletion of Trem2 partially restored microglial function, probably via restored mTOR signaling. Taken together, our findings indicated that loss of Npc1 in microglia caused changes of their morphologies and the impairment of lysosomal function, which were linked to the TREM2-mTOR signaling pathway.
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Affiliation(s)
- Liang Qiao
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xiaojing Han
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China; Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Ru Ding
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xiaodi Shang
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Lulu Xiao
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Ge Gao
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Chu Zhang
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Jing Kang
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xi Su
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yanli Liu
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Jiankai Luo
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Xin Yan
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany.
| | - Juntang Lin
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China; Henan Joint International Research Laboratory of Stem Cell Medicine, School of Medical Engineering, Xinxiang Medical University, Xinxiang, China.
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