1
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Thote V, Dinesh S, Sharma S. Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach. Syst Biol Reprod Med 2024; 70:101-112. [PMID: 38630598 DOI: 10.1080/19396368.2024.2325699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024]
Abstract
MDC1 (Mediator of DNA damage Checkpoint protein 1) functions to facilitate the localization of numerous DNA damage response (DDR) components to DNA double-strand break sites. MDC1 is an integral component in preserving genomic stability and appropriate DDR regulation. There haven't been systematic investigations of MDC1 mutations that induce cancer and genomic instability. Variations in nsSNPs have the potential to modify the protein chemistry and their function. Describing functional SNPs in disease-associated genes presents a significant conundrum for investigators, it is possible to assess potential functional SNPs before conducting larger population examinations. Multiple sequences and structure-based bioinformatics strategies were implemented in the current in-silico investigation to discern potential nsSNPs of the MDC1 genes. The nsSNPs were identified with SIFT, SNAP2, Align GVGD, PolyPhen-2, and PANTHER, and their stability was determined with MUpro. The conservation, solvent accessibility, and structural effects of the mutations were identified with ConSurf, NetSurfP-2.0, and SAAFEC-SEQ respectively. Cancer-related analysis of the nsSNPs was conducted using cBioPortal and TCGA web servers. The present study appraised five nsSNPs (P1426T, P69S, P194R, P203L, and H131Y) as probably mutilating due to their existence in highly conserved regions and propensity to deplete protein stability. The nsSNPs P194R, P203L, and H131Y were concluded as deleterious and possibly damaging from the 5 prediction tools. The functional nsSNP P194R mutation is associated with skin cutaneous melanoma while no significant records were found for other nsSNPs. The present study concludes that the highly deleterious P194R mutations can potentially induce genomic instability and contribute to various cancers' pathogenesis. Developing drugs targeting these mutations can undoubtedly be advantageous in large population-based studies, particularly in the development of precision medicine.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, India
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2
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [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: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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3
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Palma L, Sauka DH, Berry C, Peralta C. Positive selection analysis of Cyt proteins from Bacillus thuringiensis: A conservative trend driven by negative (purifying) selection. Toxicon 2024; 247:107853. [PMID: 38972359 DOI: 10.1016/j.toxicon.2024.107853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/27/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Bacillus thuringiensis is a Gram-positive entomopathogenic bacterium that produces different pesticidal proteins: vegetative insecticidal proteins (Vpb1/Vpa2, Vip3, and Vpb4) during vegetative growth, which are secreted to the culture medium, and δ-endotoxins (Cry and Cyt) during sporulation, which accumulate into parasporal crystals. Cyt proteins are the smaller subset of δ-endotoxins targeting Diptera species. While Cry and Vip3 proteins undergo positive selection, our analysis suggests that Cyt proteins evolve following a conservative trend driven negative (purifying) selection.
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Affiliation(s)
- Leopoldo Palma
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María, 1555, Argentina; Laboratorio de Control Biotecnológico de Plagas, Instituto BIOTECMED, Departamento de Genética, Universitat de València, Burjassot, València, 46100, Spain.
| | - Diego Herman Sauka
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMYZA), Hurlingham, Buenos Aires, 1686, Argentina
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Cecilia Peralta
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María, 1555, Argentina; Laboratorio de Control Biotecnológico de Plagas, Instituto BIOTECMED, Departamento de Genética, Universitat de València, Burjassot, València, 46100, Spain
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4
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Pollet L, Xia Y. Structure-guided Evolutionary Analysis of Interactome Network Rewiring at Single Residue Resolution in Yeasts. J Mol Biol 2024; 436:168641. [PMID: 38844045 DOI: 10.1016/j.jmb.2024.168641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/30/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
Protein-protein interactions (PPIs) are known to rewire extensively during evolution leading to lineage-specific and species-specific changes in molecular processes. However, the detailed molecular evolutionary mechanisms underlying interactome network rewiring are not well-understood. Here, we combine high-confidence PPI data, high-resolution three-dimensional structures of protein complexes, and homology-based structural annotation transfer to construct structurally-resolved interactome networks for the two yeasts S. cerevisiae and S. pombe. We then classify PPIs according to whether they are preserved or different between the two yeast species and compare site-specific evolutionary rates of interfacial versus non-interfacial residues for these different categories of PPIs. We find that residues in PPI interfaces evolve significantly more slowly than non-interfacial residues when using lineage-specific measures of evolutionary rate, but not when using non-lineage-specific measures. Furthermore, both lineage-specific and non-lineage-specific evolutionary rate measures can distinguish interfacial residues from non-interfacial residues for preserved PPIs between the two yeasts, but only the lineage-specific measure is appropriate for rewired PPIs. Finally, both lineage-specific and non-lineage-specific evolutionary rate measures are appropriate for elucidating structural determinants of protein evolution for residues outside of PPI interfaces. Overall, our results demonstrate that unlike tertiary structures of single proteins, PPIs and PPI interfaces can be highly volatile in their evolution, thus requiring the use of lineage-specific measures when studying their evolution. These results yield insight into the evolutionary design principles of PPIs and the mechanisms by which interactions are preserved or rewired between species, improving our understanding of the molecular evolution of PPIs and PPI interfaces at the residue level.
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Affiliation(s)
- Léah Pollet
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC, Canada
| | - Yu Xia
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC, Canada.
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5
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Liu C, Yu M, Wang M, Yang S, Fu Y, Zhang L, Zhu C, Zhang H. PCAF-mediated acetylation of METTL3 impairs mRNA translation efficiency in response to oxidative stress. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2535-x. [PMID: 39096338 DOI: 10.1007/s11427-023-2535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/08/2024] [Accepted: 08/01/2024] [Indexed: 08/05/2024]
Abstract
METTL3 methylates RNA and regulates the fate of mRNA through its methyltransferase activity. METTL3 enhances RNA translation independently of its catalytic activity. However, the underlying mechanism is still elusive. Here, we report that METTL3 is both interacted with and acetylated at lysine 177 by the acetyltransferase PCAF and deacetylated by SIRT3. Neither the methyltransferase activity nor the stability of METTL3 is affected by its acetylation at K177. Importantly, acetylation of METTL3 blocks its interaction with EIF3H, a subunit of the translation initiation factor, thereby reducing mRNA translation efficiency. Interestingly, acetylation of METTL3 responds to oxidative stress. Mechanistically, oxidative stress enhances the interaction of PCAF with METTL3, increases METTL3 acetylation, and suppresses the interaction of METTL3 with EIF3H, thereby decreasing the translation efficiency of ribosomes and inhibiting cell proliferation. Altogether, we suggest a mechanism by which oxidative stress regulates RNA translation efficiency by the modulation of METTL3 acetylation mediated by PCAF.
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Affiliation(s)
- Cheng Liu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Miao Yu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Mengyuan Wang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Siyuan Yang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Yenan Fu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Lei Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Chaoyang Zhu
- Department of General Surgery and Urological Surgery, Huaihe Hospital, Henan University, Kaifeng, 100084, China.
| | - Hongquan Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China.
- Department of Human Anatomy, Histology, and Embryology, Shenzhen University School of Medicine, Shenzhen, 518055, China.
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6
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Rodriguez DCP, Weber KC, Sundberg B, Glasgow A. MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions. Protein Sci 2024; 33:e5027. [PMID: 38989559 PMCID: PMC11237554 DOI: 10.1002/pro.5027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Quantitative tools to compile and analyze biomolecular interactions among chemically diverse binding partners would improve therapeutic design and aid in studying molecular evolution. Here we present Mapping Areas of Genetic Parsimony In Epitopes (MAGPIE), a publicly available software package for simultaneously visualizing and analyzing thousands of interactions between a single protein or small molecule ligand (the "target") and all of its protein binding partners ("binders"). MAGPIE generates an interactive three-dimensional visualization from a set of protein complex structures that share the target ligand, as well as sequence logo-style amino acid frequency graphs that show all the amino acids from the set of protein binders that interact with user-defined target ligand positions or chemical groups. MAGPIE highlights all the salt bridge and hydrogen bond interactions made by the target in the visualization and as separate amino acid frequency graphs. Finally, MAGPIE collates the most common target-binder interactions as a list of "hotspots," which can be used to analyze trends or guide the de novo design of protein binders. As an example of the utility of the program, we used MAGPIE to probe how different antibody fragments bind a viral antigen; how a common metabolite binds diverse protein partners; and how two ligands bind orthologs of a well-conserved glycolytic enzyme for a detailed understanding of evolutionarily conserved interactions involved in its activation and inhibition. MAGPIE is implemented in Python 3 and freely available at https://github.com/glasgowlab/MAGPIE, along with sample datasets, usage examples, and helper scripts to prepare input structures.
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Affiliation(s)
- Daniel C. Pineda Rodriguez
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Kyle C. Weber
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Belen Sundberg
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Anum Glasgow
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
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7
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Kovacs AS, Portelli S, Silk M, Rodrigues CHM, Ascher DB. MTR3D-AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2. Protein Sci 2024; 33:e5112. [PMID: 39031445 PMCID: PMC11258768 DOI: 10.1002/pro.5112] [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: 12/17/2023] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
The missense tolerance ratio (MTR) was developed as a novel approach to assess the deleteriousness of variants. Its three-dimensional successor, MTR3D, was demonstrated powerful at discriminating pathogenic from benign variants. However, its reliance on experimental structures and homologs limited its coverage of the proteome. We have now utilized AlphaFold2 models to develop MTR3D-AF2, which covers 89.31% of proteins and 85.39% of residues across the human proteome. This work has improved MTR3D's ability to distinguish clinically established pathogenic from benign variants. MTR3D-AF2 is freely available as an interactive web server at https://biosig.lab.uq.edu.au/mtr3daf2/.
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Affiliation(s)
- Aaron S. Kovacs
- The Australian Center for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Stephanie Portelli
- The Australian Center for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneAustralia
| | - Michael Silk
- Centre for Population Genomics, Murdoch Children's Research InstituteMelbourneAustralia
- Systems and Computational BiologyBio21 Institute, The University of MelbourneMelbourneAustralia
| | - Carlos H. M. Rodrigues
- The Australian Center for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneAustralia
| | - David B. Ascher
- The Australian Center for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneAustralia
- Systems and Computational BiologyBio21 Institute, The University of MelbourneMelbourneAustralia
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8
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Nakamura AM, Godoy AS, Kadowaki MAS, Trentin LN, Gonzalez SET, Skaf MS, Polikarpov I. Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C-terminal domain. FEBS J 2024. [PMID: 39073006 DOI: 10.1111/febs.17229] [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: 04/17/2024] [Revised: 06/06/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Carboxylesterases comprise a major class of α/β-fold hydrolases responsible for the cleavage and formation of ester bonds. Found ubiquitously in nature, these enzymes are crucial for the metabolism of both endogenous and exogenous carboxyl esters in animals, plants and microorganisms. Beyond their essential physiological roles, carboxylesterases stand out as one of the important classes of biocatalysts for biotechnology. BlEst2, an enzyme previously classified as Bacillus licheniformis esterase, remains largely uncharacterized. In the present study, we elucidate the structural biology, molecular dynamics and biochemical features of BlEst2. Our findings reveal a canonical α/β-hydrolase fold similar to the ESTHER block L of lipases, further augmented by two additional accessory C-terminal domains. Notably, the catalytic domain demonstrates two insertions, which occupy conserved locations in α/β-hydrolase proteins and commonly form the lid domain in lipase structures. Intriguingly, our in vitro cleavage of C-terminal domains revealed the structure of the active form of BlEst2. Upon activation, BlEst2 showed a markedly elevated hydrolytic activity. This observation implies that the intramolecular C-terminal domain serves as a regulatory intramolecular inhibitor. Interestingly, despite exhibiting esterase-like activity, BlEst2 structural characteristics align more closely with lipases. This suggests that BlEst2 could potentially represent a previously unrecognized subgroup within the realm of carboxyl ester hydrolases.
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Affiliation(s)
| | | | | | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas - UNICAMP, Brazil
| | - Sinkler E T Gonzalez
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas - UNICAMP, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas - UNICAMP, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil
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9
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Jia Z, Wang J, Meng X, Yang X, Tian Y, Wang B, Chen M, Yang J, Das D, Cao Y. Evolution and stress response potential of the plant splicing factor U1C. Sci Rep 2024; 14:17212. [PMID: 39060315 PMCID: PMC11282270 DOI: 10.1038/s41598-024-68190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/22/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing is a crucial process in multicellular eukaryote, facilitated by the assembly of spliceosomal complexes comprising numerous small ribonucleoproteins. At an early stage, U1C is thought to be required for 5' splice site recognition and base pairing. However, a systematic analysis of the U1C gene family in response to developmental cues and stress conditions has not yet been conducted in plants. This study identified 114 U1C genes in 72 plant species using basic bioinformatics analyses. Phylogenetic analysis was used to compare gene and protein structures, promoter motifs, and tissue- and stress-specific expression levels, revealing their functional commonalities or diversity in response to developmental cues, such as embryonic expression, or stress treatments, including drought and heat. Fluorescence quantitative expression analysis showed that U1C gene expression changed under salt, low temperature, drought, and Cd stress in rice seedlings. However, gene expression in shoots and roots was not consistent under different stress conditions, suggesting a complex regulatory mechanism. This research provides foundational insights into the U1C gene family's role in plant development and stress responses, highlighting potential targets for future studies.
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Affiliation(s)
- Zichang Jia
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Junjie Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiangfeng Meng
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Xue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jingfang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65201, USA.
| | - Yunying Cao
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China.
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10
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Geiger CJ, Wong GCL, O'Toole GA. A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14. J Bacteriol 2024; 206:e0044223. [PMID: 38832786 PMCID: PMC11270903 DOI: 10.1128/jb.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Most microbial cells found in nature exist in matrix-covered, surface-attached communities known as biofilms. This mode of growth is initiated by the ability of the microbe to sense a surface on which to grow. The opportunistic pathogen Pseudomonas aeruginosa (Pa) PA14 utilizes a single polar flagellum and type 4 pili (T4P) to sense surfaces. For Pa, T4P-dependent "twitching" motility is characterized by effectively pulling the cell across a surface through a complex process of cooperative binding, pulling, and unbinding. T4P retraction is powered by hexameric ATPases. Pa cells that have engaged a surface increase production of the second messenger cyclic AMP (cAMP) over multiple generations via the Pil-Chp system. This rise in cAMP allows cells and their progeny to become better adapted for surface attachment and activates virulence pathways through the cAMP-binding transcription factor Vfr. While many studies have focused on mechanisms of T4P twitching and regulation of T4P production and function by the Pil-Chp system, the mechanism by which Pa senses and relays a surface-engagement signal to the cell is still an open question. Here we review the current state of the surface sensing literature for Pa, with a focus on T4P, and propose an integrated model of surface sensing whereby the retraction motor PilT senses and relays the signal to the Pil-Chp system via PilJ to drive cAMP production and adaptation to a surface lifestyle.
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Affiliation(s)
- C. J. Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G. C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - G. A. O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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11
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Silverio MP, Neumann T, Schaubruch K, Heermann R, Pérez-García P, Chow J, Streit WR. Metagenome-derived SusD-homologs affiliated with Bacteroidota bind to synthetic polymers. Appl Environ Microbiol 2024; 90:e0093324. [PMID: 38953372 PMCID: PMC11267923 DOI: 10.1128/aem.00933-24] [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: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Starch utilization system (Sus)D-homologs are well known for their carbohydrate-binding capabilities and are part of the sus operon in microorganisms affiliated with the phylum Bacteroidota. Until now, SusD-like proteins have been characterized regarding their affinity toward natural polymers. In this study, three metagenomic SusD homologs (designated SusD1, SusD38489, and SusD70111) were identified and tested with respect to binding to natural and non-natural polymers. SusD1 and SusD38489 are cellulose-binding modules, while SusD70111 preferentially binds chitin. Employing translational fusion proteins with superfolder GFP (sfGFP), pull-down assays, and surface plasmon resonance (SPR) has provided evidence for binding to polyethylene terephthalate (PET) and other synthetic polymers. Structural analysis suggested that a Trp triad might be involved in protein adsorption. Mutation of these residues to Ala resulted in an impaired adsorption to microcrystalline cellulose (MC), but not so to PET and other synthetic polymers. We believe that the characterized SusDs, alongside the methods and considerations presented in this work, will aid further research regarding bioremediation of plastics. IMPORTANCE SusD1 and SusD38489 can be considered for further applications regarding their putative adsorption toward fossil-fuel based polymers. This is the first time that SusD homologs from the polysaccharide utilization loci (PUL), largely described for the phylum Bacteroidota, are characterized as synthetic polymer-binding proteins.
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Affiliation(s)
| | - Tabea Neumann
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kirsten Schaubruch
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Ralf Heermann
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Pablo Pérez-García
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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12
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Michel MA, Scutts S, Komander D. Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity. Cell Rep 2024; 43:114545. [PMID: 39052481 DOI: 10.1016/j.celrep.2024.114545] [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: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK
| | - Simon Scutts
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
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13
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Du M, Deng C, Yu T, Zhou Q, Zeng F. YjgA plays dual roles in enhancing PTC maturation. Nucleic Acids Res 2024; 52:7947-7960. [PMID: 38842932 PMCID: PMC11260487 DOI: 10.1093/nar/gkae469] [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: 01/27/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Ribosome biogenesis is a highly regulated cellular process that involves the control of numerous assembly factors. The small protein YjgA has been reported to play a role in the late stages of 50S assembly. However, the precise molecular mechanism underlying its function remains unclear. In this study, cryo-electron microscopy (cryo-EM) structures revealed that depletion of YjgA or its N-terminal loop in Escherichia coli both lead to the accumulation of immature 50S particles with structural abnormalities mainly in peptidyl transferase center (PTC) and H68/69 region. CryoDRGN analysis uncovered 8 and 6 distinct conformations of pre50S for ΔyjgA and YjgA-ΔNloop, respectively. These conformations highlighted the role of the N-terminal loop of YjgA in integrating uL16 and stabilizing H89 in PTC, which was further verified by the pull-down assays of YjgA and its mutants with uL16. Together with the function of undocking H68 through the binding of its C-terminal CTLH-like domain to the base of the L1 stalk, YjgA facilitates the maturation of PTC. This study identified critical domains of YjgA contributing to 50S assembly efficiency, providing a comprehensive understanding of the dual roles of YjgA in accelerating ribosome biogenesis and expanding our knowledge of the intricate processes governing cellular protein synthesis.
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Affiliation(s)
- Mengtan Du
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, People's Republic of China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, People's Republic of China
| | - Chenke Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, People's Republic of China
| | - Ting Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, People's Republic of China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, People's Republic of China
| | - Qixin Zhou
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, People's Republic of China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, People's Republic of China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, People's Republic of China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, People's Republic of China
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14
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Jones GD, Ellisdon AM. Understanding P-Rex regulation: structural breakthroughs and emerging perspectives. Biochem Soc Trans 2024:BST20231546. [PMID: 39023851 DOI: 10.1042/bst20231546] [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: 05/28/2024] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Rho GTPases are a family of highly conserved G proteins that regulate numerous cellular processes, including cytoskeleton organisation, migration, and proliferation. The 20 canonical Rho GTPases are regulated by ∼85 guanine nucleotide exchange factors (GEFs), with the largest family being the 71 Diffuse B-cell Lymphoma (Dbl) GEFs. Dbl GEFs promote GTPase activity through the highly conserved Dbl homology domain. The specificity of GEF activity, and consequently GTPase activity, lies in the regulation and structures of the GEFs themselves. Dbl GEFs contain various accessory domains that regulate GEF activity by controlling subcellular localisation, protein interactions, and often autoinhibition. This review focuses on the two phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3)-dependent Rac exchangers (P-Rex), particularly the structural basis of P-Rex1 autoinhibition and synergistic activation. First, we discuss structures that highlight the conservation of P-Rex catalytic and phosphoinositide binding activities. We then explore recent breakthroughs in uncovering the structural basis for P-Rex1 autoinhibition and detail the proposed minimal two-step model of how PI(3,4,5)P3 and Gβγ synergistically activate P-Rex1 at the membrane. Additionally, we discuss the further layers of P-Rex regulation provided by phosphorylation and P-Rex2-PTEN coinhibitory complex formation, although these mechanisms remain incompletely understood. Finally, we leverage the available data to infer how cancer-associated mutations in P-Rex2 destabilise autoinhibition and evade PTEN coinhibitory complex formation, leading to increased P-Rex2 GEF activity and driving cancer progression and metastasis.
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Affiliation(s)
- Gareth D Jones
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew M Ellisdon
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
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15
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Kataria A, Srivastava A, Singh DD, Haque S, Han I, Yadav DK. Systematic computational strategies for identifying protein targets and lead discovery. RSC Med Chem 2024; 15:2254-2269. [PMID: 39026640 PMCID: PMC11253860 DOI: 10.1039/d4md00223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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Affiliation(s)
- Arti Kataria
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan Jaipur India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University Jazan-45142 Saudi Arabia
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University Seoul 01897 Republic of Korea +82 32 820 4948
| | - Dharmendra Kumar Yadav
- Department of Biologics, College of Pharmacy, Gachon University Hambakmoeiro 191, Yeonsu-gu Incheon 21924 Republic of Korea
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16
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Hirata E, Sakata KT, Dearden GI, Noor F, Menon I, Chiduza GN, Menon AK. Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG. J Biol Chem 2024:107584. [PMID: 39025454 DOI: 10.1016/j.jbc.2024.107584] [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: 04/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
The oligosaccharide needed for protein N-glycosylation is assembled on a lipid carrier via a multi-step pathway. Synthesis is initiated on the cytoplasmic face of the endoplasmic reticulum (ER) and completed on the luminal side after transbilayer translocation of a heptasaccharide lipid intermediate. More than 30 Congenital Disorders of Glycosylation (CDGs) are associated with this pathway, including RFT1-CDG which results from defects in the membrane protein Rft1. Rft1 is essential for the viability of yeast and mammalian cells and was proposed as the transporter needed to flip the heptasaccharide lipid intermediate across the ER membrane. However, other studies indicated that Rft1 is not required for heptasaccharide lipid flipping in microsomes or unilamellar vesicles reconstituted with ER membrane proteins, nor is it required for the viability of at least one eukaryote. It is therefore not known what essential role Rft1 plays in N-glycosylation. Here, we present a molecular characterization of human Rft1, using yeast cells as a reporter system. We show that it is a multi-spanning membrane protein located in the ER, with its N and C-termini facing the cytoplasm. It is not N-glycosylated. The majority of RFT1-CDG mutations map to highly conserved regions of the protein. We identify key residues that are important for Rft1's ability to support N-glycosylation and cell viability. Our results provide a necessary platform for future work on this enigmatic protein.
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Affiliation(s)
- Eri Hirata
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ken-Taro Sakata
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Grace I Dearden
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Faria Noor
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - George N Chiduza
- Structure and Function of Biological Membranes - Chemistry Department, Université Libre de Bruxelles - Campus Plaine, 1050 Brussels, Belgium
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA.
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17
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Watson S, Micheloni E, Ngu L, Barnsley KK, Makowski L, Beuning PJ, Ondrechen MJ. Revisiting the Roles of Catalytic Residues in Human Ornithine Transcarbamylase. Biochemistry 2024; 63:1858-1875. [PMID: 38940639 PMCID: PMC11256359 DOI: 10.1021/acs.biochem.4c00206] [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: 04/18/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
Human ornithine transcarbamylase (hOTC) is a mitochondrial transferase protein involved in the urea cycle and is crucial for the conversion of toxic ammonia to urea. Structural analysis coupled with kinetic studies of Escherichia coli, rat, bovine, and other transferase proteins has identified residues that play key roles in substrate recognition and conformational changes but has not provided direct evidence for all of the active residues involved in OTC function. Here, computational methods were used to predict the likely active residues of hOTC; the function of these residues was then probed with site-directed mutagenesis and biochemical characterization. This process identified previously reported active residues, as well as distal residues that contribute to activity. Mutation of active site residue D263 resulted in a substantial loss of activity without a decrease in protein stability, suggesting a key catalytic role for this residue. Mutation of predicted second-layer residues H302, K307, and E310 resulted in significant decreases in enzymatic activity relative to that of wild-type (WT) hOTC with respect to l-ornithine. The mutation of fourth-layer residue H107 to produce the hOTC H107N variant resulted in a 66-fold decrease in catalytic efficiency relative to that of WT hOTC with respect to carbamoyl phosphate and a substantial loss of thermal stability. Further investigation identified H107 and to a lesser extent E98Q as key residues involved in maintaining the hOTC quaternary structure. This work biochemically demonstrates the importance of D263 in hOTC catalytic activity and shows that residues remote from the active site also play key roles in activity.
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Affiliation(s)
- Samantha
S. Watson
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Emily Micheloni
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Lisa Ngu
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kelly K. Barnsley
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Mary Jo Ondrechen
- Department
of Chemistry and Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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18
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Semper C, Watanabe N, Karimullina E, Patel DT, Di Leo R, Castellanos M, Patel DH, Chaconas G, Savchenko A. Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain. Nucleic Acids Res 2024:gkae580. [PMID: 38979576 DOI: 10.1093/nar/gkae580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Borrelia spirochetes are the causative agents of Lyme disease and relapsing fever, two of the most common tick-borne illnesses. A characteristic feature of these spirochetes is their highly segmented genomes which consists of a linear chromosome and a mixture of up to approximately 24 linear and circular extrachromosomal plasmids. The complexity of this genomic arrangement requires multiple strategies for efficient replication and partitioning during cell division, including the generation of hairpin ends found on linear replicons mediated by the essential enzyme ResT, a telomere resolvase. Using an integrative structural biology approach employing advanced modelling, circular dichroism, X-ray crystallography and small-angle X-ray scattering, we have generated high resolution structural data on ResT from B. garinii. Our data provides the first high-resolution structures of ResT from Borrelia spirochetes and revealed active site positioning in the catalytic domain. We also demonstrate that the C-terminal domain of ResT is required for both transesterification steps of telomere resolution, and is a requirement for DNA binding, distinguishing ResT from other telomere resolvases from phage and bacteria. These results advance our understanding of the molecular function of this essential enzyme involved in genome maintenance in Borrelia pathogens.
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Nobuhiko Watanabe
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Elina Karimullina
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Deepak T Patel
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, Ontario M5G 1L6, Canada
| | - Mildred Castellanos
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Dhruvin H Patel
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - George Chaconas
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, Ontario M5G 1L6, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
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19
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Stalin A, Han J, Daniel Reegan A, Ignacimuthu S, Liu S, Yao X, Zou Q. Exploring the antiviral inhibitory activity of Niloticin against the NS2B/NS3 protease of Dengue virus (DENV2). Int J Biol Macromol 2024:133791. [PMID: 38992553 DOI: 10.1016/j.ijbiomac.2024.133791] [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: 05/01/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Dengue virus (DENV2) is the cause of dengue disease and a worldwide health problem. DENV2 replicates in the host cell using polyproteins such as NS3 protease in conjugation with NS2B cofactor, making NS3 protease a promising antiviral drug-target. This study investigated the efficacy of 'Niloticin' against NS2B/NS3-protease. In silico and in vitro analyses were performed which included interaction of niloticin with NS2B/NS3-protease, protein stability and flexibility, mutation effect, betweenness centrality of residues and analysis of cytotoxicity, protein expression and WNV NS3-protease activity. Similar like acyclovir, niloticin forms strong H-bonds and hydrophobic interactions with residues LEU149, ASN152, LYS74, GLY148 and ALA164. The stability of the niloticin-NS2B/NS3-protease complex was found to be stable compared to the apo NS2B/NS3-protease in structural deviation, PCA, compactness and FEL analysis. The IC50 value of niloticin was 0.14 μM in BHK cells based on in vitro cytotoxicity analysis and showed significant activity at 2.5 μM in a concentration-dependent manner. Western blotting and qRT-PCR analyses showed that niloticin reduced DENV2 protein transcription in a dose-dependent manner. Besides, niloticin confirmed the inhibition of NS3-protease by the SensoLyte 440 WNV protease detection kit. These promising results suggest that niloticin could be an effective antiviral drug against DENV2 and other flaviviruses.
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Affiliation(s)
- Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610 054, China.
| | - Jiajia Han
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Appadurai Daniel Reegan
- National Centre for Disease Control, Bengaluru Branch, No. 8, NTI Campus, Bellary Road, Bengaluru 560 003, Karnataka, India; ICMR-Vector Control Research Centre, Indira Nagar, Gorimedu, Puducherry 605 006, India
| | - Savarimuthu Ignacimuthu
- Xavier Research Foundation, St. Xavier's College, Affiliated to Manonmaniam Sundaranar University, Palayamkottai 627 002, Tamil Nadu, India
| | - Shuwen Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Key Laboratory of Infectious Diseases Research in South China (Southern Medical University), Ministry of Education, Guangzhou 510515, China
| | - Xingang Yao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Key Laboratory of Infectious Diseases Research in South China (Southern Medical University), Ministry of Education, Guangzhou 510515, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610 054, China.
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20
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Heydarian Z, Harrington M, Hegedus DD. Defects in Glabrous 3 (GL3) functionality underlie the absence of trichomes in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38967095 DOI: 10.1111/tpj.16878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 07/06/2024]
Abstract
Previously, expression of the Arabidopsis thaliana GLABRA3 (GL3) induced trichome formation in Brassica napus. GL3 orthologues were examined from glabrous (B. oleracea), semi-glabrous (B. napus), moderately hirsute (B. rapa), and very hirsute (B. villosa) Brassica species. Ectopic expression of BnGL3, BrGL3 alleles, or BvGL3 induced trichome formation in glabrous B. napus with the effect on trichome number commensurate with density in the original accessions. Chimeric GL3 proteins in which the B. napus amino terminal region, which interacts with MYB proteins, or the middle region, which interacts with the WD40 protein TTG1, was exchanged with corresponding regions from A. thaliana were as stimulatory to trichome production as AtGL3. Exchange of the carboxy-terminal region containing a bHLH domain and an ACT domain did not alter the trichome stimulatory activity, although modeling of the ACT domain identified differences that could affect GL3 dimerization. B. napus A- and C-genomes orthologues differed in their abilities to form homo- and heterodimers. Modeling of the amino-terminal region revealed a conserved domain that may represent the MYB factor binding pocket. This region interacted with the MYB factors GL1, CPC, and TRY, as well as with JAZ8, which is involved in jasmonic acid-mediated regulation of MYC-like transcription factors. Protein interaction studies indicated that GL1 interaction with GL3 from B. napus and A. thaliana may underlie the difference in their respective abilities to induce trichome formation.
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Affiliation(s)
- Zohreh Heydarian
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
- Department of Biotechnology, School of Agriculture, University of Shiraz, Bajgah, Shiraz, Fars, Iran
| | - Myrtle Harrington
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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21
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Basu S, Ashok G, Ghosh S, Ramaiah S, Veeraraghavan B, Anbarasu A. Cefiderocol susceptibility endows hope in treating carbapenem-resistant Pseudomonas aeruginosa: insights from in vitro and in silico evidence. RSC Adv 2024; 14:21328-21341. [PMID: 38979460 PMCID: PMC11228942 DOI: 10.1039/d4ra04302b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
'High-risk' hypermutable clones of Pseudomonas aeruginosa disseminating extensive drug-resistance (XDR) have raised global health concerns with escalating mortality rates in immunocompromised patients. Mutations in conventional drug-targets under antibiotic stress necessitate structural understanding to formulate sustainable therapeutics. In the present study, the major β-lactam antibiotic target, penicillin-binding protein-3 (PBP3) with mutations F533L and T91A, were identified in carbapenemase-positive P. aeruginosa isolates (n = 6) using whole genome sequencing. Antibiotic susceptibility tests showed susceptibility to cefiderocol (MIC ≤ 4 μg ml-1) despite pan-β-lactam resistance in the isolates. Both the mutations reduced local intra-chain interactions in PBP3 that marginally increased the local flexibility (∼1%) in the structures to affect antibiotic-interactions. Molecular dynamics simulations confirmed the overall stability of the PBP3 mutants through root-mean square deviations, radius of gyration, solvent-accessibility and density curves, which favored their selection. Docking studies unveiled that the mutations in PBP3 elicited unfavorable stereochemical clashes with the conventional antibiotics thereby increasing their inhibition constants (IC) up to ∼50 fold. It was deciphered that cefiderocol retained its susceptibility despite mutations in PBP3, due to its higher average binding affinity (ΔG: -8.2 ± 0.4 kcal mol-1) towards multiple PBP-targets and lower average binding affinity (ΔG: -6.7 ± 0.7 kcal mol-1) to β-lactamases than the other β-lactam antibiotics. The molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area calculations further indicated energetically favorable binding for cefiderocol with PBP3 proteins. The study gave structural insight into emerging non-polar amino acid substitutions in PBP3 causing XDR and recommends prioritizing available antibiotics based on multi-target affinities to overcome challenges imposed by target-protein mutations.
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Affiliation(s)
- Soumya Basu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore India +91-416-2243092 +91-416-2202694
- Department of Biotechnology, NIST University Berhampur-761008 India
| | | | | | | | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College (CMC) Vellore India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore India +91-416-2243092 +91-416-2202694
- Department of Biotechnology, SBST, VIT Vellore India
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22
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Xu G, Yang S. Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity. Int J Biol Macromol 2024; 275:133635. [PMID: 38964677 DOI: 10.1016/j.ijbiomac.2024.133635] [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: 12/17/2023] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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23
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Sawyer EM, Jensen LE, Meehl JB, Larsen KP, Petito DA, Hurley JH, Voeltz GK. SigmaR1 shapes rough endoplasmic reticulum membrane sheets. Dev Cell 2024:S1534-5807(24)00382-4. [PMID: 38971154 DOI: 10.1016/j.devcel.2024.06.005] [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: 09/25/2023] [Revised: 02/12/2024] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
Rough endoplasmic reticulum (ER) sheets are a fundamental domain of the ER and the gateway into the secretory pathway. Although reticulon proteins stabilize high-curvature ER tubules, it is unclear whether other proteins scaffold the flat membranes of rough ER sheets. Through a proteomics screen using ER sheet-localized RNA-binding proteins as bait, we identify the sigma-1 receptor (SigmaR1) as an ER sheet-shaping factor. High-resolution live cell imaging and electron tomography assign SigmaR1 as an ER sheet-localized factor whose levels determine the amount of rough ER sheets in cells. Structure-guided mutagenesis and in vitro reconstitution on giant unilamellar vesicles further support a mechanism whereby SigmaR1 oligomers use their extended arrays of amphipathic helices to bind and flatten the lumenal leaflet of ER membranes to oppose membrane curvature and stabilize rough ER sheets.
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Affiliation(s)
- Eric M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Liv E Jensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Janet B Meehl
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Kevin P Larsen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Petito
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute.
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24
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Hameleers L, Gaenssle LA, Bertran‐Llorens S, Pijning T, Jurak E. Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes. FEBS Open Bio 2024; 14:1133-1146. [PMID: 38735878 PMCID: PMC11216935 DOI: 10.1002/2211-5463.13816] [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: 12/22/2023] [Revised: 03/17/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like β-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
| | - Lucie A. Gaenssle
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
| | | | - Tjaard Pijning
- Department of Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenThe Netherlands
| | - Edita Jurak
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
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25
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Liu J, Corroyer-Dulmont S, Pražák V, Khusainov I, Bahrami K, Welsch S, Vasishtan D, Obarska-Kosińska A, Thorkelsson SR, Grünewald K, Quemin ERJ, Turoňová B, Locker JK. The palisade layer of the poxvirus core is composed of flexible A10 trimers. Nat Struct Mol Biol 2024; 31:1105-1113. [PMID: 38316878 PMCID: PMC11257942 DOI: 10.1038/s41594-024-01218-5] [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: 06/11/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Due to its asymmetric shape, size and compactness, the structure of the infectious mature virus (MV) of vaccinia virus (VACV), the best-studied poxvirus, remains poorly understood. Instead, subviral particles, in particular membrane-free viral cores, have been studied with cryo-electron microscopy. Here, we compared viral cores obtained by detergent stripping of MVs with cores in the cellular cytoplasm, early in infection. We focused on the prominent palisade layer on the core surface, combining cryo-electron tomography, subtomogram averaging and AlphaFold2 structure prediction. We showed that the palisade is composed of densely packed trimers of the major core protein A10. Trimers display a random order and their classification indicates structural flexibility. A10 on cytoplasmic cores is organized in a similar manner, indicating that the structures obtained in vitro are physiologically relevant. We discuss our results in the context of the VACV replicative cycle, and the assembly and disassembly of the infectious MV.
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Affiliation(s)
- Jiasui Liu
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Simon Corroyer-Dulmont
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Iskander Khusainov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Karola Bahrami
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany
- University Clinic Frankfurt, Frankfurt am Main, Germany
| | - Sonja Welsch
- Max Planck Institute of Biophysics, Central Electron Microscopy Facility, Frankfurt am Main, Germany
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Sigurdur R Thorkelsson
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- University of Hamburg, Hamburg, Germany.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CNRS UMR9198, Université Paris-Saclay, CEA, Gif-sur-Yvette, France.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Jacomina Krijnse Locker
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany.
- Justus Liebig University of Giessen, Giessen, Germany.
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26
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Simmons HC, Finney J, Kotaki R, Adachi Y, Park Moseman A, Watanabe A, Song S, Robinson-McCarthy LR, Le Sage V, Kuraoka M, Moseman EA, Kelsoe G, Takahashi Y, McCarthy KR. A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.13.571543. [PMID: 38168412 PMCID: PMC10760138 DOI: 10.1101/2023.12.13.571543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joel Finney
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Ryutaro Kotaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Shengli Song
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Lindsey R. Robinson-McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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27
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Yadav AK, Murthy TPK, Divyashri G, Prasad N D, Prakash S, Vaishnavi V V, Shukla R, Singh TR. Computational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences. J Biomol Struct Dyn 2024; 42:5072-5091. [PMID: 37434323 DOI: 10.1080/07391102.2023.2231553] [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: 03/03/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023]
Abstract
Heme Oxygenase 1 (HMOX1) is a cytoprotective enzyme, exhibiting the highest activity in the spleen, catalyzing the heme ring breakdown into products of biological significance- biliverdin, CO, and Fe2+. In vascular cells, HMOX1 possesses strong anti-apoptotic, antioxidant, anti-proliferative, anti-inflammatory, and immunomodulatory actions. The majority of these activities are crucial for the prevention of atherogenesis. Single amino acid substitutions in proteins generated by missense non-synonymous single nucleotide polymorphism (nsSNPs) in the protein-encoding regions of genes are potent enough to cause significant medical challenges due to the alteration of protein structure and function. The current study aimed at characterizing and analyzing high-risk nsSNPs associated with the human HMOX1 gene. Preliminary screening of the total available 288 missense SNPs was performed through the lens of deleteriousness and stability prediction tools. Finally, a total of seven nsSNPs (Y58D, A131T, Y134H, F166S, F167S, R183S and M186V) were found to be most deleterious by all tools that are present at highly conserved positions. Molecular dynamics simulations (MDS) analysis explained the mutational effects on the dynamic action of the wild-type and mutant proteins. In a nutshell, R183S (rs749644285) was identified as a highly detrimental mutation that could significantly render the enzymatic activity of HMOX1. The finding of this computational analysis might help subject the experimental confirmatory analysis to characterize the role of nsSNPs in HMOX1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Gangaraju Divyashri
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Durga Prasad N
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Sriraksha Prakash
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Vijaya Vaishnavi V
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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28
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Norn C, Oliveira F, André I. Improved prediction of site-rates from structure with averaging across homologs. Protein Sci 2024; 33:e5086. [PMID: 38923241 PMCID: PMC11196898 DOI: 10.1002/pro.5086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/12/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Variation in mutation rates at sites in proteins can largely be understood by the constraint that proteins must fold into stable structures. Models that calculate site-specific rates based on protein structure and a thermodynamic stability model have shown a significant but modest ability to predict empirical site-specific rates calculated from sequence. Models that use detailed atomistic models of protein energetics do not outperform simpler approaches using packing density. We demonstrate that a fundamental reason for this is that empirical site-specific rates are the result of the average effect of many different microenvironments in a phylogeny. By analyzing the results of evolutionary dynamics simulations, we show how averaging site-specific rates across many extant protein structures can lead to correct recovery of site-rate prediction. This result is also demonstrated in natural protein sequences and experimental structures. Using predicted structures, we demonstrate that atomistic models can improve upon contact density metrics in predicting site-specific rates from a structure. The results give fundamental insights into the factors governing the distribution of site-specific rates in protein families.
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Affiliation(s)
- Christoffer Norn
- Department of Biochemistry and Structural BiologyLund UniversityLundSweden
- Bioinnovation Institute FoundationKøbenhavnDenmark
| | - Fábio Oliveira
- Department of Biochemistry and Structural BiologyLund UniversityLundSweden
| | - Ingemar André
- Department of Biochemistry and Structural BiologyLund UniversityLundSweden
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29
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McDonnell AF, Plech M, Livesey BJ, Gerasimavicius L, Owen LJ, Hall HN, FitzPatrick DR, Marsh JA, Kudla G. Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Mol Syst Biol 2024; 20:825-844. [PMID: 38849565 PMCID: PMC11219921 DOI: 10.1038/s44320-024-00043-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Nonsense and missense mutations in the transcription factor PAX6 cause a wide range of eye development defects, including aniridia, microphthalmia and coloboma. To understand how changes of PAX6:DNA binding cause these phenotypes, we combined saturation mutagenesis of the paired domain of PAX6 with a yeast one-hybrid (Y1H) assay in which expression of a PAX6-GAL4 fusion gene drives antibiotic resistance. We quantified binding of more than 2700 single amino-acid variants to two DNA sequence elements. Mutations in DNA-facing residues of the N-terminal subdomain and linker region were most detrimental, as were mutations to prolines and to negatively charged residues. Many variants caused sequence-specific molecular gain-of-function effects, including variants in position 71 that increased binding to the LE9 enhancer but decreased binding to a SELEX-derived binding site. In the absence of antibiotic selection, variants that retained DNA binding slowed yeast growth, likely because such variants perturbed the yeast transcriptome. Benchmarking against known patient variants and applying ACMG/AMP guidelines to variant classification, we obtained supporting-to-moderate evidence that 977 variants are likely pathogenic and 1306 are likely benign. Our analysis shows that most pathogenic mutations in the paired domain of PAX6 can be explained simply by the effects of these mutations on PAX6:DNA association, and establishes Y1H as a generalisable assay for the interpretation of variant effects in transcription factors.
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Affiliation(s)
- Alexander F McDonnell
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Marcin Plech
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Lukas Gerasimavicius
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Liusaidh J Owen
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hildegard Nikki Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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30
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Wang L, Wang YY, Chen ZL, Li YH. Enzymatic characterization and thermostability improvement of an acidophilic endoxylanase PphXyn11 from Paenibacillus physcomitrellae XB. Protein Expr Purif 2024; 219:106482. [PMID: 38583789 DOI: 10.1016/j.pep.2024.106482] [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: 07/11/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
GH11 enzyme is known to be specific and efficient for the hydrolysis of xylan. It has been isolated from many microorganisms, and its enzymatic characteristics and thermostability vary between species. In this study, a GH11 enzyme PphXyn11 from a novel xylan-degrading strain of Paenibacillus physcomitrellae XB was characterized, and five mutants were constructed to try to improve the enzyme's thermostability. The results showed that PphXyn11 was an acidophilic endo-β-1,4-xylanase with the optimal reaction pH of 3.0-4.0, and it could deconstruct different kinds of xylan substrates efficiently, such as beechwood xylan, wheat arabinoxylan and xylo-oligosaccharides, to produce xylobiose and xylotriose as the main products at the optimal reaction temperature of 40 °C. Improvement of the thermal stability of PphXyn11 using site-directed mutagenesis revealed that three mutants, W33C/N47C, S127C/N174C and S49E, designed by adding the disulfide bonds at the N-terminal, C-terminal and increasing the charged residues on the surface of PphXyn11 respectively, could increase the enzymatic activity and thermal stablility significantly and make the optimal reaction temperature reach 50 °C. Molecular dynamics simulations as well as computed the numbers of salt bridges and hydrogen bonds indicated that the protein structures of these three mutants were more stable than the wild type, which provided theoretical support for their improved thermal stability. Certainly, further research is necessary to improve the enzymatic characteristics of PphXyn11 to achieve the bioconversion of hemicellulosic biomass on an applicable scale.
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Affiliation(s)
- Le Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Yan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Zhi Ling Chen
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Hong Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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31
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Russo S, Rozeboom HJ, Wijma HJ, Poelarends GJ, Fraaije MW. Biochemical, kinetic, and structural characterization of a Bacillus tequilensis nitroreductase. FEBS J 2024. [PMID: 38946302 DOI: 10.1111/febs.17210] [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: 03/28/2024] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Nitroreductases (NRs) are NAD(P)H-dependent flavoenzymes that reduce nitro aromatic compounds to their corresponding arylamines via the nitroso and hydroxylamine intermediates. Because of their broad substrate scope and versatility, NRs have found application in multiple fields such as biocatalysis, bioremediation, cell-imaging and prodrug activation. However, only a limited number of members of the broad NR superfamily (> 24 000 sequences) have been experimentally characterized. Within this group of enzymes, only few are capable of amine synthesis, which is a fundamental chemical transformation for the pharmaceutical, agricultural, and textile industries. Herein, we provide a comprehensive description of a recently discovered NR from Bacillus tequilensis, named BtNR. This enzyme has previously been demonstrated to have the capability to fully convert nitro aromatic and heterocyclic compounds to their respective primary amines. In this study, we determined its biochemical, kinetic and structural properties, including its apparent melting temperature (Tm) of 59 °C, broad pH activity range (from pH 3 to 10) and a notably low redox potential (-236 ± 1 mV) in comparison to other well-known NRs. We also determined its steady-state and pre-steady-state kinetic parameters, which are consistent with other NRs. Additionally, we elucidated the crystal structure of BtNR, which resembles the well-characterized Escherichia coli oxygen-insensitive NAD(P)H nitroreductase (NfsB), and investigated the substrate binding in its active site through docking and molecular dynamics studies with four nitro aromatic substrates. Guided by these structural analyses, we probed the functional roles of active site residues by site-directed mutagenesis. Our findings provide valuable insights into the biochemical and structural properties of BtNR, as well as its potential applications in biotechnology.
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Affiliation(s)
- Sara Russo
- Molecular Enzymology Group, University of Groningen, The Netherlands
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | | | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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32
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024; 9:1713-1724. [PMID: 38806669 PMCID: PMC11222145 DOI: 10.1038/s41564-024-01707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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33
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Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S. The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. Nat Chem Biol 2024; 20:877-884. [PMID: 38172604 PMCID: PMC11253071 DOI: 10.1038/s41589-023-01521-0] [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: 04/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1.
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Affiliation(s)
- João P L Coelho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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Bazgir A, Agha Gholizadeh M, Kahani SM, Tavasoli AR, Garshasbi M. Identification of a Novel Homozygous GLS Gene Variant Associated with Developmental and Epileptic Encephalopathy (DEE) Type 71. Neurogenetics 2024; 25:225-232. [PMID: 38622440 DOI: 10.1007/s10048-024-00753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Developmental and epileptic encephalopathy (DEEs) (OMIM#618,328) is characterized by seizures, hypotonia, and brain abnormalities, often arising from mutations in genes crucial for brain function. Among these genes, GLS stands out due to its vital role in the central nervous system (CNS), with homozygous variants potentially causing DEE type 71. Using Whole Exome Sequencing (WES) on a patient exhibiting symptoms of epileptic encephalopathy, we identified a novel homozygous variant, NM_014905.5:c.1849G > T; p.(Asp617Tyr), in the GLS gene. The 5-year-old patient, born to consanguineous parents, presented with developmental delay, encephalopathy, frequent seizures, and hypotonia. Sanger sequencing further validated the GLS gene variant in both the patient and his family. Furthermore, our bioinformatics analysis indicated that this missense variant could lead to alteration of splicing, resulting in the activation of a cryptic donor site and potentially causing loss of protein function. Our finding highlights the pathogenic significance of the GLS gene, particularly in the context of brain disorders, specifically DEE71.
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Affiliation(s)
- Afsaneh Bazgir
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Seyyed Mohammad Kahani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Ali Reza Tavasoli
- Division of Pediatric Neurology, Myelin Disorders Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Neurology Division, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Department of Medical Genetics, DeNA Laboratory, Tehran, Iran.
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O'Neil PT, Swint‐Kruse L, Fenton AW. Rheostatic contributions to protein stability can obscure a position's functional role. Protein Sci 2024; 33:e5075. [PMID: 38895978 PMCID: PMC11187868 DOI: 10.1002/pro.5075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Rheostat positions, which can be substituted with various amino acids to tune protein function across a range of outcomes, are a developing area for advancing personalized medicine and bioengineering. Current methods cannot accurately predict which proteins contain rheostat positions or their substitution outcomes. To compare the prevalence of rheostat positions in homologs, we previously investigated their occurrence in two pyruvate kinase (PYK) isozymes. Human liver PYK contained numerous rheostat positions that tuned the apparent affinity for the substrate phosphoenolpyruvate (Kapp-PEP) across a wide range. In contrast, no functional rheostat positions were identified in Zymomonas mobilis PYK (ZmPYK). Further, the set of ZmPYK substitutions included an unusually large number that lacked measurable activity. We hypothesized that the inactive substitution variants had reduced protein stability, precluding detection of Kapp-PEP tuning. Using modified buffers, robust enzymatic activity was obtained for 19 previously-inactive ZmPYK substitution variants at three positions. Surprisingly, both previously-inactive and previously-active substitution variants all had Kapp-PEP values close to wild-type. Thus, none of the three positions were functional rheostat positions, and, unlike human liver PYK, ZmPYK's Kapp-PEP remained poorly tunable by single substitutions. To directly assess effects on stability, we performed thermal denaturation experiments for all ZmPYK substitution variants. Many diminished stability, two enhanced stability, and the three positions showed different thermal sensitivity to substitution, with one position acting as a "stability rheostat." The differences between the two PYK homologs raises interesting questions about the underlying mechanism(s) that permit functional tuning by single substitutions in some proteins but not in others.
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Affiliation(s)
- Pierce T. O'Neil
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansasUSA
| | - Liskin Swint‐Kruse
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansasUSA
| | - Aron W. Fenton
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansasUSA
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Mächtel R, Dobert J, Hehr U, Weiss A, Kettwig M, Laugwitz L, Groeschel S, Schmidt M, Arnold P, Regensburger M, Zunke F. Late-onset Krabbe disease presenting as spastic paraplegia - implications of GCase and CTSB/D. Ann Clin Transl Neurol 2024; 11:1715-1731. [PMID: 38837642 PMCID: PMC11251474 DOI: 10.1002/acn3.52078] [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: 10/18/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 06/07/2024] Open
Abstract
OBJECTIVE Krabbe disease (KD) is a multisystem neurodegenerative disorder with severe disability and premature death, mostly with an infancy/childhood onset. In rare cases of late-onset phenotypes, symptoms are often milder and difficult to diagnose. We here present a translational approach combining diagnostic and biochemical analyses of a male patient with a progressive gait disorder starting at the age of 44 years, with a final diagnosis of late-onset KD (LOKD). METHODS Additionally to cerebral MRI, protein structural analyses of the β-galactocerebrosidase protein (GALC) were performed. Moreover, expression, lysosomal localization, and activities of β-glucocerebrosidase (GCase), cathepsin B (CTSB), and cathepsin D (CTSD) were analyzed in leukocytes, fibroblasts, and lysosomes of fibroblasts. RESULTS Exome sequencing revealed biallelic likely pathogenic variants: GALC exons 11-17: 33 kb deletion; exon 4: missense variant (c.334A>G, p.Thr112Ala). We detected a reduced GALC activity in leukocytes and fibroblasts. While histological KD phenotypes were absent in fibroblasts, they showed a significantly decreased activities of GCase, CTSB, and CTSD in lysosomal fractions, while expression levels were unaffected. INTERPRETATION The presented LOKD case underlines the age-dependent appearance of a mildly pathogenic GALC variant and its interplay with other lysosomal proteins. As GALC malfunction results in reduced ceramide levels, we assume this to be causative for the here described decrease in CTSB and CTSD activity, potentially leading to diminished GCase activity. Hence, we emphasize the importance of a functional interplay between the lysosomal enzymes GALC, CTSB, CTSD, and GCase, as well as between their substrates, and propose their conjoined contribution in KD pathology.
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Affiliation(s)
- Rebecca Mächtel
- Department of Molecular NeurologyUniversity Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Jan‐Philipp Dobert
- Department of Molecular NeurologyUniversity Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Ute Hehr
- Center for Human GeneticsRegensburgGermany
| | - Alexander Weiss
- Department of Molecular NeurologyUniversity Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Matthias Kettwig
- Department of Pediatrics and Pediatric NeurologyUniversity Medical Center Göttingen, Georg August University GöttingenGöttingenGermany
| | - Lucia Laugwitz
- Department of Pediatric NeurologyUniversity Children's Hospital TübingenTübingenGermany
| | - Samuel Groeschel
- Department of Pediatric NeurologyUniversity Children's Hospital TübingenTübingenGermany
| | | | - Philipp Arnold
- Institute of Functional and Clinical AnatomyFAUErlangenGermany
| | - Martin Regensburger
- Department of Molecular NeurologyUniversity Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Department of Stem Cell BiologyFAUErlangenGermany
- Deutsches Zentrum Immuntherapie (DZI)University Hospital ErlangenErlangenGermany
| | - Friederike Zunke
- Department of Molecular NeurologyUniversity Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
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Girish A, Sutar S, Murthy TPK, Premanand SA, Garg V, Patil L, Shreyas S, Shukla R, Yadav AK, Singh TR. Comprehensive bioinformatics analysis of structural and functional consequences of deleterious missense mutations in the human QDPR gene. J Biomol Struct Dyn 2024; 42:5485-5501. [PMID: 37382215 DOI: 10.1080/07391102.2023.2226740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
Quinonoid dihydropteridine reductase (QDPR) is an enzyme that regulates tetrahydrobiopterin (BH4), a cofactor for enzymes involved in neurotransmitter synthesis and blood pressure regulation. Reduced QDPR activity can cause dihydrobiopterin (BH2) accumulation and BH4 depletion, leading to impaired neurotransmitter synthesis, oxidative stress, and increased risk of Parkinson's disease. A total of 10,236 SNPs were identified in the QDPR gene, with 217 being missense SNPs. Over 18 different sequence-based and structure-based tools were employed to assess the protein's biological activity, with several computational tools identifying deleterious SNPs. Additionally, the article provides detailed information about the QDPR gene and protein structure and conservation analysis. The results showed that 10 mutations were harmful and linked to brain and central nervous system disorders, and were predicted to be oncogenic by Dr. Cancer and CScape. Following conservation analysis, the HOPE server was used to analyse the effect of six selected mutations (L14P, V15G, G23S, V54G, M107K, G151S) on the protein structure. Overall, the study provides insights into the biological and functional impact of nsSNPs on QDPR activity and the potential induced pathogenicity and oncogenicity. In the future, research can be conducted to systematically evaluate QDPR gene variation through clinical studies, investigate mutation prevalence across different geographical regions, and validate computational results with conclusive experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aishwarya Girish
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | - Samruddhi Sutar
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | - T P Krishna Murthy
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | | | - Vrinda Garg
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | - Lavan Patil
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | - S Shreyas
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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Pérez-Ortín JE, Jordán-Pla A, Zhang Y, Moreno-García J, Bassot C, Barba-Aliaga M, de Campos-Mata L, Choder M, Díez J, Piazza I, Pelechano V, García-Martínez J. Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay. Yeast 2024; 41:458-472. [PMID: 38874348 DOI: 10.1002/yea.3968] [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: 07/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as "cotranslational mRNA decay." The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' → 3' decay alterations that characterize xrn1Δ cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jorge Moreno-García
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Claudio Bassot
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Leire de Campos-Mata
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mordechai Choder
- Department of Molecular Microbiology, Technion-Israel Institute of Technology, Rappaport Faculty of Medicine, Haifa, Israel
| | - Juana Díez
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
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Nila NN, Mahmud Z, Paul A, Rahman T, Hossain Howlader MZ, Hosen MI. Investigating the structural and functional consequences of germline single nucleotide polymorphisms located in the genes of the alternative lengthening of telomere (ALT) pathway. Heliyon 2024; 10:e33110. [PMID: 39021990 PMCID: PMC11253002 DOI: 10.1016/j.heliyon.2024.e33110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
Background The Alternative Lengthening of Telomeres (ALT) pathway represents a non-canonical mechanism of telomere maintenance that operates independently of the conventional telomerase activity. The three biologically significant proteins, designated as SMARCAL1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1), DAXX (Death domain-associated protein 6) and ATRX (alpha-thalassemia/mental retardation, X-linked) are associated with ALT in certain cancer types. The purpose of this study was to identify the most high-risk nsSNPs (non-synonymous Single Nucleotide Polymorphisms) within these three genes and assess their impacts on the structure and function of the proteins they encode. Methods The reported genetic polymorphisms of SMARCAL1, DAXX and ATRX genes were retrieved from the Ensembl database. Later, various computational tools like PROVEAN, PolyPhen2, SNPs and GO, SNAP2, Predict-SNP, Panther and PMut were used to predict the most deleterious nsSNPs. MutPred was used to understand the underlying molecular reasons of those nsSNPs being deleterious, followed by prediction of Post Translational Modification Sites (PTMs) using ModPred. I-Mutant and MUpro were used to predict the effect of SNP on energy stability. Later, 3D clustering analysis was done using Mutation 3D server. Moreover, ConSurf was utilized to identify the conservation scores of wild-type amino acids. Additionally, the NCBI conserved domain search tool was employed to pinpoint conserved domains within these three proteins. Project-Hope helped for biophysical validation, followed by prediction of these genes' interaction and function by using GeneMANIA. Result Analysis on SMARCAL1 protein revealed that among 665 nsSNPs, four were identified as the most deleterious: L578S, T581S, P582A, and P582S. Similarly, within the DAXX protein, among a pool of 480 nsSNPs, P284S, R230C, and R230S were found out to be the most deleterious variants. In case of ATRX protein, V178D, R246C, and V277G, from the total of 1009 nsSNPs, were predicted to be the most deleterious. All these nsSNPs were found to occur at residue positions that are 100 % conserved within protein domains and were predicted to be most damaging from both structural and functional perspectives and highly destabilizing to their corresponding proteins. Conclusion Computational investigation on the 3 proteins-SMARCAL1, DAXX and ATRX through different bioinformatics analysis tools concludes that the identified high risk nsSNPs of these proteins are pathogenic SNPs. These variants potentially exert functional and structural influences, thus making them valuable candidates for future genetic studies.
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Affiliation(s)
| | | | - Anik Paul
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Taibur Rahman
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Shi Y, Masic V, Mosaiab T, Rajaratman P, Hartley-Tassell L, Sorbello M, Goulart CC, Vasquez E, Mishra BP, Holt S, Gu W, Kobe B, Ve T. Structural characterization of macro domain-containing Thoeris antiphage defense systems. SCIENCE ADVANCES 2024; 10:eadn3310. [PMID: 38924412 PMCID: PMC11204291 DOI: 10.1126/sciadv.adn3310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD+) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Premraj Rajaratman
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Mitchell Sorbello
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cassia C. Goulart
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Biswa P. Mishra
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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Elghondakly A, Jermain MD, Winkler WC, Ferré-D'Amaré AR. Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG. Structure 2024:S0969-2126(24)00219-3. [PMID: 38959899 DOI: 10.1016/j.str.2024.06.001] [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: 12/15/2023] [Revised: 05/07/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
LoaP is a member of the universal NusG protein family. Previously, we reported that unlike other characterized homologs, LoaP binds RNA sequence-specifically, recognizing a stem-loop in the 5'-untranslated region of operons it regulates. To elucidate how this NusG homolog acquired this ability, we now determined the co-crystal structure of Thermoanaerobacter pseudethanolicus LoaP bound to its cognate 26-nucleotide dfn RNA element. Our structure reveals that the LoaP C-terminal KOW domain recognizes the helical portion of the RNA by docking into a broadened major groove, while a protruding β-hairpin of the N-terminal NusG-like domain binds the UNCG tetraloop capping the stem-loop. Major-groove RNA recognition is unusual and is made possible by conserved features of the dfn hairpin. Superposition with structures of other NusG proteins implies that LoaP can bind concurrently to the dfn RNA and the transcription elongation complex, suggesting a new level of co-transcriptional regulation by proteins of this conserved family.
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Affiliation(s)
- Amr Elghondakly
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madison D Jermain
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA; Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD, USA.
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Faridi R, Yousaf R, Inagaki S, Olszewski R, Gu S, Morell RJ, Wilson E, Xia Y, Qaiser TA, Rashid M, Fenollar-Ferrer C, Hoa M, Riazuddin S, Friedman TB. Deafness DFNB128 Associated with a Recessive Variant of Human MAP3K1 Recapitulates Hearing Loss of Map3k1-Deficient Mice. Genes (Basel) 2024; 15:845. [PMID: 39062623 PMCID: PMC11276321 DOI: 10.3390/genes15070845] [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: 05/21/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Deafness in vertebrates is associated with variants of hundreds of genes. Yet, many mutant genes causing rare forms of deafness remain to be discovered. A consanguineous Pakistani family segregating nonsyndromic deafness in two sibships were studied using microarrays and exome sequencing. A 1.2 Mb locus (DFNB128) on chromosome 5q11.2 encompassing six genes was identified. In one of the two sibships of this family, a novel homozygous recessive variant NM_005921.2:c.4460G>A p.(Arg1487His) in the kinase domain of MAP3K1 co-segregated with nonsyndromic deafness. There are two previously reported Map3k1-kinase-deficient mouse models that are associated with recessively inherited syndromic deafness. MAP3K1 phosphorylates serine and threonine and functions in a signaling pathway where pathogenic variants of HGF, MET, and GAB1 were previously reported to be associated with human deafness DFNB39, DFNB97, and DFNB26, respectively. Our single-cell transcriptome data of mouse cochlea mRNA show expression of Map3k1 and its signaling partners in several inner ear cell types suggesting a requirement of wild-type MAP3K1 for normal hearing. In contrast to dominant variants of MAP3K1 associated with Disorders of Sex Development 46,XY sex-reversal, our computational modeling of the recessive substitution p.(Arg1487His) predicts a subtle structural alteration in MAP3K1, consistent with the limited phenotype of nonsyndromic deafness.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Sayaka Inagaki
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Robert J. Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Elizabeth Wilson
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Ying Xia
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Tanveer Ahmed Qaiser
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Sector G-8/3, Ravi Road, Islamabad 44000, Pakistan;
| | - Muhammad Rashid
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Center, Jinnah Burn and Reconstructive Surgery Center, University of Health Sciences, Lahore 54550, Pakistan;
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
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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:S0092-8674(24)00649-4. [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] [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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Schoelmerich MC, Ly L, West-Roberts J, Shi LD, Shen C, Malvankar NS, Taib N, Gribaldo S, Woodcroft BJ, Schadt CW, Al-Shayeb B, Dai X, Mozsary C, Hickey S, He C, Beaulaurier J, Juul S, Sachdeva R, Banfield JF. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nat Commun 2024; 15:5414. [PMID: 38926353 PMCID: PMC11208441 DOI: 10.1038/s41467-024-49548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.
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Affiliation(s)
- Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Lynn Ly
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Ling-Dong Shi
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Deptartment of Molecular Biophysics and Biochemistry, Yale University, West Haven, CT, USA
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Deptartment of Molecular Biophysics and Biochemistry, Yale University, West Haven, CT, USA
| | - Najwa Taib
- Institut Pasteur, Université de Paris cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | - Scott Hickey
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Christine He
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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45
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Homma M, Wakabayashi T, Moriwaki Y, Shiotani N, Shigeta T, Isobe K, Okazawa A, Ohta D, Terada T, Shimizu K, Mizutani M, Takikawa H, Sugimoto Y. Insights into stereoselective ring formation in canonical strigolactone: Identification of a dirigent domain-containing enzyme catalyzing orobanchol synthesis. Proc Natl Acad Sci U S A 2024; 121:e2313683121. [PMID: 38905237 PMCID: PMC11214005 DOI: 10.1073/pnas.2313683121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/30/2024] [Indexed: 06/23/2024] Open
Abstract
Strigolactones (SLs) are plant apocarotenoids with diverse roles and structures. Canonical SLs, widespread and characterized by structural variations in their tricyclic lactone (ABC-ring), are classified into two types based on C-ring configurations. The steric C-ring configuration emerges during the BC-ring closure, downstream of the biosynthetic intermediate, carlactonoic acid (CLA). Most plants produce either type of canonical SLs stereoselectively, e.g., tomato (Solanum lycopersicum) yields orobanchol with an α-oriented C-ring. The mechanisms driving SL structural diversification are partially understood, with limited insight into functional implications. Furthermore, the exact molecular mechanism for the stereoselective BC-ring closure reaction is yet to be known. We identified an enzyme, the stereoselective BC-ring-forming factor (SRF), from the dirigent protein (DIR) family, specifically the DIR-f subfamily, whose biochemical function had not been characterized, making it a key enzyme in stereoselective canonical SL biosynthesis with the α-oriented C-ring. We first confirm the precise catalytic function of the tomato cytochrome P450 SlCYP722C, previously shown to be involved in orobanchol biosynthesis [T. Wakabayashi et al., Sci. Adv. 5, eaax9067 (2019)], to convert CLA to 18-oxocarlactonoic acid. We then show that SRF catalyzes the stereoselective BC-ring closure reaction of 18-oxocarlactonoic acid, forming orobanchol. Our methodology combines experimental and computational techniques, including SRF structure prediction and conducting molecular dynamics simulations, suggesting a catalytic mechanism based on the conrotatory 4π-electrocyclic reaction for the stereoselective BC-ring formation in orobanchol. This study sheds light on the molecular basis of how plants produce SLs with specific stereochemistry in a controlled manner.
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Affiliation(s)
- Masato Homma
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Takatoshi Wakabayashi
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Nanami Shiotani
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Takumi Shigeta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Kazuki Isobe
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
| | - Atsushi Okazawa
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Daisaku Ohta
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Masaharu Mizutani
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Yukihiro Sugimoto
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
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46
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Madhana Priya N, Sidharth Kumar N, Udhaya Kumar S, Mohanraj G, Magesh R, Zayed H, Vasudevan K, C GPD. Exploring the effect of disease causing mutations in metal binding sites of human ARSA in metachromatic leukodystrophy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:203-221. [PMID: 38960474 DOI: 10.1016/bs.apcsb.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The arylsulfatase A (ARSA) gene is observed to be deficient in patients with metachromatic leukodystrophy (MLD), a type of lysosomal storage disease. MLD is a severe neurodegenerative disorder characterized by an autosomal recessive inheritance pattern. This study aimed to map the most deleterious mutations at the metal binding sites of ARSA and the amino acids in proximity to the mutated positions. We utilized an array of computational tools, including PredictSNP, MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and ConSurf, to identify the most detrimental mutations potentially implicated in MLD collected from UniProt, ClinVar, and HGMD. Two mutations, D29N and D30H, as being extremely deleterious based on assessments of pathogenicity, conservation, biophysical characteristics, and stability analysis. The D29 and D30 are located at the metal-interacting regions of ARSA and found to undergo post-translational modification, specifically phosphorylation. Henceforth, the in-depth effect of metal binding upon mutation was examined using molecular dynamics simulations (MDS) before and after phosphorylation. The MDS results exhibited high deviation for the D29N and D30H mutations in comparison to the native, and the same was confirmed by significant residue fluctuation and reduced compactness. These structural alterations suggest that such mutations may influence protein functionality, offering potential avenues for personalized therapeutic and providing a basis for potential mutation-specific treatments for severe MLD patients.
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Affiliation(s)
- N Madhana Priya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, Tamil Nadu, India
| | - N Sidharth Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India; Department of Medicine, Division Endocrinology, Diabetes and Metabolism, Baylor College of Medicine, Houston, TX, United States
| | - G Mohanraj
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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Watanabe N, Savchenko A. Molecular insights into the initiation step of the Rcs signaling pathway. Structure 2024:S0969-2126(24)00221-1. [PMID: 38964336 DOI: 10.1016/j.str.2024.06.003] [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: 12/07/2023] [Revised: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
The Rcs pathway is repressed by the inner membrane protein IgaA under non-stressed conditions. This repression is hypothesized to be relieved by the binding of the outer membrane-anchored RcsF to IgaA. However, the precise mechanism by which RcsF binding triggers the signaling remains unclear. Here, we present the 1.8 Å resolution crystal structure capturing the interaction between IgaA and RcsF. Our comparative structural analysis, examining both the bound and unbound states of the periplasmic domain of IgaA (IgaAp), highlights rotational flexibility within IgaAp. Conversely, the conformation of RcsF remains unchanged upon binding. Our in vivo and in vitro studies do not support the model of a stable complex involving RcsF, IgaAp, and RcsDp. Instead, we demonstrate that the elements beyond IgaAp play a role in the interaction between IgaA and RcsD. These findings collectively allow us to propose a potential mechanism for the signaling across the inner membrane through IgaA.
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Affiliation(s)
- Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA.
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48
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Seneviratne S, Shi G, Szabo-Hever A, Zhang Z, Peters Haugrud AR, Running KLD, Singh G, Nandety RS, Fiedler JD, McClean PE, Xu SS, Friesen TL, Faris JD. Evolution, diversity, and function of the disease susceptibility gene Snn1 in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38923651 DOI: 10.1111/tpj.16879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/29/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a disease of durum and common wheat initiated by the recognition of pathogen-produced necrotrophic effectors (NEs) by specific wheat genes. The wheat gene Snn1 was previously cloned, and it encodes a wall-associated kinase that directly interacts with the NE SnTox1 leading to programmed cell death and ultimately the development of SNB. Here, sequence analysis of Snn1 from 114 accessions including diploid, tetraploid, and hexaploid wheat species revealed that some wheat lines possess two copies of Snn1 (designated Snn1-B1 and Snn1-B2) approximately 120 kb apart. Snn1-B2 evolved relatively recently as a paralog of Snn1-B1, and both genes have undergone diversifying selection. Three point mutations associated with the formation of the first SnTox1-sensitive Snn1-B1 allele from a primitive wild wheat were identified. Four subsequent and independent SNPs, three in Snn1-B1 and one in Snn1-B2, converted the sensitive alleles to insensitive forms. Protein modeling indicated these four mutations could abolish Snn1-SnTox1 compatibility either through destabilization of the Snn1 protein or direct disruption of the protein-protein interaction. A high-throughput marker was developed for the absent allele of Snn1, and it was 100% accurate at predicting SnTox1-insensitive lines in both durum and spring wheat. Results of this study increase our understanding of the evolution, diversity, and function of Snn1-B1 and Snn1-B2 genes and will be useful for marker-assisted elimination of these genes for better host resistance.
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Affiliation(s)
- Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Agnes Szabo-Hever
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Amanda R Peters Haugrud
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Katherine L D Running
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Raja Sekhar Nandety
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Jason D Fiedler
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Steven S Xu
- USDA-ARS Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, 94710, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
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Hirata E, Sakata KT, Dearden GI, Noor F, Menon I, Chiduza GN, Menon AK. Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587922. [PMID: 38617304 PMCID: PMC11014557 DOI: 10.1101/2024.04.03.587922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The oligosaccharide needed for protein N-glycosylation is assembled on a lipid carrier via a multi-step pathway. Synthesis is initiated on the cytoplasmic face of the endoplasmic reticulum (ER) and completed on the luminal side after transbilayer translocation of a heptasaccharide lipid intermediate. More than 30 Congenital Disorders of Glycosylation (CDGs) are associated with this pathway, including RFT1-CDG which results from defects in the membrane protein Rft1. Rft1 is essential for the viability of yeast and mammalian cells and was proposed as the transporter needed to flip the heptasaccharide lipid intermediate across the ER membrane. However, other studies indicated that Rft1 is not required for heptasaccharide lipid flipping in microsomes or unilamellar vesicles reconstituted with ER membrane proteins, nor is it required for the viability of at least one eukaryote. It is therefore not known what essential role Rft1 plays in N-glycosylation. Here, we present a molecular characterization of human Rft1, using yeast cells as a reporter system. We show that it is a multi-spanning membrane protein located in the ER, with its N and C-termini facing the cytoplasm. It is not N-glycosylated. The majority of RFT1-CDG mutations map to highly conserved regions of the protein. We identify key residues that are important for Rft1's ability to support N-glycosylation and cell viability. Our results provide a necessary platform for future work on this enigmatic protein.
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Affiliation(s)
- Eri Hirata
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ken-taro Sakata
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Grace I. Dearden
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Faria Noor
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - George N. Chiduza
- Structure and Function of Biological Membranes - Chemistry Department, Université Libre de Bruxelles - Campus Plaine, 1050 Brussels, Belgium
| | - Anant K. Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
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Villamor-Payà M, Sanchiz-Calvo M, Smak J, Pais L, Sud M, Shankavaram U, Lovgren AK, Austin-Tse C, Ganesh VS, Gay M, Vilaseca M, Arauz-Garofalo G, Palenzuela L, VanNoy G, O’Donnell-Luria A, Stracker TH. De novo TLK1 and MDM1 mutations in a patient with a neurodevelopmental disorder and immunodeficiency. iScience 2024; 27:109984. [PMID: 38868186 PMCID: PMC11166698 DOI: 10.1016/j.isci.2024.109984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/TLK2) regulate DNA replication, repair and chromatin maintenance. TLK2 variants underlie the neurodevelopmental disorder (NDD) 'Intellectual Disability, Autosomal Dominant 57' (MRD57), characterized by intellectual disability and microcephaly. Several TLK1 variants have been reported in NDDs but their functional significance is unknown. A male patient presenting with ID, seizures, global developmental delay, hypothyroidism, and primary immunodeficiency was determined to have a heterozygous TLK1 variant (c.1435C>G, p.Q479E), as well as a mutation in MDM1 (c.1197dupT, p.K400∗). Cells expressing TLK1 p.Q479E exhibited reduced cytokine responses and elevated DNA damage, but not increased radiation sensitivity or DNA repair defects. The TLK1 p.Q479E variant impaired kinase activity but not proximal protein interactions. Our study provides the first functional characterization of NDD-associated TLK1 variants and suggests that, such as TLK2, TLK1 variants may impact development in multiple tissues and should be considered in the diagnosis of rare NDDs.
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Affiliation(s)
- Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - María Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Jordann Smak
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Lynn Pais
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Malika Sud
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Uma Shankavaram
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Alysia Kern Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay S. Ganesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Lluís Palenzuela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Grace VanNoy
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O’Donnell-Luria
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
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