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Liang Y, Lv D, Liu K, Yang L, Shu H, Wen L, Lv C, Sun Q, Yin J, Liu H, Xu J, Liu Z, Ding N. MicroProteinDB: A database to provide knowledge on sequences, structures and function of ncRNA-derived microproteins. Comput Biol Med 2024; 177:108660. [PMID: 38820774 DOI: 10.1016/j.compbiomed.2024.108660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Omics-based technologies have revolutionized our comprehension of microproteins encoded by ncRNAs, revealing their abundant presence and pivotal roles within complex functional landscapes. Here, we developed MicroProteinDB (http://bio-bigdata.hrbmu.edu.cn/MicroProteinDB), which offers and visualizes the extensive knowledge to aid retrieval and analysis of computationally predicted and experimentally validated microproteins originating from various ncRNA types. Employing prediction algorithms grounded in diverse deep learning approaches, MicroProteinDB comprehensively documents the fundamental physicochemical properties, secondary and tertiary structures, interactions with functional proteins, family domains, and inter-species conservation of microproteins. With five major analytical modules, it will serve as a valuable knowledge for investigating ncRNA-derived microproteins.
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Affiliation(s)
- Yinan Liang
- The First Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Kefan Liu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150081, China
| | - Liting Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Huan Shu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Luan Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chongwen Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qisen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hui Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Zhigang Liu
- Affiliated Foshan Maternity&Child Healthcare Hospital, Southern Medical University, Guangzhou, 510000, China.
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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2
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Fulton JE, McCarron AM, Lund AR, Drobik-Czwarno W, Mullen A, Wolc A, Szadkowska J, Schmidt CJ, Taylor RL. The RHCE gene encodes the chicken blood system I. Genet Sel Evol 2024; 56:47. [PMID: 38898419 PMCID: PMC11188259 DOI: 10.1186/s12711-024-00911-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND There are 13 known chicken blood systems, which were originally detected by agglutination of red blood cells by specific alloantisera. The genomic region or specific gene responsible has been identified for four of these systems (A, B, D and E). We determined the identity of the gene responsible for the chicken blood system I, using DNA from multiple birds with known chicken I blood system serology, 600K and 54K single nucleotide polymorphism (SNP) data, and lowpass sequence information. RESULTS The gene responsible for the chicken I blood system was identified as RHCE, which is also one of the genes responsible for the highly polymorphic human Rh blood group locus, for which maternal/fetal antigenic differences can result in fetal hemolytic anemia with fetal mortality. We identified 17 unique RHCE haplotypes in the chicken, with six haplotypes corresponding to known I system serological alleles. We also detected deletions in the RHCE gene that encompass more than 6000 bp and that are predicted to remove its last seven exons. CONCLUSIONS RHCE is the gene responsible for the chicken I blood system. This is the fifth chicken blood system for which the responsible gene and gene variants are known. With rapid DNA-based testing now available, the impact of I blood system variation on response against disease, general immune function, and animal production can be investigated in greater detail.
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Affiliation(s)
- Janet E Fulton
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA.
| | - Amy M McCarron
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Ashlee R Lund
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Wioleta Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Abigail Mullen
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Anna Wolc
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Joanna Szadkowska
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Carl J Schmidt
- Department of Animal and Food Science, University of Delaware, Newark, DE, USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
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3
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Yancoskie MN, Khaleghi R, Gururajan A, Raghunathan A, Gupta A, Diethelm S, Maritz C, Sturla SJ, Krishnan M, Naegeli H. ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction. Nucleic Acids Res 2024:gkae517. [PMID: 38884271 DOI: 10.1093/nar/gkae517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C->T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Anirvinya Gururajan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aadarsh Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aryan Gupta
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich 8092, Switzerland
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
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Sosa-Fajardo A, Díaz-Muñoz C, Van der Veken D, Pradal I, Verce M, Weckx S, Leroy F. Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites. BMC Genomics 2024; 25:575. [PMID: 38849728 PMCID: PMC11161930 DOI: 10.1186/s12864-024-10490-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated. RESULTS The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms. CONCLUSIONS Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.
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Affiliation(s)
- Ana Sosa-Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - David Van der Veken
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Inés Pradal
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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5
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Frentzel H, Kraemer M, Kelner-Burgos Y, Uelze L, Bodi D. Cereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains. Int J Food Microbiol 2024; 417:110694. [PMID: 38614024 DOI: 10.1016/j.ijfoodmicro.2024.110694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
The highly potent toxin cereulide is a frequent cause of foodborne intoxications. This extremely resistant toxin is produced by Bacillus cereus group strains carrying the plasmid encoded cesHPTABCD gene cluster. It is known that the capacities to produce cereulide vary greatly between different strains but the genetic background of these variations is not clear. In this study, cereulide production capacities were associated with genetic characteristics. For this, cereulide levels in cultures of 31 strains were determined after incubation in tryptic soy broth for 24 h at 24 °C, 30 °C and 37 °C. Whole genome sequencing based data were used for an in-depth characterization of gene sequences related to cereulide production. The taxonomy, population structure and phylogenetic relationships of the strains were evaluated based on average nucleotide identity, multi-locus sequence typing (MLST), core genome MLST and single nucleotide polymorphism analyses. Despite a limited strain number, the approach of a genome wide association study (GWAS) was tested to link genetic variation with cereulide quantities. Our study confirms strain-dependent differences in cereulide production. For most strains, these differences were not explainable by sequence variations in the cesHPTABCD gene cluster or the regulatory genes abrB, spo0A, codY and pagRBc. Likewise, the population structure and phylogeny of the tested strains did not comprehensively reflect the cereulide production capacities. GWAS yielded first hints for associated proteins, while their possible effect on cereulide synthesis remains to be further investigated.
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Affiliation(s)
- Hendrik Frentzel
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Marco Kraemer
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Ylanna Kelner-Burgos
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Laura Uelze
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Sequencing and Genotyping Service Unit, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Dorina Bodi
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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6
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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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7
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Aerts T, Boonen A, Geenen L, Stulens A, Masin L, Pancho A, Francis A, Pepermans E, Baggerman G, Van Roy F, Wöhr M, Seuntjens E. Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons. Open Biol 2024; 14:240113. [PMID: 38889770 DOI: 10.1098/rsob.240113] [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: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviours. The cell adhesion molecule protocadherin10 (PCDH10) is linked to ASD in humans. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and is important for neural circuit formation. In mice, strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex (BLC) of the amygdala was observed at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the BLC at perinatal stages and vocalization-related genes were enriched in Pcdh10-expressing neurons in adult mice. An epitope-tagged Pcdh10-HAV5 mouse line revealed endogenous interactions of PCDH10 with synaptic proteins in the young postnatal telencephalon. Nuanced socio-affective communication changes in call emission rates, acoustic features and call subtype clustering were primarily observed in heterozygous pups of a conditional knockout (cKO) with selective deletion of Pcdh10 in Gsh2-lineage interneurons. These changes were less prominent in heterozygous ubiquitous Pcdh10 KO pups, suggesting that altered anxiety levels associated with Gsh2-lineage interneuron functioning might drive the behavioural effects. Together, loss of Pcdh10 specifically in interneurons contributes to behavioural alterations in socio-affective communication with relevance to ASD.
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Affiliation(s)
- Tania Aerts
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anneleen Boonen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Lieve Geenen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anne Stulens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Luca Masin
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Neural Circuit Development and Regeneration, KU Leuven , Leuven 3000, Belgium
| | - Anna Pancho
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- Developmental Genetics, Department of Biomedicine, University of Basel , Basel 4058, Switzerland
| | - Annick Francis
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Elise Pepermans
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
- Department of Computer Science, University of Antwerp , Antwerp, Belgium
| | - Frans Van Roy
- Faculty of Science, Department of Biomedical Molecular Biology; Inflammation Research Center, VIB, Ghent University , Cancer Research Institute Ghent (CRIG) 9000, Belgium
| | - Markus Wöhr
- Faculty of Psychology and Educational Sciences, Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg , Marburg 35032, Germany
- Center for Mind, Brain and Behavior, Philipps-University of Marburg , Marburg 35032, Germany
| | - Eve Seuntjens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- KU Leuven, Leuven Institute for Single Cell Omics , Leuven 3000, Belgium
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8
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Hao T, Song Z, Zhang M, Zhang L. Signaling Transduction Pathways and G-Protein-Coupled Receptors in Different Stages of the Embryonic Diapause Termination Process in Artemia. Curr Issues Mol Biol 2024; 46:3676-3693. [PMID: 38666959 PMCID: PMC11049050 DOI: 10.3390/cimb46040229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Artemia is a widely distributed small aquatic crustacean, renowned for its ability to enter a state of embryonic diapause. The embryonic diapause termination (EDT) is closely linked to environmental cues, but the precise underlying mechanisms remain elusive. In this study, ATAC-seq and RNA-seq sequencing techniques were employed to explore the gene expression profiles in Artemia cysts 30 min after EDT. These profiles were compared with those during diapause and 5 h after EDT. The regulatory mechanisms governing the EDT process were analyzed through Gene Ontology (GO) enrichment analysis of differentially expressed genes. Furthermore, the active G-protein-coupled receptors (GPCRs) were identified through structural analysis. The results unveiled that the signaling transduction during EDT primarily hinges on GPCRs and the cell surface receptor signaling pathway, but distinct genes are involved across different stages. Hormone-mediated signaling pathways and the tachykinin receptor signaling pathway exhibited heightened activity in the '0-30 min' group, whereas the Wnt signaling pathway manifested its function solely in the '30 min-5 h' group. These results imply a complete divergence in the mechanisms of signal regulation during these two stages. Moreover, through structural analysis, five GPCRs operating at different stages of EDT were identified. These findings provide valuable insights into the signal regulation mechanisms governing Artemia diapause.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (Z.S.); (M.Z.); (L.Z.)
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Chen Y, Sewsurn S, Amand S, Kunz C, Pietrancosta N, Calabro K, Buisson D, Mann S. Metabolic Investigation and Auxiliary Enzyme Modelization of the Pyrrocidine Pathway Allow Rationalization of Paracyclophane-Decahydrofluorene Formation. ACS Chem Biol 2024; 19:886-895. [PMID: 38576157 DOI: 10.1021/acschembio.3c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Fungal paracyclophane-decahydrofluorene-containing natural products are complex polycyclic metabolites derived from similar hybrid PKS-NRPS pathways. Herein we studied the biosynthesis of pyrrocidines, one representative of this family, by gene inactivation in the producer Sarocladium zeae coupled to thorough metabolic analysis and molecular modeling of key enzymes. We characterized nine pyrrocidines and analogues as well as in mutants a variety of accumulating metabolites with new structures including rare cis-decalin, cytochalasan, and fused 6/15/5 macrocycles. This diversity highlights the extraordinary plasticity of the pyrrocidine biosynthetic gene cluster. From accumulating metabolites, we delineated the scenario of pyrrocidine biosynthesis. The ring A of the decahydrofluorene is installed by PrcB, a membrane-bound cyclizing isomerase, on a PKS-NRPS-derived pyrrolidone precursor. Docking experiments in PrcB allowed us to characterize the active site suggesting a mechanism triggered by arginine-mediated deprotonation at the terminal methyl of the substrate. Next, two integral membrane proteins, PrcD and PrcE, each predicted as a four-helix bundle, perform hydroxylation of the pyrrolidone ring and paracyclophane formation, respectively. Modelization of PrcE highlights a topological homology with vitamin K oxido-reductase and the presence of a disulfide bond. Our results suggest a previously unsuspected coupling mechanism via a transient loss of aromaticity of tyrosine residue to form the strained paracyclophane motif. Finally, the lipocalin-like protein PrcX drives the exo-cycloaddition yielding ring B and C of the decahydrofluorene to afford pyrrocidine A, which is transformed by a reductase PrcI to form pyrrocidine B. These insights will greatly facilitate the microbial production of pyrrocidine analogues by synthetic biology.
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Affiliation(s)
- Youwei Chen
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Steffi Sewsurn
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Séverine Amand
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Caroline Kunz
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927, F-75005 Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, PSL University, CNRS, F-75005 Paris, France
- Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, INSERM, CNRS, F-75005 Paris, France
| | - Kevin Calabro
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Didier Buisson
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Stéphane Mann
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
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10
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Moser C, Guschtschin-Schmidt N, Silber M, Flum J, Muhle-Goll C. Substrate Selection Criteria in Regulated Intramembrane Proteolysis. ACS Chem Neurosci 2024; 15:1321-1334. [PMID: 38525994 DOI: 10.1021/acschemneuro.4c00068] [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] [Indexed: 03/26/2024] Open
Abstract
Alzheimer's disease is the most common form of dementia encountered in an aging population. Characteristic amyloid deposits of Aβ peptides in the brain are generated through cleavage of amyloid precursor protein (APP) by γ-secretase, an intramembrane protease. Cryo-EM structures of substrate γ-secretase complexes revealed details of the process, but how substrates are recognized and enter the catalytic site is still largely ignored. γ-Secretase cleaves a diverse range of substrate sequences without a common consensus sequence, but strikingly, single point mutations within the transmembrane domain (TMD) of specific substrates may greatly affect cleavage efficiencies. Previously, conformational flexibility was hypothesized to be the main criterion for substrate selection. Here we review the 3D structure and dynamics of several γ-secretase substrate TMDs and compare them with mutants shown to affect the cleavage efficiency. In addition, we present structural and dynamic data on ITGB1, a known nonsubstrate of γ-secretase. A comparison of biophysical details between these TMDs and changes generated by introducing crucial mutations allowed us to unravel common principles that differ between substrates and nonsubstrates. We identified three motifs in the investigated substrates: a highly flexible transmembrane domain, a destabilization of the cleavage region, and a basic signature at the end of the transmembrane helix. None of these appears to be exclusive. While conformational flexibility on its own may increase cleavage efficiency in well-known substrates like APP or Notch1, our data suggest that the three motifs seem to be rather variably combined to determine whether a transmembrane helix is efficiently recognized as a γ-secretase substrate.
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Affiliation(s)
- Celine Moser
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nadja Guschtschin-Schmidt
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Mara Silber
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Julia Flum
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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11
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Döring M, Brux M, Paszkowski-Rogacz M, Guillem-Gloria PM, Buchholz F, Pisabarro MT, Theis M. Nucleolar protein TAAP1/ C22orf46 confers pro-survival signaling in non-small cell lung cancer. Life Sci Alliance 2024; 7:e202302257. [PMID: 38228372 DOI: 10.26508/lsa.202302257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
Tumor cells subvert immune surveillance or lytic stress by harnessing inhibitory signals. Hence, bispecific antibodies have been developed to direct CTLs to the tumor site and foster immune-dependent cytotoxicity. Although applied with success, T cell-based immunotherapies are not universally effective partially because of the expression of pro-survival factors by tumor cells protecting them from apoptosis. Here, we report a CRISPR/Cas9 screen in human non-small cell lung cancer cells designed to identify genes that confer tumors with the ability to evade the cytotoxic effects of CD8+ T lymphocytes engaged by bispecific antibodies. We show that the gene C22orf46 facilitates pro-survival signals and that tumor cells devoid of C22orf46 expression exhibit increased susceptibility to T cell-induced apoptosis and stress by genotoxic agents. Although annotated as a non-coding gene, we demonstrate that C22orf46 encodes a nucleolar protein, hereafter referred to as "Tumor Apoptosis Associated Protein 1," up-regulated in lung cancer, which displays remote homologies to the BH domain containing Bcl-2 family of apoptosis regulators. Collectively, the findings establish TAAP1/C22orf46 as a pro-survival oncogene with implications to therapy.
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Affiliation(s)
- Marietta Döring
- https://ror.org/042aqky30 National Center for Tumor Diseases/University Cancer Center (NCT/UCC): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Melanie Brux
- https://ror.org/042aqky30 National Center for Tumor Diseases/University Cancer Center (NCT/UCC): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- https://ror.org/00e7dfm13 Medical Systems Biologyhttps://ror.org/042aqky30 , Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- https://ror.org/00e7dfm13 Medical Systems Biologyhttps://ror.org/042aqky30 , Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Pedro M Guillem-Gloria
- https://ror.org/042aqky30 Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Dresden, Germany
| | - Frank Buchholz
- https://ror.org/042aqky30 National Center for Tumor Diseases/University Cancer Center (NCT/UCC): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- https://ror.org/00e7dfm13 Medical Systems Biologyhttps://ror.org/042aqky30 , Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
| | - M Teresa Pisabarro
- https://ror.org/042aqky30 Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Dresden, Germany
| | - Mirko Theis
- https://ror.org/042aqky30 National Center for Tumor Diseases/University Cancer Center (NCT/UCC): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- https://ror.org/00e7dfm13 Medical Systems Biologyhttps://ror.org/042aqky30 , Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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12
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Song FV, Su J, Huang S, Zhang N, Li K, Ni M, Liao M. DeepSS2GO: protein function prediction from secondary structure. Brief Bioinform 2024; 25:bbae196. [PMID: 38701416 PMCID: PMC11066904 DOI: 10.1093/bib/bbae196] [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: 01/24/2024] [Revised: 03/31/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation have been extensively researched. Although obtaining a protein in three-dimensional structure through experimental or computational methods enhances the accuracy of function prediction, the sheer volume of proteins sequenced by high-throughput technologies presents a significant challenge. To address this issue, we introduce a deep neural network model DeepSS2GO (Secondary Structure to Gene Ontology). It is a predictor incorporating secondary structure features along with primary sequence and homology information. The algorithm expertly combines the speed of sequence-based information with the accuracy of structure-based features while streamlining the redundant data in primary sequences and bypassing the time-consuming challenges of tertiary structure analysis. The results show that the prediction performance surpasses state-of-the-art algorithms. It has the ability to predict key functions by effectively utilizing secondary structure information, rather than broadly predicting general Gene Ontology terms. Additionally, DeepSS2GO predicts five times faster than advanced algorithms, making it highly applicable to massive sequencing data. The source code and trained models are available at https://github.com/orca233/DeepSS2GO.
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Affiliation(s)
- Fu V Song
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China
| | - Jiaqi Su
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China
| | - Sixing Huang
- Gemini Data Japan, Kitaku Oujikamiya 1-11-11, 115-0043, Tokyo, Japan
| | - Neng Zhang
- Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Kaiyue Li
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China
| | - Ming Ni
- MGI Tech, Beishan Industrial Zone, 518083, Shenzhen, China
| | - Maofu Liao
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China
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13
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Grierson ERP, Thrimawithana AH, van Klink JW, Lewis DH, Carvajal I, Shiller J, Miller P, Deroles SC, Clearwater MJ, Davies KM, Chagné D, Schwinn KE. A phosphatase gene is linked to nectar dihydroxyacetone accumulation in mānuka (Leptospermum scoparium). THE NEW PHYTOLOGIST 2024. [PMID: 38532557 DOI: 10.1111/nph.19714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Floral nectar composition beyond common sugars shows great diversity but contributing genetic factors are generally unknown. Mānuka (Leptospermum scoparium) is renowned for the antimicrobial compound methylglyoxal in its derived honey, which originates from the precursor, dihydroxyacetone (DHA), accumulating in the nectar. Although this nectar trait is highly variable, genetic contribution to the trait is unclear. Therefore, we investigated key gene(s) and genomic regions underpinning this trait. We used RNAseq analysis to identify nectary-associated genes differentially expressed between high and low nectar DHA genotypes. We also used a mānuka high-density linkage map and quantitative trait loci (QTL) mapping population, supported by an improved genome assembly, to reveal genetic regions associated with nectar DHA content. Expression and QTL analyses both pointed to the involvement of a phosphatase gene, LsSgpp2. The expression pattern of LsSgpp2 correlated with nectar DHA accumulation, and it co-located with a QTL on chromosome 4. The identification of three QTLs, some of the first reported for a plant nectar trait, indicates polygenic control of DHA content. We have established plant genetics as a key influence on DHA accumulation. The data suggest the hypothesis of LsSGPP2 releasing DHA from DHA-phosphate and variability in LsSgpp2 gene expression contributing to the trait variability.
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Affiliation(s)
- Ella R P Grierson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | | | - John W van Klink
- PFR, Chemistry Department, University of Otago, Dunedin, 9016, New Zealand
| | - David H Lewis
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | | | - Jason Shiller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | - Poppy Miller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | | | - Michael J Clearwater
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
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14
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Wenzel M, Grüner E, Strodthoff N. Insights into the inner workings of transformer models for protein function prediction. Bioinformatics 2024; 40:btae031. [PMID: 38244570 PMCID: PMC10950482 DOI: 10.1093/bioinformatics/btae031] [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: 06/09/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
MOTIVATION We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent representations inside of transformer models, which were finetuned to Gene Ontology term and Enzyme Commission number prediction, can be inspected too. RESULTS The approach enabled us to identify amino acids in the sequences that the transformers pay particular attention to, and to show that these relevant sequence parts reflect expectations from biology and chemistry, both in the embedding layer and inside of the model, where we identified transformer heads with a statistically significant correspondence of attribution maps with ground truth sequence annotations (e.g. transmembrane regions, active sites) across many proteins. AVAILABILITY AND IMPLEMENTATION Source code can be accessed at https://github.com/markuswenzel/xai-proteins.
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Affiliation(s)
- Markus Wenzel
- Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI, Einsteinufer 37, 10587 Berlin, Germany
| | - Erik Grüner
- Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI, Einsteinufer 37, 10587 Berlin, Germany
| | - Nils Strodthoff
- School VI - Medicine and Health Services, Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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15
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Hasan ME, Samir A, Khalil MM, Shafaa MW. Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus. J Genet Eng Biotechnol 2024; 22:100336. [PMID: 38494248 PMCID: PMC10860876 DOI: 10.1016/j.jgeb.2023.100336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure-function/evolution links to both previously known and recently discovered protein structures.
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Affiliation(s)
- Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
| | - Aya Samir
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Magdy M Khalil
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt; School of Biotechnology, Badr University in Cairo, Egypt
| | - Medhat W Shafaa
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
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16
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [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: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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17
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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. Nat Commun 2024; 15:1577. [PMID: 38383452 PMCID: PMC10881494 DOI: 10.1038/s41467-024-45601-8] [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: 07/14/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%. We find that the immune system develops antibodies to human gut bacteria-infecting viruses, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - William R Morgenlander
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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18
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Deedwania A, Karmakar S, Kumar V, Shefrin S, Sundar D, Srivastava P. Construction and characterization of a temperature-sensitive pRC4 replicon for Rhodococcus and Gordonia. Gene 2024; 896:147990. [PMID: 37977321 DOI: 10.1016/j.gene.2023.147990] [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: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Temperature-sensitive plasmids are useful for genome engineering and several synthetic biology applications. There are only limited reports on temperature-sensitive plasmids for Rhodococcus and none for Gordonia. Here, we report the construction of a temperature-sensitive pRC4 replicon that is functional in Rhodococcus and Gordonia. The amino acid residues were predicted for the temperature-sensitive phenotype in the pRC4 replicon using in silico methods and molecular simulation of the DNA-binding replication protein with the origin of replication. The amino acid residues were mutated, and the temperature-sensitive phenotype was validated in Gordonia sp. IITR100. Similar results were also observed in Rhodococcus erythropolis, suggesting that the temperature-sensitive phenotype was exhibited across genera.
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Affiliation(s)
- Agrima Deedwania
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Shreyoshi Karmakar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Seyad Shefrin
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
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19
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Tillis SB, Ossiboff RJ, Wellehan JFX. Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination. Viruses 2024; 16:310. [PMID: 38400085 PMCID: PMC10892116 DOI: 10.3390/v16020310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.
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Affiliation(s)
- Steven B. Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (R.J.O.); (J.F.X.W.J.)
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20
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Andorf CM, Haley OC, Hayford RK, Portwood JL, Harding S, Sen S, Cannon EK, Gardiner JM, Kim HS, Woodhouse MR. PanEffect: a pan-genome visualization tool for variant effects in maize. Bioinformatics 2024; 40:btae073. [PMID: 38337024 PMCID: PMC10881103 DOI: 10.1093/bioinformatics/btae073] [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: 12/16/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024] Open
Abstract
SUMMARY Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 50 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to potential functional consequences. In addition, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. AVAILABILITY AND IMPLEMENTATION The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).
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Affiliation(s)
- Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
- Department of Computer Science, Iowa State University, Ames, IA 50011, United States
| | - Olivia C Haley
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Rita K Hayford
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Stephen Harding
- USDA-ARS, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, United States
| | - Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, United States
| | - Ethalinda K Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Jack M Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Hye-Seon Kim
- USDA-ARS, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, United States
| | - Margaret R Woodhouse
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
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21
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Cuy-Chaparro L, Barney-Borrero D, Arévalo-Pinzón G, Reyes C, Moreno-Pérez DA, Patarroyo MA. Babesia bovis RON2 binds to bovine erythrocytes through a highly conserved epitope. Vet Parasitol 2024; 326:110081. [PMID: 38113611 DOI: 10.1016/j.vetpar.2023.110081] [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: 06/28/2023] [Revised: 09/25/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
B. bovis invasion of bovine erythrocytes requires tight junction formation involving AMA-1/RON2 complex interaction. RON2 has been considered a vaccine candidate since antibodies targeting the protein can inhibit parasite invasion of target cells; however, the mechanism controlling B. bovis RON2 interaction with red blood cells is not yet fully understood. This study was thus aimed at identifying B. bovis RON2 protein regions associated with interaction with bovine erythrocytes. Natural selection analysis of the ron2 gene identified predominantly negative selection signals in the C-terminal region. Interestingly, protein-cell and competition assays highlighted the RON2-C region's role in peptide 42918-mediated erythrocyte binding, probably to a sialoglycoprotein receptor. This peptide (1218SFIMVKPPALHCVLKPVETL1237) lies within an intrinsically disordered region of the RON2 secondary structure flanked by two helical residues. The study provides, for the first time, valuable insights into RON2's role in interaction with its target cells. Future studies are required for studying the peptide's potential as an anti-B. bovis vaccine component.
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Affiliation(s)
- Laura Cuy-Chaparro
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia [FIDIC], Carrera 50#26-20, Bogotá DC 111321, Colombia; PhD Programme in Biotechnology, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá DC 111321, Colombia.
| | - Danny Barney-Borrero
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia [FIDIC], Carrera 50#26-20, Bogotá DC 111321, Colombia.
| | - Gabriela Arévalo-Pinzón
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia [FIDIC], Carrera 50#26-20, Bogotá DC 111321, Colombia.
| | - César Reyes
- Structure Analysis Department, Fundación Instituto de Inmunología de Colombia [FIDIC], Carrera 50#26-20, Bogotá DC 111321, Colombia.
| | - Darwin Andrés Moreno-Pérez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales [U.D.C.A.], Calle 222#55-37, Bogotá DC 111166, Colombia.
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia [FIDIC], Carrera 50#26-20, Bogotá DC 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá DC 111321, Colombia.
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22
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Dhanushkumar T, M E S, Selvam PK, Rambabu M, Dasegowda KR, Vasudevan K, George Priya Doss C. Advancements and hurdles in the development of a vaccine for triple-negative breast cancer: A comprehensive review of multi-omics and immunomics strategies. Life Sci 2024; 337:122360. [PMID: 38135117 DOI: 10.1016/j.lfs.2023.122360] [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: 10/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Triple-Negative Breast Cancer (TNBC) presents a significant challenge in oncology due to its aggressive behavior and limited therapeutic options. This review explores the potential of immunotherapy, particularly vaccine-based approaches, in addressing TNBC. It delves into the role of immunoinformatics in creating effective vaccines against TNBC. The review first underscores the distinct attributes of TNBC and the importance of tumor antigens in vaccine development. It then elaborates on antigen detection techniques such as exome sequencing, HLA typing, and RNA sequencing, which are instrumental in identifying TNBC-specific antigens and selecting vaccine candidates. The discussion then shifts to the in-silico vaccine development process, encompassing antigen selection, epitope prediction, and rational vaccine design. This process merges computational simulations with immunological insights. The role of Artificial Intelligence (AI) in expediting the prediction of antigens and epitopes is also emphasized. The review concludes by encapsulating how Immunoinformatics can augment the design of TNBC vaccines, integrating tumor antigens, advanced detection methods, in-silico strategies, and AI-driven insights to advance TNBC immunotherapy. This could potentially pave the way for more targeted and efficacious treatments.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Majji Rambabu
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - K R Dasegowda
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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23
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Ling SSM, Lilyanna S, Ng JYX, Chong JPC, Lin Q, Yong XE, Lim TK, Lin Q, Richards AM, Liew OW. Multiple circulating forms of neprilysin detected with novel epitope-directed monoclonal antibodies. Cell Mol Life Sci 2024; 81:42. [PMID: 38217709 PMCID: PMC10787894 DOI: 10.1007/s00018-023-05083-1] [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: 07/12/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/15/2024]
Abstract
Neprilysin (NEP) is an emerging biomarker for various diseases including heart failure (HF). However, major inter-assay inconsistency in the reported concentrations of circulating NEP and uncertainty with respect to its correlations with type and severity of disease are in part attributed to poorly characterized antibodies supplied in commercial ELISA kits. Validated antibodies with well-defined binding footprints are critical for understanding the biological and clinical context of NEP immunoassay data. To achieve this, we applied in silico epitope prediction and rational peptide selection to generate monoclonal antibodies (mAbs) against spatially distant sites on NEP. One of the selected epitopes contained published N-linked glycosylation sites at N285 and N294. The best antibody pair, mAb 17E11 and 31E1 (glycosylation-sensitive), were characterized by surface plasmon resonance, isotyping, epitope mapping, and western blotting. A validated two-site sandwich NEP ELISA with a limit of detection of 2.15 pg/ml and working range of 13.1-8000 pg/ml was developed with these mAbs. Western analysis using a validated commercial polyclonal antibody (PE pAb) and our mAbs revealed that non-HF and HF plasma NEP circulates as a heterogenous mix of moieties that possibly reflect proteolytic processing, post-translational modifications and homo-dimerization. Both our mAbs detected a ~ 33 kDa NEP fragment which was not apparent with PE pAb, as well as a common ~ 57-60 kDa moiety. These antibodies exhibit different affinities for the various NEP targets. Immunoassay results are dependent on NEP epitopes variably detected by the antibody pairs used, explaining the current discordant NEP measurements derived from different ELISA kits.
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Affiliation(s)
- Samantha S M Ling
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore
| | - Shera Lilyanna
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore
| | - Jessica Y X Ng
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore
| | - Jenny P C Chong
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Xin Ee Yong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - A Mark Richards
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore
- Christchurch Heart Institute, University of Otago, Otago, New Zealand
| | - Oi Wah Liew
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore, 117599, Singapore.
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24
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Basu S, Zhao B, Biró B, Faraggi E, Gsponer J, Hu G, Kloczkowski A, Malhis N, Mirdita M, Söding J, Steinegger M, Wang D, Wang K, Xu D, Zhang J, Kurgan L. DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Res 2024; 52:D426-D433. [PMID: 37933852 PMCID: PMC10767971 DOI: 10.1093/nar/gkad985] [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: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
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Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Bi Zhao
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Bálint Biró
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
- Department of Animal Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Eshel Faraggi
- Physics Department, Indiana University, Indianapolis, IN, USA
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gang Hu
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, P.R. China
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, USA
| | - Nawar Malhis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Milot Mirdita
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Johannes Söding
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Republic of Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Duolin Wang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Kui Wang
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, P.R. China
| | - Dong Xu
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang, P.R. China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
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25
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Draizen EJ, Readey J, Mura C, Bourne PE. Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinformatics 2024; 25:11. [PMID: 38177985 PMCID: PMC10768222 DOI: 10.1186/s12859-023-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence, structure, function, dynamics and evolution. As with any advance that rests upon statistical learning approaches, the recent progress in biomolecular sciences is enabled by the availability of vast volumes of sufficiently-variable data. To be useful, such data must be well-structured, machine-readable, intelligible and manipulable. These and related requirements pose challenges that become especially acute at the computational scales typical in ML. Furthermore, in structural bioinformatics such data generally relate to protein three-dimensional (3D) structures, which are inherently more complex than sequence-based data. A significant and recurring challenge concerns the creation of large, high-quality, openly-accessible datasets that can be used for specific training and benchmarking tasks in ML pipelines for predictive modeling projects, along with reproducible splits for training and testing. RESULTS Here, we report 'Prop3D', a platform that allows for the creation, sharing and extensible reuse of libraries of protein domains, featurized with biophysical and evolutionary properties that can range from detailed, atomically-resolved physicochemical quantities (e.g., electrostatics) to coarser, residue-level features (e.g., phylogenetic conservation). As a community resource, we also supply a 'Prop3D-20sf' protein dataset, obtained by applying our approach to CATH . We have developed and deployed the Prop3D framework, both in the cloud and on local HPC resources, to systematically and reproducibly create comprehensive datasets via the Highly Scalable Data Service ( HSDS ). Our datasets are freely accessible via a public HSDS instance, or they can be used with accompanying Python wrappers for popular ML frameworks. CONCLUSION Prop3D and its associated Prop3D-20sf dataset can be of broad utility in at least three ways. Firstly, the Prop3D workflow code can be customized and deployed on various cloud-based compute platforms, with scalability achieved largely by saving the results to distributed HDF5 files via HSDS . Secondly, the linked Prop3D-20sf dataset provides a hand-crafted, already-featurized dataset of protein domains for 20 highly-populated CATH families; importantly, provision of this pre-computed resource can aid the more efficient development (and reproducible deployment) of ML pipelines. Thirdly, Prop3D-20sf's construction explicitly takes into account (in creating datasets and data-splits) the enigma of 'data leakage', stemming from the evolutionary relationships between proteins.
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Affiliation(s)
- Eli J Draizen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
- School of Data Science, University of Virginia, Charlottesville, VA, USA.
| | | | - Cameron Mura
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
- School of Data Science, University of Virginia, Charlottesville, VA, USA.
| | - Philip E Bourne
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- School of Data Science, University of Virginia, Charlottesville, VA, USA
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26
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Reed CJ, Denise R, Hourihan J, Babor J, Jaroch M, Martinelli M, Hutinet G, de Crécy-Lagard V. Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.03.539116. [PMID: 37205517 PMCID: PMC10187207 DOI: 10.1101/2023.05.03.539116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that said family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3), we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most published information on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighborhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.
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Affiliation(s)
- Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Rémi Denise
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Jacob Hourihan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Jill Babor
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Maria Martinelli
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, 370 Lancaster Avenue, Haverford, PA 19041, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, Haverford College, 370 Lancaster Avenue, Haverford, PA 19041, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
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27
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Kaur R, Kumar P, Kumar A. Insights on the nuclear shuttling of H2A-H2B histone chaperones. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-13. [PMID: 38133493 DOI: 10.1080/15257770.2023.2296616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
All cellular processes that involve the unwinding of DNA also lead to the systematic shuttling of histones. Histone shuttling across the nuclear membrane is facilitated by a class of proteins known as - histone chaperones. Histone chaperones are classified based on their binding to H3/H4 histones or H2A/H2B histones. During the shuttling process, two types of signals - NLS and NES are recognized by the nuclear transport proteins. However, this is the nuclear transport protein and the mechanism of signal recognition by the protein is still unknown. Thus, in this piece of work, the NLS and NES signals are predicted on important H2A/H2B binding histone chaperones. In addition, cellular localization and potential DNA binding regions of histone chaperones are predicted. Mapping of predicted regions on the histone chaperone's structure suggested that the critical binding regions mainly lie on the disordered region of the histone chaperones. NLS and NES are present in the N- and C-terminal of the histone chaperones. Most histone chaperones contain bipartiate NLS signals. This article sheds light on the crucial aspect that in addition of being directly engaged in nucleosome synthesis and disassembly in vivo, histone chaperone also performs various specific roles via histone binding activity.
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Affiliation(s)
- Rasanpreet Kaur
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University Mathura, Bharthia, Uttar Pradesh, India
| | - Pramod Kumar
- ICMR-National Institute of Cancer Prevention and Research, Indian Council for Medical Research (ICMR-NICPR), Noida, Uttar Pradesh, India
| | - Anuj Kumar
- ICMR-National Institute of Cancer Prevention and Research, Indian Council for Medical Research (ICMR-NICPR), Noida, Uttar Pradesh, India
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28
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Domínguez-Díaz C, Avila-Arrezola KE, Rodríguez JA, del-Toro-Arreola S, Delgado-Rizo V, Fafutis-Morris M. Recombinant p40 Protein Promotes Expression of Occludin in HaCaT Keratinocytes: A Brief Communication. Microorganisms 2023; 11:2913. [PMID: 38138057 PMCID: PMC10745755 DOI: 10.3390/microorganisms11122913] [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: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The ability of epithelial barriers to perform as the first defense line against external damage derives from tight junctions, protein complexes that block microorganisms through the paracellular space. Indeed, disturbances of barrier permeability caused by bacterial metabolites and other inflammatory stimuli are the consequence of changes in protein expression in these complexes. Postbiotics, molecules derived from bacteria with beneficial effects on the host, improve barrier function through the activation of survival pathways in epithelial cells. Lacticaseibacillus rhamnosus GG secretes the muramidase p40, which protects intestinal barriers through an EGFR-dependent pathway. In this work, we cloned, expressed, and purified the recombinant p40 protein from L. rhamnosus GR-1 to evaluate its effect on cell viability, cell cytotoxicity, TEER, and protein levels of tight junctions, as well as EGFR activation via Western blot on HaCaT keratinocytes subjected to LPS. We found a novel mutation at residue 368 that does not change the structure of p40. Our protein also reduces the LPS-induced increase in cell cytotoxicity when it is added prior to this stimulus. Furthermore, although LPS did not cause changes in barrier function, p40 increased TEER and occludin expression in HaCaT, but unlike previous work with p40 from LGG, we found that recombinant p40 did not activate EGFR. This suggests that recombinant p40 enhances epithelial barrier function through distinct signaling pathways.
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Affiliation(s)
- Carolina Domínguez-Díaz
- Doctoral Program in Biomedical Sciences, Physiology Department, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Immunology and Dermatology Research Center (CIINDE), Zapopan 45190, Mexico;
| | | | - Jorge A. Rodríguez
- Department of Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan 45019, Mexico;
| | - Susana del-Toro-Arreola
- Physiology Department, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (S.d.-T.-A.); (V.D.-R.)
| | - Vidal Delgado-Rizo
- Physiology Department, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (S.d.-T.-A.); (V.D.-R.)
| | - Mary Fafutis-Morris
- Immunology and Dermatology Research Center (CIINDE), Zapopan 45190, Mexico;
- Physiology Department, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (S.d.-T.-A.); (V.D.-R.)
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29
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Zhang MF, Xie WL, Chen C, Li CX, Xu JH. Computational redesign of taxane-10β-hydroxylase for de novo biosynthesis of a key paclitaxel intermediate. Appl Microbiol Biotechnol 2023; 107:7105-7117. [PMID: 37736790 DOI: 10.1007/s00253-023-12784-x] [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: 06/22/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Paclitaxel (Taxol®) is the most popular anticancer diterpenoid predominantly present in Taxus. The core skeleton of paclitaxel is highly modified, but researches on the cytochrome P450s involved in post-modification process remain exceedingly limited. Herein, the taxane-10β-hydroxylase (T10βH) from Taxus cuspidata, which is the third post-modification enzyme that catalyzes the conversion of taxadiene-5α-yl-acetate (T5OAc) to taxadiene-5α-yl-acetoxy-10β-ol (T10OH), was investigated in Escherichia coli by combining computation-assisted protein engineering and metabolic engineering. The variant of T10βH, M3 (I75F/L226K/S345V), exhibited a remarkable 9.5-fold increase in protein expression, accompanied by respective 1.3-fold and 2.1-fold improvements in turnover frequency (TOF) and total turnover number (TTN). Upon integration into the engineered strain, the variant M3 resulted in a substantial enhancement in T10OH production from 0.97 to 2.23 mg/L. Ultimately, the titer of T10OH reached 3.89 mg/L by fed-batch culture in a 5-L bioreactor, representing the highest level reported so far for the microbial de novo synthesis of this key paclitaxel intermediate. This study can serve as a valuable reference for further investigation of other P450s associated with the artificial biosynthesis of paclitaxel and other terpenoids. KEY POINTS: • The T10βH from T. cuspidata was expressed and engineered in E. coli unprecedentedly. • The expression and activity of T10βH were improved through protein engineering. • De novo biosynthesis of T10OH was achieved in E. coli with a titer of 3.89 mg/L.
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Affiliation(s)
- Mei-Fang Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wen-Liang Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Cheng Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Zámocký M, Ferianc P. Discovering the deep evolutionary roots of serum amyloid A protein family. Int J Biol Macromol 2023; 252:126537. [PMID: 37634776 DOI: 10.1016/j.ijbiomac.2023.126537] [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: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family leading to yet unknown highly similar SAA-like sequences occurring in certain bacterial genomes is demonstrated in this contribution. Horizontal gene transfer event of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the reconstructed phylogenetic tree obtained with maximum likelihood and neighbor-joining methods, respectively. This detailed phylogeny based on totally 128 complete sequences comprised diverse serum amyloid A isoforms from various animal vertebrate and non-vertebrate phyla and also corresponding genes coding for highly similar proteins from animal gut bacteria. Typical largely conserved sequence motifs and a peculiar structural fold consisting mainly of four α-helices in a bundle within all reconstructed clades of the SAA protein family are discussed with respect to their supposed biological functions in various organisms that contain corresponding genes.
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Affiliation(s)
- Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Mlynská dolina, Ilkovičova 6, SK-84215 Bratislava, Slovakia.
| | - Peter Ferianc
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [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: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Berguido FJ, Chibssa TR, Loitsch A, Liu Y, Krstevski K, Djadjovski I, Tuppurainen E, Petrović T, Vidanović D, Caufour P, Settypalli TBK, Grünwald-Gruber C, Grabherr R, Diallo A, Cattoli G, Lamien CE. Harnessing Attenuation-Related Mutations of Viral Genomes: Development of a Serological Assay to Differentiate between Capripoxvirus-Infected and -Vaccinated Animals. Viruses 2023; 15:2318. [PMID: 38140559 PMCID: PMC10747038 DOI: 10.3390/v15122318] [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: 10/20/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Sheeppox, goatpox, and lumpy skin disease caused by the sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV), respectively, are diseases that affect millions of ruminants and many low-income households in endemic countries, leading to great economic losses for the ruminant industry. The three viruses are members of the Capripoxvirus genus of the Poxviridae family. Live attenuated vaccines remain the only efficient means for controlling capripox diseases. However, serological tools have not been available to differentiate infected from vaccinated animals (DIVA), though crucial for proper disease surveillance, control, and eradication efforts. We analysed the sequences of variola virus B22R homologue gene for SPPV, GTPV, and LSDV and observed significant differences between field and vaccine strains in all three capripoxvirus species, resulting in the truncation and absence of the B22R protein in major vaccines within each of the viral species. We selected and expressed a protein fragment present in wildtype viruses but absent in selected vaccine strains of all three species, taking advantage of these alterations in the B22R gene. An indirect ELISA (iELISA) developed using this protein fragment was evaluated on well-characterized sera from vaccinated, naturally and experimentally infected, and negative cattle and sheep. The developed wildtype-specific capripox DIVA iELISA showed >99% sensitivity and specificity for serum collected from animals infected with the wildtype virus. To the best of our knowledge, this is the first wildtype-specific, DIVA-capable iELISA for poxvirus diseases exploiting changes in nucleotide sequence alterations in vaccine strains.
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Affiliation(s)
- Francisco J. Berguido
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | | | - Angelika Loitsch
- Austrian Agency for Health and Food Safety (AGES), Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Yang Liu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Kiril Krstevski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia
| | - Eeva Tuppurainen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Tamaš Petrović
- Scientific Veterinary Institute “Novi Sad”, 21000 Novi Sad, Serbia
| | - Dejan Vidanović
- Veterinary Specialized Institute Kraljevo, Zicka 34, 36103 Kraljevo, Serbia
| | - Philippe Caufour
- UMR ASTRE Cirad-Inrae, University of Montpellier (I-MUSE), 34398 Montpellier, France
| | - Tirumala Bharani K. Settypalli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Reingard Grabherr
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Adama Diallo
- Independent Researcher, Hahngasse, 24-26, 02/07, 1090 Vienna, Austria
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
| | - Charles Euloge Lamien
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
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Höpfner D, Cichy A, Pogenberg V, Krisp C, Mezouar S, Bach NC, Grotheer J, Zarza SM, Martinez E, Bonazzi M, Feige MJ, Sieber SA, Schlüter H, Itzen A. The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol 2023; 6:1124. [PMID: 37932372 PMCID: PMC10628234 DOI: 10.1038/s42003-023-05494-7] [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: 04/14/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular bacterial pathogen Coxiella burnetii evades the host response by secreting effector proteins that aid in establishing a replication-friendly niche. Bacterial filamentation induced by cyclic AMP (Fic) enzymes can act as effectors by covalently modifying target proteins with the posttranslational AMPylation by transferring adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to a hydroxyl-containing side chain. Here we identify the gene product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at serine 10 and serine 28. We show that CbFic2 acts as a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via a C-terminal helix-turn-helix domain. We propose that CbFic2 performs AMPylation in its monomeric state, switching to a deAMPylating dimer upon DNA binding. This study unveils reversible histone modification by a specific enzyme of a pathogenic bacterium.
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Affiliation(s)
- Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Adam Cichy
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Group of Proteinchemistry, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Soraya Mezouar
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Nina C Bach
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Jan Grotheer
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Sandra Madariaga Zarza
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Martinez
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matteo Bonazzi
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Stephan A Sieber
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
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Pan S, Erdmann M, Terrell J, Cabeen MT. A putative lipase affects Pseudomonas aeruginosa biofilm matrix production. mSphere 2023; 8:e0037423. [PMID: 37754547 PMCID: PMC10597414 DOI: 10.1128/msphere.00374-23] [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] [Received: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 09/28/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is widely known for infecting patients with underlying conditions. This species often survives antibiotic therapy by forming biofilms, in which the cells produce a protective extracellular matrix. P. aeruginosa also produces virulence factors that enhance its ability to cause disease. One signaling pathway that influences virulence is the nitrogen-related phosphotransferase system (Nitro-PTS), which consists of an initial phosphotransferase, PtsP, a phosphocarrier, PtsO, and a terminal phosphate receptor, PtsN. The physiological role of the Nitro-PTS in P. aeruginosa is poorly understood. However, PtsN, when deprived of its upstream phosphotransfer proteins, has an antagonistic effect on biofilm formation. We thus conducted a transposon mutagenesis screen in an unphosphorylated-PtsN (i.e., ∆ptsP) background to identify downstream proteins with unacknowledged roles in PtsN-mediated biofilm suppression. We found an unstudied gene, PA14_04030, whose disruption restored biofilm production. This gene encodes a predicted phospholipase with signature alpha/beta hydrolase folds and a lipase signature motif with an active-site Ser residue. Hence, we renamed the gene bipL, for biofilm-impacting phospholipase. Deletion of bipL in a ∆ptsP background increased biofilm formation, supporting the idea that BipL is responsible for reducing biofilm formation in strains with unphosphorylated PtsN. Moreover, substituting the putative catalytic Ser for Ala phenocopied bipL deletion, indicating that this residue is important for the biofilm-suppressive activity of BipL in vivo. As our preliminary data suggest that BipL is a lipase, we performed lipidomics to detect changes in the lipid profile due to bipL deletion and found changes in some lipid species. IMPORTANCE Biofilm formation by bacteria occurs when cells secrete an extracellular matrix that holds them together and shields them from environmental insults. Biofilms of bacterial opportunistic human pathogens such as Pseudomonas aeruginosa pose a substantial challenge to clinical antimicrobial therapy. Hence, a more complete knowledge about the bacterial factors that influence and regulate production of the biofilm matrix is one key to formulate more effective therapeutic strategies. In this study, we screen for factors that are important for reducing biofilm matrix production in certain genetic backgrounds. We unexpectedly found a gene encoding a putative lipase enzyme and showed that its predicted catalytic site is important for its ability to reduce biofilm formation. Our findings suggest that lipase enzymes have previously uncharacterized functions in biofilm matrix regulation.
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Affiliation(s)
- Somalisa Pan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mary Erdmann
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Julia Terrell
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Matthew T. Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Durán D, Vazquez-Arias D, Blanco-Romero E, Garrido-Sanz D, Redondo-Nieto M, Rivilla R, Martín M. An Orphan VrgG Auxiliary Module Related to the Type VI Secretion Systems from Pseudomonas ogarae F113 Mediates Bacterial Killing. Genes (Basel) 2023; 14:1979. [PMID: 38002922 PMCID: PMC10671463 DOI: 10.3390/genes14111979] [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: 09/28/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector-immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.
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Affiliation(s)
- David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - David Vazquez-Arias
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
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36
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Xiang X, Vilar Gomez AA, Blomberg SP, Yuan H, Degnan BM, Degnan SM. Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica. Front Neural Circuits 2023; 17:1250694. [PMID: 37841893 PMCID: PMC10570526 DOI: 10.3389/fncir.2023.1250694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.
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Affiliation(s)
| | | | | | | | | | - Sandie M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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37
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Hu X, Xu Y, Wang C, Liu Y, Zhang L, Zhang J, Wang W, Chen Q, Liu H. Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain. Proc Natl Acad Sci U S A 2023; 120:e2305603120. [PMID: 37722056 PMCID: PMC10523638 DOI: 10.1073/pnas.2305603120] [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: 04/12/2023] [Accepted: 08/14/2023] [Indexed: 09/20/2023] Open
Abstract
An increasing number of protein interaction domains and their targets are being found to be intrinsically disordered proteins (IDPs). The corresponding target recognition mechanisms are mostly elusive because of challenges in performing detailed structural analysis of highly dynamic IDP-IDP complexes. Here, we show that by combining recently developed computational approaches with experiments, the structure of the complex between the intrinsically disordered C-terminal domain (CTD) of protein 4.1G and its target IDP region in NuMA can be dissected at high resolution. First, we carry out systematic mutational scanning using dihydrofolate reductase-based protein complementarity analysis to identify essential interaction regions and key residues. The results are found to be highly consistent with an α/β-type complex structure predicted by AlphaFold2 (AF2). We then design mutants based on the predicted structure using a deep learning protein sequence design method. The solved crystal structure of one mutant presents the same core structure as predicted by AF2. Further computational prediction and experimental assessment indicate that the well-defined core structure is conserved across complexes of 4.1G CTD with other potential targets. Thus, we reveal that an intrinsically disordered protein interaction domain uses an α/β-type structure module formed through synergistic folding to recognize broad IDP targets. Moreover, we show that computational prediction and experiment can be jointly applied to segregate true IDP regions from the core structural domains of IDP-IDP complexes and to uncover the structure-dependent mechanisms of some otherwise elusive IDP-IDP interactions.
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Affiliation(s)
- Xiuhong Hu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Yang Xu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Chenchen Wang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Yufeng Liu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Lu Zhang
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Wenning Wang
- Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai200438, China
| | - Quan Chen
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Haiyan Liu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui230027, China
- School of Data Science, University of Science and Technology of China, Hefei, Anhui230027, China
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Mechkarska M, Cunning TS, Taggart MG, Ternan NG, Leprince J, Coquet L, Jouenne T, Tena-Garcés J, Calvete JJ, Conlon JM. Identification of an Antimicrobial Peptide from the Venom of the Trinidad Thick-Tailed Scorpion Tityus trinitatis with Potent Activity against ESKAPE Pathogens and Clostridioides difficile. Antibiotics (Basel) 2023; 12:1404. [PMID: 37760701 PMCID: PMC10525828 DOI: 10.3390/antibiotics12091404] [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: 08/07/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Envenomation by the Trinidad thick-tailed scorpion Tityus trinitatis may result in fatal myocarditis and there is a high incidence of acute pancreatitis among survivors. Peptidomic analysis (reversed-phase HPLC followed by MALDI-TOF mass spectrometry and automated Edman degradation) of T. trinitatis venom led to the isolation and characterization of three peptides with antimicrobial activity. Their primary structures were established asTtAP-1 (FLGSLFSIGSKLLPGVFKLFSRKKQ.NH2), TtAP-2 (IFGMIPGLIGGLISAFK.NH2) and TtAP-3 (FFSLIPSLIGGLVSAIK.NH2). In addition, potassium channel and sodium channel toxins, present in the venom in high abundance, were identified by CID-MS/MS sequence analysis. TtAP-1 was the most potent against a range of clinically relevant Gram-positive and Gram-negative aerobes and against the anaerobe Clostridioides difficile (MIC = 3.1-12.5 µg/mL). At a concentration of 1× MIC, TtAP-1 produced rapid cell death (<15 min against Acinetobacter baumannii and Staphylococcus aureus). The therapeutic potential of TtAP-1 as an anti-infective agent is limited by its high hemolytic activity (LC50 = 18 µg/mL against mouse erythrocytes) but the peptide constitutes a template for the design of analogs that maintain the high bactericidal activity against ESKAPE pathogens but are less toxic to human cells. It is suggested that the antimicrobial peptides in the scorpion venom facilitate the action of the neurotoxins by increasing the membrane permeability of cells from either prey or predator.
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Affiliation(s)
- Milena Mechkarska
- Department of Life Sciences, Faculty of Science and Technology, St. Augustine Campus, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Taylor S. Cunning
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK; (T.S.C.); (M.G.T.); (N.G.T.)
| | - Megan G. Taggart
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK; (T.S.C.); (M.G.T.); (N.G.T.)
| | - Nigel G. Ternan
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK; (T.S.C.); (M.G.T.); (N.G.T.)
| | - Jérôme Leprince
- Université Rouen Normandie, INSERM, NorDiC UMR 1239, HeRacLeS, US 51, PRIMACEN, F-76000 Rouen, France;
| | - Laurent Coquet
- Université Rouen Normandie, INSA Rouen Normandie, CNRS, PBS UMR 6270, HeRacLeS US 51 UAR 2026 PISSARO, F-76000 Rouen, France; (L.C.); (T.J.)
| | - Thierry Jouenne
- Université Rouen Normandie, INSA Rouen Normandie, CNRS, PBS UMR 6270, HeRacLeS US 51 UAR 2026 PISSARO, F-76000 Rouen, France; (L.C.); (T.J.)
| | - Jordi Tena-Garcés
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), 46010 Valencia, Spain; (J.T.-G.); (J.J.C.)
| | - Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), 46010 Valencia, Spain; (J.T.-G.); (J.J.C.)
| | - J. Michael Conlon
- Diabetes Research Centre, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK;
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Sänger CS, Cernakova M, Wietecha MS, Garau Paganella L, Labouesse C, Dudaryeva OY, Roubaty C, Stumpe M, Mazza E, Tibbitt MW, Dengjel J, Werner S. Serine protease 35 regulates the fibroblast matrisome in response to hyperosmotic stress. SCIENCE ADVANCES 2023; 9:eadh9219. [PMID: 37647410 PMCID: PMC10468140 DOI: 10.1126/sciadv.adh9219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Hyperosmotic stress occurs in several diseases, but its long-term effects are largely unknown. We used sorbitol-treated human fibroblasts in 3D culture to study the consequences of hyperosmotic stress in the skin. Sorbitol regulated many genes, which help cells cope with the stress condition. The most robustly regulated gene encodes serine protease 35 (PRSS35). Its regulation by hyperosmotic stress was dependent on the kinases p38 and JNK and the transcription factors NFAT5 and ATF2. We identified different collagens and collagen-associated proteins as putative PRSS35 binding partners. This is functionally important because PRSS35 affected the extracellular matrix proteome, which limited cell proliferation. The in vivo relevance of these findings is reflected by the coexpression of PRSS35 and its binding partners in human skin wounds, where hyperosmotic stress occurs as a consequence of excessive water loss. These results identify PRSS35 as a key regulator of the matrisome under hyperosmotic stress conditions.
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Affiliation(s)
- Catharina S. Sänger
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Martina Cernakova
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Mateusz S. Wietecha
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
- Department of Oral Biology, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Lorenza Garau Paganella
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland
- Institute for Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Céline Labouesse
- Institute for Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Oksana Y. Dudaryeva
- Institute for Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Carole Roubaty
- Faculty of Science and Medicine, Department of Biology, University of Fribourg, Ch. du Musée 10, 1700 Fribourg, Switzerland
| | - Michael Stumpe
- Faculty of Science and Medicine, Department of Biology, University of Fribourg, Ch. du Musée 10, 1700 Fribourg, Switzerland
| | - Edoardo Mazza
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland
| | - Mark W. Tibbitt
- Institute for Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Jörn Dengjel
- Faculty of Science and Medicine, Department of Biology, University of Fribourg, Ch. du Musée 10, 1700 Fribourg, Switzerland
| | - Sabine Werner
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
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40
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Tooze RS, Miller KA, Swagemakers SMA, Calpena E, McGowan SJ, Boute O, Collet C, Johnson D, Laffargue F, de Leeuw N, Morton JV, Noons P, Ockeloen CW, Phipps JM, Tan TY, Timberlake AT, Vanlerberghe C, Wall SA, Weber A, Wilson LC, Zackai EH, Mathijssen IMJ, Twigg SRF, Wilkie AOM. Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance. Genet Med 2023; 25:100883. [PMID: 37154149 DOI: 10.1016/j.gim.2023.100883] [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: 12/22/2022] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Studies have previously implicated PRRX1 in craniofacial development, including demonstration of murine Prrx1 expression in the preosteogenic cells of the cranial sutures. We investigated the role of heterozygous missense and loss-of-function (LoF) variants in PRRX1 associated with craniosynostosis. METHODS Trio-based genome, exome, or targeted sequencing were used to screen PRRX1 in patients with craniosynostosis; immunofluorescence analyses were used to assess nuclear localization of wild-type and mutant proteins. RESULTS Genome sequencing identified 2 of 9 sporadically affected individuals with syndromic/multisuture craniosynostosis, who were heterozygous for rare/undescribed variants in PRRX1. Exome or targeted sequencing of PRRX1 revealed a further 9 of 1449 patients with craniosynostosis harboring deletions or rare heterozygous variants within the homeodomain. By collaboration, 7 additional individuals (4 families) were identified with putatively pathogenic PRRX1 variants. Immunofluorescence analyses showed that missense variants within the PRRX1 homeodomain cause abnormal nuclear localization. Of patients with variants considered likely pathogenic, bicoronal or other multisuture synostosis was present in 11 of 17 cases (65%). Pathogenic variants were inherited from unaffected relatives in many instances, yielding a 12.5% penetrance estimate for craniosynostosis. CONCLUSION This work supports a key role for PRRX1 in cranial suture development and shows that haploinsufficiency of PRRX1 is a relatively frequent cause of craniosynostosis.
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Affiliation(s)
- Rebecca S Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Sigrid M A Swagemakers
- Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Odile Boute
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, Clinique de Génétique, Lille, France
| | - Corinne Collet
- Genetics Department, Robert Debré University Hospital, APHP, Paris, France
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Fanny Laffargue
- Clinical Genetics Service and Reference Centre for Rare Developmental Abnormalities and Intellectual Disabilities, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Peter Noons
- Department of Craniofacial Surgery, Birmingham Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie M Phipps
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, New York, NY
| | - Clemence Vanlerberghe
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, Clinique de Génétique, Lille, France
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Astrid Weber
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, United Kingdom
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Elaine H Zackai
- Clinical Genetics Center, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus Medical Centre, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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41
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Lagunas-Rangel FA. Bioinformatic analysis of SIRT7 sequence and structure. J Biomol Struct Dyn 2023; 41:8081-8091. [PMID: 36148822 DOI: 10.1080/07391102.2022.2126890] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/15/2022] [Indexed: 10/14/2022]
Abstract
Sirtuins are highly conserved proteins that perform very important functions in different cellular processes. Notably, SIRT7 is the least studied human sirtuin, but it is known to be involved in a wide variety of processes in both health and disease. In this way, SIRT7 activity-regulating molecules could be beneficial for the treatment of relevant diseases such as cardiovascular and bone diseases, where SIRT7 levels are reduced, or obesity and cancer, where they are increased. In this work, using bioinformatic methods, the sequence and structure of SIRT7 orthologs in a wide variety of organisms were analyzed. Thus, the catalytic domain was found to be quite conserved (83.23% identity) and key residues such as D118, Y119, R120, D170, H187, N189, C198, C225, C228, V273, G298, F239 and V237 were identified. Furthermore, a phylogenetic tree was constructed where SIRT7 orthologs from mammals, birds, reptiles, amphibians, fish, insects, and arachnids were found to cluster in different groups. Finally, predicted three-dimensional structures showed a classic structure of the central catalytic region of most sirtuins, while the flanking N- and C-terminal regions were unique to each phylogenetic group. All this helps to understand a little more how SIRT7 works and gives clues for the future design and development of small molecules that benefit human and animal health.Communicated by Ramaswamy H. Sarma.
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42
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Kramer S, Karolak NK, Odenwald J, Gabiatti B, Castañeda Londoño P, Zavřelová A, Freire E, Almeida K, Braune S, Moreira C, Eder A, Goos C, Field M, Carrington M, Holetz F, Górna M, Zoltner M. A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 2023; 51:7520-7540. [PMID: 37309887 PMCID: PMC10415143 DOI: 10.1093/nar/gkad497] [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: 12/05/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
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Affiliation(s)
| | - Natalia Katarzyna Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Bernardo Gabiatti
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | | | - Anna Zavřelová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | | | | | - Silke Braune
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Claudia Moreira
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Amelie Eder
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Fabiola Holetz
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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Kramer DA, Narvaez-Ortiz HY, Patel U, Shi R, Shen K, Nolen BJ, Roche J, Chen B. The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton. eLife 2023; 12:e88492. [PMID: 37555826 PMCID: PMC10411975 DOI: 10.7554/elife.88492] [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: 04/10/2023] [Accepted: 05/01/2023] [Indexed: 08/10/2023] Open
Abstract
Dendrite morphogenesis is essential for neural circuit formation, yet the molecular mechanisms underlying complex dendrite branching remain elusive. Previous studies on the highly branched Caenorhabditis elegans PVD sensory neuron identified a membrane co-receptor complex that links extracellular signals to intracellular actin remodeling machinery, promoting high-order dendrite branching. In this complex, the claudin-like transmembrane protein HPO-30 recruits the WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polymerize actin. We report here our biochemical and structural analysis of this interaction, revealing that the intracellular domain (ICD) of HPO-30 is intrinsically disordered and employs two distinct mechanisms to regulate the actin cytoskeleton. First, HPO-30 ICD binding to the WRC requires dimerization and involves the entire ICD sequence, rather than a short linear peptide motif. This interaction enhances WRC activation by the GTPase Rac1. Second, HPO-30 ICD directly binds to the sides and barbed end of actin filaments. Binding to the barbed end requires ICD dimerization and inhibits both actin polymerization and depolymerization, resembling the actin capping protein CapZ. These dual functions provide an intriguing model of how membrane proteins can integrate distinct mechanisms to fine-tune local actin dynamics.
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Affiliation(s)
- Daniel A Kramer
- Roy J Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Urval Patel
- Roy J Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Rebecca Shi
- Department of Biology, Stanford UniversityStanfordUnited States
- Neurosciences IDP, Stanford UniversityStanfordUnited States
| | - Kang Shen
- Department of Biology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Julien Roche
- Roy J Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Baoyu Chen
- Roy J Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
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Garbers TB, Enders M, Neumann P, Ficner R. Crystal structure of Prp16 in complex with ADP. Acta Crystallogr F Struct Biol Commun 2023; 79:200-207. [PMID: 37548918 PMCID: PMC10416764 DOI: 10.1107/s2053230x23005721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
DEAH-box helicases play a crucial role in pre-mRNA splicing as they are responsible for major rearrangements of the spliceosome and are involved in various quality-ensuring steps. Prp16 is the driving force during spliceosomal catalysis, remodeling the C state into the C* state. Here, the first crystal structure of Prp16 from Chaetomium thermophilum in complex with ADP is reported at 1.9 Å resolution. Comparison with the other spliceosomal DEAH-box helicases Prp2, Prp22 and Prp43 reveals an overall identical domain architecture. The β-hairpin, which is a structural element of the RecA2 domain, exhibits a unique position, punctuating its flexibility. Analysis of cryo-EM models of spliceosomal complexes containing Prp16 reveals that these models show Prp16 in its nucleotide-free state, rendering the model presented here the first structure of Prp16 in complex with a nucleotide.
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Affiliation(s)
- Tim Benedict Garbers
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Marieke Enders
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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45
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Oliveira RNS, de Aguiar SRMM, Pauleta SR. Coordination of the N-Terminal Heme in the Non-Classical Peroxidase from Escherichia coli. Molecules 2023; 28:4598. [PMID: 37375153 DOI: 10.3390/molecules28124598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/28/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The non-classical bacterial peroxidase from Escherichia coli, YhjA, is proposed to deal with peroxidative stress in the periplasm when the bacterium is exposed to anoxic environments, defending it from hydrogen peroxide and allowing it to thrive under those conditions. This enzyme has a predicted transmembrane helix and is proposed to receive electrons from the quinol pool in an electron transfer pathway involving two hemes (NT and E) to accomplish the reduction of hydrogen peroxide in the periplasm at the third heme (P). Compared with classical bacterial peroxidases, these enzymes have an additional N-terminal domain binding the NT heme. In the absence of a structure of this protein, several residues (M82, M125 and H134) were mutated to identify the axial ligand of the NT heme. Spectroscopic data demonstrate differences only between the YhjA and YhjA M125A variant. In the YhjA M125A variant, the NT heme is high-spin with a lower reduction potential than in the wild-type. Thermostability was studied by circular dichroism, demonstrating that YhjA M125A is thermodynamically more unstable than YhjA, with a lower TM (43 °C vs. 50 °C). These data also corroborate the structural model of this enzyme. The axial ligand of the NT heme was validated to be M125, and mutation of this residue was proven to affect the spectroscopic, kinetic, and thermodynamic properties of YhjA.
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Affiliation(s)
- Ricardo N S Oliveira
- Microbial Stress Lab, UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sara R M M de Aguiar
- Microbial Stress Lab, UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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46
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Irvine W, Tyler M, Delgoda R. In silico characterization of the psilocybin biosynthesis pathway. Comput Biol Chem 2023; 104:107854. [PMID: 36990027 DOI: 10.1016/j.compbiolchem.2023.107854] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Nearly all mushrooms of the Psilocybe genus contain the natural product psilocybin, which is a psychoactive alkaloid derived from l-tryptophan. Considering their use in ancient times, as well as their psychedelic properties, these mushrooms have re-emerged with psychotherapeutic potential for treating depression, which has triggered increased pharmaceutical interest. However, the psilocybin biosynthesis pathway was only recently defined and, as such, little exists in the way of structural data. Accordingly, the aim of this study was to structurally characterize this pathway by generating homology models for the four Psilocybe cubensis enzymes involved in psilocybin biosynthesis (PsiD, a decarboxylase; PsiH, a monooxygenase; PsiK, a phosphotransferase; PsiM, a methyltransferase). Following initial model generation and alignment with the identified structural templates, repeated refinement of the models was carried out using secondary structure prediction, geometry evaluation, energy minimization, and molecular dynamics simulations in water. The final models were then evaluated using molecular docking interactions with their substrates, i.e., psilocybin precursors (l-tryptophan, tryptamine, 4-hydroxytryptamine, and norbaeocystin/baeocystin), all of which generated feasible binding modes for the expected biotransformation. Further plausibility of the psilocybin → aeruginascin, 4-hydroxytryptamine → norpsilocin, and tryptamine → N,N-dimethyltryptamine conversions, all mediated by the generated model for PsiM, suggests valid routes of formation for these key secondary metabolites. The structural characterization of these enzymes and their binding modes which emerged from this study can lead to a better understanding of psilocybin synthesis, thereby paving the way for the development of novel substrates and selective inhibitors, as well as improved biotechnological manipulation and production of psilocybin in vitro.
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Han F, Hu Y, Wu M, He Z, Tian H, Zhou L. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Nat Commun 2023; 14:2542. [PMID: 37248254 DOI: 10.1038/s41467-023-38158-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein complexes (I-IV). Here we report cryo-EM structures of its ~8 MDa megacomplex IV2 + (I + III2 + II)2, as well as a ~ 10.6 MDa megacomplex (IV2 + I + III2 + II)2 at lower resolution. In megacomplex IV2 + (I + III2 + II)2, each CIV2 protomer associates one copy of supercomplex I + III2 and one copy of CII, forming a half ring-shaped architecture that adapts to the membrane curvature of mitochondrial cristae. Megacomplex (IV2 + I + III2 + II)2 defines the relative position between neighbouring half rings and maintains the proximity between CIV2 and CIII2 cytochrome c binding sites. Our findings expand the current understanding of divergence in eukaryotic electron transport chain organization and how it is related to mitochondrial morphology.
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Affiliation(s)
- Fangzhu Han
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Yiqi Hu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Mengchen Wu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Zhaoxiang He
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Hongtao Tian
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Long Zhou
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
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Si Z, Cai Y, Zhao L, Han L, Wang F, Yang X, Gao X, Lu M, Liu W. Structure and function characterization of the α-L-arabinofuranosidase from the white-rot fungus Trametes hirsuta. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12561-w. [PMID: 37178306 DOI: 10.1007/s00253-023-12561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
α-L-Arabinofuranosidases (Abfs) play a crucial role in the degradation of hemicelluloses, especially arabinoxylans (AX). Most of the available characterized Abfs are from bacteria, while fungi, as natural decomposers, contain Abfs with little attention given. An arabinofuranosidase (ThAbf1), belonging to the glycoside hydrolase 51 (GH51) family, from the genome of the white-rot fungus Trametes hirsuta, was recombinantly expressed, characterized, and functionally determined. The general biochemical properties showed that the optimal conditions for ThAbf1 were pH 6.0 and 50°C. In substrate kinetics assays, ThAbf1 preferred small fragment arabinoxylo-oligosaccharides (AXOS) and could surprisingly hydrolyze di-substituted 23,33-di-L-arabinofuranosyl-xylotriose (A2,3XX). It also synergized with commercial xylanase (XYL) and increased the saccharification efficiency of arabinoxylan. The crystal structure of ThAbf1 indicated the presence of an adjacent cavity next to the catalytic pocket which led to the ability of ThAbf1 to degrade di-substituted AXOS. The narrow binding pocket prevents ThAbf1 from binding larger substrates. These findings have strengthened our understanding of the catalytic mechanism of GH51 family Abfs and provided a theoretical foundation for the development of more efficient and versatile Abfs to accelerate the degradation and biotransformation of hemicellulose in biomass. KEY POINTS: • ThAbf1 from Trametes hirsuta degraded di-substituted arabinoxylo-oligosaccharide. • ThAbf1 performed detailed biochemical characterization and kinetics. • ThAbf1 structure has been obtained to illustrate the substrate specificity.
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Affiliation(s)
- Zhenyuan Si
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yang Cai
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lang Zhao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lu Han
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Feng Wang
- Simcere Pharmaceutical Group Limited, Nanjing, 210042, PR China
| | - Xiaobing Yang
- Biology and Medicine Department, Jiangsu Industrial Technology Research Institute, Nanjing, 210031, PR China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Meiling Lu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Wei Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
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Cerrudo CS, Motta LF, Cuccovia Warlet FU, Lassalle FM, Simonin JA, Belaich MN. Protein-Gene Orthology in Baculoviridae: An Exhaustive Analysis to Redefine the Ancestrally Common Coding Sequences. Viruses 2023; 15:v15051091. [PMID: 37243176 DOI: 10.3390/v15051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Baculoviruses are entomopathogens that carry large, double-stranded circular DNA genomes and infect insect larvae of Lepidoptera, Hymenoptera and Diptera, with applications in the biological control of agricultural pests, in the production of recombinant proteins and as viral vectors for various purposes in mammals. These viruses have a variable genetic composition that differs between species, with some sequences shared by all known members, and others that are lineage-specific or unique to isolates. Based on the analysis of nearly 300 sequenced genomes, a thorough bioinformatic investigation was conducted on all the baculoviral protein coding sequences, characterizing their orthology and phylogeny. This analysis confirmed the 38 protein coding sequences currently considered as core genes, while also identifying novel coding sequences as candidates to join this set. Accordingly, homology was found among all the major occlusion body proteins, thus proposing that the polyhedrin, granulin and CUN085 genes be considered as the 39th core gene of Baculoviridae.
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Affiliation(s)
- Carolina Susana Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Lucas Federico Motta
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Franco Uriel Cuccovia Warlet
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Fernando Maku Lassalle
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
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50
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Zhao Z, Liu S, Wu C, Wang Q, Zhang Y, Wang B, Wang L, Sun R, Guo M, Ji W. Bioinformatics characteristics and expression analysis of TLR3 and its adaptor protein TRIF in Largemouth bass (Micropterus salmoides) upon Flavobacterium columnare infection. Gene 2023; 872:147450. [PMID: 37120121 DOI: 10.1016/j.gene.2023.147450] [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: 12/02/2022] [Revised: 03/19/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
TLR3 and TRIF (adaptor protein for TLR3) are vital to the MyD88-independent pathway mediated by Toll-like receptors (TLRs). In order to identify the role of TLR3 and TRIF in Micropterus salmoides, the Ms_TLR3 and Ms_TRIF (Ms: abbreviation for M. salmoides) were cloned and characterized in this study. The open reading frames (ORFs) of Ms_TLR3 and Ms_TRIF genes were 2736 bp and 1791 bp in length, encoding 911 and 596 amino acids, respectively. The protein structure of Ms_TLR3 includes a signal peptide, 18 LRR-related domains, a low complexity region, a transmembrane region, and a TIR domain. However, only a TIR domain and a coiled coil domain were found in Ms_TRIF. Both Ms_TLR3 and Ms_TRIF showed the highest homology to that of M. dolomieu. Ms_TLR3 and Ms_TRIF showed similar expression patterns in various tissues, with the highest expression level in the head kidney. After stimulation of Flavobacterium columnare, the mRNA expressions of Ms_TLR3 and Ms_TRIF were significantly up-regulated at 1 dpi in the gill, spleen and head kidney, and at 6 hpi in the trunk kidney. Furthermore, morphological changes in the gills of largemouth bass challenged with F. columnare suggested that F. columnare infection can destroy the gill filament. Taken together, Ms_TLR3 and Ms_TRIF are indeed involved in F. columnare infection and the subsequent immune response in largemouth bass. Moreover, Ms_TLR3 and Ms_TRIF might respectively play their potential roles in mucosal (mainly in the gill) and systemic (mainly in the head kidney) immune response to bacterial infection.
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Affiliation(s)
- Zhangchun Zhao
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Sixue Liu
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wu
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaqian Zhang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Bingchao Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Ruhan Sun
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengge Guo
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Ji
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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