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Cai X, He Y, Yu I, Imani A, Scholl D, Miller JF, Zhou ZH. Atomic structures of a bacteriocin targeting Gram-positive bacteria. Nat Commun 2024; 15:7057. [PMID: 39152109 PMCID: PMC11329794 DOI: 10.1038/s41467-024-51038-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024] Open
Abstract
Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; however, only those killing Gram-negative bacteria are currently known. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with target envelope differences. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.
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Affiliation(s)
- Xiaoying Cai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Yao He
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Iris Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Anthony Imani
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Dean Scholl
- Pylum Biosciences, San Francisco, CA, 94080, USA
| | - Jeff F Miller
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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2
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Sun X, Xue F, Cong C, Murtaza B, Wang L, Li X, Li S, Xu Y. Characterization of two virulent Salmonella phages and transient application in egg, meat and lettuce safety. Food Res Int 2024; 190:114607. [PMID: 38945617 DOI: 10.1016/j.foodres.2024.114607] [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: 03/05/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Salmonella, a prominent foodborne pathogen, has posed enduring challenges to the advancement of food safety and global public health. The escalating concern over antibiotic misuse, resulting in the excessive presence of drug residues in animal-derived food products, necessitates urgent exploration of alternative strategies for Salmonella control. Bacteriophages emerge as promising green biocontrol agents against pathogenic bacteria. This study delineates the identification of two novel virulent Salmonella phages, namely phage vB_SalS_ABTNLsp11241 (referred to as sp11241) and phage 8-19 (referred to as 8-19). Both phages exhibited efficient infectivity against Salmonella enterica serotype Enteritidis (SE). Furthermore, this study evaluated the effectiveness of two phages to control SE in three different foods (whole chicken eggs, raw chicken meat, and lettuce) at different MOIs (1, 100, and 10000) at 4°C. It's worth noting that sp11241 and 8-19 achieved complete elimination of SE on eggs after 3 h and 6 h at MOI = 100, and after 2 h and 5 h at MOI = 10000, respectively. After 12 h of treatment with sp11241, a maximum reduction of 3.17 log10 CFU/mL in SE was achieved on raw chicken meat, and a maximum reduction of 3.00 log10 CFU/mL was achieved on lettuce. Phage 8-19 has the same effect on lettuce as sp11241, but is slightly less effective than sp11241 on chicken meat (a maximum 2.69 log10 CFU/mL reduction). In conclusion, sp11241 and 8-19 exhibit considerable potential for controlling Salmonella contamination in food at a low temperature and represent viable candidates as green antibacterial agents for food applications.
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Affiliation(s)
- XiaoWen Sun
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Fan Xue
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Cong Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Bilal Murtaza
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - LiLi Wang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - XiaoYu Li
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - ShuYing Li
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - YongPing Xu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China.
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Hallee L, Rafailidis N, Horger C, Hong D, Gleghorn JP. Annotation Vocabulary (Might Be) All You Need. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605924. [PMID: 39131267 PMCID: PMC11312613 DOI: 10.1101/2024.07.30.605924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Protein Language Models (pLMs) have revolutionized the computational modeling of protein systems, building numerical embeddings that are centered around structural features. To enhance the breadth of biochemically relevant properties available in protein embeddings, we engineered the Annotation Vocabulary, a transformer readable language of protein properties defined by structured ontologies. We trained Annotation Transformers (AT) from the ground up to recover masked protein property inputs without reference to amino acid sequences, building a new numerical feature space on protein descriptions alone. We leverage AT representations in various model architectures, for both protein representation and generation. To showcase the merit of Annotation Vocabulary integration, we performed 515 diverse downstream experiments. Using a novel loss function and only $3 in commercial compute, our premier representation model CAMP produces state-of-the-art embeddings for five out of 15 common datasets with competitive performance on the rest; highlighting the computational efficiency of latent space curation with Annotation Vocabulary. To standardize the comparison of de novo generated protein sequences, we suggest a new sequence alignment-based score that is more flexible and biologically relevant than traditional language modeling metrics. Our generative model, GSM, produces high alignment scores from annotation-only prompts with a BERT-like generation scheme. Of particular note, many GSM hallucinations return statistically significant BLAST hits, where enrichment analysis shows properties matching the annotation prompt - even when the ground truth has low sequence identity to the entire training set. Overall, the Annotation Vocabulary toolbox presents a promising pathway to replace traditional tokens with members of ontologies and knowledge graphs, enhancing transformer models in specific domains. The concise, accurate, and efficient descriptions of proteins by the Annotation Vocabulary offers a novel way to build numerical representations of proteins for protein annotation and design.
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Affiliation(s)
- Logan Hallee
- Center for Bioinformatics and Computational Biology, University of Delaware
| | - Niko Rafailidis
- Center for Bioinformatics and Computational Biology, University of Delaware
| | - Colin Horger
- Department of Biomedical Engineering, University of Delaware
| | - David Hong
- Department of Electrical and Computer Engineering, University of Delaware
| | - Jason P Gleghorn
- Center for Bioinformatics and Computational Biology, University of Delaware
- Department of Biomedical Engineering, University of Delaware
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Martin J, Lequerica Mateos M, Onuchic JN, Coluzza I, Morcos F. Machine learning in biological physics: From biomolecular prediction to design. Proc Natl Acad Sci U S A 2024; 121:e2311807121. [PMID: 38913893 PMCID: PMC11228481 DOI: 10.1073/pnas.2311807121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024] Open
Abstract
Machine learning has been proposed as an alternative to theoretical modeling when dealing with complex problems in biological physics. However, in this perspective, we argue that a more successful approach is a proper combination of these two methodologies. We discuss how ideas coming from physical modeling neuronal processing led to early formulations of computational neural networks, e.g., Hopfield networks. We then show how modern learning approaches like Potts models, Boltzmann machines, and the transformer architecture are related to each other, specifically, through a shared energy representation. We summarize recent efforts to establish these connections and provide examples on how each of these formulations integrating physical modeling and machine learning have been successful in tackling recent problems in biomolecular structure, dynamics, function, evolution, and design. Instances include protein structure prediction; improvement in computational complexity and accuracy of molecular dynamics simulations; better inference of the effects of mutations in proteins leading to improved evolutionary modeling and finally how machine learning is revolutionizing protein engineering and design. Going beyond naturally existing protein sequences, a connection to protein design is discussed where synthetic sequences are able to fold to naturally occurring motifs driven by a model rooted in physical principles. We show that this model is "learnable" and propose its future use in the generation of unique sequences that can fold into a target structure.
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Affiliation(s)
- Jonathan Martin
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
| | - Marcos Lequerica Mateos
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Universidad del País Vasco/Euskal Herriko Unibertsitatea Science Park, Leioa48940, Spain
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of BioSciences, Rice University, Houston, TX77005
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Universidad del País Vasco/Euskal Herriko Unibertsitatea Science Park, Leioa48940, Spain
- Basque Foundation for Science, Ikerbasque, Bilbao48940, Spain
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
- Department of Bioengineering, Center for Systems Biology, University of Texas at Dallas, Richardson, TX75080
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Schwarz C, Mathieu J, Laverde Gomez J, Miller MR, Tikhonova M, Hamor C, Alvarez PJJ. Isolation and Characterization of Six Novel Fusobacterium necrophorum Phages. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:63-75. [PMID: 39119211 PMCID: PMC11304844 DOI: 10.1089/phage.2023.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Introduction Fusobacterium necrophorum, a human and animal pathogen, is the primary etiologic agent of bovine liver abscesses and a driving factor for prophylactic antibiotic use in the fed cattle industry. Considering calls to reduce agricultural antibiotic use, we isolated phages capable of killing F. necrophorum as an alternative or complementary biocontrol strategy. Methods Six novel phages (φFN37, φRTG5, φKSUM, φHugo, φPaco, and φBB) were isolated from rumen fluid or ruminal F. necrophorum isolates and subjected to host range testing on both F. necrophorum subspecies. Four F. necrophorum subspecies, necrophorum phages, were tested for cross-resistance and host growth inhibition individually and in pairs. Additionally, genomic sequencing, annotation, and analysis were performed.s. Results Four of six isolated phages were able to form lysogens, although all six contained lysogeny-related genes. φKSUM and φBB, did not form lysogens and were able to infect both subspecies. Four phages could infect F. necrophorum 8L1 (a liver abscess model challenge strain) in vitro. Genomic analysis showed that these phages belong to class Caudoviricetes with genome sizes ranging from 35 kbp to 111 kbp and GC values ranging from 26% to 36% and have extremely limited similarity to other deposited phage genomes infecting Fusobacterium or other genera. Conclusions Although all phages isolated contained sequences bearing similarities to genes implicated in lysogeny, the four selected for use in cocktails showed potential in inhibiting host growth, with several demonstrating promising attributes for biocontrol and therapeutic applications. Phage cocktails that may offer enhanced antibacterial activity were also identified, indicating the potential of some lysogenic phages to be adapted for biocontrol or therapeutic purposes when lytic phages are difficult to obtain.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | | | - Megan R. Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | | | - Clark Hamor
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
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Fan W, Hu L, Yang Y, Liu P, Feng Y, Gu RX, Liu Q. Engineering of the start condensation domain with improved N-decanoyl catalytic activity for daptomycin biosynthesis. Biotechnol J 2024; 19:e2400202. [PMID: 38896411 DOI: 10.1002/biot.202400202] [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: 04/01/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Daptomycin, a lipopeptide comprising an N-decanoyl fatty acyl chain and a peptide core, is used clinically as an antimicrobial agent. The start condensation domain (dptC1) is an enzyme that catalyzes the lipoinitiation step of the daptomycin synthesis. In this study, we integrated enzymology, protein engineering, and computer simulation to study the substrate selectivity of the start condensation domain (dptC1) and to screen mutants with improved activity for decanoyl loading. Through molecular docking and computer simulation, the fatty acyl substrate channel and the protein-protein interaction interface of dptC1 are analyzed. Key residues at the protein-protein interface between dptC1 and the acyl carrier were mutated, and a single-point mutant showed more than three-folds improved catalytic efficiency of the target n-decanoyl substrate in comparing with the wild type. Moreover, molecular dynamics simulations suggested that mutants with increased catalytic activity may correlated with a more "open" and contracted substrate binding channel. Our work provides a new perspective for the elucidation of lipopeptide natural products biosynthesis, and also provides new resources to enrich its diversity and optimize the production of important components.
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Affiliation(s)
- Wenjie Fan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lyubin Hu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Panpan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruo-Xu Gu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Wang Y, Yang Y, Liu Y, Liu C, Xu M, Fang M, Mu X. CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish. Database (Oxford) 2024; 2024:baae038. [PMID: 38803273 PMCID: PMC11130519 DOI: 10.1093/database/baae038] [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: 12/07/2023] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/29/2024]
Abstract
Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.
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Affiliation(s)
- Yuanyuan Wang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Yexin Yang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Meng Xu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Miao Fang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
| | - Xidong Mu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.1 Xingyu Road, Xilang, Liwan District, Guangzhou 510380, China
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Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, Gifford RJ. A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biol 2024; 25:120. [PMID: 38741126 PMCID: PMC11089739 DOI: 10.1186/s13059-024-03258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
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Affiliation(s)
- Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | | | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Gatseva
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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9
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Cong Z, Yin Q, Tian K, Mukoma NJ, Ouyang L, Hsiang T, Zhang L, Jiang L, Liu X. Genome Mining of Fungal Unique Trichodiene Synthase-like Sesquiterpene Synthases. J Fungi (Basel) 2024; 10:350. [PMID: 38786705 PMCID: PMC11122449 DOI: 10.3390/jof10050350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Sesquiterpenoids served as an important source for natural product drug discovery. Although genome mining approaches have revealed numerous novel sesquiterpenoids and biosynthetic enzymes, the comprehensive landscape of fungal sesquiterpene synthases (STSs) remains elusive. In this study, 123 previously reported fungal STSs were subjected to phylogenetic analysis, resulting in the identification of a fungi-specific STS family known as trichodiene synthase-like sesquiterpene synthases (TDTSs). Subsequently, the application of hidden Markov models allowed the discovery of 517 TDTSs from our in-house fungi genome library of over 400 sequenced genomes, and these TDTSs were defined into 79 families based on a sequence similarity network. Based on the novelty of protein sequences and the completeness of their biosynthetic gene clusters, 23 TDTS genes were selected for heterologous expression in Aspergillus oryzae. In total, 10 TDTSs were active and collectively produced 12 mono- and sesquiterpenes, resulting in the identification of the first chamipinene synthase, as well as the first fungi-derived cedrene, sabinene, and camphene synthases. Additionally, with the guidance of functionally characterized TDTSs, we found that TDTSs in Family 1 could produce bridged-cyclic sesquiterpenes, while those in Family 2 could synthesize spiro- and bridged-cyclic sesquiterpenes. Our research presents a new avenue for the genome mining of fungal sesquiterpenoids.
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Affiliation(s)
- Zhanren Cong
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Qiang Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Kunhong Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Njeru Joe Mukoma
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
| | - Lan Jiang
- Department of Cardiothoracic Surgery, Children’s Hospital of Nanjing Medical University, Nanjing 210093, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China (N.J.M.)
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10
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Wang S, Sun Y, Lü L, Pan Z. Contributions to the Knowledge of Nemognathinae (Coleoptera: Meloidae) from China. INSECTS 2024; 15:338. [PMID: 38786894 PMCID: PMC11122394 DOI: 10.3390/insects15050338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Despite being the most widespread blister beetle subfamily, Nemognathinae is unfairly understudied in China. In this study, a new genus and species, Sinostenoria yangi Pan, from northern China is described and illustrated. The antennae, elytra, hind wings, and claws of the new genus form a truly unique set of characteristics never observed in other genera of Nemognathini Laporte de Castelnau, 1840. Three species from China are newly recorded and illustrated: Megatrachelus sibiricus (Tauscher, 1812), Zonitomorpha dollei (Fairmaire 1889), and Stenodera djakonovi Aksentjev, 1978. The genus Oreomeloe Tan, 1981, is transferred from the tribe Meloini Gyllenhal, 1910, to Nemognathini based on an examination of the types. Aiming to test the morphology-based placement of the new genus, we conducted molecular phylogenetic analyses using two mitochondrial (COI, 16S) and three nuclear markers (28S, CAD, ITS2). The results confirm our tribal assignment of the new genus and support a clade that consists of Sinostenoriagen. n., Longizonitis Pan and Bologna, 2018, Stenoria cf. grandiceps, and Ctenopus cf. persicus.
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Affiliation(s)
- Shaopeng Wang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China;
| | - Yinuo Sun
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; (Y.S.); (L.L.)
| | - Liang Lü
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; (Y.S.); (L.L.)
| | - Zhao Pan
- Key Laboratory of Zoological Systematics and Application of Hebei Province, School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China;
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11
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Ali EAA, Hussein NA, El-Hakim AE, Amer MA, Shahein YE. Cloning and catalytic profile of Hyalomma dromedarii leucine aminopeptidase. Int J Biol Macromol 2024; 268:131778. [PMID: 38657929 DOI: 10.1016/j.ijbiomac.2024.131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Ticks have harmful impacts on both human and animal health and cause considerable economic losses. Leucine aminopeptidase enzymes (LAP) play important roles during tick infestation to liberate vital amino acids necessary for growth. The aim of the current study is to identify, express and characterize the LAP from the hard tick Hyalomma dromedarii and elucidate its biochemical characteristics. We cloned an open reading frame of 1560 bp encoding a protein of 519 amino acids. The LAP full-length was expressed in Escherichia coli BL21 (DE3) and purified. The recombinant enzyme (H.d rLAP- 6×His) had a predicted molecular mass of approximately 55 kDa. Purification and the enzymatic characteristics of H.d rLAP- 6×His were studied. The purified enzyme showed maximum activity at 37 °C and pH 8.0-8.5 using Leu-p-nitroanilide as a substrate. The activity of H.d rLAP- 6×His was sensitive to β-mercaptoethanol, dl-dithiothreitol, 1,10- phenanthroline, bestatin HCl, and EDTA and completely abolished by 0.05 % SDS. In parallel, the enzymatic activity was enhanced by Ni2+, Mn2+ and Mg2+, partially inhibited by Na+, Cu2+, Ca2+ and completely inhibited by Zn2+.
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Affiliation(s)
- Esraa A A Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Nahla A Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
| | - Amr E El-Hakim
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Mahmoud A Amer
- Zoology Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
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12
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Almeida L, Colmonero-Costeira I, da Silva MJF, Veracini C, Vasconcelos R. Insights into the Geographical Origins of the Cabo Verde Green Monkey. Genes (Basel) 2024; 15:504. [PMID: 38674438 PMCID: PMC11050204 DOI: 10.3390/genes15040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The green monkey Chlorocebus sabaeus, L. 1766, native to West Africa, was introduced to the Cabo Verde Archipelago in the 16th century. Historical sources suggest that, due to the importance of Cabo Verde as a commercial entrepôt in the Atlantic slave trade, establishing the precise place of origin of this introduced species is challenging. Non-invasive fecal samples were collected from feral and captive green monkey individuals in Cabo Verde. Two mitochondrial fragments, HVRI and cyt b, were used to confirm the taxonomic identification of the species and to tentatively determine the geographic origin of introduction to the archipelago from the African continent. By comparing the new sequences of this study to previously published ones, it was shown that Cabo Verde individuals have unique haplotypes in the HVRI, while also showing affinities to several populations from north-western coastal Africa in the cyt b, suggesting probable multiple sources of introduction and an undetermined most probable origin. The latter is consistent with historical information, but may also have resulted from solely using mtDNA as a genetic marker and the dispersal characteristics of the species. The limitations of the methodology are discussed and future directions of research are suggested.
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Affiliation(s)
- Lara Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Ivo Colmonero-Costeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Organisms and Environment Division, School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Maria J. Ferreira da Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Organisms and Environment Division, School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Cecilia Veracini
- Centre of Public and Political Administration, Institute of Social and Political Sciences, University of Lisbon, 1300-663 Lisboa, Portugal
| | - Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
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13
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Murashkina T, Sharshov K, Gadzhiev A, Petherbridge G, Derko A, Sobolev I, Dubovitskiy N, Loginova A, Kurskaya O, Kasianov N, Kabilov M, Mine J, Uchida Y, Tsunekuni R, Saito T, Alekseev A, Shestopalov A. Avian Influenza Virus and Avian Paramyxoviruses in Wild Waterfowl of the Western Coast of the Caspian Sea (2017-2020). Viruses 2024; 16:598. [PMID: 38675939 PMCID: PMC11054612 DOI: 10.3390/v16040598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The flyways of many different wild waterfowl pass through the Caspian Sea region. The western coast of the middle Caspian Sea is an area with many wetlands, where wintering grounds with large concentrations of birds are located. It is known that wild waterfowl are a natural reservoir of the influenza A virus. In the mid-2000s, in the north of this region, the mass deaths of swans, gulls, and pelicans from high pathogenicity avian influenza virus (HPAIV) were noted. At present, there is still little known about the presence of avian influenza virus (AIVs) and different avian paramyxoviruses (APMVs) in the region's waterfowl bird populations. Here, we report the results of monitoring these viruses in the wild waterfowl of the western coast of the middle Caspian Sea from 2017 to 2020. Samples from 1438 individuals of 26 bird species of 7 orders were collected, from which 21 strains of AIV were isolated, amounting to a 1.46% isolation rate of the total number of samples analyzed (none of these birds exhibited external signs of disease). The following subtypes were determined and whole-genome nucleotide sequences of the isolated strains were obtained: H1N1 (n = 2), H3N8 (n = 8), H4N6 (n = 2), H7N3 (n = 2), H8N4 (n = 1), H10N5 (n = 1), and H12N5 (n = 1). No high pathogenicity influenza virus H5 subtype was detected. Phylogenetic analysis of AIV genomes did not reveal any specific pattern for viruses in the Caspian Sea region, showing that all segments belong to the Eurasian clades of classic avian-like influenza viruses. We also did not find the amino acid substitutions in the polymerase complex (PA, PB1, and PB2) that are critical for the increase in virulence or adaptation to mammals. In total, 23 hemagglutinating viruses not related to influenza A virus were also isolated, of which 15 belonged to avian paramyxoviruses. We were able to sequence 12 avian paramyxoviruses of three species, as follows: Newcastle disease virus (n = 4); Avian paramyxovirus 4 (n = 5); and Avian paramyxovirus 6 (n = 3). In the Russian Federation, the Newcastle disease virus of the VII.1.1 sub-genotype was first isolated from a wild bird (common pheasant) in the Caspian Sea region. The five avian paramyxovirus 4 isolates obtained belonged to the common clade in Genotype I, whereas phylogenetic analysis of three isolates of Avian paramyxovirus 6 showed that two isolates, isolated in 2017, belonged to Genotype I and that an isolate identified in 2020 belonged to Genotype II. The continued regular monitoring of AIVs and APMVs, the obtaining of data on the biological properties of isolated strains, and the accumulation of information on virus host species will allow for the adequate planning of epidemiological measures, suggest the most likely routes of spread of the virus, and assist in the prediction of the introduction of the viruses in the western coastal region of the middle Caspian Sea.
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Affiliation(s)
- Tatyana Murashkina
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Alimurad Gadzhiev
- Faculty of Ecology and Sustainable Development, Dagestan State University, Makhachkala 367016, Russia;
| | - Guy Petherbridge
- Caspian Centre for Nature Conservation, International Institute of Ecology and Sustainable Development, Association of Universities and Research Centres of Caspian Region States, Makhachkala 367016, Russia;
| | - Anastasiya Derko
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Ivan Sobolev
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Arina Loginova
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Olga Kurskaya
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Nikita Kasianov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia;
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Alexander Alekseev
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
- Caspian Centre for Nature Conservation, International Institute of Ecology and Sustainable Development, Association of Universities and Research Centres of Caspian Region States, Makhachkala 367016, Russia;
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14
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Cai X, He Y, Yu I, Imani A, Scholl D, Miller JF, Zhou ZH. Atomic structures of a bacteriocin targeting Gram-positive bacteria. RESEARCH SQUARE 2024:rs.3.rs-4007122. [PMID: 38586031 PMCID: PMC10996793 DOI: 10.21203/rs.3.rs-4007122/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Due to envelope differences between Gram-positive and Gram-negative bacteria1, engineering precision bactericidal contractile nanomachines2 requires atomic-level understanding of their structures; however, only those killing a Gram-negative bacterium are currently known3,4. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar protein linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with differences between their targeted envelopes. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire length of the diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.
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Affiliation(s)
- Xiaoying Cai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Yao He
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Iris Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Anthony Imani
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Dean Scholl
- Pylum Biosciences, 100 Kimball Way S. San Francisco, CA 94080, USA
| | - Jeff F. Miller
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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15
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Jahan K, Battaje RR, Pratap V, Ahire G, Pushpakaran A, Ashtam A, Bharatam PV, Panda D. Identification of ethyl-6-bromo-2((phenylthio)methyl)imidazo[1,2-a]pyridine-3-carboxylate as a narrow spectrum inhibitor of Streptococcus pneumoniae and its FtsZ. Eur J Med Chem 2024; 267:116196. [PMID: 38350359 DOI: 10.1016/j.ejmech.2024.116196] [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: 11/17/2023] [Revised: 01/19/2024] [Accepted: 01/28/2024] [Indexed: 02/15/2024]
Abstract
Filamentous temperature-sensitive mutant Z (FtsZ) is a key cell-division protein recognized as an important target for anti-bacterial drug discovery, especially in the context of rising multi-drug resistance. A respiratory pathogen, Streptococcus pneumoniae, is rapidly evolving antibiotic resistance, thus posing a clinical risk in the developing world. Inhibiting the conserved protein FtsZ, leading to the arrest of cell division, is an attractive alternative strategy for inhibiting S. pneumoniae. Previously, Vitamin K3 was identified as an FtsZ-targeting agent against S. pneumoniae. In the present work, docking studies were used to identify potential anti-FtsZ agents that bind to the Vitamin K3-binding region of a homology model generated for S. pneumoniae FtsZ. Compounds with imidazo[1,2-a]pyridine-3-carboxylate core were synthesized and screened for their anti-proliferative activity against S. pneumoniae. Remarkably, the hit compound IP-01 showed anti-bacterial action against S. pneumoniae without any activity on other bacteria. In S. pneumoniae, IP-01 showed similar inhibitory action on FtsZ and cell division as Vitamin K3. Sequence alignment identified three unique residues within S. pneumoniae FtsZ that IP-01 binds to, providing a structural basis for the observed specificity. IP-01 is one of the first narrow-spectrum agents identified against S. pneumoniae that targets FtsZ, and we present it as a promising lead for the design of narrow-spectrum anti-FtsZ anti-pneumococcal compounds.
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Affiliation(s)
- Kousar Jahan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India.
| | - Rachana Rao Battaje
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Vidyadhar Pratap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Ganesh Ahire
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India.
| | - Athira Pushpakaran
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Anvesh Ashtam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India.
| | - Dulal Panda
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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16
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Okmane L, Fitkin L, Sandgren M, Ståhlberg J. The first crystal structure of a family 45 glycoside hydrolase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A. FEBS Open Bio 2024; 14:505-514. [PMID: 38311343 PMCID: PMC10909974 DOI: 10.1002/2211-5463.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Here we describe the first crystal structure of a beta-1,4-endoglucanase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A, which belongs to subfamily C of glycoside hydrolase family 45 (GH45). GtCel45A is ~ 18 kDa in size and the crystal structure contains 179 amino acids. The structure is refined at 1.30 Å resolution and Rfree 0.18. The enzyme consists of a single catalytic module folded into a six-stranded double-psi beta-barrel domain surrounded by long loops. GtCel45A is very similar in sequence (82% identity) and structure to PcCel45A from the white-rot fungus Phanerochaete chrysosporium. Surprisingly though, initial hydrolysis of barley beta-glucan was almost twice as fast in GtCel45A as compared to PcCel45A.
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Affiliation(s)
- Laura Okmane
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Louise Fitkin
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Mats Sandgren
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Jerry Ståhlberg
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
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17
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Brady MJ, Cheam M, Gent JI, Dawe RK. The maize striate leaves2 ( sr2) gene encodes a conserved DUF3732 domain and is homologous to the rice yss1 gene. PLANT DIRECT 2024; 8:e567. [PMID: 38357415 PMCID: PMC10864124 DOI: 10.1002/pld3.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Maize striate leaves2 (sr2) is a mutant that causes white stripes on leaves that has been used in mapping studies for decades though the underlying gene has not been identified. The sr2 locus has been previously mapped to small regions of normal chromosome 10 (N10) and a rearranged variant called abnormal chromosome 10 (Ab10). A comparison of assembled genomes carrying N10 and Ab10 revealed only five candidate sr2 genes. Analysis of a stock carrying the sr2 reference allele (sr2-ref) showed that one of the five genes has a transposon insertion that disrupts its protein sequence and has a severe reduction in mRNA. An independent Mutator transposon insertion in the gene (sr2-Mu) failed to complement the sr2-ref mutation, and plants homozygous for sr2-Mu showed white striped leaf margins. The sr2 gene encodes a DUF3732 protein with strong homology to a rice gene with a similar mutant phenotype called young seedling stripe1 (yss1). These and other published data suggest that sr2 may have a function in plastid gene expression.
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Affiliation(s)
| | - Maya Cheam
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Jonathan I. Gent
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - R. Kelly Dawe
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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18
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Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F. TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Res 2024; 52:D1465-D1477. [PMID: 37713619 PMCID: PMC10767903 DOI: 10.1093/nar/gkad751] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
Target discovery is one of the essential steps in modern drug development, and the identification of promising targets is fundamental for developing first-in-class drug. A variety of methods have emerged for target assessment based on druggability analysis, which refers to the likelihood of a target being effectively modulated by drug-like agents. In the therapeutic target database (TTD), nine categories of established druggability characteristics were thus collected for 426 successful, 1014 clinical trial, 212 preclinical/patented, and 1479 literature-reported targets via systematic review. These characteristic categories were classified into three distinct perspectives: molecular interaction/regulation, human system profile and cell-based expression variation. With the rapid progression of technology and concerted effort in drug discovery, TTD and other databases were highly expected to facilitate the explorations of druggability characteristics for the discovery and validation of innovative drug target. TTD is now freely accessible at: https://idrblab.org/ttd/.
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Affiliation(s)
- Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Donghai Zhao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Shen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven 06510, USA
| | - Yuan Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Yunqing Qiu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Yuzong Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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19
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Zhang L, Sun W, Gao W, Zhang Y, Zhang P, Liu Y, Chen T, Yang D. Genome-wide identification and analysis of the GGCT gene family in wheat. BMC Genomics 2024; 25:32. [PMID: 38177998 PMCID: PMC10768367 DOI: 10.1186/s12864-023-09934-w] [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: 10/30/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND γ-glutamylcyclotransferase (GGCT), an enzyme to maintain glutathione homeostasis, plays a vital role in the response to plant growth and development as well as the adaptation to various stresses. Although the GGCT gene family analysis has been conducted in Arabidopsis and rice, the family genes have not yet been well identified and analyzed at the genome-wide level in wheat (Triticum aestivum L.). RESULTS In the present study, 20 TaGGCT genes were identified in the wheat genome and widely distributed on chromosomes 2A, 2B, 2D, 3A, 4A, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B, and 7D. Phylogenetic and structural analyses showed that these TaGGCT genes could be classified into three subfamilies: ChaC, GGGACT, and GGCT-PS. They exhibited similar motif compositions and distribution patterns in the same subgroup. Gene duplication analysis suggested that the expansion of TaGGCT family genes was facilitated by segmental duplications and tandem repeats in the wheat evolutionary events. Identification of diverse cis-acting response elements in TaGGCT promoters indicated their potential fundamental roles in response to plant development and abiotic stresses. The analysis of transcriptome data combined with RT-qPCR results revealed that the TaGGCTs genes exhibited ubiquitous expression across plant organs, with highly expressed in roots, stems, and developing grains. Most TaGGCT genes were up-regulated after 6 h under 20% PEG6000 and ABA treatments. Association analysis revealed that two haplotypes of TaGGCT20 gene displayed significantly different Thousand-kernel weight (TKW), Kernel length (KL), and Kernel width (KW) in wheat. The geographical and annual distribution of the two haplotypes of TaGGCT20 gene further revealed that the frequency of the favorable haplotype TaGGCT20-Hap-I was positively selected in the historical breeding process of wheat. CONCLUSION This study investigated the genome-wide identification, structure, evolution, and expression analysis of TaGGCT genes in wheat. The motifs of TaGGCTs were highly conserved throughout the evolutionary history of wheat. Most TaGGCT genes were highly expressed in roots, stems, and developing grains, and involved in the response to drought stresses. Two haplotypes were developed in the TaGGCT20 gene, where TaGGCT20-Hap-I, as a favorable haplotype, was significantly associated with higher TKW, KL, and KW in wheat, suggesting that the haplotype is used as a function marker for the selection in grain yield in wheat breeding.
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Affiliation(s)
- Long Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Wanting Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
| | - Yuan Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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20
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Lasalle A, Benech-Correa G, Brunet FG, Vizziano-Cantonnet D. hsd17b1 is a key gene for ovarian differentiation of the Siberian sturgeon. Mol Reprod Dev 2024; 91:e23729. [PMID: 38282315 DOI: 10.1002/mrd.23729] [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: 06/21/2023] [Revised: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
This is the first work using gonads from undifferentiated, genetically-sexed Siberian sturgeon describing expression changes in genes related to steroid synthesis and female and male sex differentiation. One factor identified as relevant for ovarian differentiation was the gene coding for the enzyme Hsd17b1, which converts estrone into estradiol-17β. hsd17b1 was highly activated in female gonads at 2.5 months of age, around the onset of sex differentiation, preceding activation of two other genes involved in estrogen production (cyp19a1 and foxl2). hsd17b1 was also strongly repressed in males. Two known foxl2 paralogs are found in Siberian sturgeon-foxl2 and foxl2l-but only foxl2 appeared to be associated with ovarian differentiation. With regard to the male pathway, neither 11-oxygenated androgens nor classic male genes (amh, dmrt1, sox9, and dhh) were found to be involved in male sex differentiation, leaving open the question of which genes participate in early male gonad development in this ancient fish. Taken together, these results indicate an estrogen-dependence of female sex differentiation and 11-oxygenated androgen-independence of male sex differentiation.
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Affiliation(s)
- André Lasalle
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Germán Benech-Correa
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard, Lyon, France
| | - Denise Vizziano-Cantonnet
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
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21
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He X, Zhang X, Deng Y, Yang R, Yu LX, Jia S, Zhang T. Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species. Int J Mol Sci 2023; 24:17334. [PMID: 38139163 PMCID: PMC10743518 DOI: 10.3390/ijms242417334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Plant mitochondria are crucial for species evolution, phylogenetics, classification, and identification as maternal genetic material. However, the presence of numerous repetitive sequences, complex structures, and a low number of genes in the mitochondrial genome has hindered its complete assembly and related research endeavors. In this study, we assembled two mitochondrial genomes of alfalfa varieties of Zhongmu No.1 (299,123 bp) and Zhongmu No.4 (306,983 bp), based on a combination of PacBio, Illumina, and Hi-C sequences. The comparison of genome assemblies revealed that the same number of mitochondrial genes, including thirty-three protein-coding genes, sixteen tRNA genes, and three rRNA genes existed in the two varieties. Additionally, large fragments of repetitive sequences were found underlying frequent mitochondrial recombination events. We observed extensive transfer of mitochondrial fragments into the nuclear genome of Zhongmu No.4. Analysis of the cox1 and rrn18s genes in 35 Medicago accessions revealed the presence of population-level deletions and substitutions in the rrn18s gene. We propose that mitochondrial structural reorganizations may contribute to alfalfa evolution.
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Affiliation(s)
- Xiaofan He
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Xiaopeng Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Yantian Deng
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Rui Yang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA;
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
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22
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Djulbegovic M, Taylor Gonzalez DJ, Antonietti M, Uversky VN, Shields CL, Karp CL. Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma. Int J Biol Macromol 2023; 250:126027. [PMID: 37506796 PMCID: PMC11182630 DOI: 10.1016/j.ijbiomac.2023.126027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Class 2 uveal melanomas are associated with the inactivation of the BRCA1 ((breast cancer type 1 susceptibility protein)-associated protein 1 (BAP1)) gene. Inactivation of BAP1 promotes the upregulation of vitamin K-dependent protein S (PROS1), which interacts with the tyrosine-protein kinase Mer (MERTK) receptor on M2 macrophages to induce an immunosuppressive environment. METHODS We simulated the interaction of PROS1 with MERTK with ColabFold. We evaluated PROS1 and MERTK for the presence of intrinsically disordered protein regions (IDPRs) and disorder-to-order (DOT) regions to understand their protein-protein interaction (PPI). We first evaluated the structure of each protein with AlphaFold. We then analyzed specific sequence-based features of the PROS1 and MERTK with a suite of bioinformatics tools. RESULTS With high-resolution, moderate confidence, we successfully modeled the interaction between PROS1 and MERTK (predicted local distance difference test score (pDLLT) = 70.68). Our structural analysis qualitatively demonstrated IDPRs (i.e., spaghetti-like entities) in PROS1 and MERK. PROS1 was 23.37 % disordered, and MERTK was 23.09 % disordered, classifying them as moderately disordered and flexible proteins. PROS1 was significantly enriched in cysteine, the most order-promoting residue (p-value <0.05). Our IUPred analysis demonstrated that there are two disorder-to-order transition (DOT) regions in PROS1. MERTK was significantly enriched in proline, the most disorder-promoting residue (p-value <0.05), but did not contain DOT regions. Our STRING analysis demonstrated that the PPI network between PROS1 and MERTK is more complex than their assumed one-to-one binding (p-value <2.0 × 10-6). CONCLUSION Our findings present a novel prediction for the interaction between PROS1 and MERTK. Our findings show that PROS1 and MERTK contain elements of intrinsic disorder. PROS1 has two DOT regions that are attractive immunotherapy targets. We recommend that IDPRs and DOT regions found in PROS1 and MERTK should be considered when developing immunotherapies targeting this PPI.
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Affiliation(s)
- Mak Djulbegovic
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | | | | | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Carol L Karp
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA.
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23
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Wang W, Qin L, Zhang W, Tang L, Zhang C, Dong X, Miao P, Shen M, Du H, Cheng H, Wang K, Zhang X, Su M, Lu H, Li C, Gao Q, Zhang X, Huang Y, Liang C, Zhou JM, Chen YH. WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance. Cell 2023; 186:2656-2671.e18. [PMID: 37295403 DOI: 10.1016/j.cell.2023.05.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Li Qin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Linghui Tang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pei Miao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Hangyuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyun Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Min Su
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Huang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Yu-Hang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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