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Biswas D, Benson S, Matunis A, Gebretsadik G, Wertz A, StPierre BJ, Schacht N, Yan Y, Gebremichael HY, Wong PK, Baughn AD, Medina SH. Lead Informed Artificial Intelligence Mining of Antitubercular Host Defense Peptides. Biomacromolecules 2025; 26:3167-3179. [PMID: 40310992 PMCID: PMC12076502 DOI: 10.1021/acs.biomac.5c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 05/03/2025]
Abstract
Identifying host defense peptides (HDPs) that are effective against drug-resistant infections is challenging due to their vast sequence space. Artificial intelligence (AI)-guided design can accelerate HDP discovery, but it traditionally requires large data sets to operationalize. We report an AI workflow that utilizes limited data sets (∼100 peptides) to uncover potent, selective, and safe HDPs by informing selection through lead candidate mutational scanning. This approach, referred to as Lead Informed Machine Interrogation of Therapeutic Sequences (LIMITS), is applied against the exemplary pathogen Mycobacterium tuberculosis. Experimental validation of predicted sequences shows nearly an order of magnitude improvement in potency, selectivity, and safety, relative to the initial template. Post hoc analysis suggests sequence length may be a unique and underappreciated driver of antitubercular HDP activity. These results demonstrate that, with continued development, the LIMITS approach can identify selective HDPs under data-limited conditions and elucidate structure-function-performance relationships previously hidden in biologic complexity.
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Affiliation(s)
- Diptomit Biswas
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Molecular,
Cellular, and Integrative Biosciences Graduate Program, Penn State University, University Park, Pennsylvania 16802, United States
| | - Sara Benson
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Aidan Matunis
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, Penn
State University, University Park, Pennsylvania 16802, United States
| | - Gebremichal Gebretsadik
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adam Wertz
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Ben J. StPierre
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Nathan Schacht
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yue Yan
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Hanna Y. Gebremichael
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Pak Kin Wong
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Anthony D. Baughn
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Scott H. Medina
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Molecular,
Cellular, and Integrative Biosciences Graduate Program, Penn State University, University Park, Pennsylvania 16802, United States
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2
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Berdieva M, Kalinina V, Palii O, Skarlato S. Putative MutS2 Homologs in Algae: More Goods in Shopping Bag? J Mol Evol 2024; 92:815-833. [PMID: 39365456 DOI: 10.1007/s00239-024-10210-y] [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: 04/12/2024] [Accepted: 09/20/2024] [Indexed: 10/05/2024]
Abstract
MutS2 proteins are presumably involved in either control of recombination or translation quality control in bacteria. MutS2 homologs have been found in plants and some algae; however, their actual diversity in eukaryotes remains unknown. We found putative MutS2 homologs in various species of photosynthetic eukaryotes and performed a detailed analysis of the revealed amino acid sequences. Three groups of homologs were distinguished depending on their domain composition: MutS2 homologs with full set of specific domains, MutS2-like sequences without endonuclease Smr domain, and MutS2-like homologs lacking Smr and clamp in domain IV, the extreme form of which are proteins with only a complete ATPase domain. We clarified the information about amino acid composition and set of specific motifs in the conserved domains in MutS2 and MutS2-like sequences. The models of the predicted tertiary structure were obtained for each group of homologs. The phylogenetic analysis demonstrated that all eukaryotic sequences split into two large groups. The first group included homologs belonging to species of Archaeplastida and a subset of haptophyte homologs, while the second-sequences of organisms from CASH groups (cryptophytes, alveolates, stramenopiles, haptophytes) and chlorarachniophytes. The cyanobacterial MutS2 clustered together with the first group, and proteins belonging to Deltaproteobacteria (orders Myxococcales and Bradymonadales) showed phylogenetic affinity to the CASH-including group with strong support. The observed tree pattern did not support a clear differentiation of eukaryotes into lineages with red and green algae-derived plastids. The results are discussed in the context of current conceptions of serial endosymbioses and genetic mosaicism in algae with complex plastids.
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Affiliation(s)
- Mariia Berdieva
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064, St. Petersburg, Russia.
| | - Vera Kalinina
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064, St. Petersburg, Russia
| | - Olga Palii
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064, St. Petersburg, Russia
| | - Sergei Skarlato
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064, St. Petersburg, Russia
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3
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Karki BR, Macmillan AC, Vicente-Muñoz S, Greis KD, Romick LE, Cunningham JT. Evolutionary origins and innovations sculpting the mammalian PRPS enzyme complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.01.616059. [PMID: 39411161 PMCID: PMC11476008 DOI: 10.1101/2024.10.01.616059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The phosphoribosyl pyrophosphate synthetase (PRPS) enzyme conducts a chokepoint reaction connecting central carbon metabolism and nucleotide production pathways, making it essential for life1,2. Here, we show that the presence of multiple PRPS-encoding genes is a hallmark trait of eukaryotes, and we trace the evolutionary origins and define the individual functions of each of the five mammalian PRPS homologs - three isozymes (one testis-restricted)3,4 and two non-enzymatic associated proteins (APs)5,6 - which we demonstrate operate together as a large molecular weight complex capable of attaining a heterogeneous array of functional multimeric configurations. Employing a repertoire of isogenic fibroblast clones in all viable individual or combinatorial assembly states, we define preferential interactions between subunits, and we show that cells lacking PRPS2, PRPSAP1, and PRPSAP2 render PRPS1 into aberrant homo-oligomeric assemblies with diminished metabolic flux and impaired proliferative capacity. We demonstrate how numerous evolutionary innovations in the duplicated genes have created specialized roles for individual complex members and identify translational control mechanisms that enable fine-tuned regulation of PRPS assembly and activity, which provide clues into the positive and negative selective pressures that facilitate metabolic flexibility and tissue specialization in advanced lifeforms. Collectively, our study demonstrates how evolution has transformed a single PRPS gene into a multimeric complex endowed with functional and regulatory features that govern cellular biochemistry.
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Affiliation(s)
- Bibek R. Karki
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Austin C. Macmillan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sara Vicente-Muñoz
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lindsey E. Romick
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA
| | - J. Tom Cunningham
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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4
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Wang Z, Peng Y, Li J, Li J, Yuan H, Yang S, Ding X, Xie A, Zhang J, Wang S, Li K, Shi J, Xing G, Shi W, Yan J, Liu J. DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions. PLANT COMMUNICATIONS 2024; 5:100985. [PMID: 38859587 DOI: 10.1016/j.xplc.2024.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been developed for predicting gene expression. However, existing methods do not take into consideration the effect of chromatin interactions on target gene expression, thus potentially reducing the accuracy of gene expression prediction and mining of important regulatory elements. In this study, we developed a highly accurate deep learning-based gene expression prediction model (DeepCBA) based on maize chromatin interaction data. Compared with existing models, DeepCBA exhibits higher accuracy in expression classification and expression value prediction. The average Pearson correlation coefficients (PCCs) for predicting gene expression using gene promoter proximal interactions, proximal-distal interactions, and both proximal and distal interactions were 0.818, 0.625, and 0.929, respectively, representing an increase of 0.357, 0.16, and 0.469 over the PCCs obtained with traditional methods that use only gene proximal sequences. Some important motifs were identified through DeepCBA; they were enriched in open chromatin regions and expression quantitative trait loci and showed clear tissue specificity. Importantly, experimental results for the maize flowering-related gene ZmRap2.7 and the tillering-related gene ZmTb1 demonstrated the feasibility of DeepCBA for exploration of regulatory elements that affect gene expression. Moreover, promoter editing and verification of two reported genes (ZmCLE7 and ZmVTE4) demonstrated the utility of DeepCBA for the precise design of gene expression and even for future intelligent breeding. DeepCBA is available at http://www.deepcba.com/ or http://124.220.197.196/.
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Affiliation(s)
- Zhenye Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiying Li
- Microsoft Corporation, Redmond, WA 98052, USA
| | - Hao Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shangpo Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinru Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiangling Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouzhe Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Keqin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Shi
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangjie Xing
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weihan Shi
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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5
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Thagun C, Odahara M, Kodama Y, Numata K. Identification of a highly efficient chloroplast-targeting peptide for plastid engineering. PLoS Biol 2024; 22:e3002785. [PMID: 39298532 PMCID: PMC11444414 DOI: 10.1371/journal.pbio.3002785] [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: 12/23/2023] [Revised: 10/01/2024] [Accepted: 08/03/2024] [Indexed: 09/22/2024] Open
Abstract
Plastids are pivotal target organelles for comprehensively enhancing photosynthetic and metabolic traits in plants via plastid engineering. Plastidial proteins predominantly originate in the nucleus and must traverse membrane-bound multiprotein translocons to access these organelles. This import process is meticulously regulated by chloroplast-targeting peptides (cTPs). Whereas many cTPs have been employed to guide recombinantly expressed functional proteins to chloroplasts, there is a critical need for more efficient cTPs. Here, we performed a comprehensive exploration and comparative assessment of an advanced suite of cTPs exhibiting superior targeting capabilities. We employed a multifaceted approach encompassing computational prediction, in planta expression, fluorescence tracking, and in vitro chloroplast import studies to identify and analyze 88 cTPs associated with Arabidopsis thaliana mutants with phenotypes linked to chloroplast function. These polypeptides exhibited distinct abilities to transport green fluorescent protein (GFP) to various compartments within leaf cells, particularly chloroplasts. A highly efficient cTP derived from Arabidopsis plastid ribosomal protein L35 (At2g24090) displayed remarkable effectiveness in chloroplast localization. This cTP facilitated the activities of chloroplast-targeted RNA-processing proteins and metabolic enzymes within plastids. This cTP could serve as an ideal transit peptide for precisely targeting biomolecules to plastids, leading to advancements in plastid engineering.
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Affiliation(s)
- Chonprakun Thagun
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Kyoto, Japan
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Masaki Odahara
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Kyoto, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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6
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Gontijo M, Pereira Teles M, Martins Correia H, Pérez Jorge G, Rodrigues Santos Goes IC, Fasabi Flores AJ, Braz M, de Moraes Ceseti L, Zonzini Ramos P, Rosa e Silva I, Pereira Vidigal PM, Kobarg J, Miguez Couñago R, Alvarez-Martinez CE, Pereira C, Freire CSR, Almeida A, Brocchi M. Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001462. [PMID: 38739436 PMCID: PMC11170124 DOI: 10.1099/mic.0.001462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 μg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 μg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 μg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 μg ml-1) and P. aeruginosa P2307 (65.00 μg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.
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Affiliation(s)
- Marco Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mateus Pereira Teles
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Hugo Martins Correia
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Genesy Pérez Jorge
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Research Group Statistics and Mathematical Modeling Applied to Educational Quality (GEMMA), University of Sucre, Sincelejo, Sucre, Colombia
| | - Isabella Carolina Rodrigues Santos Goes
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Anthony Jhoao Fasabi Flores
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Márcia Braz
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Lucas de Moraes Ceseti
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Ivan Rosa e Silva
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Viçosa, MG 36570-900, Brazil
| | - Jörg Kobarg
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Rafael Miguez Couñago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Cristina Elisa Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Carla Pereira
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Carmen S. R. Freire
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
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7
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Monzón S, Varona S, Negredo A, Vidal-Freire S, Patiño-Galindo JA, Ferressini-Gerpe N, Zaballos A, Orviz E, Ayerdi O, Muñoz-Gómez A, Delgado-Iribarren A, Estrada V, García C, Molero F, Sánchez-Mora P, Torres M, Vázquez A, Galán JC, Torres I, Causse Del Río M, Merino-Diaz L, López M, Galar A, Cardeñoso L, Gutiérrez A, Loras C, Escribano I, Alvarez-Argüelles ME, Del Río L, Simón M, Meléndez MA, Camacho J, Herrero L, Jiménez P, Navarro-Rico ML, Jado I, Giannetti E, Kuhn JH, Sanchez-Lockhart M, Di Paola N, Kugelman JR, Guerra S, García-Sastre A, Cuesta I, Sánchez-Seco MP, Palacios G. Monkeypox virus genomic accordion strategies. Nat Commun 2024; 15:3059. [PMID: 38637500 PMCID: PMC11026394 DOI: 10.1038/s41467-024-46949-7] [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: 09/06/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. Person-to-person transmission appears higher than for clade I or subclade IIa MPXV, possibly caused by genomic changes in subclade IIb MPXV. Key genomic changes could occur in the genome's low-complexity regions (LCRs), which are challenging to sequence and are often dismissed as uninformative. Here, using a combination of highly sensitive techniques, we determine a high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This reveals significant variation in short tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of single-nucleotide polymorphisms (SNPs) and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs), including OPG153, OPG204, and OPG208, could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. We posit that genomic studies focusing on phenotypic MPXV differences should consider LCR variability.
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Affiliation(s)
- Sara Monzón
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Sarai Varona
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Universidad Nacional de Educación a Distancia (UNED), 2832, Madrid, Spain
| | - Anabel Negredo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Santiago Vidal-Freire
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Angel Zaballos
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Oskar Ayerdi
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Ana Muñoz-Gómez
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | | | - Vicente Estrada
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Cristina García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Francisca Molero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Patricia Sánchez-Mora
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Montserrat Torres
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ana Vázquez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan-Carlos Galán
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Ignacio Torres
- Servicio de Microbiología, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, 46010, Valencia, Spain
| | - Manuel Causse Del Río
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, 14004, Córdoba, Spain
| | - Laura Merino-Diaz
- Unidad Clínico de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013, Sevilla, Spain
| | - Marcos López
- Servicio de Microbiología y Parasitología, Hospital Universitario Puerta de Hierro Majadahonda, 28222, Madrid, Spain
| | - Alicia Galar
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, 28007, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiología, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, 28006, Madrid, Spain
| | - Almudena Gutiérrez
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Cristina Loras
- Servicio de Microbiología, Hospital General y Universitario, 13005, Ciudad Real, Spain
| | - Isabel Escribano
- Servicio de Microbiología, Hospital General Universitario Dr. Balmis, 03010, Alicante, Spain
| | | | | | - María Simón
- Servicio de Microbiología, Hospital Central de la Defensa "Gómez Ulla", 28947, Madrid, Spain
| | - María Angeles Meléndez
- Servicio de Microbiología y Parasitología, Hospital Universitario 12 de Octubre, 28041, Madrid, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Laura Herrero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Jiménez
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Luisa Navarro-Rico
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel Jado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Elaina Giannetti
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
| | - Mariano Sanchez-Lockhart
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Nicholas Di Paola
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Jeffrey R Kugelman
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Susana Guerra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departmento de Medicina Preventiva, Salud Publica y Microbiología, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Isabel Cuesta
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maripaz P Sánchez-Seco
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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8
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Xu K, Yu S, Wang K, Tan Y, Zhao X, Liu S, Zhou J, Wang X. AI and Knowledge-Based Method for Rational Design of Escherichia coli Sigma70 Promoters. ACS Synth Biol 2024; 13:402-407. [PMID: 38176073 DOI: 10.1021/acssynbio.3c00578] [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: 01/06/2024]
Abstract
Expanding sigma70 promoter libraries can support the engineering of metabolic pathways and enhance recombinant protein expression. Herein, we developed an artificial intelligence (AI) and knowledge-based method for the rational design of sigma70 promoters. Strong sigma70 promoters were identified by using high-throughput screening (HTS) with enhanced green fluorescent protein (eGFP) as a reporter gene. The features of these strong promoters were adopted to guide promoter design based on our previous reported deep learning model. In the following case study, the obtained strong promoters were used to express collagen and microbial transglutaminase (mTG), resulting in increased expression levels by 81.4% and 33.4%, respectively. Moreover, these constitutive promoters achieved soluble expression of mTG-activating protease and contributed to active mTG expression in Escherichia coli. The results suggested that the combined method may be effective for promoter engineering.
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Affiliation(s)
- Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shangyang Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kun Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinyi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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9
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Perez LJ, Cloherty GA, Berg MG. Parallel evolution of picobirnaviruses from distinct ancestral origins. Microbiol Spectr 2023; 11:e0269323. [PMID: 37888988 PMCID: PMC10714727 DOI: 10.1128/spectrum.02693-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Picobirnaviruses (PBVs) are highly heterogeneous viruses encoding a capsid and RdRp. Detected in a wide variety of animals with and without disease, their association with gastrointestinal and respiratory infections, and consequently their public health importance, has rightly been questioned. Determining the "true" host of Picobirnavirus lies at the center of this debate, as evidence exists for them having both vertebrate and prokaryotic origins. Using integrated and time-stamped phylogenetic approaches, we show they are contemporaneous viruses descending from two different ancestors: avian Reovirus and fungal Partitivirus. The fungal PBV-R2 species emerged with a single segment (RdRp) until it acquired a capsid from vertebrate PBV-R1 and PBV-R3 species. Protein and RNA folding analyses revealed how the former came to resemble the latter over time. Thus, parallel evolution from disparate hosts has driven the adaptation and genetic diversification of the Picobirnaviridae family.
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Affiliation(s)
- Lester J. Perez
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Chicago, Illinois, USA
| | - Gavin A. Cloherty
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Chicago, Illinois, USA
| | - Michael G. Berg
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Chicago, Illinois, USA
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10
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Wang X, Xu K, Tan Y, Yu S, Zhao X, Zhou J. Deep Learning-Assisted Design of Novel Promoters in Escherichia coli. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2300184. [PMID: 38099247 PMCID: PMC10716054 DOI: 10.1002/ggn2.202300184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Indexed: 12/17/2023]
Abstract
Deep learning (DL) approaches have the ability to accurately recognize promoter regions and predict their strength. Here, the potential for controllably designing active Escherichia coli promoter is explored by combining multiple deep learning models. First, "DRSAdesign," which relies on a diffusion model to generate different types of novel promoters is created, followed by predicting whether they are real or fake and strength. Experimental validation showed that 45 out of 50 generated promoters are active with high diversity, but most promoters have relatively low activity. Next, "Ndesign," which relies on generating random sequences carrying functional -35 and -10 motifs of the sigma70 promoter is introduced, and their strength is predicted using the designed DL model. The DL model is trained and validated using 200 and 50 generated promoters, and displays Pearson correlation coefficients of 0.49 and 0.43, respectively. Taking advantage of the DL models developed in this work, possible 6-mers are predicted as key functional motifs of the sigma70 promoter, suggesting that promoter recognition and strength prediction mainly rely on the accommodation of functional motifs. This work provides DL tools to design promoters and assess their functions, paving the way for DL-assisted metabolic engineering.
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Affiliation(s)
- Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Shangyang Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Xinyi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan UniversityWuxi214122China
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11
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Yang L, Yang Y, Huang L, Cui X, Liu Y. From single- to multi-omics: future research trends in medicinal plants. Brief Bioinform 2022; 24:6840072. [PMID: 36416120 PMCID: PMC9851310 DOI: 10.1093/bib/bbac485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022] Open
Abstract
Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies of medicinal plants have been performed to identify molecular markers of species and functional genes controlling key biological traits, as well as to understand biosynthetic pathways of bioactive metabolites and the regulatory mechanisms of environmental responses. Omics technologies have been widely applied to medicinal plants, including as taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics and mutagenomics. However, because of the complex biological regulation network, single omics usually fail to explain the specific biological phenomena. In recent years, reports of integrated multi-omics studies of medicinal plants have increased. Until now, there have few assessments of recent developments and upcoming trends in omics studies of medicinal plants. We highlight recent developments in omics research of medicinal plants, summarise the typical bioinformatics resources available for analysing omics datasets, and discuss related future directions and challenges. This information facilitates further studies of medicinal plants, refinement of current approaches and leads to new ideas.
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Affiliation(s)
- Lifang Yang
- Kunming University of Science and Technology, China
| | - Ye Yang
- Kunming University of Science and Technology, China
| | - Luqi Huang
- the academician of the Chinese Academy of Engineering, studies the development of traditional Chinese medicine, Chinese Academy of Chinese Medical Sciences, China
| | - Xiuming Cui
- Corresponding authors. X. M. Cui, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail: ; Y. Liu, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail:
| | - Yuan Liu
- Corresponding authors. X. M. Cui, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail: ; Y. Liu, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail:
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12
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Cordeiro TFVB, Gontijo MTP, Jorge GP, Brocchi M. EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes. Microorganisms 2022; 10:microorganisms10101945. [PMID: 36296221 PMCID: PMC9610160 DOI: 10.3390/microorganisms10101945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022] Open
Abstract
Genomic compaction is an essential characteristic of living organisms. Nucleoid-associated proteins (NAPs) are a group of small proteins that play crucial roles in chromosome architecture and affect DNA replication, transcription, and recombination by imposing topological alterations in genomic DNA, thereby modulating global gene expression. EbfC/YbaB was first described as a DNA-binding protein of Borrelia burgdorferi that regulates the expression of surface lipoproteins with roles in virulence. Further studies indicated that this protein binds specifically and non-specifically to DNA and colocalises with nucleoids in this bacterium. The data showed that this protein binds to DNA as a homodimer, although it can form other organised structures. Crystallography analysis indicated that the protein possesses domains responsible for protein–protein interactions and forms a “tweezer” structure probably involved in DNA binding. Moreover, sequence analysis revealed conserved motifs that may be associated with dimerisation. Structural analysis also showed that the tridimensional structure of EbfC/YbaB is highly conserved within the bacterial domain. The DNA-binding activity was observed in different bacterial species, suggesting that this protein can protect DNA during stress conditions. These findings indicate that EbfC/YbaB is a broadly distributed NAP. Here, we present a review of the existing data on this NAP.
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