1
|
Fernandez-de-Cossio-Diaz J. Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines. Methods Mol Biol 2025; 2847:163-175. [PMID: 39312143 DOI: 10.1007/978-1-0716-4079-1_11] [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: 09/25/2024]
Abstract
In this chapter, we discuss the potential application of Restricted Boltzmann machines (RBM) to model sequence families of structured RNA molecules. RBMs are a simple two-layer machine learning model able to capture intricate sequence dependencies induced by secondary and tertiary structure, as well as mechanisms of structural flexibility, resulting in a model that can be successfully used for the design of allosteric RNA such as riboswitches. They have recently been experimentally validated as generative models for the SAM-I riboswitch aptamer domain sequence family. We introduce RBM mathematically and practically, providing self-contained code examples to download the necessary training sequence data, train the RBM, and sample novel sequences. We present in detail the implementation of algorithms necessary to use RBMs, focusing on applications in biological sequence modeling.
Collapse
|
2
|
Li D, Li H, Feng H, Qi P, Wu Z. Unveiling kiwifruit TCP genes: evolution, functions, and expression insights. PLANT SIGNALING & BEHAVIOR 2024; 19:2338985. [PMID: 38597293 PMCID: PMC11008546 DOI: 10.1080/15592324.2024.2338985] [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: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.
Collapse
Affiliation(s)
- Donglin Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Haibo Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Huimin Feng
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Ping Qi
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhicheng Wu
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| |
Collapse
|
3
|
Theodosiou T, Vrettos K, Baltsavia I, Baltoumas F, Papanikolaou N, Antonakis AΝ, Mossialos D, Ouzounis CA, Promponas VJ, Karaglani M, Chatzaki E, Brandau S, Pavlopoulos GA, Andreakos E, Iliopoulos I. BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery. Comput Struct Biotechnol J 2024; 23:3247-3253. [PMID: 39279874 PMCID: PMC11399685 DOI: 10.1016/j.csbj.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/18/2024] Open
Abstract
The process of navigating through the landscape of biomedical literature and performing searches or combining them with bioinformatics analyses can be daunting, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related repositories. Herein, we present BioTextQuest v2.0, a tool for biomedical literature mining. BioTextQuest v2.0 is an open-source online web portal for document clustering based on sets of selected biomedical terms, offering efficient management of information derived from PubMed abstracts. Employing established machine learning algorithms, the tool facilitates document clustering while allowing users to customize the analysis by selecting terms of interest. BioTextQuest v2.0 streamlines the process of uncovering valuable insights from biomedical research articles, serving as an agent that connects the identification of key terms like genes/proteins, diseases, chemicals, Gene Ontology (GO) terms, functions, and others through named entity recognition, and their application in biological research. Instead of manually sifting through articles, researchers can enter their PubMed-like query and receive extracted information in two user-friendly formats, tables and word clouds, simplifying the comprehension of key findings. The latest update of BioTextQuest leverages the EXTRACT named entity recognition tagger, enhancing its ability to pinpoint various biological entities within text. BioTextQuest v2.0 acts as a research assistant, significantly reducing the time and effort required for researchers to identify and present relevant information from the biomedical literature.
Collapse
Affiliation(s)
- Theodosios Theodosiou
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Konstantinos Vrettos
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Ismini Baltsavia
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Fotis Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Athens 16672, Greece
| | - Nikolas Papanikolaou
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Andreas Ν Antonakis
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Dimitrios Mossialos
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Christos A Ouzounis
- Biological Computation & Computational Biology Group, AIIA Lab, School of Informatics, Aristotle University of Thessalonica, 57001 Thessalonica, Greece
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia 1678, Cyprus
| | - Makrina Karaglani
- Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ekaterini Chatzaki
- Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Sven Brandau
- Experimental and Translational Research, Department of Otorhinolaryngology, University Hospital Essen, Essen, Germany
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Athens 16672, Greece
| | - Evangelos Andreakos
- Center for Immunology and Transplantation, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Ioannis Iliopoulos
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| |
Collapse
|
4
|
Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
Collapse
Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| |
Collapse
|
5
|
Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [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: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
Collapse
Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| |
Collapse
|
6
|
Chanket W, Pipatthana M, Sangphukieo A, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T, Phanchana M. The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective. Comput Struct Biotechnol J 2024; 23:2358-2374. [PMID: 38873647 PMCID: PMC11170357 DOI: 10.1016/j.csbj.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.
Collapse
Affiliation(s)
- Wannarat Chanket
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Methinee Pipatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
7
|
Pham C, Stogios PJ, Savchenko A, Mahadevan R. Computation-guided transcription factor biosensor specificity engineering for adipic acid detection. Comput Struct Biotechnol J 2024; 23:2211-2219. [PMID: 38817964 PMCID: PMC11137364 DOI: 10.1016/j.csbj.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
Transcription factor (TF)-based biosensors that connect small-molecule sensing with readouts such as fluorescence have proven to be useful synthetic biology tools for applications in biotechnology. However, the development of specific TF-based biosensors is hindered by the limited repertoire of TFs specific for molecules of interest since current construction methods rely on a limited set of characterized TFs. In this study, we present an approach for engineering the specificity of TFs through a computation-based workflow using molecular docking that enables targeted alteration of TF ligand specificity. Using this method, we engineer the LysR family BenM TF to alter its specificity from its cognate ligand cis,cis-muconic acid to adipic acid through a single amino acid substitution identified by our computational workflow. When implemented in a cell-free system, the engineered biosensor shows higher ligand sensitivity, expanding the potential applications of this circuit. We further investigate ligand binding through molecular dynamics to analyze the substitution, elucidating the impact of modulating a single amino acid position on the mechanism of BenM ligand binding. This study represents the first application of biomolecular modeling methods for altering BenM specificity and for gaining insights into how mutations influence the structural dynamics of BenM. Such methods can potentially be applied to other TFs to alter specificity and analyze the dynamics responsible for these changes, highlighting the applicability of computational tools for informing experiments. In addition, our developed adipic acid biosensor can be applied for the identification and engineering of enzymes to produce adipic acid.
Collapse
Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
- The Institute of Biomedical Engineering, University of Toronto, Ontario, Canada
| |
Collapse
|
8
|
Nana Teukam YG, Kwate Dassi L, Manica M, Probst D, Schwaller P, Laino T. Language models can identify enzymatic binding sites in protein sequences. Comput Struct Biotechnol J 2024; 23:1929-1937. [PMID: 38736695 PMCID: PMC11087710 DOI: 10.1016/j.csbj.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 05/14/2024] Open
Abstract
Recent advances in language modeling have had a tremendous impact on how we handle sequential data in science. Language architectures have emerged as a hotbed of innovation and creativity in natural language processing over the last decade, and have since gained prominence in modeling proteins and chemical processes, elucidating structural relationships from textual/sequential data. Surprisingly, some of these relationships refer to three-dimensional structural features, raising important questions on the dimensionality of the information encoded within sequential data. Here, we demonstrate that the unsupervised use of a language model architecture to a language representation of bio-catalyzed chemical reactions can capture the signal at the base of the substrate-binding site atomic interactions. This allows us to identify the three-dimensional binding site position in unknown protein sequences. The language representation comprises a reaction-simplified molecular-input line-entry system (SMILES) for substrate and products, and amino acid sequence information for the enzyme. This approach can recover, with no supervision, 52.13% of the binding site when considering co-crystallized substrate-enzyme structures as ground truth, vastly outperforming other attention-based models.
Collapse
Affiliation(s)
| | - Loïc Kwate Dassi
- IBM Research Europe, Saümerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Matteo Manica
- IBM Research Europe, Saümerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Daniel Probst
- IBM Research Europe, Saümerstrasse 4, 8803 Rüschlikon, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Switzerland
| | - Philippe Schwaller
- IBM Research Europe, Saümerstrasse 4, 8803 Rüschlikon, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Switzerland
| | - Teodoro Laino
- IBM Research Europe, Saümerstrasse 4, 8803 Rüschlikon, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Switzerland
| |
Collapse
|
9
|
Qin T, Han J, Fan C, Sun H, Rauf N, Wang T, Yin Z, Chen X. Unveiling axolotl transcriptome for tissue regeneration with high-resolution annotation via long-read sequencing. Comput Struct Biotechnol J 2024; 23:3186-3198. [PMID: 39263210 PMCID: PMC11388199 DOI: 10.1016/j.csbj.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024] Open
Abstract
Axolotls are known for their remarkable regeneration ability. Exploring their transcriptome provides insight into regenerative mechanisms. However, the current annotation of the axolotl transcriptome is limited, leaving the role of unannotated transcripts in regeneration unknown. To discourse this challenge, we exploited long-read sequencing technology, which enables direct observation of full-length RNA transcripts, greatly enhancing the coverage and accuracy of axolotl transcriptome annotation. By utilizing this method, we identified 222 novel gene loci and 4775 novel transcripts, which were quantified using short-read sequencing data. Through the inclusive analysis, we discovered novel homologs, potential functional proteins, noncoding RNAs, and alternative splicing events in key regeneration pathways. In particular, we identified novel transcripts with high protein-coding potential implicated in cell cycle regulation and musculoskeletal development, and regeneration were identified. Interestingly, alternative splice variants were also detected across diverse pathways critical to regeneration. This specifies that these novel transcripts potentially play vital roles underpinning the robust regenerative capacities of axolotls. Single-cell transcriptomic analysis further revealed these isoforms to predominantly exist in axolotl limb chondrocytes and mature tissue cell populations. Overall, the findings significantly advanced consideration of the axolotl transcriptome and provided a new perspective for understanding the mechanisms of regenerative abilities of axolotls.
Collapse
Affiliation(s)
- Tian Qin
- Department of Orthopedic Surgery of Sir Run Run Shaw Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| | - Jie Han
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunmei Fan
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Heng Sun
- Medical 3D Printing Center, Orthopedic Institute, Department of Orthopedic Surgery, The First Affiliated Hospital, School of Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Naveed Rauf
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zi Yin
- Department of Orthopedic Surgery of Sir Run Run Shaw Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| | - Xiao Chen
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| |
Collapse
|
10
|
Rieseberg TP, Holzhausen A, Bierenbroodspot MJ, Zhang W, Abreu IN, de Vries J. Conserved carotenoid pigmentation in reproductive organs of Charophyceae. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230372. [PMID: 39343025 PMCID: PMC11449214 DOI: 10.1098/rstb.2023.0372] [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: 03/15/2024] [Revised: 05/10/2024] [Accepted: 06/19/2024] [Indexed: 10/01/2024] Open
Abstract
Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red-probably protectant-pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'.
Collapse
Affiliation(s)
- Tim P Rieseberg
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Anja Holzhausen
- Department of Crop Physiology, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty Heimann-Str. 5 , Halle (Saale) 06120, Germany
| | - Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Wanchen Zhang
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Ilka N Abreu
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Plant Biochemistry, Albrecht Haller Institute of Plant Science, Justus-von-Liebig-Weg, University of Goettingen , Goettingen 37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, Justus-von-Liebig Weg 11, University of Goettingen , Goettingen 37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Applied Bioinformatics, Campus Institute Data Science, University of Goettingen , Goettingen 37077, Germany
| |
Collapse
|
11
|
Alvarez D, Yang Y, Saito Y, Balakrishna A, Goto K, Gojobori T, Al-Babili S. Characterization of a β-carotene isomerase from the cyanobacterium Cyanobacteria aponinum. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230360. [PMID: 39343012 PMCID: PMC11449226 DOI: 10.1098/rstb.2023.0360] [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: 06/08/2024] [Accepted: 06/26/2024] [Indexed: 10/01/2024] Open
Abstract
Carotenoids are essential components of the photosynthetic apparatus and precursors of plant hormones, such as strigolactones (SLs). SLs are involved in various aspects of plant development and stress-response processes, including the establishment of root and shoot architecture. SL biosynthesis begins with the reversible isomerization of all-trans-carotene into 9-cis-β-carotene, catalysed by DWARF27 β-carotene isomerase (D27). Sequence comparisons have revealed the presence of D27-related proteins in photosynthetic eukaryotes and cyanobacteria lacking SLs. To gain insight into the evolution of SL biosynthesis, we characterized the activity of a cyanobacterial D27 protein (CaD27) from Cyanobacterim aponinum, using carotenoid-accumulating Escherichia coli cells and in vitro enzymatic assays. Our results demonstrate that CaD27 is an all-trans/cis and cis/cis-β-carotene isomerase, with a cis/cis conversion preference. CaD27 catalysed 13-cis/15-cis-, all-trans/9-cis-β-carotene, and neurosporene isomerization. Compared with plant enzymes, it exhibited a lower 9-cis-/all-trans-β-carotene conversion ratio. A comprehensive genome survey revealed the presence of D27 as a single-copy gene in the genomes of 20 out of 200 cyanobacteria species analysed. Phylogenetic and enzymatic analysis of CaD27 indicated that cyanobacterial D27 genes form a single orthologous group, which is considered an ancestral type of those found in photosynthetic eukaryotes. This article is part of the theme issue 'The evolution of plant metabolism'.
Collapse
Affiliation(s)
- Derry Alvarez
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
| | - Yu Yang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
| | - Yoshimoto Saito
- Marine Open Innovation (MaOI) Institute, 9-25 Hinodecho, Shimizu-ku, Shizuoka424-0922, Japan
| | - Aparna Balakrishna
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
| | - Kosuke Goto
- Marine Open Innovation (MaOI) Institute, 9-25 Hinodecho, Shimizu-ku, Shizuoka424-0922, Japan
| | - Takashi Gojobori
- Marine Open Innovation (MaOI) Institute, 9-25 Hinodecho, Shimizu-ku, Shizuoka424-0922, Japan
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal23955-6900, Saudi Arabia
| |
Collapse
|
12
|
Chen T, Deng C, Li S, Li B, Liang Y, Zhang Y, Li J, Xu N, Yu K. Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135669. [PMID: 39208627 DOI: 10.1016/j.jhazmat.2024.135669] [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: 06/22/2024] [Revised: 07/30/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.
Collapse
Affiliation(s)
- Tianyi Chen
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China
| | - Chunfang Deng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China.
| | - Shaoyang Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Bing Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Yuanyan Zhang
- Jiangxi Academy of Eco-Environmental Sciences & Planning, Nanchang 330029, PR China
| | - Jiarui Li
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China
| | - Nan Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| |
Collapse
|
13
|
Teixeira CSS, Carriço-Sá B, Villa C, Mafra I, Costa J. Can Physicochemical Properties Alter the Potency of Aeroallergens? Part 1 - Aeroallergen Protein Families. Curr Allergy Asthma Rep 2024; 24:591-607. [PMID: 39302571 PMCID: PMC11464574 DOI: 10.1007/s11882-024-01172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2024] [Indexed: 09/22/2024]
Abstract
PURPOSE OF REVIEW Respiratory allergies are non-communicable diseases caused by the hypersensitivity of the immune system to environmental aeroallergens. The culprits are aero-transported proteins eliciting respiratory symptoms in sensitized/allergic individuals. This review intends to provide a holistic overview on the categorization of aeroallergens into protein families (Part 1) and to exploit the impact of physicochemical properties on inhalant protein allergenicity (Part 2). This first part will focus particularly on aeroallergen organization into families and how this classification fits their physicochemical properties. RECENT FINDINGS Aeroallergen classification into protein families facilitates the identification of common physicochemical properties, thus aiding a better comprehension of known allergens, while predicting the behavior of novel ones. The available online databases gathering important features of aeroallergens are currently scarce. Information on distinct aeroallergen classification is still lacking, as data is dispersed and often outdated, hampering an efficient evaluation of new aeroallergens.
Collapse
Affiliation(s)
- Carla S S Teixeira
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Bruno Carriço-Sá
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
| |
Collapse
|
14
|
Olivieri FA, Marti MA, Wetzler DE. Phosphorylation Mechanism Switching in Histidine Kinases Is a Tool for Fast Protein Evolution: Insights From AlphaFold Models. Proteins 2024; 92:1276-1286. [PMID: 38884545 DOI: 10.1002/prot.26708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/08/2024] [Accepted: 05/25/2024] [Indexed: 06/18/2024]
Abstract
Histidine kinases (HKs) are a central part of bacterial environmental-sensing two-component systems. They provide their hosts with the ability to respond to a wide range of physical and chemical signals. HKs are multidomain proteins consisting of at least a sensor domain, dimerization and phosphorylation domain (DHp), and a catalytic domain. They work as homodimers and the existence of two different autophosphorylation mechanisms (cis and trans) has been proposed as relevant for pathway specificity. Although several HKs have been intensively studied, a precise sequence-to-structure explanation of why and how either cis or trans phosphorylation occurs is still unavailable nor is there any evolutionary analysis on the subject. In this work, we show that AlphaFold can accurately determine whether an HK dimerizes in a cis or trans structure. By modeling multiple HKs we show that both cis- and trans-acting HKs are common in nature and the switch between mechanisms has happened multiple times in the evolutionary history of the family. We then use AlphaFold modeling to explore the molecular determinants of the phosphorylation mechanism. We conclude that it is the difference in lengths of the helices surrounding the DHp loop that determines the mechanism. We also show that very small changes in these helices can cause a mechanism switch. Despite this, previous evidence shows that for a particular HK the phosphorylation mechanism is conserved. This suggests that the phosphorylation mechanism participates in system specificity and mechanism switching provides these systems with a way to diverge.
Collapse
Affiliation(s)
- Federico A Olivieri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
| | - Diana E Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
| |
Collapse
|
15
|
Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with FecB BB genotype. Anim Biotechnol 2024; 35:2312393. [PMID: 38421365 DOI: 10.1080/10495398.2024.2312393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
BACKGROUND The thyroid gland is an important endocrine gland in animals that secretes thyroid hormones and acts on various organs throughout the body. lncRNAs are long non-coding RNAs that play an important role in animal reproduction; however, there is a lack of understanding of their expression patterns and potential roles in the thyroid gland of the Small Tail Han (STH) sheep. In this study, we used RNA-Seq technology to examine the transcriptome expression pattern of the thyroid from the luteal phase (LP) and follicular phase (FP) of FecB BB (MM) STH sheep. RESULTS We identified a total of 122 and 1287 differential expression lncRNAs (DELs) and differential expression mRNAs (DEGs), respectively, which were significantly differentially expressed. These DELs target genes and DEGs can be enriched in several signalling pathways related to the animal reproduction process. CONCLUSIONS The expression profiles of DELs and DEGs in thyroid glands provide a more comprehensive resource for elucidating the reproductive regulatory mechanisms of STH sheep.
Collapse
Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
16
|
Barbosa PGP, Rosse I, Bessa MASEF, Silva DF, Saraiva MAF, Cunha AC, Moraes L, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM, Trópia MJM, Castro IM, Brandão RL. Genomic approachesidentifySTT4 as a new component in glucose-induced activation of yeast plasma membrane H +-ATPase. Cell Calcium 2024; 123:102909. [PMID: 38861767 DOI: 10.1016/j.ceca.2024.102909] [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: 04/09/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
Many studies have focused on identifying the signaling pathway by which addition of glucose triggers post-translational activation of the plasma membrane H+-ATPase in yeast. They have revealed that calcium signaling is involved in the regulatory pathway, supported for instance by the phenotype of mutants inARG82 that encodes an inositol kinase that phosphorylates inositol triphosphate (IP3). Strong glucose-induced calcium signaling, and high glucose-induced plasma membrane H+-ATPase activation have been observed in a specific yeast strain with the PJ genetic background. In this study, we have applied pooled-segregant whole genome sequencing, QTL analysis and a new bioinformatics methodology for determining SNP frequencies to identify the cause of this discrepancy and possibly new components of the signaling pathway. This has led to the identification of an STT4 allele with 6 missense mutations as a major causative allele, further supported by the observation that deletion of STT4 in the inferior parent caused a similar increase in glucose-induced plasma membrane H+-ATPase activation. However, the effect on calcium signaling was different indicating the presence of additional relevant genetic differences between the superior and reference strains. Our results suggest that phosphatidylinositol-4-phosphate might play a role in the glucose-induced activation of plasma membrane H+-ATPase by controlling intracellular calcium release through the modulation of the activity of phospholipase C.
Collapse
Affiliation(s)
| | - Izinara Rosse
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia; Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | | | - Débora Faria Silva
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia
| | | | - Aureliano Claret Cunha
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia
| | - Lauro Moraes
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia; Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium; Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium; Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium; Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | | | - Ieso Miranda Castro
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia.
| |
Collapse
|
17
|
Chow CFW, Ghosh S, Hadarovich A, Toth-Petroczy A. SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences. Proc Natl Acad Sci U S A 2024; 121:e2401622121. [PMID: 39383002 DOI: 10.1073/pnas.2401622121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/30/2024] [Indexed: 10/11/2024] Open
Abstract
Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite them comprising ~21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment-based approaches in assessing evolutionary homology in unalignable sequences. Furthermore, it correctly identified dissimilar but functionally analogous IDRs in IDR-replacement experiments reported in the literature, whereas alignment-based tools were incapable of detecting such functional relationships. SHARK-dive not only predicts functionally similar IDRs at a proteome-wide scale but also identifies cryptic sequence properties and motifs that drive remote homology and analogy, thereby providing interpretable and experimentally verifiable hypotheses of the sequence determinants that underlie such relationships. SHARK-dive acts as an alternative to alignment to facilitate systematic analysis and functional annotation of the unalignable protein universe.
Collapse
Affiliation(s)
- Chi Fung Willis Chow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden 01062, Germany
| | - Soumyadeep Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
| | - Anna Hadarovich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden 01062, Germany
| |
Collapse
|
18
|
Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS. Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. Proc Natl Acad Sci U S A 2024; 121:e2408249121. [PMID: 39388274 DOI: 10.1073/pnas.2408249121] [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: 04/24/2024] [Accepted: 08/29/2024] [Indexed: 10/12/2024] Open
Abstract
ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here, we identify C12orf29 (RLIG1) as an atypical ATP-grasp enzyme that ligates RNA. Human RLIG1 and its homologs autoadenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. RLIG1 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Transcriptomic analyses of Rlig1 knockout mice revealed significant alterations in global tRNA levels in the brains of female mice, but not in those of male mice. Furthermore, crystal structures of a RLIG1 homolog from Yasminevirus bound to nucleotides revealed a minimal and atypical RNA ligase fold with a conserved active site architecture that participates in catalysis. Collectively, our results identify RLIG1 as an RNA ligase and suggest its involvement in tRNA biology.
Collapse
Affiliation(s)
- Yingjie Hu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Victor A Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hengyi Xu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, University of Texas at Austin, Austin, TX 78712
| | - James P Pfister
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bing Song
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Alan M Lambowitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, University of Texas at Austin, Austin, TX 78712
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| |
Collapse
|
19
|
Salcedo-Tacuma D, Howells GD, McHose C, Gutierrez-Diaz A, Schupp J, Smith DM. ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life. BMC Genomics 2024; 25:951. [PMID: 39396964 DOI: 10.1186/s12864-024-10864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 10/03/2024] [Indexed: 10/15/2024] Open
Abstract
The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were experimentally tested by pulldowns, confirming that they directly interact with the proteasome, with one of them directly activating it. ProEnd's extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer.
Collapse
Affiliation(s)
- David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Giovanni D Howells
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Coleman McHose
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Aimer Gutierrez-Diaz
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Jane Schupp
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
| |
Collapse
|
20
|
Chen C, Buscaill P, Sanguankiattichai N, Huang J, Kaschani F, Kaiser M, van der Hoorn RAL. Extracellular plant subtilases dampen cold-shock peptide elicitor levels. NATURE PLANTS 2024:10.1038/s41477-024-01815-8. [PMID: 39394507 DOI: 10.1038/s41477-024-01815-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/05/2024] [Indexed: 10/13/2024]
Abstract
Recognizing pathogen-associated molecular patterns on the cell surface is crucial for plant immunity. The proteinaceous nature of many of these patterns suggests that secreted proteases play important roles in their formation and stability. Here we demonstrate that the apoplastic subtilase SBT5.2a inactivates the immunogenicity of cold-shock proteins (CSPs) of the bacterial plant pathogen Pseudomonas syringae by cleaving within the immunogenic csp22 epitope. Consequently, mutant plants lacking SBT5.2a activity retain higher levels of csp22, leading to enhanced immune responses and reduced pathogen growth. SBT5.2 sensitivity is influenced by sequence variation surrounding the cleavage site and probably extends to CSPs from other bacterial species. These findings suggest that variations in csp22 stability among bacterial pathogens are a crucial factor in plant-bacteria interactions and that pathogens exploit plant proteases to avoid pattern recognition.
Collapse
Affiliation(s)
- Changlong Chen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Pierre Buscaill
- Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | | | - Jie Huang
- Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | |
Collapse
|
21
|
Cauldron NC, Shea T, Cuomo CA. Improved genome assembly of Candida auris strain B8441 and annotation of B11205. Microbiol Resour Announc 2024; 13:e0051224. [PMID: 39177371 PMCID: PMC11465782 DOI: 10.1128/mra.00512-24] [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: 05/16/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
Candida auris is a fungal pathogen of significant worldwide concern, typically resistant to one or more antifungal drugs. We report a completed genome for clade Ia isolate B8441 and gene annotations of clade Ic isolate B11205. These resources will support public health investigations and population genomic studies of this pathogen.
Collapse
Affiliation(s)
- Nicholas C. Cauldron
- Department of Molecular Microbiology & Immunology, Brown University, Providence, Rhode Island, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christina A. Cuomo
- Department of Molecular Microbiology & Immunology, Brown University, Providence, Rhode Island, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
22
|
Berner K, Zoza-Veloz M, Nolan M, Graham D, Ivanova N, Seshadri R, Spring S, Escobar M. Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615 T) and Butyrivibrio fibrisolvens DSM 3071 (D1 T). Microbiol Resour Announc 2024; 13:e0051724. [PMID: 39194265 PMCID: PMC11465783 DOI: 10.1128/mra.00517-24] [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: 05/14/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Here, we report the draft genome sequences of two Butyrivibrio-type strains isolated from rumen fluid. The genome sequence of Butyrivibrio hungatei DSM 14810 was 3.3 Mb with 3,093 predicted genes, while the Butyrivibrio fibrisolvens DSM 3071 genome sequence was 4.8 Mb with 4,132 predicted genes.
Collapse
Affiliation(s)
- Keely Berner
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Michelle Zoza-Veloz
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Matt Nolan
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Danielle Graham
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthew Escobar
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| |
Collapse
|
23
|
Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y. Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response. CELL GENOMICS 2024; 4:100654. [PMID: 39288763 DOI: 10.1016/j.xgen.2024.100654] [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: 06/21/2023] [Revised: 04/04/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024]
Abstract
Type I interferon (IFN-I) plays an important role in the innate immune response through inducing IFN-I-stimulated genes (ISGs). However, how alternative splicing (AS) events, especially over time, affect their function remains poorly understood. We generated an annotation (113,843 transcripts) for IFN-I-stimulated human B cells called isoISG using high-accuracy long-read sequencing data from PacBio Sequel II/IIe. Transcript isoform profiling using isoISG revealed that isoform switching occurred in the early response to IFN-I so that ISGs would gain functional domains (e.g., C4B) or higher protein production (e.g., IRF3). Conversely, isoforms lacking functional domains increased during the late phase of IFN-I response, mainly due to intron retention events. This suggests that isoform switching both triggers and terminates IFN-I responses at the translation and protein levels. Furthermore, genetic variants influencing the isoform ratio of ISGs were associated with immunological and infectious diseases. AS has essential roles in regulating innate immune response and associated diseases.
Collapse
Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Jun Inamo
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA; Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mihoko Shimada
- National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Kensuke Yamaguchi
- Biomedical Engineering Research Innovation Center, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
24
|
Samuel B, Mittelman K, Croitoru SY, Ben Haim M, Burstein D. Diverse anti-defence systems are encoded in the leading region of plasmids. Nature 2024:10.1038/s41586-024-07994-w. [PMID: 39385022 DOI: 10.1038/s41586-024-07994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
Abstract
Plasmids are major drivers of gene mobilization by means of horizontal gene transfer and play a key role in spreading antimicrobial resistance among pathogens1,2. Despite various bacterial defence mechanisms such as CRISPR-Cas, restriction-modification systems and SOS-response genes that prevent the invasion of mobile genetic elements3, plasmids robustly transfer within bacterial populations through conjugation4,5. Here we show that the leading region of plasmids, the first to enter recipient cells, is a hotspot for an extensive repertoire of anti-defence systems, encoding anti-CRISPR, anti-restriction, anti-SOS and other counter-defence proteins. We further identified in the leading region a prevalence of promoters known to allow expression from single-stranded DNA6, potentially facilitating rapid protection against bacterial immunity during the early stages of plasmid establishment. We demonstrated experimentally the importance of anti-defence gene localization in the leading region for efficient conjugation. These results indicate that focusing on the leading region of plasmids could lead to the discovery of diverse anti-defence genes. Combined, our findings show a new facet of plasmid dissemination and provide theoretical foundations for developing efficient conjugative delivery systems for natural microbial communities.
Collapse
Affiliation(s)
- Bruria Samuel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Karin Mittelman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shirly Ynbal Croitoru
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Ben Haim
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
| |
Collapse
|
25
|
de Oliveira FS, Azambuja M, Schemberger MO, Nascimento VD, Oliveira JIN, Wolf IR, Nogaroto V, Martins C, Vicari MR. Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp. Mol Genet Genomics 2024; 299:96. [PMID: 39382723 DOI: 10.1007/s00438-024-02190-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 09/28/2024] [Indexed: 10/10/2024]
Abstract
DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.
Collapse
Affiliation(s)
- Fernanda Souza de Oliveira
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Viviane Demetrio Nascimento
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Jordana Inácio Nascimento Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil.
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil.
| |
Collapse
|
26
|
Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution. Cell Host Microbe 2024; 32:1853-1867.e5. [PMID: 39293438 PMCID: PMC11466702 DOI: 10.1016/j.chom.2024.08.016] [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: 03/08/2024] [Revised: 06/27/2024] [Accepted: 08/22/2024] [Indexed: 09/20/2024]
Abstract
Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.
Collapse
Affiliation(s)
- Zhenrun J Zhang
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Cody G Cole
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Michael J Coyne
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Rita C Smith
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Téa E Pappas
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Shannon A Townson
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Nina Laliwala
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Emily Waligurski
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Che Woodson
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Jessica C Little
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - David Moran
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Amber Rose
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Mary McMillin
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Emma McSpadden
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Eric G Pamer
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, 5841 South Maryland Ave., Chicago, IL 60637, USA; Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA.
| | - Laurie E Comstock
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA.
| |
Collapse
|
27
|
Rhodes J, Jacobs J, Dennis EK, Manjari SR, Banavali NK, Marlow R, Rokebul MA, Chaturvedi S, Chaturvedi V. What makes Candida auris pan-drug resistant? Integrative insights from genomic, transcriptomic, and phenomic analysis of clinical strains resistant to all four major classes of antifungal drugs. Antimicrob Agents Chemother 2024; 68:e0091124. [PMID: 39297640 PMCID: PMC11459930 DOI: 10.1128/aac.00911-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 09/25/2024] Open
Abstract
The global epidemic of drug-resistant Candida auris continues unabated. The initial report on pan-drug resistant (PDR) C. auris strains in a hospitalized patient in New York was unprecedented. PDR C. auris showed both known and unique mutations in the prominent gene targets of azoles, amphotericin B, echinocandins, and flucytosine. However, the factors that allow C. auris to acquire pan-drug resistance are not known. Therefore, we conducted a genomic, transcriptomic, and phenomic analysis to better understand PDR C. auris. Among 1,570 genetic variants in drug-resistant C. auris, 299 were unique to PDR strains. The whole-genome sequencing results suggested perturbations in genes associated with nucleotide biosynthesis, mRNA processing, and nuclear export of mRNA. Whole transcriptome sequencing of PDR C. auris revealed two genes to be significantly differentially expressed-a DNA repair protein and DNA replication-dependent chromatin assembly factor 1. Of 59 novel transcripts, 12 transcripts had no known homology. We observed no fitness defects among multi-drug resistant (MDR) and PDR C. auris strains grown in nutrient-deficient or -enriched media at different temperatures. Phenotypic profiling revealed wider adaptability to nitrogenous nutrients and increased utilization of substrates critical in upper glycolysis and tricarboxylic acid cycle. Structural modeling of a 33-amino acid deletion in the gene for uracil phosphoribosyl transferase suggested an alternate route in C. auris to generate uracil monophosphate that does not accommodate 5-fluorouracil as a substrate. Overall, we find evidence of metabolic adaptations in MDR and PDR C. auris in response to antifungal drug lethality without deleterious fitness costs.
Collapse
Affiliation(s)
- Johanna Rhodes
- Department of Medical Microbiology, Radboudumc, Nijmegen, the Netherlands
- MRC GIDA, Imperial College London, London, United Kingdom
| | - Jonathan Jacobs
- American Type Culture Collection, University Blvd, Manassas, Virginia, USA
| | - Emily K. Dennis
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Swati R. Manjari
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Nilesh K. Banavali
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- School of Public Health, University of Albany, Albany, New York, USA
| | - Robert Marlow
- American Type Culture Collection, University Blvd, Manassas, Virginia, USA
| | | | - Sudha Chaturvedi
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- School of Public Health, University of Albany, Albany, New York, USA
| | - Vishnu Chaturvedi
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Westchester Medical Center/New York Medical College, Valhalla, New York, USA
| |
Collapse
|
28
|
Sun H, Chen Y, Ma L. MDVarP: modifier ~ disease-causing variant pairs predictor. BioData Min 2024; 17:39. [PMID: 39379981 PMCID: PMC11460193 DOI: 10.1186/s13040-024-00392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 09/28/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Modifiers significantly impact disease phenotypes by modulating the effects of disease-causing variants, resulting in varying disease manifestations among individuals. However, identifying genetic interactions between modifier and disease-causing variants is challenging. RESULTS We developed MDVarP, an ensemble model comprising 1000 random forest predictors, to identify modifier ~ disease-causing variant combinations. MDVarP achieves high accuracy and precision, as verified using an independent dataset with published evidence of genetic interactions. We identified 25 novel modifier ~ disease-causing variant combinations and obtained supporting evidence for these associations. MDVarP outputs a class label ("Associated-pair" or "Nonrelevant-pair") and two prediction scores indicating the probability of a true association. CONCLUSIONS MDVarP prioritizes variant pairs associated with phenotypic modulations, enabling more effective mapping of functional contributions from disease-causing and modifier variants. This framework interprets genetic interactions underlying phenotypic variations in human diseases, with potential applications in personalized medicine and disease prevention.
Collapse
Affiliation(s)
- Hong Sun
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China.
| | - Yunqin Chen
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, 200237, China
| | - Liangxiao Ma
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, Shanghai, 200031, China
| |
Collapse
|
29
|
Liu D, Luo C, Dai R, Huang X, Chen X, He L, Mao H, Li J, Zhang L, Yang QY, Mei Z. AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research. Nucleic Acids Res 2024:gkae833. [PMID: 39377391 DOI: 10.1093/nar/gkae833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/28/2024] [Accepted: 09/16/2024] [Indexed: 10/09/2024] Open
Abstract
As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR's capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.
Collapse
Affiliation(s)
- Dongxu Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengfang Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyan Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongxia Mao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Linna Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Yong Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572025, China
| | - Zhinan Mei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
30
|
Rigkos K, Filis G, Antonopoulou I, de Oliveira Maciel A, Saridis P, Zarafeta D, Skretas G. Biomimetic CO 2 Capture Unlocked through Enzyme Mining: Discovery of a Highly Thermo- and Alkali-Stable Carbonic Anhydrase. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17732-17742. [PMID: 39311668 PMCID: PMC11465738 DOI: 10.1021/acs.est.4c04291] [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: 04/30/2024] [Revised: 08/30/2024] [Accepted: 09/11/2024] [Indexed: 10/09/2024]
Abstract
Taking immediate action to combat the urgent threat of CO2-driven global warming is crucial for ensuring a habitable planet. Decarbonizing the industrial sector requires implementing sustainable carbon-capture technologies, such as biomimetic hot potassium carbonate capture (BioHPC). BioHPC is superior to traditional amine-based strategies due to its eco-friendly nature. This innovative technology relies on robust carbonic anhydrases (CAs), enzymes that accelerate CO2 hydration and endure harsh industrial conditions like high temperature and alkalinity. Thus, the discovery of highly stable CAs is crucial for the BioHPC technology advancement. Through high-throughput bioinformatics analysis, we identified a highly thermo- and alkali-stable CA, termed CA-KR1, originating from a metagenomic sample collected at a hot spring in Kirishima, Japan. CA-KR1 demonstrates remarkable stability at high temperatures and pH, with a half-life of 24 h at 80 °C and retains activity and solubility even after 30 d in a 20% (w/v) K2CO3/pH 11.5 solution─a standard medium for HPC. In pressurized batch reactions, CA-KR1 enhanced CO2 absorption by >90% at 90 °C, 20% K2CO3, and 7 bar. To our knowledge, CA-KR1 constitutes the most resilient CA biocatalyst for efficient CO2 capture under HPC-relevant conditions, reported to date. CA-KR1 integration into industrial settings holds great promise in promoting efficient BioHPC, a potentially game-changing development for enhancing carbon-capture capacity toward industrial decarbonization.
Collapse
Affiliation(s)
- Konstantinos Rigkos
- Institute
of Chemical Biology, National Hellenic Research
Foundation, Athens 11635, Greece
- Department
of Biological Applications and Technologies, University of Ioannina, Ioannina 45500, Greece
- Institute
for Bio-Innovation, Biomedical Sciences
Research Center “Alexander Fleming”, Vari 16672, Greece
| | - Georgios Filis
- Institute
of Chemical Biology, National Hellenic Research
Foundation, Athens 11635, Greece
- Institute
for Bio-Innovation, Biomedical Sciences
Research Center “Alexander Fleming”, Vari 16672, Greece
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
| | - Io Antonopoulou
- Biochemical
Process Engineering, Division of Chemical Engineering, Department
of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå 97187, Sweden
| | - Ayanne de Oliveira Maciel
- Biochemical
Process Engineering, Division of Chemical Engineering, Department
of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå 97187, Sweden
| | - Pavlos Saridis
- Institute
of Chemical Biology, National Hellenic Research
Foundation, Athens 11635, Greece
- Faculty of
Biology, National and Kapodistrian University
of Athens, Athens 15772, Greece
| | - Dimitra Zarafeta
- Institute
of Chemical Biology, National Hellenic Research
Foundation, Athens 11635, Greece
- Institute
for Bio-Innovation, Biomedical Sciences
Research Center “Alexander Fleming”, Vari 16672, Greece
| | - Georgios Skretas
- Institute
of Chemical Biology, National Hellenic Research
Foundation, Athens 11635, Greece
- Institute
for Bio-Innovation, Biomedical Sciences
Research Center “Alexander Fleming”, Vari 16672, Greece
| |
Collapse
|
31
|
Jaryenneh J, Krishna R, Schoeniger JS, Mageeney CM. Complete genome sequence of Rhodococcus qingshengii phage Perlina. Microbiol Resour Announc 2024:e0086924. [PMID: 39377611 DOI: 10.1128/mra.00869-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 09/05/2024] [Indexed: 10/09/2024] Open
Abstract
Rhodococcus phage Perlina is a novel phage isolated on Rhodococcus qingshengii S10. Perlina encodes 112 open reading frames with typical phage structural genes identified and 3 tRNAs (tRNA-Ile, tRNA-Met, and tRNA-Asn). Few close relatives can be identified at the nucleotide level, suggesting a new phage species.
Collapse
Affiliation(s)
| | - Rohan Krishna
- Sandia National Laboratories, Livermore, California, USA
| | | | | |
Collapse
|
32
|
Smit SJ, Whitehead C, James SR, Jeffares DC, Godden G, Peng D, Sun H, Lichman BR. Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata. G3 (BETHESDA, MD.) 2024; 14:jkae172. [PMID: 39047060 DOI: 10.1093/g3journal/jkae172] [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: 05/02/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
The Nepetoideae, a subfamily of Lamiaceae (mint family), is rich in aromatic plants, many of which are sought after for their use as flavors and fragrances or for their medicinal properties. Here, we present genome assemblies for two species in Nepetiodeae: Drepanocaruym sewerzowii and Marmoritis complanata. Both assemblies were generated using Oxford Nanopore Q20 + reads with contigs anchored to nine pseudomolecules that resulted in 335 Mb and 305 Mb assemblies, respectively, and BUSCO scores above 95% for both the assembly and annotation. We furthermore provide a species tree for the Lamiaceae using only genome-derived gene models, complementing existing transcriptome and marker-based phylogenies.
Collapse
Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Caragh Whitehead
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Sally R James
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Daniel C Jeffares
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Deli Peng
- School of Life Science, Yunnan Normal University, Kunming 650092, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
33
|
Liu G, Li X, Guan J, Tai C, Weng Y, Chen X, Ou HY. oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements. Nucleic Acids Res 2024:gkae869. [PMID: 39373502 DOI: 10.1093/nar/gkae869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/12/2024] [Accepted: 09/23/2024] [Indexed: 10/08/2024] Open
Abstract
Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.
Collapse
Affiliation(s)
- Guitian Liu
- Department of Infectious Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai 519000, China
| | - Jiahao Guan
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqing Weng
- Department of Pulmonary and Critical Care Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai 519000, China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Hong-Yu Ou
- Department of Infectious Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
34
|
Coyle MC, Elya CN, Bronski MJ, Eisen MB. Entomophthovirus: an insect-derived iflavirus that infects a behavior-manipulating fungal pathogen of dipterans. G3 (BETHESDA, MD.) 2024; 14:jkae198. [PMID: 39158097 PMCID: PMC11457076 DOI: 10.1093/g3journal/jkae198] [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: 05/07/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 08/20/2024]
Abstract
We report a virus infecting Entomophthora muscae, a behavior-manipulating fungal pathogen of dipterans. The virus, which we name Berkeley Entomophthovirus, is a positive-strand RNA virus in the iflaviridae family of capsid-forming viruses, which are mostly known to infect insects. The viral RNA is expressed at high levels in fungal cells in vitro and during in vivo infections of Drosophila melanogaster, and virus particles can be seen intracellularly in E. muscae. This virus, of which we find two closely related variants in our culture of E. muscae, is also closely related to three different viruses reported from metagenomic surveys, two of which were isolated from wild dipterans, and a third isolated from wild ticks. By analyzing sequencing data from these earlier reports, we find abundant reads aligning to E. muscae specifically in the samples from which viral reads were sequenced. These data establish a wide and perhaps obligate association with E. muscae in the wild, consistent with our laboratory data that E. muscae is the host for these closely related viruses. Because of this, we propose the name Entomophthovirus (EV) for this group of highly related virus variants. As other members of the iflaviridae have been reported to cause behavioral changes in insects, we speculate on the possibility that EV plays a role in the behavioral manipulation of flies infected with E. muscae.
Collapse
Affiliation(s)
- Maxwell C Coyle
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carolyn N Elya
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael J Bronski
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
35
|
Singh G, Pasinato A, Yriarte ALC, Pizarro D, Divakar PK, Schmitt I, Dal Grande F. Are there conserved biosynthetic genes in lichens? Genome-wide assessment of terpene biosynthetic genes suggests ubiquitous distribution of the squalene synthase cluster. BMC Genomics 2024; 25:936. [PMID: 39375591 PMCID: PMC11457338 DOI: 10.1186/s12864-024-10806-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 09/17/2024] [Indexed: 10/09/2024] Open
Abstract
Lichen-forming fungi (LFF) are prolific producers of functionally and structurally diverse secondary metabolites, most of which are taxonomically exclusive and play lineage-specific roles. To date, widely distributed, evolutionarily conserved biosynthetic pathways in LFF are not known. However, this idea stems from polyketide derivatives, since most biochemical research on lichens has concentrated on polyketide synthases (PKSs). Here, we present the first systematic identification and comparison of terpene biosynthetic genes of LFF using all the available Lecanoromycete reference genomes and 22 de novo sequenced ones (111 in total, representing 60 genera and 23 families). We implemented genome mining and gene networking approaches to identify and group the biosynthetic gene clusters (BGCs) into networks of similar BGCs. Our large-scale analysis led to the identification of 724 terpene BGCs with varying degrees of pairwise similarity. Most BGCs in the dataset were unique with no similarity to a previously known fungal or bacterial BGC or among each other. Remarkably, we found two BGCs that were widely distributed in LFF. Interestingly, both conserved BGCs contain the same core gene, i.e., putatively a squalene/phytoene synthase (SQS), involved in sterol biosynthesis. This indicates that early gene duplications, followed by gene losses/gains and gene rearrangement are the major evolutionary factors shaping the composition of these widely distributed SQS BGCs across LFF. We provide an in-depth overview of these BGCs, including the transmembrane, conserved, variable and LFF-specific regions. Our study revealed that lichenized fungi do have a highly conserved BGC, providing the first evidence that a biosynthetic gene may constitute essential genes in lichens.
Collapse
Affiliation(s)
- Garima Singh
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121, Padua, Italy.
- Botanical Garden of Padova, University of Padova, Padua, Italy.
| | - Anna Pasinato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121, Padua, Italy
| | | | - David Pizarro
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, 28040, Spain
| | - Pradeep K Divakar
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, 28040, Spain
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt Am Main, 60325, Germany
- Department of Biosciences, Institute of Ecology Evolution and Diversity, Goethe UniversityFrankfurt,, Max-Von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt Am Main, 60325, Germany
| | - Francesco Dal Grande
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121, Padua, Italy
- Botanical Garden of Padova, University of Padova, Padua, Italy
| |
Collapse
|
36
|
Schmidt S, Murphy R, Vizueta J, Schierbech SK, Conlon BH, Kreuzenbeck NB, Vreeburg SME, van de Peppel LJJ, Aanen DK, Silué KS, Kone NA, Beemelmanns C, Weber T, Poulsen M. Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species (Termitomyces) farmed by termites. Commun Biol 2024; 7:1269. [PMID: 39369058 PMCID: PMC11455885 DOI: 10.1038/s42003-024-06887-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: 02/02/2024] [Accepted: 09/12/2024] [Indexed: 10/07/2024] Open
Abstract
The use of compounds produced by hosts or symbionts for defence against antagonists has been identified in many organisms, including in fungus-farming termites (Macrotermitinae). The obligate mutualistic fungus Termitomyces plays a pivotal role in plant biomass decomposition and as the primary food source for these termites. Despite the isolation of various specialized metabolites from different Termitomyces species, our grasp of their natural product repertoire remains incomplete. To address this knowledge gap, we conducted a comprehensive analysis of 39 Termitomyces genomes, representing 21 species associated with members of five termite host genera. We identified 754 biosynthetic gene clusters (BGCs) coding for specialized metabolites and categorized 660 BGCs into 61 biosynthetic gene cluster families (GCFs) spanning five compound classes. Seven GCFs were shared by all 21 Termitomyces species and 21 GCFs were present in all genomes of subsets of species. Evolutionary constraint analyses on the 25 most abundant GCFs revealed distinctive evolutionary histories, signifying that millions of years of termite-fungus symbiosis have influenced diverse biosynthetic pathways. This study unveils a wealth of non-random and largely undiscovered chemical potential within Termitomyces and contributes to our understanding of the intricate evolutionary trajectories of biosynthetic gene clusters in the context of long-standing symbiosis.
Collapse
Affiliation(s)
- Suzanne Schmidt
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Robert Murphy
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Joel Vizueta
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Signe Kjærsgaard Schierbech
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Benjamin H Conlon
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Nina B Kreuzenbeck
- Group of Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sabine M E Vreeburg
- Laboratory of Genetics, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | | | - Duur K Aanen
- Laboratory of Genetics, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Kolotchèlèma S Silué
- Unité de Formation et de Recherche Sciences de la Nature (UFR-SN), Laboratoire d'Ecologie et de Développement Durable (UREB), Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
- Centre de Recherche en Écologie (CRE), Station de Recherche en Ecologie du Parc national de la Comoé, Bouna, Côte d'Ivoire
| | - N'Golo A Kone
- Unité de Formation et de Recherche Sciences de la Nature (UFR-SN), Laboratoire d'Ecologie et de Développement Durable (UREB), Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
- Centre de Recherche en Écologie (CRE), Station de Recherche en Ecologie du Parc national de la Comoé, Bouna, Côte d'Ivoire
| | - Christine Beemelmanns
- Group of Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Department Anti-infectives from Microbiota, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8, 66123, Saarbrücken, Germany
- Universität des Saarlandes, Campus E8, 66123, Saarbrücken, Germany
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| |
Collapse
|
37
|
Li D, Liu Z, Zhang L, Bian X, Wu J, Li L, Chen Y, Luo L, Pan L, Kong L, Xiao Y, Wang J, Zhang X, Wang W, Toma M, Piipponen M, Sommar P, Xu Landén N. The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing. Nat Commun 2024; 15:8637. [PMID: 39366968 PMCID: PMC11452505 DOI: 10.1038/s41467-024-52783-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 09/18/2024] [Indexed: 10/06/2024] Open
Abstract
The cell transition from an inflammatory phase to a subsequent proliferative phase is crucial for wound healing, yet the driving mechanism remains unclear. By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identify SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. Snhg26-deficient mice exhibit impaired wound repair characterized by delayed re-epithelization accompanied by exacerbated inflammation. Single-cell transcriptome analysis combined with gain-of-function and loss-of-function of SNHG26 in vitro and ex vivo reveals its specific role in facilitating inflammatory-to-proliferative state transition of keratinocyte progenitors. A mechanistic study unravels that SNHG26 interacts with and relocates the transcription factor ILF2 from inflammatory genomic loci, such as JUN, IL6, IL8, and CCL20, to the genomic locus of LAMB3. Collectively, our findings suggest that lncRNAs play cardinal roles in expediting tissue repair and regeneration and may constitute an invaluable reservoir of therapeutic targets in reparative medicine.
Collapse
Affiliation(s)
- Dongqing Li
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China.
| | - Zhuang Liu
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Letian Zhang
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Xiaowei Bian
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Jianmin Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, Wenzhou Medical University, 325035, Wenzhou, China
| | - Li Li
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Yongjian Chen
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Lihua Luo
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Ling Pan
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Lingzhuo Kong
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Yunting Xiao
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Jiating Wang
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Xiya Zhang
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042, Nanjing, China
| | - Wang Wang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Maria Toma
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Minna Piipponen
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Pehr Sommar
- Department of Plastic and Reconstructive Surgery, Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden.
| |
Collapse
|
38
|
Bhardwaj S, Lee M, O'Carroll D, McDonald J, Osborne K, Khan S, Pickford R, Coleman N, O'Farrell C, Richards S, Manefield MJ. Biotransformation of 6:2/4:2 fluorotelomer alcohols by Dietzia aurantiaca J3: Enzymes and proteomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135510. [PMID: 39178776 DOI: 10.1016/j.jhazmat.2024.135510] [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: 03/29/2024] [Revised: 07/12/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are recalcitrant synthetic organohalides known to negatively impact human health. Short-chain fluorotelomer alcohols are considered the precursor of various perfluorocarboxylic acids (PFCAs) in the environment. Their ongoing production and widespread detection motivate investigations of their biological transformation. Dietzia aurantiaca strain J3 was isolated from PFAS-contaminated landfill leachate using 6:2 fluorotelomer sulphonate (6:2 FTS) as a sulphur source. Resting cell experiments were used to test if strain J3 could transform fluorotelomer alcohols (6:2 and 4:2 FTOH). Strain J3 transformed fluorotelomer alcohols into PFCAs, polyfluorocarboxylic acids and transient intermediates. Over 6 days, 80 % and 58 % of 6:2 FTOH (0.1 mM) and 4:2 FTOH (0.12 mM) were degraded with 6.4 % and 14 % fluoride recovery respectively. Fluorotelomer unsaturated carboxylic acid (6:2 FTUCA) was the most abundant metabolite, accounting for 21 to 30 mol% of 6:2 FTOH (0.015 mM) applied on day zero. Glutathione (GSH) conjugates of 6:2/4:2 FTOH and 5:3 FTCA adducts were also structurally identified. Proteomics studies conducted to identify enzymes in the biotransformation pathway have revealed the role of various enzymes involved in β oxidation. This is the first report of 6:2/4:2 FTOH glutathione conjugates and 5:3 FTCA adducts in prokaryotes, and the first study to explore the biotransformation of 4:2 FTOH by pure bacterial strain.
Collapse
Affiliation(s)
- Shefali Bhardwaj
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Denis O'Carroll
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - James McDonald
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Keith Osborne
- Environment Protection Science, NSW Department of Climate Change, Energy, the Environment and Water, Lidcombe, NSW 2141, Australia
| | - Stuart Khan
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Russell Pickford
- UNSW Mark Wainwright Analytical Centre, UNSW, Sydney, NSW 2052, Australia
| | - Nicholas Coleman
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | | | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia.
| |
Collapse
|
39
|
Vishwakarma A, Padmashali N, Thiyagarajan S. AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function. J Proteome Res 2024; 23:4296-4302. [PMID: 39215721 DOI: 10.1021/acs.jproteome.4c00251] [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: 09/04/2024]
Abstract
The rapid expansion of biological sequence databases due to high-throughput genomic and proteomic sequencing methods has left a considerable number of identified protein sequences with unclear or incomplete functional annotations. Domains of unknown function (DUFs) are protein domains that lack functional annotations but are present in numerous proteins. To address the challenge of finding functional annotations for DUFs, we have developed a computational method that efficiently identifies and annotates these enigmatic protein domains by utilizing the position-specific iterative basic local alignment search tool (PSI-BLAST) and data mining techniques. Our pipeline identifies putative potential functionalities of DUFs, thereby decreasing the gap between known sequences and functions. The tool can also take user input sequences to annotate. We executed our pipeline on 5111 unique DUF sequences obtained from Pfam, resulting in putative annotations for 2007 of these. These annotations were subsequently incorporated into a comprehensive database and interfaced with a web-based server named "AnnoDUF". AnnoDUF is freely accessible to both academic and industrial users, via the World Wide Web at the link http://bts.ibab.ac.in/annoduf.php. All scripts used in this study are uploaded to the GitHub repository, and these can be accessed from https://github.com/BioToolSuite/AnnoDUF.
Collapse
Affiliation(s)
- Aman Vishwakarma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City Phase 1, Bengaluru 560100, KA, India
| | - Namrata Padmashali
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City Phase 1, Bengaluru 560100, KA, India
| | - Saravanamuthu Thiyagarajan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City Phase 1, Bengaluru 560100, KA, India
| |
Collapse
|
40
|
Yu M, Bai M, Chen M, Zhang G, Zhao Y, Ma Q, Yang L, Gu C. Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica. Genetica 2024:10.1007/s10709-024-00215-2. [PMID: 39365430 DOI: 10.1007/s10709-024-00215-2] [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: 06/07/2024] [Accepted: 09/24/2024] [Indexed: 10/05/2024]
Abstract
The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.
Collapse
Affiliation(s)
- Mengxin Yu
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Mingzhu Bai
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Mengmeng Chen
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Guozhe Zhang
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Yu Zhao
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Qingqing Ma
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Liyuan Yang
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Cuihua Gu
- College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| |
Collapse
|
41
|
Ospina JA, Lopez-Alvarez D, Gimode W, Wenzl P, Carvajal-Yepes M. Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America. Sci Rep 2024; 14:23141. [PMID: 39367150 PMCID: PMC11452518 DOI: 10.1038/s41598-024-74161-6] [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: 06/26/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024] Open
Abstract
Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world's largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.
Collapse
Affiliation(s)
- Jessica A Ospina
- International Center for Tropical Agriculture, CIAT, Palmira, 6713, Colombia
- Universidad Nacional de Colombia, Palmira, Colombia
| | | | - Winnie Gimode
- International Center for Tropical Agriculture, CIAT, Palmira, 6713, Colombia
| | - Peter Wenzl
- International Center for Tropical Agriculture, CIAT, Palmira, 6713, Colombia
| | | |
Collapse
|
42
|
Liu W, Wang P, Zhuang X, Ling Y, Liu H, Wang S, Yu H, Ma L, Jiang Y, Zhao G, Yan X, Zhou Z, Zhang G. RDBSB: a database for catalytic bioparts with experimental evidence. Nucleic Acids Res 2024:gkae844. [PMID: 39360609 DOI: 10.1093/nar/gkae844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/10/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
Catalytic bioparts are fundamental to the design, construction and optimization of biological systems for specific metabolic pathways. However, the functional characterization information of these bioparts is frequently dispersed across multiple databases and literature sources, posing significant challenges to the effective design and optimization of specific chassis or cell factories. We developed the Registry and Database of Bioparts for Synthetic Biology (RDBSB), a comprehensive resource encompassing 83 193 curated catalytic bioparts with experimental evidences. RDBSB offers their detailed qualitative and quantitative catalytic information, including critical parameters such as activities, substrates, optimal pH and temperature, and chassis specificity. The platform features an interactive search engine, visualization tools and analysis utilities such as biopart finder, structure prediction and pathway design tools. Additionally, RDBSB promotes community engagement through a catalytic bioparts submission system to facilitate rapid data sharing and utilization. To date, RDBSB has supported the contribution of >1000 catalytic bioparts. We anticipate that the database will significantly enhance the resources available for pathway design in synthetic biology and serve essential tools for researchers. RDBSB is freely available at https://www.biosino.org/rdbsb/.
Collapse
Affiliation(s)
- Wan Liu
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Feng Lin Road, Shanghai 200032, China
| | - Xinhao Zhuang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yunchao Ling
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230026, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., 4/F, Youyue Building, No. 298, Xiangke Road, Pudong New District, Shanghai 200030, China
| | - Haihan Yu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230026, China
| | - Liangxiao Ma
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yuguo Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, and Chenshan Science Research Center, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences (CAS), 3888 Chenhua Road, Shanghai 201602, China
| | - Guoping Zhao
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Feng Lin Road, Shanghai 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Feng Lin Road, Shanghai 200032, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| |
Collapse
|
43
|
Sweet P, Burroughs M, Jang S, Contreras L. TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs. Microbiol Spectr 2024; 12:e0383823. [PMID: 39235252 PMCID: PMC11466087 DOI: 10.1128/spectrum.03838-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/20/2024] [Indexed: 09/06/2024] Open
Abstract
The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria. IMPORTANCE Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.
Collapse
Affiliation(s)
- Philip Sweet
- McKetta Department of
Chemical Engineering, University of Texas at
Austin, Austin,
Texas, USA
| | - Matthew Burroughs
- McKetta Department of
Chemical Engineering, University of Texas at
Austin, Austin,
Texas, USA
| | - Sungyeon Jang
- McKetta Department of
Chemical Engineering, University of Texas at
Austin, Austin,
Texas, USA
| | - Lydia Contreras
- McKetta Department of
Chemical Engineering, University of Texas at
Austin, Austin,
Texas, USA
| |
Collapse
|
44
|
Magar S, Kolte V, Sharma G, Govindarajan S. Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study. Microbiol Spectr 2024; 12:e0420023. [PMID: 39264185 PMCID: PMC11448039 DOI: 10.1128/spectrum.04200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/07/2024] [Indexed: 09/13/2024] Open
Abstract
Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities. IMPORTANCE Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.
Collapse
Affiliation(s)
- Sharayu Magar
- Department of Biological Sciences, SRM University AP, Amaravati, Andhra Pradesh, India
| | - Vaishnavi Kolte
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad, India
| | | |
Collapse
|
45
|
Berndsen CE, Bell JK. The structural biology and dynamics of malate dehydrogenases. Essays Biochem 2024; 68:57-72. [PMID: 39113569 DOI: 10.1042/ebc20230082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 10/04/2024]
Abstract
Malate dehydrogenase (MDH) enzymes catalyze the reversible oxidoreduction of malate to oxaloacetate using NAD(P) as a cofactor. This reaction is vital for metabolism and the exchange of reducing equivalents between cellular compartments. There are more than 100 structures of MDH in the Protein Data Bank, representing species from archaea, bacteria, and eukaryotes. This conserved family of enzymes shares a common nucleotide-binding domain, substrate-binding domain, and subunits associate to form a dimeric or a tetrameric enzyme. Despite the variety of crystallization conditions and ligands in the experimental structures, the conformation and configuration of MDH are similar. The quaternary structure and active site dynamics account for most conformational differences in the experimental MDH structures. Oligomerization appears essential for activity despite each subunit having a structurally independent active site. There are two dynamic regions within the active site that influence substrate binding and possibly catalysis, with one of these regions adjoining the subunit interface. In this review, we introduce the reader to the general structural framework of MDH highlighting the conservation of certain features and pointing out unique differences that regulate MDH enzyme activity.
Collapse
Affiliation(s)
- Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, U.S.A
| | - Jessica K Bell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, U.S.A
| |
Collapse
|
46
|
Stark GF, Truchon AR, Wilhelm SW. Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype. BMC Genomics 2024; 25:922. [PMID: 39363260 PMCID: PMC11448079 DOI: 10.1186/s12864-024-10839-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024] Open
Abstract
The Microcystis mobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain, Microcystis aeruginosa PCC 7086, and a non-toxigenic genetic mutant, Microcystis aeruginosa PCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyB strain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyB isolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights how Microcystis strains continue to "evolve" in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences between Microcystis strains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments.
Collapse
Affiliation(s)
- Gwendolyn F Stark
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Alexander R Truchon
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA.
| |
Collapse
|
47
|
Wu P, Li S, Yu X, Guo S, Gao L. Identification of long-chain acyl-CoA synthetase gene family reveals that SlLACS1 is essential for cuticular wax biosynthesis in tomato. Int J Biol Macromol 2024; 277:134438. [PMID: 39098676 DOI: 10.1016/j.ijbiomac.2024.134438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/22/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
Long-chain acyl-CoA synthetases (LACSs), belonging to the acyl-activating enzyme superfamily, play crucial roles in lipid biosynthesis and fatty acid catabolism. Here, we identified 11 LACS genes in the tomato reference genome, and these genes were clustered into six subfamilies. Gene structure and conserved motif analyses indicated that LACSs from the same subfamily shared conserved gene and protein structures. Expression analysis revealed that SlLACS1 was highly expressed in the outer epidermis of tomato fruits and leaves. Subcellular localization assay results showed that SlLACS1 was located in the endoplasmic reticulum. Compared with wild-type plants, the wax content on leaves and fruits decreased by 22.5-34.2 % in SlLACS1 knockout lines, confirming that SlLACS1 was involved in wax biosynthesis in both leaves and fruits. Water loss, chlorophyll extraction, water-deficit, and toluidine blue assays suggested that cuticle permeability was elevated in SlLACS1 knockout lines, resulting in reduction in both drought stress resistance and fruit shelf-life. Overall, our analysis of the LACSs in tomato, coupled with investigations of SlLACS1 function, yielded a deeper understanding of the evolutionary patterns of LACS members and revealed the involvement of SlLACS1 in wax accumulation contribute to drought resistance and extended fruit shelf-life in tomato.
Collapse
Affiliation(s)
- Pan Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofen Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sumin Guo
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Lei Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| |
Collapse
|
48
|
Rey Redondo E, Leung SKK, Yung CCM. Genomic and biogeographic characterisation of the novel prasinovirus Mantoniella tinhauana virus 1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70020. [PMID: 39392286 PMCID: PMC11467894 DOI: 10.1111/1758-2229.70020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024]
Abstract
Mamiellophyceae are a ubiquitous class of unicellular green algae in the global ocean. Their ecological importance is highlighted in studies focused on the prominent genera Micromonas, Ostreococcus, and Bathycoccus. Mamiellophyceae are susceptible to prasinoviruses, double-stranded DNA viruses belonging to the nucleocytoplasmic large DNA virus group. Our study represents the first isolation of a prasinovirus in the South China Sea and the only one to infect the globally distributed genus Mantoniella. We conducted a comparative analysis with previously identified viral relatives, encompassing morphological characteristics, host specificity, marker-based phylogenetic placement, and whole-genome sequence comparisons. Although it shares morphological and genetic similarities with established prasinoviruses, this novel virus showed distinct genetic traits, confining its infection to the species Mantoniella tinhauana. We also explored the global biogeography of this prasinovirus and its host by mapping metagenomic data and analysing their relationship with various environmental parameters. Our results demonstrate a pronounced link between the virus and its host, both found predominantly in higher latitudes in the surface ocean. By gaining an increased understanding of the relationships between viruses, hosts, and environments, researchers can better make predictions and potentially implement measures to mitigate the consequences of climate change on oceanic processes.
Collapse
Affiliation(s)
- Elvira Rey Redondo
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| | - Shara Ka Kiu Leung
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| | - Charmaine Cheuk Man Yung
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| |
Collapse
|
49
|
Zeng Y, Jiang R, Deng J, Cheng D, Wang W, Ye J, He C, Zhang C, Zhang H, Zheng H. Characterization of MKK family genes and their responses to temperature stress and Vibrio parahaemolyticus infection in noble scallop Chlamys nobilis. MARINE ENVIRONMENTAL RESEARCH 2024; 201:106695. [PMID: 39205359 DOI: 10.1016/j.marenvres.2024.106695] [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: 05/05/2024] [Revised: 07/21/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Mitogen-activated protein kinase kinase (MKK), the key element of the Mitogen-activated protein kinase (MAPK) signaling pathway, is crucial for the immune response to adverse environments in aquatic animals. Nevertheless, there is limited information regarding the role of the MKK gene family in mollusks. In our study, genome data and transcriptome were used to identify four MKK genes (CnMKK4, CnMKK5, CnMKK6, and CnMKK7) in the noble scallop. The result of the gene structure, motif analysis, and phylogenetic tree revealed that MKK genes are relatively conserved in bivalves. Moreover, four CnMKK genes were significantly highly expressed in immune-related tissues, suggesting that CnMKKs may related to bivalve immunity. Furthermore, CnMKK6 and CgMKK4 were significantly differentially expressed (P < 0.05) under 24 h of temperature stress, and all CnMKKs were significantly differentially expressed (P < 0.05) under 24 h of Vibrio parahaemolyticus infection. These results showed that the CnMKKs may have a significant impact under biotic and abiotic stresses. In conclusion, the result of the CnMKKs provides valuable insights into comprehending the function of MKK genes in mollusks.
Collapse
Affiliation(s)
- Yetao Zeng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Ruolin Jiang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Jingwen Deng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Dewei Cheng
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources of the People's Republic of China, Beihai, 536009, China
| | - Weili Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Jianming Ye
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Cheng He
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Chuanxu Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China
| | - Hongkuan Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China.
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Marine Sciences Institute, Shantou University, Shantou, 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou, 515063, China.
| |
Collapse
|
50
|
Coclet C, Camargo AP, Roux S. MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes. mSystems 2024:e0088824. [PMID: 39352141 DOI: 10.1128/msystems.00888-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 09/09/2024] [Indexed: 10/12/2024] Open
Abstract
While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.
Collapse
Affiliation(s)
- Clément Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|