1
|
Sharma G, Paul P, Dviwedi A, Kaur P, Kumar P, Gupta VK, Saha SB, Kulshrestha S. In silico screening and evaluation of antiviral peptides as inhibitors against ORF9b protein of SARS-CoV-2. 3 Biotech 2024; 14:192. [PMID: 39118822 PMCID: PMC11303353 DOI: 10.1007/s13205-024-04032-4] [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: 11/25/2022] [Accepted: 07/14/2024] [Indexed: 08/10/2024] Open
Abstract
The present study investigated antiviral peptides (AVPs) as inhibitors of SARS-CoV-2 Orf9b protein, a novel target for disrupting the Orf9b-TOM70 complex crucial for viral infection. In silico screening via molecular docking and MD simulations identified AVP1442 and AVP1896 with high binding affinities to Orf9b (- 846.3 kcal mol-1 and - 820 kcal mol-1, respectively), comparable to the Orf9b-TOM70 complex (- 810.99 kcal mol-1). These AVPs interacted with key amino acid residues in Orf9b, including phosphorylation sites. In addition, AVPs also closely interacted with conserved regions in Orf9b. AVP1896 formed a hydrogen bond with Orf9b's threonine at position 84. AVP1442 interacted with Orf9b's leucine at position 15. Favorable Ramachandran plots and compactness during MD simulations for up to 100 ns suggest good stability of formed complexes. These non-toxic AVPs warrant further in vitro and in vivo evaluation, potentially as components of drug cocktails with small molecules or interferon-based therapies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04032-4.
Collapse
Affiliation(s)
- Gaurav Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 Himachal Pradesh India
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad, 382424 Gujarat India
| | - Prateek Paul
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Prayagraj, 211007 Uttar Pradesh India
| | - Ananya Dviwedi
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 Himachal Pradesh India
- Rajiv Gandhi Institute of Information Technology and Biotechnology, Pune, 411045 Maharashtra India
| | - Parneet Kaur
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 Himachal Pradesh India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 Himachal Pradesh India
- Department of Forensic Science, Himachal Pradesh University, Summer Hill, Shimla, 171005 Himachal Pradesh India
| | - V. Kumar Gupta
- Department of Applied Biology, University of Science and Technology, Meghalaya, 793101 India
| | - Saurav Bhaskar Saha
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Prayagraj, 211007 Uttar Pradesh India
| | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 Himachal Pradesh India
| |
Collapse
|
2
|
Caballero I, Castellví A, Triviño J, Jiménez E, Soler N, Borges R, Usón I. ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins. Protein Sci 2024; 33:e5136. [PMID: 39150227 PMCID: PMC11328115 DOI: 10.1002/pro.5136] [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: 03/30/2024] [Revised: 07/07/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.
Collapse
Affiliation(s)
- Iracema Caballero
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Albert Castellví
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Josep Triviño
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Elisabet Jiménez
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Nicolas Soler
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Rafael Borges
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| |
Collapse
|
3
|
Rahimzadeh F, Mohammad Khanli L, Salehpoor P, Golabi F, PourBahrami S. Unveiling the evolution of policies for enhancing protein structure predictions: A comprehensive analysis. Comput Biol Med 2024; 179:108815. [PMID: 38986287 DOI: 10.1016/j.compbiomed.2024.108815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Predicting protein structure is both fascinating and formidable, playing a crucial role in structure-based drug discovery and unraveling diseases with elusive origins. The Critical Assessment of Protein Structure Prediction (CASP) serves as a biannual battleground where global scientists converge to untangle the intricate relationships within amino acid chains. Two primary methods, Template-Based Modeling (TBM) and Template-Free (TF) strategies, dominate protein structure prediction. The trend has shifted towards Template-Free predictions due to their broader sequence coverage with fewer templates. The predictive process can be broadly classified into contact map, binned-distance, and real-valued distance predictions, each with distinctive strengths and limitations manifested through tailored loss functions. We have also introduced revolutionary end-to-end, and all-atom diffusion-based techniques that have transformed protein structure predictions. Recent advancements in deep learning techniques have significantly improved prediction accuracy, although the effectiveness is contingent upon the quality of input features derived from natural bio-physiochemical attributes and Multiple Sequence Alignments (MSA). Hence, the generation of high-quality MSA data holds paramount importance in harnessing informative input features for enhanced prediction outcomes. Remarkable successes have been achieved in protein structure prediction accuracy, however not enough for what structural knowledge was intended to, which implies need for development in some other aspects of the predictions. In this regard, scientists have opened other frontiers for protein structural prediction. The utilization of subsampling in multiple sequence alignment (MSA) and protein language modeling appears to be particularly promising in enhancing the accuracy and efficiency of predictions, ultimately aiding in drug discovery efforts. The exploration of predicting protein complex structure also opens up exciting opportunities to deepen our knowledge of molecular interactions and design therapeutics that are more effective. In this article, we have discussed the vicissitudes that the scientists have gone through to improve prediction accuracy, and examined the effective policies in predicting from different aspects, including the construction of high quality MSA, providing informative input features, and progresses in deep learning approaches. We have also briefly touched upon transitioning from predicting single-chain protein structures to predicting protein complex structures. Our findings point towards promoting open research environments to support the objectives of protein structure prediction.
Collapse
Affiliation(s)
- Faezeh Rahimzadeh
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | | | - Pedram Salehpoor
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Faegheh Golabi
- Department of Biomedical Engineering, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahin PourBahrami
- Department of Computer Engineering, Technical and Vocational University (TVU), Tehran, Iran
| |
Collapse
|
4
|
Mathew B, Lee AS, Chen K, Kaczmarski M, Oommen N, Mehaboob A, Patel V, Patel Y, Saji H, Shamsi MA, Gibb B. Complete genome sequences of Arthrobacter globiformis phages Uzumaki and Argan of cluster AU6. Microbiol Resour Announc 2024; 13:e0029324. [PMID: 38990022 PMCID: PMC11320949 DOI: 10.1128/mra.00293-24] [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: 03/23/2024] [Accepted: 06/05/2024] [Indexed: 07/12/2024] Open
Abstract
Bacteriophages Uzumaki and Argan infect Arthrobacter globiformis B-2880 isolated from soil samples in Long Island, New York. These bacteriophages have lambda-like morphology with prolate capsid and share 97% gene content similarity. These traits place them in cluster AU6 with other related Arthrobacter phages.
Collapse
Affiliation(s)
- Brandon Mathew
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Andrew Sean Lee
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Katie Chen
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Michael Kaczmarski
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Nigel Oommen
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Asweel Mehaboob
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Vrushali Patel
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Yamini Patel
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Hannah Saji
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Muhammad Ayaan Shamsi
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Bryan Gibb
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| |
Collapse
|
5
|
Berry NE, Cassford MS, Agostino CJ, Dionne EN, Schmitt OJ, Butela KA, Jacobs-Sera D, DeGiorgis JA, Cornely K. Genomic sequences of Mycobacterium smegmatis A cluster phages LBerry, Pembroke, and Zolita. Microbiol Resour Announc 2024; 13:e0050424. [PMID: 38980043 PMCID: PMC11320968 DOI: 10.1128/mra.00504-24] [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: 05/12/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect Mycobacterium smegmatis mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.
Collapse
Affiliation(s)
- Nathan E. Berry
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marly S. Cassford
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Colby J. Agostino
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Ethan N. Dionne
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Olivia J. Schmitt
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| |
Collapse
|
6
|
Hossain A, Gnanagobal H, Cao T, Chakraborty S, Chukwu-Osazuwa J, Soto-Dávila M, Vasquez I, Santander J. Role of cold shock proteins B and D in Aeromonas salmonicida subsp. salmonicida physiology and virulence in lumpfish ( Cyclopterus lumpus). Infect Immun 2024; 92:e0001124. [PMID: 38920386 PMCID: PMC11320987 DOI: 10.1128/iai.00011-24] [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: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Cold shock proteins (Csp) are pivotal nucleic acid binding proteins known for their crucial roles in the physiology and virulence of various bacterial pathogens affecting plant, insect, and mammalian hosts. However, their significance in bacterial pathogens of teleost fish remains unexplored. Aeromonas salmonicida subsp. salmonicida (hereafter A. salmonicida) is a psychrotrophic pathogen and the causative agent of furunculosis in marine and freshwater fish. Four csp genes (cspB, cspD, cspA, and cspC) have been identified in the genome of A. salmonicida J223 (wild type). Here, we evaluated the role of DNA binding proteins, CspB and CspD, in A. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus). A. salmonicida ΔcspB, ΔcspD, and the double ΔcspBΔcspD mutants were constructed and characterized. A. salmonicida ΔcspB and ΔcspBΔcspD mutants showed a faster growth at 28°C, and reduced virulence in lumpfish. A. salmonicida ΔcspD showed a slower growth at 28°C, biofilm formation, lower survival in low temperatures and freezing conditions (-20°C, 0°C, and 4°C), deficient in lipopolysaccharide synthesis, and low virulence in lumpfish. Additionally, ΔcspBΔcspD mutants showed less survival in the presence of bile compared to the wild type. Transcriptome analysis revealed that 200, 37, and 921 genes were differentially expressed in ΔcspB, ΔcspD, and ΔcspBΔcspD, respectively. In ΔcspB and ΔcspBΔcspD virulence genes in the chromosome and virulence plasmid were downregulated. Our analysis indicates that CspB and CspD mostly act as a transcriptional activator, influencing cell division (e.g., treB), virulence factors (e.g., aexT), and ultimately virulence.
Collapse
Affiliation(s)
- Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Joy Chukwu-Osazuwa
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Manuel Soto-Dávila
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| |
Collapse
|
7
|
Grafakou A, Mosterd C, Beck MH, Kelleher P, McDonnell B, de Waal PP, van Rijswijck IMH, van Peij NNME, Cambillau C, Mahony J, van Sinderen D. Discovery of antiphage systems in the lactococcal plasmidome. Nucleic Acids Res 2024:gkae671. [PMID: 39119896 DOI: 10.1093/nar/gkae671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Until the late 2000s, lactococci substantially contributed to the discovery of various plasmid-borne phage defence systems, rendering these bacteria an excellent antiphage discovery resource. Recently, there has been a resurgence of interest in identifying novel antiphage systems in lactic acid bacteria owing to recent reports of so-called 'defence islands' in diverse bacterial genera. Here, 321 plasmid sequences from 53 lactococcal strains were scrutinized for the presence of antiphage systems. Systematic evaluation of 198 candidates facilitated the discovery of seven not previously described antiphage systems, as well as five systems, of which homologues had been described in other bacteria. All described systems confer resistance against the most prevalent lactococcal phages, and act post phage DNA injection, while all except one behave like abortive infection systems. Structure and domain predictions provided insights into their mechanism of action and allow grouping of several genetically distinct systems. Although rare within our plasmid collection, homologues of the seven novel systems appear to be widespread among bacteria. This study highlights plasmids as a rich repository of as yet undiscovered antiphage systems.
Collapse
Affiliation(s)
- Andriana Grafakou
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Cas Mosterd
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Matthias H Beck
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Paul P de Waal
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Irma M H van Rijswijck
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Noël N M E van Peij
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255 Marseille, France
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| |
Collapse
|
8
|
Pruneda JN, Nguyen JV, Nagai H, Kubori T. Bacterial usurpation of the OTU deubiquitinase fold. FEBS J 2024; 291:3303-3316. [PMID: 36636866 PMCID: PMC10338644 DOI: 10.1111/febs.16725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/10/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023]
Abstract
The extensive cellular signalling events controlled by posttranslational ubiquitination are tightly regulated through the action of specialized proteases termed deubiquitinases. Among them, the OTU family of deubiquitinases can play very specialized roles in the regulation of discrete subtypes of ubiquitin signals that control specific cellular functions. To exert control over host cellular functions, some pathogenic bacteria have usurped the OTU deubiquitinase fold as a secreted virulence factor that interferes with ubiquitination inside infected cells. Herein, we provide a review of the function of bacterial OTU deubiquitinases during infection, the structural basis for their deubiquitinase activities and the bioinformatic approaches leading to their identification. Understanding bacterial OTU deubiquitinases holds the potential for discoveries not only in bacterial pathogenesis but in eukaryotic biology as well.
Collapse
Affiliation(s)
- Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Justine V. Nguyen
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, Gifu 501-1194, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| |
Collapse
|
9
|
Trost CN, Yang J, Garcia B, Hidalgo-Reyes Y, Fung BCM, Wang J, Lu WT, Maxwell KL, Wang Y, Davidson AR. An anti-CRISPR that pulls apart a CRISPR-Cas complex. Nature 2024; 632:375-382. [PMID: 38961300 DOI: 10.1038/s41586-024-07642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
In biological systems, the activities of macromolecular complexes must sometimes be turned off. Thus, a wide variety of protein inhibitors has evolved for this purpose. These inhibitors function through diverse mechanisms, including steric blocking of crucial interactions, enzymatic modification of key residues or substrates, and perturbation of post-translational modifications1. Anti-CRISPRs-proteins that block the activity of CRISPR-Cas systems-are one of the largest groups of inhibitors described, with more than 90 families that function through diverse mechanisms2-4. Here, we characterize the anti-CRISPR AcrIF25, and we show that it inhibits the type I-F CRISPR-Cas system by pulling apart the fully assembled effector complex. AcrIF25 binds to the predominant CRISPR RNA-binding components of this complex, comprising six Cas7 subunits, and strips them from the RNA. Structural and biochemical studies indicate that AcrIF25 removes one Cas7 subunit at a time, starting at one end of the complex. Notably, this feat is achieved with no apparent enzymatic activity. To our knowledge, AcrIF25 is the first example of a protein that disassembles a large and stable macromolecular complex in the absence of an external energy source. As such, AcrIF25 establishes a paradigm for macromolecular complex inhibitors that may be used for biotechnological applications.
Collapse
Affiliation(s)
- Chantel N Trost
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jing Yang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yurima Hidalgo-Reyes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Beatrice C M Fung
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jiuyu Wang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wang-Ting Lu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yanli Wang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of the Chinese Academy of Sciences, Beijing, China.
| | - Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
10
|
Kumar H, Kim P. Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective. Clin Transl Med 2024; 14:e1789. [PMID: 39090739 PMCID: PMC11294035 DOI: 10.1002/ctm2.1789] [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: 03/22/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three-dimensional (3D) structures of fusion proteins remains a difficult task because the current AI-based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template-based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi-level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta and D-I-TASSER for modelling the 3D structures. HIGHLIGHTS: This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein. This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step. This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models. This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures.
Collapse
Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Pora Kim
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| |
Collapse
|
11
|
Guzman C, Mohri K, Nakamura R, Miyake M, Tsuchiya Y, Tomii K, Watanabe H. Neuronal and non-neuronal functions of the synaptic cell adhesion molecule neurexin in Nematostella vectensis. Nat Commun 2024; 15:6495. [PMID: 39090098 PMCID: PMC11294457 DOI: 10.1038/s41467-024-50818-8] [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: 03/20/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
The evolutionary transition from diffusion-mediated cell-cell communication to faster, targeted synaptic signaling in animal nervous systems is still unclear. Genome sequencing analyses have revealed a widespread distribution of synapse-related genes among early-diverging metazoans, but how synaptic machinery evolved remains largely unknown. Here, we examine the function of neurexins (Nrxns), a family of presynaptic cell adhesion molecules with critical roles in bilaterian chemical synapses, using the cnidarian model, Nematostella vectensis. Delta-Nrxns are expressed mainly in neuronal cell clusters that exhibit both peptidergic and classical neurotransmitter signaling. Knockdown of δ-Nrxn reduces spontaneous peristalsis of N. vectensis polyps. Interestingly, gene knockdown and pharmacological studies suggest that δ-Nrxn is involved in glutamate- and glycine-mediated signaling rather than peptidergic signaling. Knockdown of the epithelial α-Nrxn reveals a major role in cell adhesion between ectodermal and endodermal epithelia. Overall, this study provides molecular, functional, and cellular insights into the pre-neural function of Nrxns, as well as key information for understanding how and why they were recruited to the synaptic machinery.
Collapse
Affiliation(s)
- Christine Guzman
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Biology, Institute of Zoology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Kurato Mohri
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Ryotaro Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Minato Miyake
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuko Tsuchiya
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| |
Collapse
|
12
|
Chen L, Li Q, Nasif KFA, Xie Y, Deng B, Niu S, Pouriyeh S, Dai Z, Chen J, Xie CY. AI-Driven Deep Learning Techniques in Protein Structure Prediction. Int J Mol Sci 2024; 25:8426. [PMID: 39125995 PMCID: PMC11313475 DOI: 10.3390/ijms25158426] [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: 07/15/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established protein modeling to state-of-the-art artificial intelligence (AI) frameworks. The paper will start with a brief introduction to protein structures, protein modeling, and AI. The section on established protein modeling will discuss homology modeling, ab initio modeling, and threading. The next section is deep learning-based models. It introduces some state-of-the-art AI models, such as AlphaFold (AlphaFold, AlphaFold2, AlphaFold3), RoseTTAFold, ProteinBERT, etc. This section also discusses how AI techniques have been integrated into established frameworks like Swiss-Model, Rosetta, and I-TASSER. The model performance is compared using the rankings of CASP14 (Critical Assessment of Structure Prediction) and CASP15. CASP16 is ongoing, and its results are not included in this review. Continuous Automated Model EvaluatiOn (CAMEO) complements the biennial CASP experiment. Template modeling score (TM-score), global distance test total score (GDT_TS), and Local Distance Difference Test (lDDT) score are discussed too. This paper then acknowledges the ongoing difficulties in predicting protein structure and emphasizes the necessity of additional searches like dynamic protein behavior, conformational changes, and protein-protein interactions. In the application section, this paper introduces some applications in various fields like drug design, industry, education, and novel protein development. In summary, this paper provides a comprehensive overview of the latest advancements in established protein modeling and deep learning-based models for protein structure predictions. It emphasizes the significant advancements achieved by AI and identifies potential areas for further investigation.
Collapse
Affiliation(s)
- Lingtao Chen
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Qiaomu Li
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Kazi Fahim Ahmad Nasif
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Ying Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Bobin Deng
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Shuteng Niu
- Department of Computer Science, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Seyedamin Pouriyeh
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| | - Zhiyu Dai
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Jiawei Chen
- College of Computing, Data Science and Society, University of California, Berkeley, CA 94720, USA;
| | - Chloe Yixin Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (Q.L.); (K.F.A.N.); (Y.X.); (B.D.); (S.P.)
| |
Collapse
|
13
|
Wu Z, Guo L, Wu Y, Yang M, Du S, Shao J, Zhang Z, Zhao Y. Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family. mSphere 2024; 9:e0045824. [PMID: 38926906 PMCID: PMC11288001 DOI: 10.1128/msphere.00458-24] [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: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine Roseobacter group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the Roseobacter CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11, Poseidonocella, and Sphingomonadaceae. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages. IMPORTANCE The Roseobacter CHUG lineage, affiliated with the Pelagic Roseobacter Cluster (PRC), is widely distributed in the global oceans and is active in oligotrophic seawater. However, knowledge of the bacteriophages that infect CHUG members is limited. In this study, a CHUG phage, CRP-810, that infects the CHUG strain FZCC0198, was isolated and shown to have a novel genomic architecture. In addition, 251 uncultured viral genomes closely related to CRP-810 were recovered and included in the analyses. Phylogenomic analyses revealed that the CRP-810-type phages represent a new phage family containing at least eight genus-level subgroups. Members of this family were predicted to infect various marine bacteria. We also demonstrated that the CRP-810-type phages are widely distributed in global oceans and display distinct biogeographic patterns related to latitude. Collectively, this study provides important insights into the genomic organization, diversity, and ecology of a novel phage family that infect ecologically important bacteria in the global ocean.
Collapse
Affiliation(s)
- Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Luyuan Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiabing Shao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
14
|
Li S, Wei B, Xu L, Cong C, Murtaza B, Wang L, Li X, Li J, Xu M, Yin J, Xu Y. In vivo efficacy of phage cocktails against carbapenem resistance Acinetobacter baumannii in the rat pneumonia model. J Virol 2024; 98:e0046724. [PMID: 38864621 PMCID: PMC11265278 DOI: 10.1128/jvi.00467-24] [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: 03/11/2024] [Accepted: 04/22/2024] [Indexed: 06/13/2024] Open
Abstract
Acinetobacter baumannii, an opportunistic pathogen, poses a significant threat in intensive care units, leading to severe nosocomial infections. The rise of multi-drug-resistant strains, particularly carbapenem-resistant A. baumannii, has created formidable challenges for effective treatment. Given the prolonged development cycle and high costs associated with antibiotics, phages have garnered clinical attention as an alternative for combating infections caused by drug-resistant bacteria. However, the utilization of phage therapy encounters notable challenges, including the narrow host spectrum, where each phage targets a limited subset of bacteria, increasing the risk of phage resistance development. Additionally, uncertainties in immune system dynamics during treatment hinder tailoring symptomatic interventions based on patient-specific states. In this study, we isolated two A. baumannii phages from wastewater and conducted a comprehensive assessment of their potential applications. This evaluation included sequencing analysis, genome classification, pH and temperature stability assessments, and in vitro bacterial inhibition assays. Further investigations involved analyzing histological and cytokine alterations in rats undergoing phage cocktail treatment for pneumonia. The therapeutic efficacy of the phages was validated, and transcriptomic studies of rat lung tissue during phage treatment revealed crucial changes in the immune system. The findings from our study underscore the potential of phages for future development as a treatment strategy and offer compelling evidence regarding immune system dynamics throughout the treatment process.IMPORTANCEDue to the growing problem of multi-drug-resistant bacteria, the use of phages is being considered as an alternative to antibiotics, and the genetic safety and application stability of phages determine the potential of phage application. The absence of drug resistance genes and virulence genes in the phage genome can ensure the safety of phage application, and the fact that phage can remain active in a wide range of temperatures and pH is also necessary for application. In addition, the effect evaluation of preclinical studies is especially important for clinical application. By simulating the immune response situation during the treatment process through mammalian models, the changes in animal immunity can be observed, and the effect of phage therapy can be further evaluated. Our study provides compelling evidence that phages hold promise for further development as therapeutic agents for Acinetobacter baumannii infections.
Collapse
Affiliation(s)
- Shibin Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed Science, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Le Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Cong Cong
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Jibin Li
- R&D Centre, Liaoning Innovation Center for Phage Application Professional Technology, Dalian, China
| | - Mu Xu
- R&D Department, Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, China
| | - Jiajun Yin
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
- R&D Department, Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, China
| |
Collapse
|
15
|
Pelagalli C, Sera DJ, DeGiorgis JA, Cornely K. Mycobacteriophage maravista: a cluster F1 phage discovered on Cape Cod, Massachusetts. Microbiol Resour Announc 2024; 13:e0050224. [PMID: 38860805 PMCID: PMC11256854 DOI: 10.1128/mra.00502-24] [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: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Mycobacterium virus Maravista, a member of the family Gracegardnervirianae and species Cheoctovirus, is an F1 cluster phage that infects Mycobacterium smegmatis mc²155. The Maravista genome has 61.3% GC content, is 60,140 bp in length, and encodes 104 putative genes. Maravista encodes two putative glycosyltransferases, suggesting glycosylation of its capsid protein.
Collapse
Affiliation(s)
- Charles Pelagalli
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Debbie-Jacobs Sera
- Department of Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| |
Collapse
|
16
|
Patel Y, Patel VP, Syeda A, Saji H, Gibb BP. Genome sequence of bacteriophage Janeemi isolated on Arthrobacter globiformis from soil collected in New York. Microbiol Resour Announc 2024; 13:e0017724. [PMID: 38860811 PMCID: PMC11256828 DOI: 10.1128/mra.00177-24] [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: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Janeemi is a bacteriophage that infects Arthrobacter globiformis B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted genes. Based on gene content similarity to phages in the actinobacteriophage database, Janeemi is assigned to phage cluster AZ1.
Collapse
Affiliation(s)
- Yamini Patel
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Vrushali P. Patel
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Amna Syeda
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Hannah Saji
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Bryan P. Gibb
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| |
Collapse
|
17
|
Sun Y, Wang L, Zhang M, Jie J, Guan Q, Fu J, Chu X, Chen D, Li C, Song L, Luo ZQ. Acinetobacter nosocomialis utilizes a unique type VI secretion system to promote its survival in niches with prey bacteria. mBio 2024; 15:e0146824. [PMID: 38916378 PMCID: PMC11253628 DOI: 10.1128/mbio.01468-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 06/26/2024] Open
Abstract
Pathogenic bacteria of the Acinetobacter genus pose a severe threat to human health worldwide due to their strong adaptability, tolerance, and antibiotic resistance. Most isolates of these bacteria harbor a type VI secretion system (T6SS) that allows them to outcompete co-residing microorganisms, but whether this system is involved in acquiring nutrients from preys remains less studied. In this study, we found that Ab25, a clinical isolate of Acinetobacter nosocomialis, utilizes a T6SS to kill taxonomically diverse microorganisms, including bacteria and fungi. The T6SS of Ab25 is constitutively expressed, and among the three predicted effectors, T6e1, a member of the RHS effector family, contributes the most for its antimicrobial activity. T6e1 undergoes self-cleavage, and a short carboxyl fragment with nuclease activity is sufficient to kill target cells via T6SS injection. Interestingly, strain Ab25 encodes an orphan VgrG protein, which when overexpressed blocks the firing of its T6SS. In niches such as dry plastic surfaces, the T6SS promotes prey microorganism-dependent survival of Ab25. These results reveal that A. nosocomialis employs T6SSs that are highly diverse in their regulation and effector composition to gain a competitive advantage in environments with scarce nutrient supply and competing microbes.IMPORTANCEThe type VI secretion system (T6SS) plays an important role in bacterial adaptation to environmental challenges. Members of the Acinetobacter genus, particularly A. baumannii and A. nosocomialis, are notorious for their multidrug resistance and their ability to survive in harsh environments. In contrast to A. baumannii, whose T6SS has been well-studied, few research works have focused on A. nosocomialis. In this study, we found that an A. nosocomialis strain utilizes a contitutively active T6SS to kill diverse microorganisms, including bacteria and fungi. Although T6SS structural proteins of A. nosocomialis are similar to those of A. baumannii, the effector repertoire differs greatly. Interestingly, the T6SS of the A. nosocomialis strain codes for an ophan VgrG protein, which blocks the firing of the system when overexpressed, suggesting the existence of a new regulatory mechanism for the T6SS. Importantly, although the T6SS does not provide an advantage when the bacterium is grown in nutrient-rich medium, it allows A. nosocomialis to survive better in dry surfaces that contain co-existing bacteria. Our results suggest that killing of co-residing microorganisms may increase the effectiveness of strategies designed to reduce the fitness of Acinetobacter bacteria by targeting their T6SS.
Collapse
Affiliation(s)
- Yu Sun
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
- Department of Gastroenterology, Endoscopy center, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Ming Zhang
- Department of Ultrasound, The First Hospital of Jilin University, Changchun, China
| | - Jing Jie
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Qingtian Guan
- Bioinformatics Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Jiaqi Fu
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Xiao Chu
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Dong Chen
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Chunxiuli Li
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
18
|
Ananya, Panchariya DC, Karthic A, Singh SP, Mani A, Chawade A, Kushwaha S. Vaccine design and development: Exploring the interface with computational biology and AI. Int Rev Immunol 2024:1-20. [PMID: 38982912 DOI: 10.1080/08830185.2024.2374546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Computational biology involves applying computer science and informatics techniques in biology to understand complex biological data. It allows us to collect, connect, and analyze biological data at a large scale and build predictive models. In the twenty first century, computational resources along with Artificial Intelligence (AI) have been widely used in various fields of biological sciences such as biochemistry, structural biology, immunology, microbiology, and genomics to handle massive data for decision-making, including in applications such as drug design and vaccine development, one of the major areas of focus for human and animal welfare. The knowledge of available computational resources and AI-enabled tools in vaccine design and development can improve our ability to conduct cutting-edge research. Therefore, this review article aims to summarize important computational resources and AI-based tools. Further, the article discusses the various applications and limitations of AI tools in vaccine development.
Collapse
Affiliation(s)
- Ananya
- National Institute of Animal Biotechnology, Hyderabad, India
| | | | | | | | - Ashutosh Mani
- Motilal Nehru National Institute of Technology, Prayagraj, India
| | - Aakash Chawade
- Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | |
Collapse
|
19
|
Chong Qui E, Habtehyimer F, Germroth A, Grant J, Kosanovic L, Singh I, Hancock SP. Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection. Int J Mol Sci 2024; 25:7466. [PMID: 39000573 PMCID: PMC11242194 DOI: 10.3390/ijms25137466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Stephen P. Hancock
- Department of Chemistry, Towson University, Towson, MD 21252, USA; (E.C.Q.); (F.H.); (A.G.); (J.G.); (L.K.); (I.S.)
| |
Collapse
|
20
|
Huang YJ, Montelione GT. Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600902. [PMID: 38979209 PMCID: PMC11230435 DOI: 10.1101/2024.06.26.600902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Recent advances in molecular modeling using deep learning can revolutionize our understanding of dynamic protein structures. NMR is particularly well-suited for determining dynamic features of biomolecular structures. The conventional process for determining biomolecular structures from experimental NMR data involves its representation as conformation-dependent restraints, followed by generation of structural models guided by these spatial restraints. Here we describe an alternative approach: generating a distribution of realistic protein conformational models using artificial intelligence-(AI-) based methods and then selecting the sets of conformers that best explain the experimental data. We applied this conformational selection approach to redetermine the solution NMR structure of the enzyme Gaussia luciferase. First, we generated a diverse set of conformer models using AlphaFold2 (AF2) with an enhanced sampling protocol. The models that best-fit NOESY and chemical shift data were then selected with a Bayesian scoring metric. The resulting models include features of both the published NMR structure and the standard AF2 model generated without enhanced sampling. This "AlphaFold-NMR" protocol also generated an alternative "open" conformational state that fits nearly as well to the overall NMR data but accounts for some NOESY data that is not consistent with first "closed" conformational state; while other NOESY data consistent with this second state are not consistent with the first conformational state. The structure of this "open" structural state differs from that of the "closed" state primarily by the position of a thumb-shaped loop between α-helices H5 and H6, revealing a cryptic surface pocket. These alternative conformational states of Gluc are supported by "double recall" analysis of NOESY data and AF2 models. Additional structural states are also indicated by backbone chemical shift data indicating partially-disordered conformations for the C-terminal segment. Considered as a multistate ensemble, these multiple states of Gluc together fit the NOESY and chemical shift data better than the "restraint-based" NMR structure and provide novel insights into its structure-dynamic-function relationships. This study demonstrates the potential of AI-based modeling with enhanced sampling to generate conformational ensembles followed by conformer selection with experimental data as an alternative to conventional restraint satisfaction protocols for protein NMR structure determination.
Collapse
Affiliation(s)
- Yuanpeng J. Huang
- Dept of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
| | - Gaetano T. Montelione
- Dept of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
| |
Collapse
|
21
|
Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH. Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599552. [PMID: 38948817 PMCID: PMC11213020 DOI: 10.1101/2024.06.21.599552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Transposase genes are ubiquitous in all domains of life and provide a rich reservoir for the evolution of novel protein functions. Here we report deep evolutionary links between bacterial IS110 transposases, which catalyze RNA-guided DNA recombination using bridge RNAs, and archaeal/eukaryotic Nop5-family proteins, which promote RNA-guided RNA 2'-O-methylation using C/D-box snoRNAs. Based on conservation in the protein primary sequence, domain architecture, and three-dimensional structure, as well as common architectural features of the non-coding RNA components, we propose that programmable RNA modification emerged via exaptation of components derived from IS110-like transposons. Alongside recent studies highlighting the origins of CRISPR-Cas9 and Cas12 in IS605-family transposons, these findings underscore how recurrent domestication events of transposable elements gave rise to complex RNA-guided biological mechanisms.
Collapse
Affiliation(s)
- Hugo Vaysset
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
- AgroParisTech, Université Paris-Saclay, Paris, France
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jean Cury
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Aude Bernheim
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| |
Collapse
|
22
|
Wu H, Li W, Zeng C, Li J, Wu H. Complete genome of a novel mycobacteriophage WXIN isolated in Wuhan, China. BMC Genom Data 2024; 25:62. [PMID: 38890591 PMCID: PMC11186097 DOI: 10.1186/s12863-024-01244-8] [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: 03/01/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
OBJECTIVES The rising of antibiotic resistance has sparked a renewed interest in mycobacteriophage as alternative therapeutic strategies against mycobacterial infections. So far, the vast majority of mycobacteriophages have been isolated using the model species Mycobacterium smegmatis, implying an overwhelming majority of mycobacteriophages in the environment remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. This study was undertaken to isolate and characterize novel mycobacteriophages targeting Mycobacterium septicum. DATA DESCRIPTION Here a novel mycobacteriophage WXIN against M. septicum was isolated from soil samples in Wuhan, China. Whole genome analysis indicates that the phage genome consists of 115,158 bp with a GC content of 61.9%. Of the 260 putative open reading frames, 46 may be associated with phage packaging, structure, lysis, lysogeny, genome modification/replication, and other functional roles. The limited genome-wide similarity, along with phylogenetic trees constructed based on viral proteome and orthologous genes show that phage WXIN represents a novel cluster distantly related to cluster J mycobacteriophages (genus Omegavirus). Overall, these results provide novel insights into the genomic properties of mycobacteriophages, highlighting the great genetic diversity of mycobacteriophages in relation to their hosts.
Collapse
Affiliation(s)
- Haoming Wu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Wenxin Li
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Chi Zeng
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jiaxin Li
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Huan Wu
- Department of Laboratory Medicine, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430019, China
| |
Collapse
|
23
|
Ravi J, Anantharaman V, Chen SZ, Brenner EP, Datta P, Aravind L, Gennaro ML. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 2024; 9:e0084723. [PMID: 38809013 PMCID: PMC11237479 DOI: 10.1128/msystems.00847-23] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.
Collapse
Affiliation(s)
- Janani Ravi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Samuel Zorn Chen
- Computer Science Engineering Undergraduate Program, Michigan State University, East Lansing, Michigan, USA
| | - Evan Pierce Brenner
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Pratik Datta
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| |
Collapse
|
24
|
Calvopina-Chavez DG, Bursey DM, Tseng YJ, Patil LM, Bewley KD, Bennallack PR, McPhie JM, Wagstaff KB, Daley A, Miller SM, Moody JD, Price JC, Griffitts JS. Micrococcin cysteine-to-thiazole conversion through transient interactions between the scaffolding protein TclI and the modification enzymes TclJ and TclN. Appl Environ Microbiol 2024; 90:e0024424. [PMID: 38780510 PMCID: PMC11218655 DOI: 10.1128/aem.00244-24] [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: 02/14/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase, and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, demonstrate complex formation between TclI, TclJ, and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core. IMPORTANCE Thiopeptides are a family of antimicrobial peptides characterized for having sulfur-containing heterocycles and for being highly post-translationally modified. Numerous thiopeptides have been identified; almost all of which inhibit protein synthesis in gram-positive bacteria. These intrinsic antimicrobial properties make thiopeptides promising candidates for the development of new antibiotics. The thiopeptide micrococcin is synthesized by the ribosome and undergoes several post-translational modifications to acquire its bioactivity. In this study, we identify key interactions within the enzymatic complex that carries out cysteine to thiazole conversion in the biosynthesis of micrococcin.
Collapse
Affiliation(s)
| | - Devan M. Bursey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Yi-Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Leena M. Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Kathryn D. Bewley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - Philip R. Bennallack
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Josh M. McPhie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Kimberly B. Wagstaff
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Anisha Daley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Susan M. Miller
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - John C. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| |
Collapse
|
25
|
Milhaven M, Bakry HA, Batra A, Bermingham AM, Grama G, Kebe J, Martinez SS, Mudunuri RV, Nelson MR, Nguyen ET, Peterson MM, Pruitt A, Tran K, Brar A, Cerna G, Chaffee E, Caruso SM, Pfeifer SP. Complete genome sequence of the Streptomyces bacteriophage Amabiko. Microbiol Resour Announc 2024; 13:e0018224. [PMID: 38651927 PMCID: PMC11237712 DOI: 10.1128/mra.00182-24] [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: 02/22/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei-a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and one tmRNA. Amabiko is closely related to Streptomyces bacteriophage MindFlayer (gene content similarity: 86.5%).
Collapse
Affiliation(s)
- Mark Milhaven
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Heba A. Bakry
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Anuvi Batra
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | | | - Gloria Grama
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Jacob Kebe
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona, USA
| | - Shawn S. Martinez
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Rishika V. Mudunuri
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Megan R. Nelson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Department of Psychology, Arizona State University, Tempe, Arizona, USA
| | - Evie T. Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Mia M. Peterson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Alexis Pruitt
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Kristan Tran
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Akarshi Brar
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Gabriella Cerna
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elaine Chaffee
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Susanne P. Pfeifer
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
26
|
Jo SJ, Giri SS, Lee YM, Park JH, Hwang MH, Lee SB, Jung WJ, Kim SG, Roh E, Park SC. Genomic insights into novel Erwinia bacteriophages: unveiling their Henunavirus membership and host infection strategies. Curr Microbiol 2024; 81:204. [PMID: 38831133 DOI: 10.1007/s00284-024-03713-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/21/2024] [Indexed: 06/05/2024]
Abstract
Erwinia amylovora, the primary causative agent of blight disease in rosaceous plants, poses a significant threat to agricultural yield worldwide, with limited effective countermeasures. The emergence of sustainable alternative agents such as bacteriophages is a promising solution for fire blight that specifically targets Erwinia. In this study, we isolated pEp_SNUABM_01 and pEa_SNUABM_55 from a South Korean apple orchard soil, analyzed their genomic DNA sequences, and performed a comprehensive comparative analysis of Hena1 in four distinct sections. This study aimed to unveil distinctive features of these phages, with a focus on host recognition, which will provide valuable insights into the evolution and characteristics of Henunavirus bacteriophages that infect plant pathogenic Erwinia spp. By elucidating the distinct genomic features of these phages, particularly in terms of host recognition, this study lays a foundation for their potential application in mitigating the risks associated with fire blight in Rosaceae plants on a global scale.
Collapse
Affiliation(s)
- Su Jin Jo
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hong Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mae Hyun Hwang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Guen Kim
- Laboratory of Phage and Microbial Resistance, Department of Biological Sciences, Kyonggi University, Suwon, 16227, Republic of Korea.
| | - Eunjung Roh
- Crop Protection Division, Rural Development Administration, National Institute of Agriculture Sciences, Wanju, 55365, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
27
|
Javid M, Shahverdi AR, Ghasemi A, Moosavi-Movahedi AA, Ebrahim-Habibi A, Sepehrizadeh Z. Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics. Protein J 2024; 43:522-543. [PMID: 38662183 DOI: 10.1007/s10930-024-10195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
Collapse
Affiliation(s)
- Mehri Javid
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azadeh Ebrahim-Habibi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
28
|
Dos Santos ER, de Camargo BR, da Silva LA, Laumann RA, Ribeiro BM, Ardisson-Araújo DMP. The multispecies stinkbug iflavirus Halyomorpha halys virus detected in the multispecies stinkbug egg parasitoid microwasp, Telenomus podisi (Ashmead) (Hymenoptera: Platygastridae). Braz J Microbiol 2024; 55:1913-1921. [PMID: 38615311 PMCID: PMC11153462 DOI: 10.1007/s42770-024-01340-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: 01/12/2024] [Accepted: 03/27/2024] [Indexed: 04/15/2024] Open
Abstract
Wasps are important parasitoids of stinkbugs and frequently exposed to various types of microorganisms through environmental contact and fecal-oral transmission route. Many parasitize stinkbug eggs and are commercially used in the field to control insect population. The parasitoid T. podisi is known for its high parasitism capacity and ability to target multiple species of stinkbugs. In this study we asked whether T. podisi exposed to eggs infected by a multispecies asymptomatic stinkbug virus, the Halyomorpha halys virus (HhV) would get infected. HhV is a geographically distributed multispecies iflavirus previously found to infect four stinkbug hosts, including three Brazilian species, Chinavia ubica, Euschistus heros and Diceraeus melacanthus, and T. posidi can parasitize all of them. As results, RT-PCR screening revealed positive samples for the HhV genome in two out of four tested pools of T. podisi, whereas the antigenome, indicative of replicative activity, was not detected. The wasps were raised in E. heros eggs that presented both the genome and the antigenome forms of the HhV genome. Subsequent RNA-deep sequencing of HhV positive T. podisi RNA pools yielded a complete genome of HhV with high coverage. Phylogenetic analysis positioned the isolate HhV-Tp (isolate Telenomus podisi) alongside with the stinkbug HhV. Analysis of transcriptomes from several hymenopteran species revealed HhV-Tp reads in four species. However, the transmission mechanism and the ecological significance of HhV remain elusive, warranting further studies to illuminate both the transmission process and its capacity for environmental propagation using T. podisi as a potential vector.
Collapse
Affiliation(s)
- Ethiane Rozo Dos Santos
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Brenda Rabelo de Camargo
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Leonardo Assis da Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Raul Alberto Laumann
- Laboratory of Chemical Ecology, EMBRAPA Genetic Resources and Biotechnology, Brasília, DF, 70770-900, Brazil
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| |
Collapse
|
29
|
Zhao N, Wu T, Wang W, Zhang L, Gong X. Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure. Interdiscip Sci 2024; 16:261-288. [PMID: 38955920 DOI: 10.1007/s12539-024-00626-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: 10/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 07/04/2024]
Abstract
Protein complexes perform diverse biological functions, and obtaining their three-dimensional structure is critical to understanding and grasping their functions. In many cases, it's not just two proteins interacting to form a dimer; instead, multiple proteins interact to form a multimer. Experimentally resolving protein complex structures can be quite challenging. Recently, there have been efforts and methods that build upon prior predictions of dimer structures to attempt to predict multimer structures. However, in comparison to monomeric protein structure prediction, the accuracy of protein complex structure prediction remains relatively low. This paper provides an overview of recent advancements in efficient computational models for predicting protein complex structures. We introduce protein-protein docking methods in detail and summarize their main ideas, applicable modes, and related information. To enhance prediction accuracy, other critical protein-related information is also integrated, such as predicting interchain residue contact, utilizing experimental data like cryo-EM experiments, and considering protein interactions and non-interactions. In addition, we comprehensively review computational approaches for end-to-end prediction of protein complex structures based on artificial intelligence (AI) technology and describe commonly used datasets and representative evaluation metrics in protein complexes. Finally, we analyze the formidable challenges faced in current protein complex structure prediction tasks, including the structure prediction of heteromeric complex, disordered regions in complex, antibody-antigen complex, and RNA-related complex, as well as the evaluation metrics for complex assessment. We hope that this work will provide comprehensive knowledge of complex structure predictions to contribute to future advanced predictions.
Collapse
Affiliation(s)
- Nan Zhao
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Tong Wu
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Wenda Wang
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Lunchuan Zhang
- School of Mathematics, Renmin University of China, Beijing, 100872, China.
| | - Xinqi Gong
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China.
- School of Mathematics, Renmin University of China, Beijing, 100872, China.
- Beijing Academy of Artificial Intelligence, Beijing, 100084, China.
| |
Collapse
|
30
|
Salgado JCS, Alnoch RC, Polizeli MDLTDM, Ward RJ. Microenzymes: Is There Anybody Out There? Protein J 2024; 43:393-404. [PMID: 38507106 DOI: 10.1007/s10930-024-10193-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20-60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions.
Collapse
Affiliation(s)
- Jose Carlos Santos Salgado
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil.
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil.
| | - Robson Carlos Alnoch
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| |
Collapse
|
31
|
Wolyniak MJ, Frazier RH, Gemborys PK, Loehr HE. Malate dehydrogenase: a story of diverse evolutionary radiation. Essays Biochem 2024:EBC20230076. [PMID: 38813783 DOI: 10.1042/ebc20230076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.
Collapse
Affiliation(s)
- Michael J Wolyniak
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943, U.S.A
| | - Robert H Frazier
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943, U.S.A
| | - Peter K Gemborys
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943, U.S.A
| | - Henry E Loehr
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943, U.S.A
| |
Collapse
|
32
|
Griffiths SC, Tan J, Wagner A, Blazer LL, Adams JJ, Srinivasan S, Moghisaei S, Sidhu SS, Siebold C, Ho HYH. Structure and function of the ROR2 cysteine-rich domain in vertebrate noncanonical WNT5A signaling. eLife 2024; 13:e71980. [PMID: 38780011 PMCID: PMC11219042 DOI: 10.7554/elife.71980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
The receptor tyrosine kinase ROR2 mediates noncanonical WNT5A signaling to orchestrate tissue morphogenetic processes, and dysfunction of the pathway causes Robinow syndrome, brachydactyly B, and metastatic diseases. The domain(s) and mechanisms required for ROR2 function, however, remain unclear. We solved the crystal structure of the extracellular cysteine-rich (CRD) and Kringle (Kr) domains of ROR2 and found that, unlike other CRDs, the ROR2 CRD lacks the signature hydrophobic pocket that binds lipids/lipid-modified proteins, such as WNTs, suggesting a novel mechanism of ligand reception. Functionally, we showed that the ROR2 CRD, but not other domains, is required and minimally sufficient to promote WNT5A signaling, and Robinow mutations in the CRD and the adjacent Kr impair ROR2 secretion and function. Moreover, using function-activating and -perturbing antibodies against the Frizzled (FZ) family of WNT receptors, we demonstrate the involvement of FZ in WNT5A-ROR signaling. Thus, ROR2 acts via its CRD to potentiate the function of a receptor super-complex that includes FZ to transduce WNT5A signals.
Collapse
Affiliation(s)
- Samuel C Griffiths
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Jia Tan
- Department of Cell Biology and Human Anatomy, University of California, Davis School of MedicineDavisUnited States
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | - Levi L Blazer
- School of Pharmacy, University of WaterlooWaterlooCanada
| | | | - Srisathya Srinivasan
- Department of Cell Biology and Human Anatomy, University of California, Davis School of MedicineDavisUnited States
| | - Shayan Moghisaei
- Department of Cell Biology and Human Anatomy, University of California, Davis School of MedicineDavisUnited States
| | | | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Hsin-Yi Henry Ho
- Department of Cell Biology and Human Anatomy, University of California, Davis School of MedicineDavisUnited States
| |
Collapse
|
33
|
Donizetti A, Calicchio M, Romano MZ, Rosati L, Turco M, Carrese AM, del Gaudio R, Ferrandino I, Aniello F. Expression of Insl3 Protein in Adult Danio rerio. Int J Mol Sci 2024; 25:5419. [PMID: 38791457 PMCID: PMC11122137 DOI: 10.3390/ijms25105419] [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: 04/03/2024] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Insulin-like peptide 3 (INSL3) is a biomarker for Leydig cells in the testes of vertebrates, and it is principally involved in spermatogenesis through specific binding with the RXFP2 receptor. This study reports the insl3 gene transcript and the Insl3 prepropeptide expression in both non-reproductive and reproductive tissues of Danio rerio. An immunohistochemistry analysis shows that the hormone is present at a low level in the Leydig cells and germ cells at all stages of Danio rerio testis differentiation. Considering that the insl3 gene is transcribed in Leydig cells, our results highlight an autocrine and paracrine function of this hormone in the Danio rerio testis, adding new information on the Insl3 mode of action in reproduction. We also show that Insl3 and Rxfp2 belonging to Danio rerio and other vertebrate species share most of the amino acid residues involved in the ligand-receptor interaction and activation, suggesting a conserved mechanism of action during vertebrate evolution.
Collapse
Affiliation(s)
- Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Mauro Calicchio
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Maria Zelinda Romano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Luigi Rosati
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Manuela Turco
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Anna Maria Carrese
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Rosanna del Gaudio
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Ida Ferrandino
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (A.D.); (M.C.); (L.R.); (M.T.); (A.M.C.); (R.d.G.); (I.F.)
| |
Collapse
|
34
|
Ahammad I, Bushra Lamisa A, Sharmin S, Bhattacharjee A, Mahmud Chowdhury Z, Ahamed T, Uzzal Hossain M, Chandra Das K, Salimullah M, Ara Keya C. Subtractive genomics study for the identification of therapeutic targets against Cronobacter sakazakii: A threat to infants. Heliyon 2024; 10:e30332. [PMID: 38707387 PMCID: PMC11066692 DOI: 10.1016/j.heliyon.2024.e30332] [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: 06/04/2023] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen that has been associated with severe infection in neonates such as necrotizing enterocolitis (NEC), neonatal meningitis, and bacteremia. This pathogen can survive in a relatively dry environment, especially in powdered infant formula (PIF). Unfortunately, conventional drugs that were once effective against C. sakazakii are gradually losing their efficacy due to rising antibiotic resistance. In this study, a subtractive genomic approach was followed in order to identify potential therapeutic targets in the pathogen. The whole proteome of the pathogen was filtered through a step-by-step process, which involved removing paralogous proteins, human homologs, sequences that are less essential for survival, proteins with shared metabolic pathways, and proteins that are located in cells other than the cytoplasmic membrane. As a result, nine novel drug targets were identified. Further, the analysis also unveiled that the FDA-approved drug Terbinafine can be repurposed against the Glutathione/l-cysteine transport system ATP-binding/permease protein CydC of C. sakazakii. Moreover, molecular docking and dynamics studies of Terbinafine and CydC suggested that this drug can be used to treat C. sakazakii infection in neonates. However, for clinical purposes further in vitro and in vivo studies are necessary.
Collapse
Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Anika Bushra Lamisa
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Sadia Sharmin
- Department of Biotechnology & Genetic Engineering, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Tanvir Ahamed
- Department of Biotechnology & Genetic Engineering, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| |
Collapse
|
35
|
Wu Y, Ding C, Sharif B, Weinreb A, Swaim G, Hao H, Yogev S, Watanabe S, Hammarlund M. Polarized localization of kinesin-1 and RIC-7 drives axonal mitochondria anterograde transport. J Cell Biol 2024; 223:e202305105. [PMID: 38470363 PMCID: PMC10932739 DOI: 10.1083/jcb.202305105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/17/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Mitochondria transport is crucial for axonal mitochondria distribution and is mediated by kinesin-1-based anterograde and dynein-based retrograde motor complexes. While Miro and Milton/TRAK were identified as key adaptors between mitochondria and kinesin-1, recent studies suggest the presence of additional mechanisms. In C. elegans, ric-7 is the only single gene described so far, other than kinesin-1, that is absolutely required for axonal mitochondria localization. Using CRISPR engineering in C. elegans, we find that Miro is important but is not essential for anterograde traffic, whereas it is required for retrograde traffic. Both the endogenous RIC-7 and kinesin-1 act at the leading end to transport mitochondria anterogradely. RIC-7 binding to mitochondria requires its N-terminal domain and partially relies on MIRO-1, whereas RIC-7 accumulation at the leading end depends on its disordered region, kinesin-1, and metaxin2. We conclude that transport complexes containing kinesin-1 and RIC-7 polarize at the leading edge of mitochondria and are required for anterograde axonal transport in C. elegans.
Collapse
Affiliation(s)
- Youjun Wu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Chen Ding
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Behrang Sharif
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Weinreb
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Grace Swaim
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyan Hao
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marc Hammarlund
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
36
|
Embry A, Baggett NS, Heisler DB, White A, de Jong MF, Kocsis BL, Tomchick DR, Alto NM, Gammon DB. Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery. PLoS Pathog 2024; 20:e1012010. [PMID: 38753575 PMCID: PMC11098378 DOI: 10.1371/journal.ppat.1012010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.
Collapse
Affiliation(s)
- Aaron Embry
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Nina S. Baggett
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - David B. Heisler
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Addison White
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Maarten F. de Jong
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Benjamin L. Kocsis
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Neal M. Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| | - Don B. Gammon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United State of America
| |
Collapse
|
37
|
Hernandez CA, Delesalle VA, Krukonis GP, DeCurzio JM, Koskella B. Genomic and phenotypic signatures of bacteriophage coevolution with the phytopathogen Pseudomonas syringae. Mol Ecol 2024; 33:e16850. [PMID: 36651263 DOI: 10.1111/mec.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023]
Abstract
The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail-associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype-phenotype relationship.
Collapse
Affiliation(s)
- Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
| | | | - Greg P Krukonis
- Department of Biology, Angelo State University, San Angelo, Texas, USA
| | - Jenna M DeCurzio
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
38
|
Sahin E, Edis G, Keskin E, Akata I. Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus. Arch Virol 2024; 169:110. [PMID: 38664287 DOI: 10.1007/s00705-024-06027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 05/24/2024]
Abstract
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.
Collapse
Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
| | - Gulce Edis
- Graduate School of Natural and Applied Sciences, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, Tandogan, Ankara, 06100, Turkey
| |
Collapse
|
39
|
Ortiz Charneco G, Kelleher P, Buivydas A, de Waal PP, van Rijswijck IM, van Peij NN, Cambillau C, Mahony J, Van Sinderen D. Discovering genetic determinants for cell-to-cell adhesion in two prevalent conjugative lactococcal plasmids. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100239. [PMID: 38706493 PMCID: PMC11067333 DOI: 10.1016/j.crmicr.2024.100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
Plasmids pNP40 and pUC11B encode two prevalent yet divergent conjugation systems, which have been characterized in detail recently. Here, we report the elucidation of the putative adhesins of the pNP40 and pUC11B conjugation systems, encoded by traAd and trsAd, respectively. Despite their significant sequence divergence, TraAd and TrsAd represent the most conserved component between the pNP40- and the pUC11B-encoded conjugation systems and share similar peptidoglycan-hydrolase domains. Protein structure prediction using AlphaFold2 highlighted the structural similarities between their predicted domains, as well as the potential homo-dimeric state of both proteins. Expression of the putative surface adhesins resulted in a cell clumping phenotype not only among cells expressing these surface adhesins but also between adhesin-expressing and non-producing cells. Furthermore, mutant derivatives of plasmids pNP40 or pUC11B carrying a mutation in traAd or trsAd, respectively, were shown to act as efficient donors provided the corresponding recipient expresses either traAd or trsAd, thus demonstrating in trans reciprocal complementarity of these proteins in conjugation systems.
Collapse
Affiliation(s)
- Guillermo Ortiz Charneco
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Paul P. de Waal
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Irma M.H. van Rijswijck
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Noël N.M.E. van Peij
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Christian Cambillau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université – CNRS, UMR 7255, Marseille, France
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| |
Collapse
|
40
|
Vargas-Pérez MDLÁ, Devos DP, López-Lluch G. An AlphaFold Structure Analysis of COQ2 as Key a Component of the Coenzyme Q Synthesis Complex. Antioxidants (Basel) 2024; 13:496. [PMID: 38671943 PMCID: PMC11047366 DOI: 10.3390/antiox13040496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Coenzyme Q (CoQ) is a lipidic compound that is widely distributed in nature, with crucial functions in metabolism, protection against oxidative damage and ferroptosis and other processes. CoQ biosynthesis is a conserved and complex pathway involving several proteins. COQ2 is a member of the UbiA family of transmembrane prenyltransferases that catalyzes the condensation of the head and tail precursors of CoQ, which is a key step in the process, because its product is the first intermediate that will be modified in the head by the next components of the synthesis process. Mutations in this protein have been linked to primary CoQ deficiency in humans, a rare disease predominantly affecting organs with a high energy demand. The reaction catalyzed by COQ2 and its mechanism are still unknown. Here, we aimed at clarifying the COQ2 reaction by exploring possible substrate binding sites using a strategy based on homology, comprising the identification of available ligand-bound homologs with solved structures in the Protein Data Bank (PDB) and their subsequent structural superposition in the AlphaFold predicted model for COQ2. The results highlight some residues located on the central cavity or the matrix loops that may be involved in substrate interaction, some of which are mutated in primary CoQ deficiency patients. Furthermore, we analyze the structural modifications introduced by the pathogenic mutations found in humans. These findings shed new light on the understanding of COQ2's function and, thus, CoQ's biosynthesis and the pathogenicity of primary CoQ deficiency.
Collapse
Affiliation(s)
- María de los Ángeles Vargas-Pérez
- Departamento de Fisiología, Anatomía y Biología Celular, Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Carretera de Utrera km1, 41013 Seville, Spain;
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Seville, Spain;
| | - Guillermo López-Lluch
- Departamento de Fisiología, Anatomía y Biología Celular, Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Carretera de Utrera km1, 41013 Seville, Spain;
| |
Collapse
|
41
|
Bearhart JM, Bethke JL, Christian CS, Cour FN, Creasey KR, Crowe EJ, Dahl JG, Hanson LA, Jaecks AL, Lamantia VA, Madison M, Roskowiak AL, Scheberl JD, VanEperen BM, Wurst ME, Klyczek KK. Complete genome sequence of Microbacterium paraoxydans phage Damascus. Microbiol Resour Announc 2024; 13:e0128723. [PMID: 38624212 PMCID: PMC11080557 DOI: 10.1128/mra.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Phage Damascus was isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The Damascus genome is 56,477 bp with 3' single-stranded overhangs and 56.5% G+C content. Damascus was assigned to cluster EL and shares 42.6%-91.7% gene content with the three other phages in this cluster.
Collapse
Affiliation(s)
- Julisa M. Bearhart
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Jenna L. Bethke
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Cassie S. Christian
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Faith N. Cour
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karleigh R. Creasey
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Emily J. Crowe
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Julia G. Dahl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Lindsey A. Hanson
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Abby L. Jaecks
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Vincent A. Lamantia
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Mercedes Madison
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Autumn L. Roskowiak
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Justin D. Scheberl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Bekkah M. VanEperen
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Morgan E. Wurst
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| |
Collapse
|
42
|
Akter A, Ananna NF, Ullah H, Islam S, Al Amin M, Kibria KMK, Mahmud S. Computational approach for identifying immunogenic epitopes and optimizing peptide vaccine through in-silico cloning against Mycoplasma genitalium. Heliyon 2024; 10:e28223. [PMID: 38596014 PMCID: PMC11002066 DOI: 10.1016/j.heliyon.2024.e28223] [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: 07/11/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
Mycoplasma genitalium is a pathogenic microorganism linked to a variety of severe health conditions including ovarian cancer, prostate cancer, HIV transmission, and sexually transmitted diseases. A more effective approach to address the challenges posed by this pathogen, given its high antibiotic resistance rates, could be the development of a peptide vaccine. In this study, we used experimentally validated 13 membrane proteins and their immunogenicity to identify suitable vaccine candidates. Thus, based on immunogenic properties and high conservation among other Mycoplasma genitalium sub-strains, the P110 surface protein is considered for further investigation. Later on, we identified T-cell epitopes and B-cell epitopes from the P110 protein to construct a multiepitope-based vaccine. As a result, the 'NIAPISFSFTPFTAA' T-cell epitope and 'KVKYESSGSNNISFDS' B-cell epitope have shown 99.53% and 87.50% population coverage along with 100% conservancy among the subspecies, and both epitopes were found to be non-allergenic. Furthermore, focusing on molecular docking analysis showed the lowest binding energy for MHC-I (-137.5 kcal/mol) and MHC-II (-183.3 kcal/mol), leading to a satisfactory binding strength between the T-cell epitopes and the MHC molecules. However, the constructed multiepitope vaccine (MEV) consisting of 54 amino acids demonstrates favorable characteristics for a vaccine candidate, including a theoretical pI of 4.25 with a scaled solubility of 0.812 and high antigenicity probabilities. Additionally, structural analyses reveal that the MEV displays substantial alpha helices and extended strands, vital for its immunogenicity. Molecular docking with the human Toll-like receptors TLR1/2 heterodimer shows strong binding affinity, reinforcing its potential to elicit an immune response. Our immune simulation analysis demonstrates immune memory development and robust immunity, while codon adaptation suggests optimal expression in E. coli using the pET-28a(+) vector. These findings collectively highlight the MEV's potential as a valuable vaccine candidate against M. genitalium.
Collapse
Affiliation(s)
- Asma Akter
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Natasha Farhin Ananna
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Hedayet Ullah
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Sirajul Islam
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Md Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| |
Collapse
|
43
|
Wang S, Han Z, Strick TR. Single-molecule characterization of Sen1 translocation properties provides insights into eukaryotic factor-dependent transcription termination. Nucleic Acids Res 2024; 52:3249-3261. [PMID: 38261990 PMCID: PMC11013386 DOI: 10.1093/nar/gkae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Sen1 is an essential helicase for factor-dependent transcription termination in Saccharomyces cerevisiae, whose molecular-motor mechanism has not been well addressed. Here, we use single-molecule experimentation to better understand the molecular-motor determinants of its action on RNA polymerase II (Pol II) complex. We quantify Sen1 translocation activity on single-stranded DNA (ssDNA), finding elevated translocation rates, high levels of processivity and ATP affinities. Upon deleting the N- and C-terminal domains, or further deleting different parts of the prong subdomain, which is an essential element for transcription termination, Sen1 displays changes in its translocation properties, such as slightly reduced translocation processivities, enhanced translocation rates and statistically identical ATP affinities. Although these parameters fulfil the requirements for Sen1 translocating along the RNA transcript to catch up with a stalled Pol II complex, we observe significant reductions in the termination efficiencies as well as the factions of the formation of the previously described topological intermediate prior to termination, suggesting that the prong may preserve an interaction with Pol II complex during factor-dependent termination. Our results underscore a more detailed rho-like mechanism of Sen1 and a critical interaction between Sen1 and Pol II complex for factor-dependent transcription termination in eukaryotes.
Collapse
Affiliation(s)
- Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190 Beijing, China
- Songshan Lake Materials Laboratory, 523808 Dongguan, Guangdong, China
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Zhong Han
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Terence R Strick
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
- Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| |
Collapse
|
44
|
Valentin Caban K, Kalesnik E, Green KA, Negro CJ, Nunez Rodriguez U, Peele MC, Nguyen CT, Cahill S, Dougherty K, Logue M, Hargraves S, Radziak H, Willette L, Ogunyinka E, Campbell DC, Adebamiro O, Schmeltzer C, Onimus J, Asaka HA, Bangura W, Shimp CM, Alade A, Sequira DM, Jimenez T, Swerdlow SJ, Harrison MK, Fallest-Strobl PC, Mastropaolo MD. Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker. Microbiol Resour Announc 2024; 13:e0125123. [PMID: 38451225 PMCID: PMC11008123 DOI: 10.1128/mra.01251-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the host Microbacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sydney Cahill
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Melissa Logue
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | - Luke Willette
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | | | | | | | | | | | | | - Ameera Alade
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Tommy Jimenez
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | - Neumann University Phage Discovery Group
- Sciences, Neumann University, Aston, Pennsylvania, USA
- Biological Sciences, University of Pittsburgh Greensburg, Greensburg, Pennsylvania, USA
- Sciences, Cabrini University, Radnor, Pennsylvania, USA
| | - Sarah J. Swerdlow
- Biological Sciences, University of Pittsburgh Greensburg, Greensburg, Pennsylvania, USA
| | | | | | | |
Collapse
|
45
|
Tatum B, Murray P, Bicknell C, Webb SA, Kanak A. Genome sequence and annotation of Arthrobacter globiformis phage Ruchi (AS1) isolated from soil in Lumpkin County, Georgia. Microbiol Resour Announc 2024; 13:e0122423. [PMID: 38466103 PMCID: PMC11008183 DOI: 10.1128/mra.01224-23] [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: 12/23/2023] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
Ruchi, a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host Arthrobacter globiformis, possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus revealed 64 predicted reading frames, no predicted tRNA genes, and a close evolutionary relationship to AS1 phage Basilisk.
Collapse
Affiliation(s)
- Brooke Tatum
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Payton Murray
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Claire Bicknell
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A. Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| |
Collapse
|
46
|
Kumar SV, Schaffer N, Bharmal Z, Mood Q, Erill I, Caruso SM. Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using Streptomyces mirabilis NRRL B-2400 in Columbia, MD. Microbiol Resour Announc 2024; 13:e0006824. [PMID: 38394246 PMCID: PMC11008112 DOI: 10.1128/mra.00068-24] [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: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.
Collapse
Affiliation(s)
- Soven Verma Kumar
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Nicholas Schaffer
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Zainab Bharmal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Quinn Mood
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | | | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Departament d’Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| |
Collapse
|
47
|
Abreu G, Garcia E, Oliveira A, Oliveira H. Genome sequence of Erwinia amylovora bacteriophage Omen. Microbiol Resour Announc 2024; 13:e0012224. [PMID: 38526096 PMCID: PMC11008144 DOI: 10.1128/mra.00122-24] [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: 02/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
We report the genome of Erwinia amylovora phage Omen, isolated from a Portuguese orchard. Omen has a genome size of 85,304 bp, belongs to the genus Kolesnikvirus (myovirus morphotype), and shares over 80% nucleotide identity with various Erwinia phage genomes.
Collapse
Affiliation(s)
- Gabriel Abreu
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Edgar Garcia
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
48
|
Bailey DS, Dotson DR, Berkes C, Agbede O, Augustin M, Blackman-Murray I, Chambers T, Felber N, Fleming D, Frazier L, Gray N, Harrison A, Hernandez G, Iwuchukwu N, Iwuji C, Jackson T, Jefferson A, Jordan D, Jordan M, Nicolas B, Person M, Richardson G, Roman A, Stevens C, Suggs M, Thompson N, Timmons-Smith S, Wilfong S, Wilson-Wheatley M. Complete genome sequence of Mycobacterium smegmatis phage Rummer, a subcluster A3 actinophage. Microbiol Resour Announc 2024; 13:e0126823. [PMID: 38466105 PMCID: PMC11008113 DOI: 10.1128/mra.01268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Bacteriophage Rummer is a siphovirus morphology actinophage isolated from Mycobacterium smegmatis. Rummer has a 50,908 base pair genome encoding 89 predicted protein-coding genes and three tRNAs. Based on gene content similarity to sequenced actinobacteriophages, Rummer is assigned to phage subcluster A3.
Collapse
Affiliation(s)
- Dondra S. Bailey
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dominique R. Dotson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Charlotte Berkes
- Department of Biology, Merrimack College, North Andover, Massachusetts, USA
| | - Oluwanifemi Agbede
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Marcelaine Augustin
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | | | - Talaeya Chambers
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nicolas Felber
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dy'Mon Fleming
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Loretta Frazier
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Natalie Gray
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ayanna Harrison
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Genesis Hernandez
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nina Iwuchukwu
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Chika Iwuji
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Taysha Jackson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Angelic Jefferson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Daya Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Miracle Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Brian Nicolas
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Monae Person
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ga'Nayah Richardson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ashley Roman
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Christian Stevens
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - My'Sean Suggs
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nahshon Thompson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Summer Timmons-Smith
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Shiaishea Wilfong
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | | |
Collapse
|
49
|
Adams RM, Britton HA, Bruce ED, De La Paz Y, Kratz EN, Pfeifer EJ, Priddy DE, Schotter BI, Stuffle WA, Wagner J, Weiss MR, Watt DK, Connerly PL, Rueschhoff EE. Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta . Microbiol Resour Announc 2024; 13:e0120423. [PMID: 38526095 PMCID: PMC11008160 DOI: 10.1128/mra.01204-23] [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: 12/07/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024] Open
Abstract
Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host Gordonia rubripertincta NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.
Collapse
Affiliation(s)
- Reese M. Adams
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Holly A. Britton
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily D. Bruce
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Yucita De La Paz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily N. Kratz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emma J. Pfeifer
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Daisy E. Priddy
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Brooklyn I. Schotter
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Wyatt A. Stuffle
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Jordyn Wagner
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Meredith R. Weiss
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Danielle K. Watt
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Pamela L. Connerly
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | | |
Collapse
|
50
|
Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
Collapse
Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|