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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.
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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
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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; 43:361-380. [PMID: 38982912 DOI: 10.1080/08830185.2024.2374546] [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: 03/22/2024] [Revised: 04/29/2024] [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.
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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
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53
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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.
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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.)
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54
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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.
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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
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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.
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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
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56
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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.
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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
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57
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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.
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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
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58
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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.
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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
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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%).
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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
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60
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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.
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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.
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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.
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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.
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62
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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.
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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.
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63
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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.
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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.
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64
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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.
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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
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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.
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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
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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.
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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.)
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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.
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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
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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.
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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
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69
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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.
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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
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70
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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.
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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
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71
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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.
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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
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72
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Golomidova A, Kulikov E, Kuznetsov A, Pechenov PY, Belalov I, Letarov A, Galyov E. Isolation and complete genome sequence of Aeromonas bacteriophage Gekk3-15. F1000Res 2024; 13:380. [PMID: 39233781 PMCID: PMC11372344 DOI: 10.12688/f1000research.144007.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2024] [Indexed: 09/06/2024] Open
Abstract
Bacteria of the genus Aeromonas, especially A. hydrophila and A. veronii are recognized as important fish pathogens that cause significant economic losses in aquaculture. Environmentally friendly bacteriophage-based solutions for the treatment of fish and for the reduction of colonization by pathogenic bacteria in production facilities are currently in high demand. The bacteriophage Gekk3-15 was isolated during a search for novel phage strains potentially suitable for Aeromonas biocontrol applications. Genome sequencing revealed that this virus is a relatively small myovirus with a 64847 bp long dsDNA genome, which is consistent with virion electron microscopy data. Bacteriophage Gekk3-15 is distinct in its nucleotide and encoded aa sequences from all other sequenced bacteriophage genomes, and may represent a new viral taxon at the genus or subfamily level.
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Affiliation(s)
- A.K. Golomidova
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - E.E. Kulikov
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - A.S. Kuznetsov
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - P. Yu. Pechenov
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - I.S. Belalov
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - A.V. Letarov
- Winogradsky Institute of Microbiology, Research Center “Fundamentals of Biotechnology” RAS, Moscow, Russian Federation
| | - E.E. Galyov
- Genetics and Genome Biology, University of Leicester, Leicester, UK
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73
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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.
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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
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74
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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.
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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;
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75
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Wottrich S, Mendonca S, Safarpour C, Nguyen C, Marinelli LJ, Hancock SP, Modlin RL, Parker JM. Putative pseudolysogeny-dependent phage gene implicated in the superinfection resistance of Cutibacterium acnes. MICROBIOME RESEARCH REPORTS 2024; 3:27. [PMID: 39421248 PMCID: PMC11480721 DOI: 10.20517/mrr.2023.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 10/19/2024]
Abstract
Objectives: Cutibacterium acnes, formerly Propionibacterium acnes, is a bacterial species characterized by tenacious acne-contributing pathogenic strains. Therefore, bacteriophage therapy has become an attractive treatment route to circumvent issues such as evolved bacterial antibiotic resistance. However, medical and commercial use of phage therapy for C. acnes has been elusive, necessitating ongoing exploration of phage characteristics that confer bactericidal capacity. Methods: A novel phage (Aquarius) was isolated and analyzed. Testing included genomic sequencing and annotation, electron microscopy, patch testing, reinfection assays, and qPCR to confirm pseudolysogeny and putative superinfection exclusion (SIE) protein expression. Results: Given a superinfection-resistant phenotype was observed, reinfection assays and patch tests were performed, which confirmed the re-cultured bacteria were resistant to superinfection. Subsequent qPCR indicated pseudolysogeny was a concomitantly present phenomenon. Phage genomic analysis identified the presence of a conserved gene (gp41) with a product containing Ltp family-like protein signatures which may contribute to phage-mediated bacterial superinfection resistance (SIR) in a pseudolysogeny-dependent manner. qPCR was performed to analyze and roughly quantify gp41 activity, and mRNA expression was high during infection, implicating a role for the protein during the phage life cycle. Conclusions: This study confirms that C. acnes bacteria are capable of harboring phage pseudolysogens and suggests that this phenomenon plays a role in bacterial SIR. This mechanism may be conferred by the expression of phage proteins while the phage persists within the host in the pseudolysogenic state. This parameter must be considered in future endeavors for efficacious application of C. acnes phage-based therapeutics.
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Affiliation(s)
- Stephanie Wottrich
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90024, USA
- Department of Neurology, Dell Seton Medical Center at the University of Texas at Austin, Austin, TX 78701, USA
| | - Stacee Mendonca
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Cameron Safarpour
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Christine Nguyen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Laura J. Marinelli
- UCLA Dermatology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Robert L. Modlin
- UCLA Dermatology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90024, USA
- Department of Biomedical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA 91101, USA
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76
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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.
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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
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77
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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.
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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
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78
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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.
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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
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79
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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.
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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
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80
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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.
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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
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81
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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.
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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
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82
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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.
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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
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83
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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.
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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
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84
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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.
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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
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85
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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.
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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
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86
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Fricke LC, Lindsey ARI. Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia. Genome Biol Evol 2024; 16:evae036. [PMID: 38530785 PMCID: PMC11019157 DOI: 10.1093/gbe/evae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/28/2024] Open
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
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Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
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87
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Willner DL, Paudel S, Halleran AD, Solini GE, Gray V, Saha MS. Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1. BMC Microbiol 2024; 24:107. [PMID: 38561651 PMCID: PMC10986025 DOI: 10.1186/s12866-024-03241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. RESULTS By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production. CONCLUSIONS The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.
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Affiliation(s)
- Dana L Willner
- Data Science Program, William & Mary, Williamsburg, VA, USA
| | - Sudip Paudel
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Wyss Institute, Harvard University, Cambridge, MA, USA
| | - Andrew D Halleran
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Atalaya Capital Management, New York, NY, USA
| | - Grace E Solini
- Department of Biology, William & Mary, Williamsburg, VA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Veronica Gray
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Georgetown University School of Medicine, Washington, DC, USA
| | - Margaret S Saha
- Department of Biology, William & Mary, Williamsburg, VA, USA.
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88
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O'Connell LM, Coffey A, O'Mahony JM. Genomic analysis of seven mycobacteriophages identifies three novel species with differing phenotypic stabilities. Heliyon 2024; 10:e27932. [PMID: 38515691 PMCID: PMC10955285 DOI: 10.1016/j.heliyon.2024.e27932] [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] [Received: 08/31/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Recently, case studies have been published regarding the application of mycobacteriophage (MP) therapy (MPT) in patients with multi-antibiotic-resistant infections. A major limitation in the development of MPT is the paucity of therapeutically useful MP. As there are approximately 10,000 MP that have yet to be sequenced, it is possible that characterization of this cohort would increase the repertoire of useful MP. This study aims to contribute to such a strategy, by characterizing a cohort of 7 mycobacteriophages. Sequencing analyses revealed that the MP have unique sequences, and subsequent gene annotation revealed differences in gene organization. Notably, MP LOCARD has the largest genome and operons encoding for glycosyltransferases. Taxonomic analysis executed with VIRIDIC, Gegenees and VICTOR revealed that LOCARD belongs to a different genus than the other phages and is the foundational member of one of three novel species identified in this study. LOCARD, LOCV2, and LOCV5 were selected as representative members of their species and subjected to phenotypic analyses to compare their stability under biologically and industrially relevant conditions. Again LOCARD stood out, as it was unaffected by the typical temperatures (37 °C) and salinity (0.9%) experienced in mammals, while the viability of LOCV2 and LOCV5 was significantly reduced. LOCARD was also tolerant to pH 10, low levels of antiviral detergent and was the least impacted by a single freeze-thaw cycle. When all these results are considered, it indicates that LOCARD in particular, has potential therapeutic and/or diagnostics applications, given its resilience towards physiological and storage conditions.
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Affiliation(s)
- Laura M. O'Connell
- Munster Technological University, Rossa Avenue, Bishopstown, Cork, T12 P928, Ireland
| | - Aidan Coffey
- Munster Technological University, Rossa Avenue, Bishopstown, Cork, T12 P928, Ireland
| | - Jim M. O'Mahony
- Munster Technological University, Rossa Avenue, Bishopstown, Cork, T12 P928, Ireland
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89
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Updegrove TB, Delerue T, Anantharaman V, Cho H, Chan C, Nipper T, Choo-Wosoba H, Jenkins LM, Zhang L, Su Y, Shroff H, Chen J, Bewley CA, Aravind L, Ramamurthi KS. Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587046. [PMID: 38903092 PMCID: PMC11188070 DOI: 10.1101/2024.03.27.587046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation non-uniformly to secure against the possibility that favorable growth conditions, which puts sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early utilize a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay non-sporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.
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Affiliation(s)
- Taylor B. Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hyomoon Cho
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carissa Chan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Nipper
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hyoyoung Choo-Wosoba
- Biostatistics and Data Management Support Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa M. Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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90
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Do H, Nguyen DL, Ahn YY, Nam Y, Kang Y, Oh H, Hwang J, Han SJ, Kim K, Lee JH. Structural and functional characterization of sulfurtransferase from Frondihabitans sp. PAMC28461. PLoS One 2024; 19:e0298999. [PMID: 38526988 PMCID: PMC10962793 DOI: 10.1371/journal.pone.0298999] [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: 12/03/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
Sulfurtransferases transfer of sulfur atoms from thiols to acceptors like cyanide. They are categorized as thiosulfate sulfurtransferases (TSTs) and 3-mercaptopyruvate sulfurtransferases (MSTs). TSTs transfer sulfur from thiosulfate to cyanide, producing thiocyanate. MSTs transfer sulfur from 3-mercaptopyruvate to cyanide, yielding pyruvate and thiocyanate. The present study aimed to isolate and characterize the sulfurtransferase FrST from Frondihabitans sp. PAMC28461 using biochemical and structural analyses. FrST exists as a dimer and can be classified as a TST rather than an MST according to sequence-based clustering and enzyme activity. Furthermore, the discovery of activity over a wide temperature range and the broad substrate specificity exhibited by FrST suggest promising prospects for its utilization in industrial applications, such as the detoxification of cyanide.
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Affiliation(s)
- Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Dieu Linh Nguyen
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Yong-Yoon Ahn
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Yewon Nam
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
| | - YoonJi Kang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
| | - HoeJung Oh
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Se Jong Han
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Kitae Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
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91
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Wang J, Zhang M, Pei J, Yi W, Fan L, Wang C, Xiao X. Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates. Front Cell Infect Microbiol 2024; 14:1361045. [PMID: 38572320 PMCID: PMC10987712 DOI: 10.3389/fcimb.2024.1361045] [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: 12/24/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Over the past decade, Corynebacterium striatum (C. striatum), an emerging multidrug-resistant (MDR) pathogen, has significantly challenged healthcare settings, especially those involving individuals with weakened immune systems. The rise of these superbugs necessitates innovative solutions. Methods This study aimed to isolate and characterize bacteriophages targeting MDR-C. striatum. Utilizing 54 MDR-C. striatum isolates from a local hospital as target strains, samples were collected from restroom puddles for phage screening. Dot Plaque and Double-layer plate Assays were employed for screening. Results A novel temperate bacteriophage, named CSP1, was identified through a series of procedures, including purification, genome extraction, sequencing, and one-step growth curves. CSP1 possesses a 39,752 base pair circular double-stranded DNA genome with HK97-like structural proteins and potential for site-specific recombination. It represents a new species within the unclassified Caudoviricetes class, as supported by transmission electron microscopy, genomic evolutionary analysis, and collinearity studies. Notably, CSP1 infected and lysed 21 clinical MDR-C. striatum isolates, demonstrating a wide host range. The phage remained stable in conditions ranging from -40 to 55°C, pH 4 to 12, and in 0.9% NaCl buffer, showing no cytotoxicity. Discussion The identification of CSP1 as the first phage targeting clinical C. striatum strains opens new possibilities in bacteriophage therapy research, and the development of diagnostic and therapeutic tools against pathogenic bacteria.
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Affiliation(s)
- Jiao Wang
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Meng Zhang
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Wei Yi
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Li Fan
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Chunhua Wang
- Department of Clinical Laboratory, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xiao Xiao
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
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92
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Chuhran L, Whitlow C, Teems C, Kanak A, Webb SA. Genome sequence and annotation of Arthrobacter globiformis phage Vulpecula (AS1) isolated from soil in Dahlonega, Georgia. Microbiol Resour Announc 2024; 13:e0009024. [PMID: 38385671 DOI: 10.1128/mra.00090-24] [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: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
Vulpecula, a temperate bacteriophage collected from soil in Dahlonega, Georgia using host Arthrobacter globiformis, is an AS1 subcluster virus of 37,766 bp (67.7% GC). Genome annotation suggests 64 open reading frames, no predicted tRNA genes, and ~98% sequence similarity to AS1 phages Ruchi (from GA) and Jamun (New Hampshire).
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Affiliation(s)
- Lily Chuhran
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Chase Whitlow
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Carson Teems
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
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93
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Diggins AE, Gubitose MG, Hinrichsen EG, Jones PT, Kearns BS, Lord CE, Parsons MT, Pitt RA, Woods IA, Zarakotas TR, Wilkes BM. Genome sequence of Arthrobacter globiformis phage MaGuCo. Microbiol Resour Announc 2024; 13:e0117923. [PMID: 38376341 DOI: 10.1128/mra.01179-23] [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: 11/29/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
MaGuCo is a temperate phage isolated from soil collected in Alton, NH, USA, using Arthrobacter globiformis. Its genome is 43,924 base pairs long and contains 63 protein-encoding genes, 44 of which were assigned putative functions. MaCuGo is assigned to cluster AZ2 based on gene content similarity to actinobacteriophages.
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Affiliation(s)
- Amanda E Diggins
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary G Gubitose
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Elijah G Hinrichsen
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Patrick T Jones
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Brian S Kearns
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Caitlynn E Lord
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary T Parsons
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Rachel A Pitt
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Isabella A Woods
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Teagan R Zarakotas
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Beth M Wilkes
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
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94
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Migueletti MR, García Rey J, Micheloni J, Lomanto C, Martelli E, Sánchez G, Colombo JM, Vallecillo LM, Lamagni F, Giusti T, Acosta F, Villagrán F, Gvozdenovich M, Pricco Frakich A, Pianesi T, Tulin G, Mascali FC, Petitti TD, Torres Manno MA, Fusari CM, Buttigliero L, Giordana MF, Gramajo H, Diacovich L, Espariz M, Mussi MA. Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24. Microbiol Resour Announc 2024; 13:e0121523. [PMID: 38315107 DOI: 10.1128/mra.01215-23] [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: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
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Affiliation(s)
- Matías R Migueletti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julieta García Rey
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Micheloni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Lomanto
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa Martelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gastón Sánchez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julián M Colombo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano M Vallecillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Francisco Lamagni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Giusti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabrina Acosta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Villagrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Gvozdenovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Abril Pricco Frakich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tulio Pianesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gonzalo Tulin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia C Mascali
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás D Petitti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano A Torres Manno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Corina M Fusari
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Espariz
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Alejandra Mussi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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95
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Oliveros AM, McDougall SA, Snyder MA, Snowden SK, Richard JD, Rao CM, Ponce M, Pitonza CJ, Ozcelik M, Mannina SS, Magna JR, Lopez AS, Gustafson LC, Glackin BK, Dolge AE, DeLancy ND, Davis ABC, Davis TP, Blagodar M, Natale SN, Dennis MK, Godin EA. Genome sequence of bacteriophage Djungelskog isolated from an Arthrobacter globiformis culture. Microbiol Resour Announc 2024; 13:e0129423. [PMID: 38376224 DOI: 10.1128/mra.01294-23] [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: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Actinobacteriophage Djungelskog was isolated from a sample of degraded organic material in Poughkeepsie, NY, using Arthrobacter globiformis B-2979. Its genome is 54,512 bp and encodes 86 putative protein-coding genes. Djungelskog has a siphovirus morphology and is assigned to cluster AW based on gene content similarity to actinobacteriophages.
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Affiliation(s)
| | | | - Miles A Snyder
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sara K Snowden
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Joseph D Richard
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Marybeth Ponce
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Mira Ozcelik
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sofia S Mannina
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Juliana R Magna
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew S Lopez
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Brynn K Glackin
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Abigail E Dolge
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Nate D DeLancy
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew B C Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Thomas P Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Max Blagodar
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sydney N Natale
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Megan K Dennis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
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96
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Nielander M, Maybank M, Massimino C, Fitzgerald J, Blossum H, Douthitt C, Holland C, Hunter WB, Carrol M, D'Elia T. Complete genome sequences of StopSmel and Aussie, two Mu-like bacteriophages of Sinorhizobium meliloti. Microbiol Resour Announc 2024; 13:e0123023. [PMID: 38385668 DOI: 10.1128/mra.01230-23] [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: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
We report the complete genome sequences of two bacteriophages, Aussie and StopSmel, isolated from soil using the host Sinorhizobium meliloti NRRL L-50. The genomes are similar in length and gene content and share 76% nucleotide identity. Comparative analysis of Aussie and StopSmel identified core functional modules associated with Mu-like bacteriophages.
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Affiliation(s)
- Macy Nielander
- Department of Biomedical Engineering and Science, Florida Institute of Technology, Melbourne, Florida, USA
| | - Mya Maybank
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Crissy Massimino
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - John Fitzgerald
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Hannah Blossum
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Cayce Douthitt
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Chris Holland
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Wayne B Hunter
- USDA-ARS, US Horticultural Research Laboratory, Fort Pierce, Florida, USA
| | - Megan Carrol
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, USA
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97
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Bass S, Coates D, Frasketi N, James S, Marella V, Pulla R, Stoecker K, Tupurani S, Johnson AA. Complete genome sequences of mycobacteriophages Ageofdapage, Aubs, BABullseye, CheetoDust, ShaboiShabazz, and TomBrady. Microbiol Resour Announc 2024; 13:e0125323. [PMID: 38334400 DOI: 10.1128/mra.01253-23] [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: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
We report genome sequences of six mycobacteriophages. Each virus was isolated from a soil sample and belongs to the siphovirus morphology. Genomes are 41,901-60,613 bp in length, contain between 62 and 103 protein-coding genes, with up to 40% of those genes having a predicted function.
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Affiliation(s)
- Shelbie Bass
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Danielle Coates
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Nina Frasketi
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Smeetha James
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vishnu Marella
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Riya Pulla
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Kyle Stoecker
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Srichandra Tupurani
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Allison A Johnson
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
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98
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Ngove Z, Matthews R, Goedken J, Huntington S, Kirkle L, Coleman ST. Complete genome sequences of bacteriophages Guetzie and SirVictor, isolated from Microbacterium foliorum. Microbiol Resour Announc 2024; 13:e0107423. [PMID: 38294214 DOI: 10.1128/mra.01074-23] [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: 11/07/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024] Open
Abstract
Cluster EA4 Guetzie and SirVictor are lytic siphoviral bacteriophages that were isolated from soil in Waverly, Iowa, using Microbacterium foliorum NRRL B-24224 as the host. The Guetzie and SirVictor genomes are both 39,758 bp each, and both contain 58 predicted protein-coding genes with one tRNA gene each.
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Affiliation(s)
- Zefanias Ngove
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Jack Goedken
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Lauren Kirkle
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | - Sean T Coleman
- Biology Department, Wartburg College, Waverly, Iowa, USA
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99
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Zhao Q, Bao J, Li H, Hu W, Kong Y, Zhong Y, Fu Q, Xu G, Liu F, Jiao X, Jin J, Ming Z. Structural and biochemical basis of FLS2-mediated signal activation and transduction in rice. PLANT COMMUNICATIONS 2024; 5:100785. [PMID: 38158656 PMCID: PMC10943584 DOI: 10.1016/j.xplc.2023.100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/11/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
The receptor-like kinase FLAGELLIN-SENSITIVE 2 (FLS2) functions as a bacterial flagellin receptor localized on the cell membrane of plants. In Arabidopsis, the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) cooperates with FLS2 to detect the flagellin epitope flg22, resulting in formation of a signaling complex that triggers plant defense responses. However, the co-receptor responsible for recognizing and signaling the flg22 epitope in rice remains to be determined, and the precise structural mechanism underlying FLS2-mediated signal activation and transduction has not been clarified. This study presents the structural characterization of a kinase-dead mutant of the intracellular kinase domain of OsFLS2 (OsFLS2-KDD1013A) in complex with ATP or ADP, resolved at resolutions of 1.98 Å and 2.09 Å, respectively. Structural analysis revealed that OsFLS2 can adopt an active conformation in the absence of phosphorylation, although it exhibits only weak basal catalytic activity for autophosphorylation. Subsequent investigations demonstrated that OsSERK2 effectively phosphorylates OsFLS2, which reciprocally phosphorylates OsSERK2, leading to complete activation of OsSERK2 and rapid phosphorylation of the downstream substrate receptor-like cytoplasmic kinases OsRLCK176 and OsRLCK185. Through mass spectrometry experiments, we successfully identified critical autophosphorylation sites on OsSERK2, as well as sites transphosphorylated by OsFLS2. Furthermore, we demonstrated the interaction between OsSERK2 and OsFLS2, which is enhanced in the presence of flg22. Genetic evidence suggests that OsRLCK176 and OsRLCK185 may function downstream of the OsFLS2-mediated signaling pathway. Our study reveals the molecular mechanism by which OsFLS2 mediates signal transduction pathways in rice and provides a valuable example for understanding RLK-mediated signaling pathways in plants.
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Affiliation(s)
- Qiaoqiao Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Jinlin Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Huailong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Wei Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Yanqiong Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Yifeng Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Qiang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Fenmei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China.
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100
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Borujeni PM, Salavati R. Functional domain annotation by structural similarity. NAR Genom Bioinform 2024; 6:lqae005. [PMID: 38298181 PMCID: PMC10830352 DOI: 10.1093/nargab/lqae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/03/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Traditional automated in silico functional annotation uses tools like Pfam that rely on sequence similarities for domain annotation. However, structural conservation often exceeds sequence conservation, suggesting an untapped potential for improved annotation through structural similarity. This approach was previously overlooked before the AlphaFold2 introduction due to the need for more high-quality protein structures. Leveraging structural information especially holds significant promise to enhance accurate annotation in diverse proteins across phylogenetic distances. In our study, we evaluated the feasibility of annotating Pfam domains based on structural similarity. To this end, we created a database from segmented full-length protein structures at their domain boundaries, representing the structure of Pfam seeds. We used Trypanosoma brucei, a phylogenetically distant protozoan parasite as our model organism. Its structome was aligned with our database using Foldseek, the ultra-fast structural alignment tool, and the top non-overlapping hits were annotated as domains. Our method identified over 400 new domains in the T. brucei proteome, surpassing the benchmark set by sequence-based tools, Pfam and Pfam-N, with some predictions validated manually. We have also addressed limitations and suggested avenues for further enhancing structure-based domain annotation.
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Affiliation(s)
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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