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Narh JK, Casillas-Vega NG, Zarate X. LL-37_Renalexin hybrid peptide exhibits antimicrobial activity at lower MICs than its counterpart single peptides. Appl Microbiol Biotechnol 2024; 108:126. [PMID: 38229302 DOI: 10.1007/s00253-023-12887-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 01/18/2024]
Abstract
An alarming global public health and economic peril has been the emergence of antibiotic resistance resulting from clinically relevant bacteria pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species constantly exhibiting intrinsic and extrinsic resistance mechanisms against last-resort antibiotics like gentamycin, ciprofloxacin, tetracycline, colistin, and standard ampicillin prescription in clinical practices. The discovery and applications of antimicrobial peptides (AMPs) with antibacterial properties have been considered and proven as alternative antimicrobial agents to antibiotics. In this study, we have designed, produced, and purified a recombinant novel multifunctional hybrid antimicrobial peptide LL-37_Renalexin for the first time via the application of newly designed flexible GS peptide linker coupled with the use of our previously characterized small metal-binding proteins SmbP and CusF3H+ as carrier proteins that allow for an enhanced bacterial expression, using BL21(DE3) and SHuffle T7(DE3) Escherichia coli strains, and purification of the hybrid peptide via immobilized metal affinity chromatography. The purified tag-free LL-37_Renalexin hybrid peptide exhibited above 85% reduction in bacteria colony-forming units and broad-spectrum antimicrobial effects against Staphylococcus aureus, Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), and Klebsiella pneumoniae bacteria clinical isolates at a lower minimum inhibition concentration level (10-33 μM) as compared to its counterpart single-AMPs LL-37 and Renalexin (50-100 μM). KEY POINTS: • The hybrid antimicrobial peptide LL-37_Renalexin has been designed using a GS linker. • The peptide was expressed with the carrier proteins SmbP and CusF3H+. • The hybrid peptide shows antibacterial potency against clinical bacterial isolates.
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Affiliation(s)
- Julius Kwesi Narh
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, 66455, San Nicolas de los Garza, NL, Mexico
| | - Nestor G Casillas-Vega
- Departamento de Patologia Clinica, Hospital Universitario Dr. Jose Eleuterio Gonzalez, Universidad Autonoma de Nuevo Leon, 64460, Monterrey, NL, Mexico
| | - Xristo Zarate
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, 66455, San Nicolas de los Garza, NL, Mexico.
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2
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Graf J, Schöpperle M, Pernil R, Schleiff E. Two TonB-dependent outer membrane transporters involved in heme uptake in Anabaena sp. PCC 7120. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:16-28. [PMID: 38234586 PMCID: PMC10792254 DOI: 10.15698/mic2024.01.812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024]
Abstract
Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium Anabaena sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by alr2153 (hutA1) and alr3242 (hutA2) are assigned as outer membrane heme transporters. Indeed, Anabaena sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll a synthesis and in an increase of the chlorophyll a content. Moreover, iron starvation induced the expression of hutA1, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in hutA2 induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that Anabaena sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.
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Affiliation(s)
- Julia Graf
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Martin Schöpperle
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Current address: Lonza Cologne GmbH, Köln, Germany:
| | - Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Max von Laue Str. 11, 60438 Frankfurt, Germany
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Azemin WA, Ishak NF, Saedin MAA, Shamsir MS, Razali SA. Molecular docking and simulation studies of Chloroquine, Rimantadine and CAP-1 as potential repurposed antivirals for decapod iridescent virus 1 (DIV1). FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100120. [PMID: 37854946 PMCID: PMC10579962 DOI: 10.1016/j.fsirep.2023.100120] [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] [Indexed: 10/20/2023] Open
Abstract
Drug repurposing is a methodology of identifying new therapeutic use for existing drugs. It is a highly efficient, time and cost-saving strategy that offers an alternative approach to the traditional drug discovery process. Past in-silico studies involving molecular docking have been successful in identifying potential repurposed drugs for the various treatment of diseases including aquaculture diseases. The emerging shrimp hemocyte iridescent virus (SHIV) or Decapod iridescent virus 1 (DIV1) is a viral pathogen that causes severe disease and high mortality (80 %) in farmed shrimps caused serious economic losses and presents a new threat to the shrimp farming industry. Therefore, effective antiviral drugs are critically needed to control DIV1 infections. The aim of this study is to investigate the interaction of potential existing antiviral drugs, Chloroquine, Rimantadine, and CAP-1 with DIV1 major capsid protein (MCP) with the intention of exploring the potential of drug repurposing. The interaction of the DIV1 MCP and three antivirals were characterised and analysed using molecular docking and molecular dynamics simulation. The results showed that CAP-1 is a more promising candidate against DIV1 with the lowest binding energy of -8.46 kcal/mol and is more stable compared to others. We speculate that CAP-1 binding may induce the conformational changes in the DIV1 MCP structure by phosphorylating multiple residues (His123, Tyr162, and Thr395) and ultimately block the viral assembly and maturation of DIV1 MCP. To the best of our knowledge, this is the first report regarding the structural characterisation of DIV1 MCP docked with repurposing drugs.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Pulau, Minden, Pinang 11800, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohamad Amirul Asyraf Saedin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Malaysia
| | - Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
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Ribeiro IC, de Moraes JVB, Mariotini-Moura C, Polêto MD, da Rocha Torres Pavione N, de Castro RB, Miranda IL, Sartori SK, Alves KLS, Bressan GC, de Souza Vasconcellos R, Meyer-Fernandes JR, Diaz-Muñoz G, Fietto JLR. Synthesis of new non-natural L-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1). Purinergic Signal 2023:10.1007/s11302-023-09974-7. [PMID: 37975950 DOI: 10.1007/s11302-023-09974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Trypanosoma cruzi is the pathogen of Chagas disease, a neglected tropical disease that affects more than 6 million people worldwide. There are no vaccines to prevent infection, and the therapeutic arsenal is very minimal and toxic. The unique E-NTPDase of T. cruzi (TcNTPDase1) plays essential roles in adhesion and infection and is a virulence factor. Quercetin is a flavonoid with antimicrobial, antiviral, and antitumor activities. Its potential as a partial inhibitor of NTPDases has also been demonstrated. In this work, we synthesized the non-natural L-glycoside derivatives of quercetin and evaluated them as inhibitors of recombinant TcNTPDase1 (rTcNTPDase1). These compounds, and quercetin and miquelianin, a natural quercetin derivative, were also tested. Compound 16 showed the most significant inhibitory effect (94%). Quercetin, miquelianin, and compound 14 showed inhibition close to 50%. We thoroughly investigated the inhibitory effect of 16. Our data suggested a competitive inhibition with a Ki of 8.39 μM (± 0.90). To better understand the interaction of compound 16 and rTcNTPDase1, we performed molecular dynamics simulations of the enzyme and docking analyses with the compounds. Our predictions show that compound 16 binds to the enzyme's catalytic site and interacts with important residues for NTPDase activity. As an inhibitor of a critical T. cruzi enzyme, (16) could be helpful as a starting point in the developing of a future treatment for Chagas disease. Furthermore, the discovery of (16) as an inhibitor of TcNTPDase1 may open new avenues in the study and development of new inhibitors of E-NTPDases.
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Affiliation(s)
- Isadora Cunha Ribeiro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Christiane Mariotini-Moura
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Medicine and Nursing Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Depolo Polêto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Raissa Barbosa de Castro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Izabel Luzia Miranda
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Suélen Karine Sartori
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kryssia Lohayne Santos Alves
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Costa Bressan
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - José Roberto Meyer-Fernandes
- Laboratory of Cellular Biochemistry, Institute of Medical Biochemistry Leopoldo de Meis, Health Sciences Center, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gaspar Diaz-Muñoz
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Juliana Lopes Rangel Fietto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Montero DA, Garcia-Betancourt R, Vidal RM, Velasco J, Palacios PA, Schneider D, Vega C, Gómez L, Montecinos H, Soto-Shara R, Oñate Á, Carreño LJ. A chimeric protein-based vaccine elicits a strong IgG antibody response and confers partial protection against Shiga toxin-producing Escherichia coli in mice. Front Immunol 2023; 14:1186368. [PMID: 37575242 PMCID: PMC10413102 DOI: 10.3389/fimmu.2023.1186368] [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: 03/14/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Background Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that causes gastrointestinal infections, ranging from acute diarrhea and dysentery to life-threatening diseases such as Hemolytic Uremic Syndrome. Currently, a vaccine to prevent STEC infection is an unmet medical need. Results We developed a chimeric protein-based vaccine targeting seven virulence factors of STEC, including the Stx2B subunit, Tir, Intimin, EspA, Cah, OmpT, and AggA proteins. Immunization of mice with this vaccine candidate elicited significant humoral and cellular immune responses against STEC. High levels of specific IgG antibodies were found in the serum and feces of immunized mice. However, specific IgA antibodies were not detected in either serum or feces. Furthermore, a significantly higher percentage of antigen-specific CD4+ T cells producing IFN-γ, IL-4, and IL-17 was observed in the spleens of immunized mice. Notably, the immunized mice showed decreased shedding of STEC O157:H7 and STEC O91:H21 strains and were protected against weight loss during experimental infection. Additionally, infection with the STEC O91:H21 strain resulted in kidney damage in control unimmunized mice; however, the extent of damage was slightly lower in immunized mice. Our findings suggest that IgG antibodies induced by this vaccine candidate may have a role in inhibiting bacterial adhesion and complement-mediated killing. Conclusion This study provides evidence that IgG responses are involved in the host defense against STEC. However, our results do not rule out that other classes of antibodies also participate in the protection against this pathogen. Additional work is needed to improve the protection conferred by our vaccine candidate and to elucidate the relevant immune responses that lead to complete protection against this pathogen.
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Affiliation(s)
- David A. Montero
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Richard Garcia-Betancourt
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto M. Vidal
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juliana Velasco
- Unidad de Paciente Crítico, Clínica Hospital del Profesor, Santiago, Chile
- Programa de Formación de Especialista en Medicina de Urgencia, Universidad Andrés Bello, Santiago, Chile
| | - Pablo A. Palacios
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela Schneider
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Carolina Vega
- Plataforma Experimental, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Leonardo Gómez
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Hernán Montecinos
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Soto-Shara
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Ángel Oñate
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Leandro J. Carreño
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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Cherene MB, Taveira GB, Almeida-Silva F, da Silva MS, Cavaco MC, da Silva-Ferreira AT, Perales JEA, de Oliveira Carvalho A, Venâncio TM, da Motta OV, Rodrigues R, Castanho MARB, Gomes VM. Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10112-3. [PMID: 37365421 DOI: 10.1007/s12602-023-10112-3] [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] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
The emergence of resistant microorganisms has reduced the effectiveness of currently available antimicrobials, necessitating the development of new strategies. Plant antimicrobial peptides (AMPs) are promising candidates for novel drug development. In this study, we aimed to isolate, characterize, and evaluate the antimicrobial activities of AMPs isolated from Capsicum annuum. The antifungal potential was tested against Candida species. Three AMPs from C. annuum leaves were isolated and characterized: a protease inhibitor, a defensin-like protein, and a lipid transporter protein, respectively named CaCPin-II, CaCDef-like, and CaCLTP2. All three peptides had a molecular mass between 3.5 and 6.5 kDa and caused morphological and physiological changes in four different species of the genus Candida, such as pseudohyphae formation, cell swelling and agglutination, growth inhibition, reduced cell viability, oxidative stress, membrane permeabilization, and metacaspase activation. Except for CaCPin-II, the peptides showed low or no hemolytic activity at the concentrations used in the yeast assays. CaCPin-II inhibited α-amylase activity. Together, these results suggest that these peptides have the potential as antimicrobial agents against species of the genus Candida and can serve as scaffolds for the development of synthetic peptides for this purpose.
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Affiliation(s)
- Milena Bellei Cherene
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Gabriel Bonan Taveira
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Marciele Souza da Silva
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Marco Calvinho Cavaco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | | | | | - André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Thiago Motta Venâncio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Olney Vieira da Motta
- Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Rosana Rodrigues
- Laboratório de Melhoramento e Genética Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | | | - Valdirene Moreira Gomes
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
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Zhang Y, Pan D, Xiao P, Xu Q, Geng F, Zhang X, Zhou X, Xu H. A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation. Front Microbiol 2023; 14:1097492. [PMID: 37007517 PMCID: PMC10057547 DOI: 10.3389/fmicb.2023.1097492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMO) are expected to change the current status of chitin resource utilization. This study reports that targeted enrichment of the microbiota was performed with chitin by the selective gradient culture technique, and a novel LPMO (M2822) was identified from the enrichment microbiota metagenome. First, soil samples were screened based on soil bacterial species and chitinase biodiversity. Then gradient enrichment culture with different chitin concentrations was carried out. The efficiency of chitin powder degradation was increased by 10.67 times through enrichment, and chitin degradation species Chitiniphilus and Chitinolyticbacter were enriched significantly. A novel LPMO (M2822) was found in the metagenome of the enriched microbiota. Phylogenetic analysis showed that M2822 had a unique phylogenetic position in auxiliary activity (AA) 10 family. The analysis of enzymatic hydrolysate showed that M2822 had chitin activity. When M2822 synergized with commercial chitinase to degrade chitin, the yield of N-acetyl glycosamine was 83.6% higher than chitinase alone. The optimum temperature and pH for M2822 activity were 35°C and 6.0. The synergistic action of M2822 and chitin-degrading enzymes secreted by Chitiniphilus sp. LZ32 could efficiently hydrolyze shrimp shell powder. After 12 h of enzymatic hydrolysis, chitin oligosaccharides (COS) yield reached 4,724 μg/mL. To our knowledge, this work is the first study to mine chitin activity LPMO in the metagenome of enriched microbiota. The obtained M2822 showed application prospects in the efficient production of COS.
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Affiliation(s)
- Yang Zhang
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Delong Pan
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Peiyao Xiao
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Qianqian Xu
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Fan Geng
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Xinyu Zhang
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Xiuling Zhou
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- *Correspondence: Xiuling Zhou,
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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8
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Antonelli AC, Almeida VP, da Fonseca SG. Immunoinformatics Vaccine Design for Zika Virus. Methods Mol Biol 2023; 2673:411-429. [PMID: 37258930 DOI: 10.1007/978-1-0716-3239-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Zika virus (ZIKV) is an emerging virus from the Flaviviridae family and Flavivirus genus that has caused important outbreaks around the world. ZIKV infection is associated with severe neuropathology in newborns and adults. Until now, there is no licensed vaccine available for ZIKV infection. Therefore, the development of a safe and effective vaccine against ZIKV is an urgent need. Recently, we designed an in silico multi-epitope vaccine for ZIKV based on immunoinformatics tools. To construct this in silico ZIKV vaccine, we used a consensus sequence generated from ZIKV sequences available in databank. Then, we selected CD4+ and CD8+ T cell epitopes from all ZIKV proteins based on the binding prediction to class II and class I human leukocyte antigen (HLA) molecules, promiscuity, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the construct and B cell epitopes were identified. Adjuvants were associated to increase immunogenicity. Distinct linkers were used for connecting the CD4+ and CD8+ T cell epitopes, EDIII, and adjuvants. Several analyses, such as antigenicity, population coverage, allergenicity, autoimmunity, and secondary and tertiary structures of the vaccine, were evaluated using various immunoinformatics tools and online web servers. In this chapter, we present the protocols with the rationale and detailed steps needed for this in silico multi-epitope ZIKV vaccine design.
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Affiliation(s)
- Ana Clara Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Simone Gonçalves da Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Dineshkumar K, Antony G. Computational identification of putative copper-binding proteins in pomegranate bacterial blight pathogen Xanthomonas citri pv. punicae. Arch Microbiol 2022; 204:362. [DOI: 10.1007/s00203-022-02982-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
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10
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Costa LC, Hu X, Malapi-Wight M, O'Connell M, Hendrickson LM, Turner RS, McFarland C, Foster J, Hurtado-Gonzales OP. Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis. Arch Virol 2021; 167:261-265. [PMID: 34757504 DOI: 10.1007/s00705-021-05294-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022]
Abstract
In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤ 70.80% in RdPp and ≤ 34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.
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Affiliation(s)
- Larissa C Costa
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Xiaojun Hu
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Martha Malapi-Wight
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.,USDA-APHIS, Biotechnology Regulatory Services, Biotechnology Risk Analysis Program, Riverdale, MD, USA
| | - Mary O'Connell
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Leticia M Hendrickson
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Roy S Turner
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | | | - Joseph Foster
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Oscar P Hurtado-Gonzales
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.
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11
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Alsulami AF, Torres PHM, Moghul I, Arif SM, Chaplin AK, Vedithi SC, Blundell TL. COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. Brief Bioinform 2021; 22:bbab220. [PMID: 34137435 PMCID: PMC8574963 DOI: 10.1093/bib/bbab220] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 01/25/2023] Open
Abstract
Mutations in hallmark genes are believed to be the main drivers of cancer progression. These mutations are reported in the Catalogue of Somatic Mutations in Cancer (COSMIC). Structural appreciation of where these mutations appear, in protein-protein interfaces, active sites or deoxyribonucleic acid (DNA) interfaces, and predicting the impacts of these mutations using a variety of computational tools are crucial for successful drug discovery and development. Currently, there are 723 genes presented in the COSMIC Cancer Gene Census. Due to the complexity of the gene products, structures of only 87 genes have been solved experimentally with structural coverage between 90% and 100%. Here, we present a comprehensive, user-friendly, web interface (https://cancer-3d.com/) of 714 modelled cancer-related genes, including homo-oligomers, hetero-oligomers, transmembrane proteins and complexes with DNA, ribonucleic acid, ligands and co-factors. Using SDM and mCSM software, we have predicted the impacts of reported mutations on protein stability, protein-protein interfaces affinity and protein-nucleic acid complexes affinity. Furthermore, we also predicted intrinsically disordered regions using DISOPRED3.
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Affiliation(s)
- Ali F Alsulami
- Department of Biochemistry at the University of Cambridge, Cambridge CB2 1GA, UK
| | - Pedro H M Torres
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | | | | | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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12
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Sierra Cacho D, Zamorano Sánchez DS, Xiqui-Vázquez ML, Viruega Góngora VI, Ramírez-Mata A, Baca BE. CdgC, a Cyclic-di-GMP Diguanylate Cyclase of Azospirillum baldaniorum Is Involved in Internalization to Wheat Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:748393. [PMID: 34745182 PMCID: PMC8564387 DOI: 10.3389/fpls.2021.748393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Azospirillum baldaniorum is a plant growth-promoting rhizobacterium (PGPR) capable of fixing nitrogen, the synthesis of several phytohormones including indole-acetic acid, and induction of plant defenses against phytopathogens. To establish a successful and prolonged bacteria-plant interaction, A. baldaniorum can form biofilms, bacterial communities embedded in a self-made matrix formed by extracellular polymeric substances which provide favorable conditions for survival. A key modulator of biofilm formation is the second messenger bis-(3'-5')-cyclic-dimeric-GMP (c-di-GMP), which is synthesized by diguanylate cyclases (DGC) and degraded by specific phosphodiesterases. In this study, we analyzed the contribution of a previously uncharacterized diguanylate cyclase designated CdgC, to biofilm formation and bacterial-plant interaction dynamics. We showed that CdgC is capable of altering c-di-GMP levels in a heterologous host, strongly supporting its function as a DGC. The deletion of cdgC resulted in alterations in the three-dimensional structure of biofilms in a nitrogen-source dependent manner. CdgC was required for optimal colonization of wheat roots. Since we also observed that CdgC played an important role in exopolysaccharide production, we propose that this signaling protein activates a physiological response that results in the strong attachment of bacteria to the roots, ultimately contributing to an optimal bacterium-plant interaction. Our results demonstrate that the ubiquitous second messenger c-di-GMP is a key factor in promoting plant colonization by the PGPR A. baldaniorum by allowing proficient internalization in wheat roots. Understanding the molecular basis of PGPR-plant interactions will enable the design of better biotechnological strategies of agro-industrial interest.
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Affiliation(s)
- Daniel Sierra Cacho
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - David S. Zamorano Sánchez
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Maria Luisa Xiqui-Vázquez
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Víctor Iván Viruega Góngora
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Alberto Ramírez-Mata
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Beatriz E. Baca
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
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13
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Alaalm L, Crunden JL, Butcher M, Obst U, Whealy R, Williamson CE, O'Brien HE, Schaffitzel C, Ramage G, Spencer J, Diezmann S. Identification and Phenotypic Characterization of Hsp90 Phosphorylation Sites That Modulate Virulence Traits in the Major Human Fungal Pathogen Candida albicans. Front Cell Infect Microbiol 2021; 11:637836. [PMID: 34513723 PMCID: PMC8431828 DOI: 10.3389/fcimb.2021.637836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/24/2021] [Indexed: 01/13/2023] Open
Abstract
The highly conserved, ubiquitous molecular chaperone Hsp90 is a key regulator of cellular proteostasis and environmental stress responses. In human pathogenic fungi, which kill more than 1.6 million patients each year worldwide, Hsp90 governs cellular morphogenesis, drug resistance, and virulence. Yet, our understanding of the regulatory mechanisms governing fungal Hsp90 function remains sparse. Post-translational modifications are powerful components of nature’s toolbox to regulate protein abundance and function. Phosphorylation in particular is critical in many cellular signaling pathways and errant phosphorylation can have dire consequences for the cell. In the case of Hsp90, phosphorylation affects its stability and governs its interactions with co-chaperones and clients. Thereby modulating the cell’s ability to cope with environmental stress. Candida albicans, one of the leading human fungal pathogens, causes ~750,000 life-threatening invasive infections worldwide with unacceptably high mortality rates. Yet, it remains unknown if and how Hsp90 phosphorylation affects C. albicans virulence traits. Here, we show that phosphorylation of Hsp90 is critical for expression of virulence traits. We combined proteomics, molecular evolution analyses and structural modeling with molecular biology to characterize the role of Hsp90 phosphorylation in this non-model pathogen. We demonstrated that phosphorylation negatively affects key virulence traits, such as the thermal stress response, morphogenesis, and drug susceptibility. Our results provide the first record of a specific Hsp90 phosphorylation site acting as modulator of fungal virulence. Post-translational modifications of Hsp90 could prove valuable in future exploitations as antifungal drug targets.
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Affiliation(s)
- Leenah Alaalm
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Julia L Crunden
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mark Butcher
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Ulrike Obst
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Ryann Whealy
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Heath E O'Brien
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | | | - Gordon Ramage
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Stephanie Diezmann
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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14
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Thorsing M, Krogh TJ, Vitved L, Nawrocki A, Jakobsen R, Larsen MR, Chakraborty S, Bourgeois AL, Andersen AZ, Boysen A. Linking inherent O-Linked Protein Glycosylation of YghJ to Increased Antigen Potential. Front Cell Infect Microbiol 2021; 11:705468. [PMID: 34490144 PMCID: PMC8417355 DOI: 10.3389/fcimb.2021.705468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a WHO priority pathogen and vaccine target which causes infections in low-income and middle-income countries, travelers visiting endemic regions. The global urgent demand for an effective preventive intervention has become more pressing as ETEC strains have become increasingly multiple antibiotic resistant. However, the vaccine development pipeline has been slow to address this urgent need. To date, vaccine development has focused mainly on canonical antigens such as colonization factors and expressed toxins but due to genomic plasticity of this enteric pathogen, it has proven difficult to develop effective vaccines. In this study, we investigated the highly conserved non-canonical vaccine candidate YghJ/SsLE. Using the mass spectrometry-based method BEMAP, we demonstrate that YghJ is hyperglycosylated in ETEC and identify 54 O-linked Set/Thr residues within the 1519 amino acid primary sequence. The glycosylation sites are evenly distributed throughout the sequence and do not appear to affect the folding of the overall protein structure. Although the glycosylation sites only constitute a minor subpopulation of the available epitopes, we observed a notable difference in the immunogenicity of the glycosylated YghJ and the non-glycosylated protein variant. We can demonstrate by ELISA that serum from patients enrolled in an ETEC H10407 controlled infection study are significantly more reactive with glycosylated YghJ compared to the non-glycosylated variant. This study provides an important link between O-linked glycosylation and the relative immunogenicity of bacterial proteins and further highlights the importance of this observation in considering ETEC proteins for inclusion in future broad coverage subunit vaccine candidates.
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Affiliation(s)
| | | | - Lars Vitved
- Department of Cancer and Inflammation Research, University of Southern Denmark, Odense, Denmark
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Subhra Chakraborty
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - A. Louis Bourgeois
- Center for Vaccine Innovation and Access, PATH, Washington, DC, United States
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15
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Pratama AA, Bolduc B, Zayed AA, Zhong ZP, Guo J, Vik DR, Gazitúa MC, Wainaina JM, Roux S, Sullivan MB. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ 2021; 9:e11447. [PMID: 34178438 PMCID: PMC8210812 DOI: 10.7717/peerj.11447] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). RESULTS The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. CONCLUSION Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Zhi-Ping Zhong
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States of America
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Dean R. Vik
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | | | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Infectious Diseases Institute at The Ohio State University, Ohio State University, Columbus, OH, United States of America
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Environmental and Geodetic Engineering, Ohio State University, Department of Civil, Columbus, OH, United States of America
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16
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Kar RK. Computational Resources for Bioscience Education. Appl Biochem Biotechnol 2021; 193:3418-3424. [PMID: 34101113 PMCID: PMC8184869 DOI: 10.1007/s12010-021-03601-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]
Abstract
With the ongoing laboratory restrictions, it is often challenging for bioscience students to make satisfactory progress in their projects. A long-standing practice in multi-disciplinary research is to use computational and theoretical method to corroborate with experiment findings. In line with the lack of opportunity to access laboratory instruments, the pandemic situation is a win-win scenario for scholars to focus on computational methods. This communication outline some of the standalone tools and webservers that bioscience students can successfully learn and adopt to obtain in-depth insights into biochemistry, biophysics, biotechnology, and bioengineering research work.
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Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623, Berlin, Germany.
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17
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Soto-Ospina A, Araque Marín P, Bedoya G, Sepulveda-Falla D, Villegas Lanau A. Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site. Front Mol Biosci 2021; 8:649990. [PMID: 34150846 PMCID: PMC8206637 DOI: 10.3389/fmolb.2021.649990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer's disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.
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Affiliation(s)
- Alejandro Soto-Ospina
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- School of Life Sciences, Research and Innovation in Chemistry Formulations Group, EIA University, Envigado, Colombia
| | - Gabriel Bedoya
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrés Villegas Lanau
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
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18
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Czerwonka G, Gmiter D, Durlik-Popińska K. Draft Genome of Proteus mirabilis Serogroup O18 Elaborating Phosphocholine-Decorated O Antigen. Front Cell Infect Microbiol 2021; 11:620010. [PMID: 33842384 PMCID: PMC8027243 DOI: 10.3389/fcimb.2021.620010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Proteus mirabilis is a pathogenic, Gram-negative, rod-shaped bacterium that causes ascending urinary tract infections. Swarming motility, urease production, biofilm formation, and the properties of its lipopolysaccharide (LPS) are all factors that contribute to the virulence of this bacterium. Uniquely, members of the O18 serogroup elaborate LPS molecules capped with O antigen polymers built of pentasaccharide repeats; these repeats are modified with a phosphocholine (ChoP) moiety attached to the proximal sugar of each O unit. Decoration of the LPS with ChoP is an important surface modification of many pathogenic and commensal bacteria. The presence of ChoP on the bacterial envelope is correlated with pathogenicity, as decoration with ChoP plays a role in bacterial adhesion to mucosal surfaces, resistance to antimicrobial peptides and sensitivity to complement-mediated killing in several species. The genome of P. mirabilis O18 is 3.98 Mb in size, containing 3,762 protein-coding sequences and an overall GC content of 38.7%. Annotation performed using the RAST Annotation Server revealed genes associated with choline phosphorylation, uptake and transfer. Moreover, amino acid sequence alignment of the translated licC gene revealed it to be homologous to LicC from Streptococcus pneumoniae encoding CTP:phosphocholine cytidylyltransferase. Recognized homologs are located in the O antigen gene clusters of Proteus species, near the wzx gene encoding the O antigen flippase, which translocates lipid-linked O units across the inner membrane. This study reveals the genes potentially engaged in LPS decoration with ChoP in P. mirabilis O18.
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Affiliation(s)
- Grzegorz Czerwonka
- Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | - Dawid Gmiter
- Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
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19
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Urbániková Ľ. CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. 3 Biotech 2021; 11:84. [PMID: 33505839 DOI: 10.1007/s13205-020-02575-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/01/2020] [Indexed: 01/23/2023] Open
Abstract
Bioinformatics analysis was focused on unique acetylesterases annotated in the CAZy database within the CE16 family and simultaneously belonging to the SGNH hydrolase superfamily. The CE16 acetylesterases were compared to structurally related SGNH hydrolases: (i) selected members of the CE2, CE3, CE6, CE12 and CE17 family of the CAZy database and (ii) structural representatives of the Lipase_GDSL and Lipase_GDSL_2 families according to the Pfam database. Sequence alignment based on four conserved sequence regions (CSRs) containing active-site residues was used to calculate sequence logos specific for each CE family and to construct a phylogenetic tree. In many members of the CE16 family, aspartic acid from the Ser-His-Asp catalytic triad has been replaced by asparagine, and based on structure-sequence comparison, an alternative catalytic dyad mechanism was predicted for these enzymes. In addition to four conserved regions, CSR-I, CSR-II, CSR-III and CSR-V, containing catalytic and oxyanion-hole residues, CSR-IV was found in the CE16 family as the only CAZy family. Tertiary structures of the characterized CE16 members prepared by homology modeling showed that the α/β/α sandwich fold as well as the topology of their active sites are preserved. The phylogenetic tree and sequence alignment indicate the existence of a subfamily in the CE16 family fully consistent with the known biochemical data. In addition, nonstandard CE16 members that differ from others were analyzed and their active-site residues were predicted. A better understanding of the structure-function relationship of acetylesterases can help in the targeted design of these enzymes for biotechnology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02575-w.
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20
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De Oliveira TV, Guimarães AP, Bressan GC, Maia ER, Coimbra JSDR, Polêto MD, De Oliveira EB. Structural and molecular bases of angiotensin-converting enzyme inhibition by bovine casein-derived peptides: an in silico molecular dynamics approach. J Biomol Struct Dyn 2020; 39:1386-1403. [PMID: 32066337 DOI: 10.1080/07391102.2020.1730243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The angiotensin-converting enzyme (ACE) plays a key role in blood pressure regulation process, and its inhibition is one of the main drug targets for the treatment of hypertension. Though various peptides from milk proteins are well-known for their ACE-inhibitory capacity, research devoted to understand the molecular bases of such property remain scarce, specifically for such peptides. Therefore, in this work, computational molecular docking and molecular dynamics calculations were performed to enlighten the intermolecular interactions involved in ACE inhibition by six different casein-derived peptides (FFVAPFPEVFGK, FALPQYLK, ALNEINQFYQK, YLGYLEQLLR, HQGLPQEVLNENLLR and NAVPITPTLNR). Two top ranked docking poses for each peptide (one with N- and the other C-terminal peptide extremity oriented towards the ACE active site) were selected for dynamic simulations (50 ns; GROMOS53A6 force field), and the results were correlated to in vitro ACE inhibition capacity. Two molecular features appeared to be essential for peptides to present high ACE inhibition capacity in vitro: i) to interact with the S1 active site residues (Ala354, Glu384, and Tyr523) by hydrogen bonds; ii) to interact with Zn2+ coordinated residues (His383, His387, and Glu411) by short-lenght hydrogen bonds, as observed in the cases of ALNEINQFYQK (IACE = 80.7%), NAVPITPTLNR (IACE = 80.7%), and FALPQYLK (IACE = 79.0%). Regardless of the temporal stability of these strong interactions, they promoted some disruption of Zn2+ tetrahedral coordination during the molecular dynamics trajectories, and were pointed as the main reason for the greatest ACE inhibition by these peptides. On the other hand, peptides with intermediate inhibition capacity (50% < IACE < 45%) interacted mainly by weaker interactions (e.g.: electrostatic and hydrophobic) with the Zn2+ coordinated residues, and were not able to change significantly its tetrahedral coordination structure. These findings may: i) assist the discrimination in silico of "good" and "bad" ACE-inhibitory peptides from other food sources, and/or ii) aid in designing de novo new molecules with ACE-inhibitory capacity. Communicated by Ramaswamy Sarma.
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Affiliation(s)
| | - Ana Paula Guimarães
- Departamento de Química (DEQ), Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
| | - Gustavo Costa Bressan
- Departamento de Bioquímica e Biologia Molecular (DBB), Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
| | - Elaine Rose Maia
- Laboratório de Estudos Estruturais Moleculares (LEEM), Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Marcelo Depólo Polêto
- Departamento de Biologia Geral (DBG), Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
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Mattila HK, Mäkinen M, Lundell T. Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:26. [PMID: 32123543 PMCID: PMC7038570 DOI: 10.1186/s13068-020-01677-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fungal decomposition of wood is considered as a strictly aerobic process. However, recent findings on wood-decaying fungi to produce ethanol from various lignocelluloses under oxygen-depleted conditions lead us to question this. We designed gene expression study of the white rot fungus Phlebia radiata (isolate FBCC0043) by adopting comparative transcriptomics and functional genomics on solid lignocellulose substrates under varying cultivation atmospheric conditions. RESULTS Switch to fermentative conditions was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides. Changes in the expression profiles of CAZy (carbohydrate-active enzyme) encoding genes upon oxygen depletion, lead into an alternative wood decomposition strategy. Surprisingly, we noticed higher cellulolytic activity under fermentative conditions in comparison to aerobic cultivation. In addition, our results manifest how oxygen depletion affects over 200 genes of fungal primary metabolism including several transcription factors. We present new functions for acetate generating phosphoketolase pathway and its potential regulator, Adr1 transcription factor, in carbon catabolism under oxygen depletion. CONCLUSIONS Physiologically resilient wood-decomposing Basidiomycota species P. radiata is capable of thriving under respirative and fermentative conditions utilizing only untreated lignocellulose as carbon source. Hypoxia-response mechanism in the fungus is, however, divergent from the regulation described for Ascomycota fermenting yeasts or animal-pathogenic species of Basidiomycota.
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Affiliation(s)
- Hans Kristian Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
| | - Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
- Present Address: VTT Technical Research Centre of Finland Ltd, 02044 VTT Espoo, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
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22
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Futagi Y, Kobayashi M, Narumi K, Furugen A, Iseki K. Homology modeling and site-directed mutagenesis identify amino acid residues underlying the substrate selection mechanism of human monocarboxylate transporters 1 (hMCT1) and 4 (hMCT4). Cell Mol Life Sci 2019; 76:4905-4921. [PMID: 31101938 PMCID: PMC11105385 DOI: 10.1007/s00018-019-03151-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/21/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Human monocarboxylate transporters (hMCTs/SLC16As) mediate the transport of monocarboxylic compounds across plasma membranes. Among the hMCTs, hMCT1 and hMCT4 are expressed in various tissues, and transport substrates involved in energy metabolism. Both transporters mediate L-lactate transport, but, although hMCT1 also transports L-5-oxoproline (L-OPro), this compound is minimally transported by hMCT4. Thus, we were interested in the molecular mechanism responsible for the difference in substrate specificity between hMCT1 and hMCT4. Therefore, we generated 3D structure models of hMCT1 and hMCT4 to identify amino acid residues involved in the substrate specificity of these transporters. We found that the substrate specificity of hMCT1 was regulated by residues involved in turnover number (M69) and substrate affinity (F367), and these residues were responsible for recognizing (directly or indirectly) the -NH- moiety of L-OPro. Furthermore, our homology model of hMCT1 predicted that M69 and F367 participate in hydrophobic interactions with another region of hMCT1, emphasizing its potentially important role in the binding and translocation cycle of L-OPro. Mutagenesis experiments supported this model, showing that efficient L-OPro transport required a hydrophobic, long linear structure at position 69 and a hydrophobic, γ-branched structure at position 367. Our work demonstrated that the amino acid residues, M69 and F367, are key molecular elements for the transport of L-OPro by hMCT1. These two residues may be involved in substrate recognition and/or substrate-induced conformational changes.
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Affiliation(s)
- Yuya Futagi
- Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
- Japan Society for the Promotion of Science (JSPS), 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Masaki Kobayashi
- Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan.
- Department of Pharmacy, Hokkaido University Hospital, Kita-14-jo, Nishi-5-chome, Kita-ku, Sapporo, 060-8648, Japan.
| | - Katsuya Narumi
- Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Ayako Furugen
- Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Ken Iseki
- Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan.
- Department of Pharmacy, Hokkaido University Hospital, Kita-14-jo, Nishi-5-chome, Kita-ku, Sapporo, 060-8648, Japan.
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Munsamy G, Soliman MES. Unveiling a New Era in Malaria Therapeutics: A Tailored Molecular Approach Towards the Design of Plasmepsin IX Inhibitors. Protein J 2019; 38:616-627. [DOI: 10.1007/s10930-019-09871-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Molecular docking studies of bioactive compounds from Annona muricata Linn as potential inhibitors for Bcl-2, Bcl-w and Mcl-1 antiapoptotic proteins. Apoptosis 2019; 23:27-40. [PMID: 29204721 DOI: 10.1007/s10495-017-1434-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Annona muricata Linn or usually identified as soursop is a potential anticancer plant that has been widely reported to contain valuable chemopreventive agents known as annonaceous acetogenins. The antiproliferative and anticancer activities of this tropical and subtropical plant have been demonstrated in cell culture and animal studies. A. muricata L. exerts inhibition against numerous types of cancer cells, involving multiple mechanism of actions such as apoptosis, a programmed cell death that are mainly regulated by Bcl-2 family of proteins. Nonetheless, the binding mode and the molecular interactions of the plant's bioactive constituents have not yet been unveiled for most of these mechanisms. In the current study, we aim to elucidate the binding interaction of ten bioactive phytochemicals of A. muricata L. to three Bcl-2 family of antiapoptotic proteins viz. Bcl-2, Bcl-w and Mcl-1 using an in silico molecular docking analysis software, Autodock 4.2. The stability of the complex with highest affinity was evaluated using MD simulation. We compared the docking analysis of these substances with pre-clinical Bcl-2 inhibitor namely obatoclax. The study identified the potential chemopreventive agent among the bioactive compounds. We also characterized the important interacting residues of protein targets which involve in the binding interaction. Results displayed that anonaine, a benzylisoquinoline alkaloid, showed a high affinity towards the Bcl-2, thus indicating that this compound is a potent inhibitor of the Bcl-2 antiapoptotic family of proteins.
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25
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Kotowska M, Świat M, Zarȩba-Pasławska J, Jaworski P, Pawlik K. A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2). Front Microbiol 2019; 10:1451. [PMID: 31297104 PMCID: PMC6608401 DOI: 10.3389/fmicb.2019.01451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
Bacteria from the genus Streptomyces have been long exploited as the most prolific producers of antibiotics, other secondary metabolites and enzymes. They are important members of soil microbial communities that can adapt to changing conditions thank to the fine regulation of gene expression in response to environmental signals. Streptomyces coelicolor A3(2) is a model organism for molecular studies with the most deeply recognized interactions within the complex metabolic and regulatory network. However, details about molecular signals recognized by specialized regulatory proteins as well as their direct targets are often missing. We describe here a zinc-binding protein HypR (SCO6294) which belongs to FadR subfamily of GntR-like regulators. The DNA sequence 5'-TACAATGTCAC-3' recognized by the HypR protein in its own promoter region was identified by DNase I footprinting. Binding of six DNA fragments containing similar sequences located in other promoter regions were confirmed by the electrophoretic mobility shift assay (EMSA). The sequences of 7 in vitro-determined binding sites were assembled to generate a logo of the HypR binding motif, 5'-CTNTGC(A/C)ATGTCAC-3'. Comparison of luciferase reporter genes expression under the control of cloned promoter regions in S. coelicolor A3(2) wild type and deletion mutant strains revealed, that the HypR protein acts as a repressor of its target genes. Genes belonging to the regulon of HypR code for enzymes putatively involved in collagen degradation and utilization of L-hydroxyproline (L-Hyp) as concluded from predicted structure and conserved domains. Their transcription is induced in the wild type strain by the addition of L-Hyp to the culture medium. Moreover, knockout of one of the genes from the predicted L-Hyp utilization operon abolished the ability of the strain to grow on L-Hyp as a sole source of carbon. To our knowledge, this work is the first indication of the existence of the pathway of L-hydroxyproline catabolism in Streptomycetes.
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Affiliation(s)
- Magdalena Kotowska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | | | | | | | - Krzysztof Pawlik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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26
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Mougari S, Bekliz M, Abrahao J, Di Pinto F, Levasseur A, La Scola B. Guarani Virophage, a New Sputnik-Like Isolate From a Brazilian Lake. Front Microbiol 2019; 10:1003. [PMID: 31130943 PMCID: PMC6510173 DOI: 10.3389/fmicb.2019.01003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/18/2019] [Indexed: 01/23/2023] Open
Abstract
Virophages are critical regulators of viral population dynamics and potential actors in the stability of the microbial networks. These small biological entities predate the replicative cycle of giant viruses, such as the members of the Mimiviridae family or their distant relatives, which produce within the cytoplasm of their host cells a viral factory harboring a complex biochemistry propitious to the growth of the smaller parasites. In this paper, we describe the isolation and the characterization of a new virophage, the eighth, that we named Guarani. We observed that Guarani exhibits a late replication cycle compared to its giant virus host. In addition, like all Sputnik strains, Guarani is able to infect the three lineages A, B and C of the Mimiviridae family, and affects the replication and the infectivity of its host virus. In terms of genetic content, Guarani has a 18,967 bp long double-stranded DNA genome encoding 22 predicted genes very similar to Sputnik genes, except for ORF19 and ORF12. The former is more related to Zamilon while the latter seems to be novel. The architecture of the Guarani genome is closely related to Sputnik and Zamilon strains, suggesting a common origin for all these virophages.
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Affiliation(s)
- Said Mougari
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Meriem Bekliz
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Jonatas Abrahao
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fabrizio Di Pinto
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Department of Medicine, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
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27
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de Macêdo Mendes C, Teixeira DG, Lima JPMS, Lanza DCF. Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome. BMC STRUCTURAL BIOLOGY 2019; 19:8. [PMID: 30999895 PMCID: PMC6474068 DOI: 10.1186/s12900-019-0106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/28/2019] [Indexed: 01/07/2023]
Abstract
Background White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Until now, the functions of these proteins were little studied. In this work, sequences and putative proteins encoded by WSSV variable regions were characterized in silico. Results The in silico approach enabled determining the variability of some sequences, as well as the identification of some domains resembling the Formin homology 2, RNA recognition motif, Xeroderma pigmentosum group D repair helicase, Hemagglutinin and Ankyrin motif. The information obtained from the sequences and the analysis of secondary and tertiary structure models allow to infer that some of these proteins possibly have functions related to protein modulation/degradation, intracellular transport, recombination and endosome fusion events. Conclusions The bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497. Electronic supplementary material The online version of this article (10.1186/s12900-019-0106-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cayro de Macêdo Mendes
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Diego Gomes Teixeira
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - João Paulo Matos Santos Lima
- Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
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28
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Warneys R, Gaucher M, Robert P, Aligon S, Anton S, Aubourg S, Barthes N, Braud F, Cournol R, Gadenne C, Heintz C, Brisset MN, Degrave A. Acibenzolar- S-Methyl Reprograms Apple Transcriptome Toward Resistance to Rosy Apple Aphid. FRONTIERS IN PLANT SCIENCE 2018; 9:1795. [PMID: 30619387 PMCID: PMC6299034 DOI: 10.3389/fpls.2018.01795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/19/2018] [Indexed: 05/09/2023]
Abstract
Acibenzolar-S-methyl (ASM) is a chemical compound, which is able to induce resistance in several model and non-model plants, but the end-players of this induced defense remain ill-defined. Here, we test the hypothesis that treatment with ASM can protect apple (Malus × domestica) against the rosy apple aphid (Dysaphis plantaginea) and investigate the defense molecules potentially involved in resistance. We measured aphid life traits and performed behavioral assays to study the effect of ASM on plant resistance against the aphid, and then combined transcriptomic, bioinformatics, metabolic and biochemical analyses to identify the plant compounds involved in resistance. Plants treated with ASM negatively affected several life traits of the aphid and modified its feeding and host seeking behaviors. ASM treatment elicited up-regulation of terpene synthase genes in apple and led to the emission of (E,E)-α-farnesene, a sesquiterpene that was repellent to the aphid. Several genes encoding amaranthin-like lectins were also strongly up-regulated upon treatment and the corresponding proteins accumulated in leaves, petioles and stems. Our results link the production of specific apple proteins and metabolites to the antibiosis and antixenosis effects observed against Dysaphis plantaginea, providing insight into the mechanisms underlying ASM-induced herbivore resistance.
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Affiliation(s)
- Romain Warneys
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Matthieu Gaucher
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Philippe Robert
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Sophie Aligon
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Sylvia Anton
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, Angers, France
| | - Sébastien Aubourg
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Nicolas Barthes
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS – Université de Montpellier – Université Paul Valery Montpellier 3 – EPHE – IRD, Montpellier, France
| | - Ferréol Braud
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Raphaël Cournol
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Christelle Heintz
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Marie-Noëlle Brisset
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Alexandre Degrave
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
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Hecox-Lea BJ, Mark Welch DB. Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers. BMC Evol Biol 2018; 18:177. [PMID: 30486781 PMCID: PMC6264785 DOI: 10.1186/s12862-018-1288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022] Open
Abstract
Background Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2–4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. Results We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75–100% of genes involved in MMR and HR are present in 0–2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3–8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. Conclusion The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids. Electronic supplementary material The online version of this article (10.1186/s12862-018-1288-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biology, Northeastern University, Boston, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
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30
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Benler S, Cobián-Güemes AG, McNair K, Hung SH, Levi K, Edwards R, Rohwer F. A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. MICROBIOME 2018; 6:191. [PMID: 30352623 PMCID: PMC6199706 DOI: 10.1186/s40168-018-0573-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs. RESULTS This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle. The majority of phage-encoded DGRs were identified as prophages in bacterial hosts from the phyla Bacteroidetes, Proteobacteria, and Firmicutes. Sequence reads from these previously unidentified prophages were present in viral metagenomes (viromes), indicating these prophages can produce functional viruses. Five phages possessed hypervariable proteins with structural similarity to the tail fiber of BPP-1, whereas the functions of the remaining DGR target proteins were unknown. A novel temperate phage that harbors a DGR cassette targeting a protein of unknown function was induced from Bacteroides dorei. This phage, here named Bacteroides dorei Hankyphage, lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively. CONCLUSIONS Here, the number of known DGR-containing phages is increased from four to 92. All of these phages exhibit a temperate lifestyle, including a cosmopolitan human-associated phage. Targeted hypervariation by temperate phages may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.
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Affiliation(s)
- Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | | | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Shr-Hau Hung
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Rob Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
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Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
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Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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Castillo A, Tello M, Ringwald K, Acuña LG, Quatrini R, Orellana O. A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species. RNA Biol 2017; 15:492-499. [PMID: 29168417 DOI: 10.1080/15476286.2017.1408765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNAAla. This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAcaTY.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved. By means of site directed mutagenesis, target site deletions and in vivo integrations assays in the heterologous model Escherichia coli, we assessed the target sequence requirements for site-specific recombination to be catalyzed by these integrases. We determined that each enzyme recognizes a specific small DNA segment encoding the anticodon stem/loop of the tRNA as target site and that specific positions in these regions are well conserved in the target attB sites of orthologous integrases. Also, we demonstrate that the local genetic context of the target sequence is not relevant for the integration to take place. These findings shed new light on the mechanism of site-specific integration of integrative-conjugative elements in members of Acidithiobacillus genus.
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Affiliation(s)
- Andrés Castillo
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina , Universidad de Chile , Santiago , Región Metropolitana , Chile
| | - Mario Tello
- b Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología , Universidad de Santiago de Chile , Santiago , Chile
| | - Kenneth Ringwald
- c Carl R. Woese Institute for Genomic Biology, Department of Microbiology , University of Illinois , Urbana-Champaign , Illinois , United States
| | - Lillian G Acuña
- d Fundación Ciencia y Vida. Ave. Zañartu 1482 - Ñuñoa, Santiago , Región Metropolitana , Chile
| | - Raquel Quatrini
- d Fundación Ciencia y Vida. Ave. Zañartu 1482 - Ñuñoa, Santiago , Región Metropolitana , Chile
| | - Omar Orellana
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina , Universidad de Chile , Santiago , Región Metropolitana , Chile
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Thayer KM. Structure prediction and analysis of neuraminidase sequence variants. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:361-376. [PMID: 26900942 DOI: 10.1002/bmb.20963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/29/2015] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
Analyzing protein structure has become an integral aspect of understanding systems of biochemical import. The laboratory experiment endeavors to introduce protein folding to ascertain structures of proteins for which the structure is unavailable, as well as to critically evaluate the quality of the prediction obtained. The model system used is the highly mutable influenza virus protein neuraminidase, which is the key target in the development of therapeutics. In light of recent pandemics, understanding how mutations confer drug resistance, which translates at the molecular level to understanding how different sequence variants differ, constitutes an area of great interest because of the ramifications in public health. This lab targets upper level undergraduate biochemistry students, and aims to introduce tools to be used to explore protein folding and protein visualization in the context of the neuraminidase case study. Students proceed to critically evaluate the folded models by comparison with crystallographic structures. When validity is established, they fold a neuraminidase sequence for which a structure is not available. Through structural alignment and visual inspection of the 150 loop, students gain molecular insight into two possible conformations of the protein, which are actively being studied. Folding the third chosen sequence mimics a true research environment in allowing students to generate a structure from a sequence for which a structure was not previously available, and to assess whether their particular variant has an open or closed loop. From this vantage, they are then challenged to speculate about the connection between loop conformation and drug susceptibility. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):361-376, 2016.
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Affiliation(s)
- Kelly M Thayer
- From the Department of Chemistry, Vassar College, Poughkeepsie, New York, 12604
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