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Chakma V, Barman DN, Das SC, Hossain A, Momin MB, Tasneem M, Gupta SD. In silico analysis of a novel hypothetical protein (YP_498675.1) from Staphylococcus aureus unravels the protein of tryptophan synthase beta superfamily (Try-synth-beta_ II). J Genet Eng Biotechnol 2023; 21:135. [PMID: 37995054 PMCID: PMC10667181 DOI: 10.1186/s43141-023-00613-7] [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: 02/11/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Staphylococcus aureus is a gram-positive spherical bacteria and the most common cause of nosocomial infections in the world. Given its clinical significance, the genome sequence of S. aureus has been elucidated to enhance our comprehension of its lifestyle and pathogenicity. The research aimed to summarize a potential hypothetical protein that may play an important role in S. aureus virulence and pathogenicity, covering its anticipated structure, probable biological functions, and importance in this context. RESULTS A hypothetical protein, YP_498675.1 with 281 amino acid residues of S. aureus, was chosen for analysis and modeling by several bioinformatics tools and databases in this work. According to primary and secondary structure analyses, YP_498675.1 is a stable hydrophilic protein with a significant proportion of α-helices. Subcellular localization predictions by CELLO, PSORTb, and SOSUI server indicate that it is a cytoplasmic protein. NCBI-CDD, Pfam, and InterProScan functional genomics research revealed that the hypothetical protein may include the pyridoxal phosphate (PLP)-dependent 2, 3-diaminopropionate biosynthesis protein SbnA domain. In the homology modeling method, the HHpred server was employed to create its 3D structure using the template structure of a Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP (PDB ID: 5D84_A), an X-ray diffraction model having 100% sequence identity with the hypothetical protein. After energy minimization, several quality assessments and validation factors determined that the generated protein model was reliable and of reasonable quality. CONCLUSION The present study has characterized and functionally annotated the hypothetical protein YP_498675.1 of S. aureus. Further experimental validation would aid in determining the actual function of YP_498675.1 as well as confirm the protein's value as a therapeutic target.
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Affiliation(s)
- Vivian Chakma
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Dhirendra Nath Barman
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Shuvo Chandra Das
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Anwar Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Monira Binte Momin
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Maisha Tasneem
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Shipan Das Gupta
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
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Masum MHU, Rajia S, Bristi UP, Akter MS, Amin MR, Shishir TA, Ferdous J, Ahmed F, Rahaman MM, Saha O. In Silico Functional Characterization of a Hypothetical Protein From Pasteurella Multocida Reveals a Novel S-Adenosylmethionine-Dependent Methyltransferase Activity. Bioinform Biol Insights 2023; 17:11779322231184024. [PMID: 37424709 PMCID: PMC10328030 DOI: 10.1177/11779322231184024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Genomes may now be sequenced in a matter of weeks, leading to an influx of "hypothetical" proteins (HP) whose activities remain a mystery in GenBank. The information included inside these genes has quickly grown in prominence. Thus, we selected to look closely at the structure and function of an HP (AFF25514.1; 246 residues) from Pasteurella multocida (PM) subsp. multocida str. HN06. Possible insights into bacterial adaptation to new environments and metabolic changes might be gained by studying the functions of this protein. The PM HN06 2293 gene encodes an alkaline cytoplasmic protein with a molecular weight of 28352.60 Da, an isoelectric point (pI) of 9.18, and an overall average hydropathicity of around -0.565. One of its functional domains, tRNA (adenine (37)-N6)-methyltransferase TrmO, is a S-adenosylmethionine (SAM)-dependent methyltransferase (MTase), suggesting that it belongs to the Class VIII SAM-dependent MTase family. The tertiary structures represented by HHpred and I-TASSER models were found to be flawless. We predicted the model's active site using the Computed Atlas of Surface Topography of Proteins (CASTp) and FTSite servers, and then displayed it in 3 dimensional (3D) using PyMOL and BIOVIA Discovery Studio. Based on molecular docking (MD) results, we know that HP interacts with SAM and S-adenosylhomocysteine (SAH), 2 crucial metabolites in the tRNA methylation process, with binding affinities of 7.4 and 7.5 kcal/mol, respectively. Molecular dynamic simulations (MDS) of the docked complex, which included only modest structural adjustments, corroborated the strong binding affinity of SAM and SAH to the HP. Evidence for HP's possible role as an SAM-dependent MTase was therefore given by the findings of Multiple sequence alignment (MSA), MD, and molecular dynamic modeling. These in silico data suggest that the investigated HP might be used as a useful adjunct in the investigation of Pasteurella infections and the development of drugs to treat zoonotic pasteurellosis.
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Affiliation(s)
- Md. Habib Ullah Masum
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Sultana Rajia
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Uditi Paul Bristi
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mir Salma Akter
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Ruhul Amin
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Tushar Ahmed Shishir
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Jannatul Ferdous
- Department of Medicine, Abdul Malek Ukil Medical College, Noakhali, Bangladesh
| | - Firoz Ahmed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
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Miftahussurur M, Alfaray RI, Fauzia KA, Dewayani A, Doohan D, Waskito LA, Rezkitha YAA, Utomo DH, Somayana G, Fahrial Syam A, Lubis M, Akada J, Matsumoto T, Yamaoka Y. Low-grade intestinal metaplasia in Indonesia: Insights into the expression of proinflammatory cytokines during Helicobacter pylori infection and unique East-Asian CagA characteristics. Cytokine 2023; 163:156122. [PMID: 36640695 DOI: 10.1016/j.cyto.2022.156122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023]
Abstract
Helicobacter pylori infection is a major cause of intestinal metaplasia. In this study, we aimed to understand the reason underlying the low grade and incidence of intestinal metaplasia in Indonesia, based on the expression of genes encoding proinflammatory cytokines in gastric biopsy specimens. The possible reasons for the lesser virulence of the East-Asian-type CagA in Indonesia than that of the Western-type CagA, which is not common in other countries, were also investigated. The mRNA expression of cytokines was evaluated using real-time PCR. CagA characteristics were analyzed using in silico analysis. The expression of cytokines was typically not robust, among H. pylori-infected subjects in Indonesia, despite them predominantly demonstrating the East-Asian-type CagA. This might partially be explained by the characteristics of the East-Asian-type CagA in Indonesia, which showed a higher instability index and required higher energy to interact with proteins related to the cytokine induction pathway compared with the other types (p < 0.001 and p < 0.05, respectively). Taken together, besides the low prevalence of H. pylori, the low inflammatory response of the host and low CagA virulence, even among populations with high infection rates, may play an essential role in the low grade and low incidence of intestinal metaplasia in Indonesia. We believe that these findings would be relevant for better understanding of intestinal metaplasia, which is closely associated with the development of gastric cancer.
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Affiliation(s)
- Muhammad Miftahussurur
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Jalan Mayjend Prof, Dr. Moestopo, No. 6-8, Surabaya, Surabaya 60131, Indonesia; Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia.
| | - Ricky Indra Alfaray
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Kartika Afrida Fauzia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Astri Dewayani
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Infectious Disease Control, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Dalla Doohan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Physiology and Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia; Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Yudith Annisa Ayu Rezkitha
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Internal Medicine, Faculty of Medicine, University of Muhammadiyah, Surabaya, Surabaya 60113, Indonesia.
| | - Didik Huswo Utomo
- Research and Education Center for Bioinformatics, Indonesia Institute of Bioinformatics, Malang 65162, Indonesia.
| | - Gde Somayana
- Gastroentero Hepatology Division, Department of Internal Medicine, Faculty of Medicine-Sanglah Hospital, Udayana University, Denpasar, Bali 80114, Indonesia.
| | - Ari Fahrial Syam
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, University of Indonesia, Jakarta 10430, Indonesia.
| | - Masrul Lubis
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, Universitas Sumatera Utara, Medan 20222, Indonesia
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA.
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Rajapaksha LGTG, Gunasekara CWR, de Alwis PS. In silico detection and characterization of novel virulence proteins of the emerging poultry pathogen Gallibacterium anatis. Genomics Inform 2022; 20:e41. [PMID: 36617648 PMCID: PMC9847380 DOI: 10.5808/gi.22006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/14/2022] [Indexed: 12/31/2022] Open
Abstract
The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.
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Affiliation(s)
- L. G. T. G Rajapaksha
- Veterinary Medical Center and College of Veterinary Medicine, Jeonbuk National University, Jeonju 54596, Korea
| | - C. W. R Gunasekara
- College of Fisheries Science, Pukyong National University, Busan 48513, Korea,Corresponding author: E-mail:
| | - P. S. de Alwis
- College of Fisheries Science, Pukyong National University, Busan 48513, Korea
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Singh V, Dhankhar P, Dalal V, Tomar S, Kumar P. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. J Mol Graph Model 2022; 116:108262. [PMID: 35839717 DOI: 10.1016/j.jmgm.2022.108262] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022]
Abstract
Klebsiella pneumonia is known to cause several nosocomial infections in immunocompromised patients. It has developed resistance against a broad range of presently available antibiotics, resulting in high mortality rates in patients and declared an urgent threat. Therefore, exploration of possible novel drug targets against this opportunistic bacteria needs to be undertaken. In the present study, we performed an extensive in-silico analysis for functional and structural annotation and characterized HP CP995_08280 from K. pneumonia as a drug target and aimed to identify potent drug candidates. The functional and structural studies using several bioinformatics tools and databases predicted that HP CP995_08280 is a cytosolic protein that belongs to the β-lactamase family and shares structural similarity with FmtA protein from Staphylococcus aureus (PDB ID: 5ZH8). The structure of HP CP995_08280 was successfully modeled followed by structure-based virtual screening, docking, molecular dynamics, and Molecular mechanic/Poisson-Boltzmann surface area (MMPBSA) were performed to identify the potential compounds. We have found five potent antibacterial molecules, namely BDD 24083171, BDD 24085737, BDE 25098678, BDE 33638819, and BDE 33672484, which exhibited high binding affinity (>-7.5 kcal/mol) and were stabilized by hydrogen bonding and hydrophobic interactions with active site residues (Ser42, Lys45, Tyr126, and Asp128) of protein. Molecular dynamics and MMPBSA revealed that HP CP995_08280 - ligand(s) complexes were less dynamic and more stable than native HP CP995_08280. Hence, the present study may serve as a potential lead for developing inhibitors against drug-resistant Klebsiella pneumonia.
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Affiliation(s)
- Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India.
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Arteaga-Resendiz NK, Rodea GE, Ribas-Aparicio RM, Olivares-Cervantes AL, Castelán-Vega JA, Olivares-Trejo JDJ, Mendoza-Elizalde S, López-Villegas EO, Colín C, Aguilar-Rodea P, Reyes-López A, Salazar García M, Velázquez-Guadarrama N. HP0953 - hypothetical virulence factor overexpresion and localization during Helicobacter pylori infection of gastric epithelium. World J Gastroenterol 2022; 28:3886-3902. [PMID: 36157534 PMCID: PMC9367236 DOI: 10.3748/wjg.v28.i29.3886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/26/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The high prevalence and persistence of Helicobacter pylori (H. pylori) infection, as well as the diversity of pathologies related to it, suggest that the virulence factors used by this microorganism are varied. Moreover, as its proteome contains 340 hypothetical proteins, it is important to investigate them to completely understand the mechanisms of its virulence and survival. We have previously reported that the hypothetical protein HP0953 is overexpressed during the first hours of adhesion to inert surfaces, under stress conditions, suggesting its role in the environmental survival of this bacterium and perhaps as a virulence factor.
AIM To investigate the expression and localization of HP0953 during adhesion to an inert surface and against gastric (AGS) cells.
METHODS Expression analysis was performed for HP0953 during H. pylori adhesion. HP0953 expression at 0, 3, 12, 24, and 48 h was evaluated and compared using the Kruskal-Wallis equality-of-populations rank test. Recombinant protein was produced and used to obtain polyclonal antibodies for immunolocalization. Immunogold technique was performed on bacterial sections during adherence to inert surfaces and AGS cells, which was analyzed by transmission electron microscopy. HP0953 protein sequence was analyzed to predict the presence of a signal peptide and transmembrane helices, both provided by the ExPASy platform, and using the GLYCOPP platform for glycosylation sites. Different programs, via, I-TASSER, RaptorX, and HHalign-Kbest, were used to perform three-dimensional modeling.
RESULTS HP0953 exhibited its maximum expression at 12 h of infection in gastric epithelium cells. Immunogold technique revealed HP0953 localization in the cytoplasm and accumulation in some peripheral areas of the bacterial body, with greater expression when it is close to AGS cells. Bioinformatics analysis revealed the presence of a signal peptide that interacts with the transmembrane region and then allows the release of the protein to the external environment. The programs also showed a similarity with the Tip-alpha protein of H. pylori. Tip-alpha is an exotoxin that penetrates cells and induces tumor necrosis factor alpha production, and HP0953 could have a similar function as posttranslational modification sites were found; modifications in turn require enzymes located in eukaryotic cells. Thus, to be functional, HP0953 may necessarily need to be translocated inside the cell where it can trigger different mechanisms producing cellular damage.
CONCLUSION The location of HP0953 around infected cells, the probable posttranslational modifications, and its similarity to an exotoxin suggest that this protein is a virulence factor.
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Affiliation(s)
- Nancy K Arteaga-Resendiz
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
- Posgrado en Biomedicina y Biotecnología Molecular, Laboratorio de Producción y Control de Biológicos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gerardo E Rodea
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Rosa María Ribas-Aparicio
- Posgrado en Biomedicina y Biotecnología Molecular, Laboratorio de Producción y Control de Biológicos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Alma L Olivares-Cervantes
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Juan Arturo Castelán-Vega
- Posgrado en Biomedicina y Biotecnología Molecular, Laboratorio de Producción y Control de Biológicos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - José de Jesús Olivares-Trejo
- Laboratorio de Adquisición de Hierro, Universidad Autónoma de la Ciudad México, Posgrado Ciencias Genómica, Mexico City 03100, Mexico
| | - Sandra Mendoza-Elizalde
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Edgar O López-Villegas
- Laboratorio Central de Microscopía, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Christian Colín
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Pamela Aguilar-Rodea
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Alfonso Reyes-López
- Centro de estudios económicos y sociales en salud, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Marcela Salazar García
- Laboratorio de Investigación en Biología del Desarrollo y Teratogénesis Experimental, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Norma Velázquez-Guadarrama
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
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Rabbi MF, Akter SA, Hasan MJ, Amin A. In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System. Bioinform Biol Insights 2021; 15:11779322211011140. [PMID: 33994781 PMCID: PMC8076777 DOI: 10.1177/11779322211011140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
Shigellosis caused by Shigella dysenteriae is a major public health concern worldwide, particularly in developing countries. The bacterial genome is known, but there are many hypothetical proteins whose functions are yet to be discovered. A hypothetical protein (accession no. WP_128879999.1, 161 residues) of S. dysenteriae ATCC 12039 strain was selected in this study for comprehensive structural and functional analysis. Subcellular localization and different physicochemical properties of this hypothetical protein were estimated indicating it as a stable, soluble, and extracellular protein. Functional annotation tools, such as NCBI-CD Search, Pfam, and InterProScan, predicted our target protein to be an amidase effector protein 4 (Tae4) of type-VI secretion system (T6SS). Multiple sequence alignment of the homologous sequences coincided with previous findings. Random coil was found to be predominant in secondary structure. Three-dimensional (3D) structure of the protein was obtained using homology modeling method by SWISS-MODEL server using a template protein (PDB ID: 4J30) of 80.12% sequence identity. The 3D structure became more stable after YASARA energy minimization and was validated by several quality assessment tools like PROCHECK, QMEAN, Verify3D, and ERRAT. Superimposition of the target with the template protein by UCSF Chimera generated RMSD value of 0.115 Å, suggesting a reliable 3D structure. The active site of the modeled structure was predicted and visualized by CASTp server and PyMOL. Interestingly, similar binding affinity and key interacting residues were found for the target protein and a Salmonella enterica Tae4 protein with the ligand L-Ala D-Glu-mDAP by molecular docking analysis. Protein-protein docking was also performed between the target protein and hemolysin coregulated protein 1 of T6SS. Finally, the protein was found to be a unique protein of S. dysenteriae nonhomologous to human by comparative genomics approach indicating a potential therapeutic target. Most pathogens harboring T6SS in their system pose a significant threat to the human health. Many T6SSs and their effectors are associated with interbacterial competition, pathogenesis, and virulency; however, relationships between these effectors and pathogenicity of S. dysenteriae are yet to be determined. The study findings provide a lucrative platform for future antibacterial treatment.
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Affiliation(s)
- Md Fazley Rabbi
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Saiwda Asma Akter
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Jaimol Hasan
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Al Amin
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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Identification of positive and negative regulators in the stepwise developmental progression towards infectivity in Trypanosoma brucei. Sci Rep 2021; 11:5755. [PMID: 33707699 PMCID: PMC7952579 DOI: 10.1038/s41598-021-85225-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/25/2021] [Indexed: 11/17/2022] Open
Abstract
Trypanosoma brucei is a protozoan parasite that causes important human and livestock diseases in sub-Saharan Africa. By overexpressing a single RNA-binding protein, RBP6, in non-infectious procyclics trypanosomes, we previously recapitulated in vitro the events occurring in the tsetse fly vector, namely the development of epimastigotes and infectious, quiescent metacyclic parasites. To identify genes involved in this developmental progression, we individually targeted 86 transcripts by RNAi in the RBP6 overexpression cell line and assessed the loss-of-function phenotypes on repositioning the kinetoplast, an organelle that contains the mitochondrial genome, the expression of BARP or brucei alanine rich protein, a marker for epimastigotes, and metacyclic variant surface glycoprotein. This screen identified 22 genes that positively or negatively regulate the stepwise progression towards infectivity at different stages. Two previously uncharacterized putative nucleic acid binding proteins emerged as potent regulators, namely the cold shock domain-containing proteins CSD1 and CSD2. RNA-Seq data from a selected group of cell lines further revealed that the components of gene expression regulatory networks identified in this study affected the abundance of a subset of transcripts in very similar fashion. Finally, our data suggest a considerable overlap between the genes that regulate the formation of stumpy bloodstream form trypanosomes and the genes that govern the development of metacyclic form parasites.
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Araújo CL, Blanco I, Souza L, Tiwari S, Pereira LC, Ghosh P, Azevedo V, Silva A, Folador A. In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PeerJ 2020; 8:e9643. [PMID: 32913672 PMCID: PMC7456259 DOI: 10.7717/peerj.9643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/10/2020] [Indexed: 12/30/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.
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Affiliation(s)
- Carlos Leonardo Araújo
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Iago Blanco
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Luciana Souza
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lino César Pereira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adriana Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Pranavathiyani G, Prava J, Rajeev AC, Pan A. Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. Front Cell Infect Microbiol 2020; 10:109. [PMID: 32318354 PMCID: PMC7146069 DOI: 10.3389/fcimb.2020.00109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein–protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were “novel”. Furthermore, a host–pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.
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Affiliation(s)
- G Pranavathiyani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Amir M, Kumar V, Dohare R, Islam A, Ahmad F, Hassan MI. Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family. J Evol Biol 2018; 31:1903-1917. [PMID: 30267552 DOI: 10.1111/jeb.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/28/2022]
Abstract
The cold shock domain (CSD) belongs to the oligosaccharide/oligonucleotide-binding fold superfamily which is highly conserved from prokaryotes to higher eukaryotes, and appears to function as RNA chaperones. CSD is involved in diverse cellular processes, including adaptation to low temperatures, nutrient stress, cellular growth and developmental processes. Structural Classification of Proteins (SCOP) database broadly classifies OB fold proteins into 18 different superfamilies, including nucleic acid-binding superfamily (NAB). The NAB is further divided into 17 families together with cold shock DNA-binding protein family (CSDB). The CSDB have more than 240 000 sequences in UniProt database consisting of 32 domains including CSD. Among these domains, CSD is the second largest sequence contributor (> 40 398 sequences). Herein, we have systematically analysed the relative abundance and distribution of CSD proteins based on sequences, structures, repeats and gene ontology (GO) molecular functions in all domains of life. Analysis of sequence distribution suggesting that CSDs are largely found in bacteria (83-94%) with single CSD repeat. However, repeat distribution in eukaryota varies from 1 to 5 in combination with other auxiliary domain that makes CSD proteins functionally more diverse compared to the bacterial counterparts. Further, analysis of repeats distributions on evolutionary scale suggest that existence of CSD in multiple repeats is mainly driven through speciation, gene shuffling and gene duplication events.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Amity Institute of Neuropsychology & Neurosciences, Amity University Noida, UP, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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da Costa WLO, Araújo CLDA, Dias LM, Pereira LCDS, Alves JTC, Araújo FA, Folador EL, Henriques I, Silva A, Folador ARC. Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS One 2018; 13:e0198965. [PMID: 29940001 PMCID: PMC6016940 DOI: 10.1371/journal.pone.0198965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.
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Affiliation(s)
- Wana Lailan Oliveira da Costa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Carlos Leonardo de Aragão Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Larissa Maranhão Dias
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Lino César de Sousa Pereira
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Jorianne Thyeska Castro Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraiba, João Pessoa, Paraíba, Brazil
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
- * E-mail: ,
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Abstract
As Helicobacter pylori infects half the world's population and displays an extensive intraspecies diversity, genomics is a powerful tool to understand evolution and disease, to identify factors that confer higher risk of severe sequelae, and to find new approaches for therapy both among bacterial and host targets. In line with these objectives, this review article summarizes the major findings in Helicobacter genomics in papers published between April 2016 and March 2017.
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Affiliation(s)
- Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Philippe Lehours
- INSERM, Univ. Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, Bordeaux, France
| | - Filipa F Vale
- Faculty of Pharmacy, Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Universidade de Lisboa, Lisbon, Portugal
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Turab Naqvi AA, Rahman S, Rubi, Zeya F, Kumar K, Choudhary H, Jamal MS, Kim J, Hassan MI. Genome analysis of Chlamydia trachomatis for functional characterization of hypothetical proteins to discover novel drug targets. Int J Biol Macromol 2016; 96:234-240. [PMID: 27993657 DOI: 10.1016/j.ijbiomac.2016.12.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/05/2016] [Accepted: 12/15/2016] [Indexed: 01/28/2023]
Abstract
C. trachomatis is a Gram-negative bacterium that causes trachoma and sexually transmitted disease (STD) Chlamydia in humans. Chlamydial genital infections are the most frequent among all communicable diseases. The D/UW-3/Cx strain of C. trachomatis contains 935 genes and three pseudogenes. Out of these genes, 887 genes code for proteins while six for rRNA, 37 tRNA, and three genes translate into other RNAs. The proteome of C. trachomatis made of 887 proteins contains 269 Hypothetical proteins (HPs) that are subjected to functional characterization. This study suggests some known methods of functional characterization of such HPs. All of these methods are explicitly used to assign functions to the HPs with the accuracy of more than 90%. After extensive analysis of all the HPs, we have successfully assigned functions to 89 HPs with high precision. In the newly assigned HPs, there are enzymes, transporters, binding proteins, proteins involved in biosynthesis and regulatory processes and proteins with miscellaneous functions. The study suggests that the functionally annotated HPs may play a vital role in the growth and pathogenesis of this organism. Therefore, they can be considered potential drug targets.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 712-749, South Korea
| | - Rubi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Firdaus Zeya
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Kundan Kumar
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Hani Choudhary
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Center of Innovation in Personalized Medicine, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box: 80216, Jeddah 21589, Saudi Arabia
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 712-749, South Korea.
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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