Functional and Structural Annotation of a Hypothetical Protein (PA2373) from...

[Full title: Functional and Structural Annotation of a Hypothetical Protein (PA2373) from Pseudomonas aeruginosa PA01]

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OPEN ACCESS International Journal of Pharmacology ISSN 1811-7775 DOI: 10.3923/ijp.2021.262.270 Research Article Functional and Structural Annotation of a Hypothetical Protein (PA 2373) from Pseudomonas aeruginosa PA 01 1 Alariqi Reem, 2 Rokayya Sami, 3 Marwa. Y.F. Koko, 4 Abeer Essam Noman, 5 Yousif A. Algabri, 6 Raj Aditya Kumar, 2 Ebtihal Khojah and 1 Zhao-Hua Zhong 1 Department of Microbiology, Harbin Medical University, 157 Baojian Road, Harbin 150081, China 2 Department of Food Science and Nutrition, College of Sciences, Taif University, P.O. 11099, Taif 21944, Saudi Arabia 3 Department of Food Science, Grease and Vegetable Protein, Northeast Agriculture University, China 4 College of Food Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China 5 Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, 250061, China 6 Department of Physiology, Harbin Medical University,157 Baojian Road, Harbin 150081 China Abstract Background and Objective: A comprehensive study of Pseudomonas aeruginosa proteomics found that 25% of proteins are retained as hypothetical proteins whose functions have not yet been ultimately determined. In this study, itʼs attempted to assign a particular role to one such hypothetical protein PA 2373 for which no experimental knowledge is currently available. Materials and Methods: To achieve this, the newest versions of bioinformatics tools was applied that provide various information, such as regarding amino acid sequences, protein families, sequence-function relationships and motifs. To identify homologous proteins, sequence similarities were searched using accessible bioinformatics databases. Results: Obtained results showed that PA 2373 has two functional domains, including VI̲Rhs̲Vgr and 5 superfamilies. Functional annotation showed that PA 2373 could be a Vgr protein and type VI secretion system. In addition, protein-protein interactions of selected hypothetical proteins show that certain functional partners play a significant role in pathogen survival. Conclusion: This study's findings may help better understand the mechanisms of virulence, drug resistance and pathogenesis of P. aeruginosa infections and to innovate the treatment strategies subsequently Key words: Hypothetical protein, VgrG 1, T 6 SSs, virulence, P. aeruginosa, PA 2373 Citation: Reem, A., R. Sami, M.Y.F. Koko, A.E. Noman, Y.A. Algabri, R.A. Kumar, E. Khojah and Z.H. Zhong, 2021. Functional and structural annotation of a hypothetical protein (PA 2373) from Pseudomonas aeruginosa PA 01. Int. J. Pharmacol., 17: 262-270 Corresponding Author: Rokayya Sami, Department of Food Science and Nutrition, College of Sciences, Taif University, P.O. 11099, Taif 21944, Saudi Arabia Zhao-Hua Zhong, Department of Microbiology, Harbin Medical University, 157 Baojian Road, Harbin 150081, China Copyright: © 2021 Alariqi Reem et al. This is an open access article distributed under the terms of the creative commons attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. Competing Interest: The authors have declared that no competing interest exists Data Availability: All relevant data are within the paper and its supporting information files.

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Int. J. Pharmacol., 17 (5): 262-270, 2021 INTRODUCTION Secretion systems of proteins are essential for bacteria to grow and survive in various environments. In some cases, pathogenic bacteria use secretion systems to control host immunity and create a replica space 1 . In eukaryotic cells, this secretory strategy entails the translocation of altered molecules from the inside to the outside of the cell, as well as the transport of effector molecules such as toxins, enzymes or proteins. Therefore, secretion is a vital part of the pathogenesis and virulence of bacteria 2 . There are different types of bacterial secretion systems; the type VI secretion system (T 6 SS) is the sixth and the most recently known bacterial secretion system 3 . T 6 SS has been identified in P. aeruginosa and included in antibacterial competition and virulence 4 . Virulence factors are microorganism-secreted molecules that allow them to colonize the host, suppress the host's immune responses and cause illness. Thus, understanding the molecular mechanisms of bacterial virulence plays a vital role in bacterial pathogenesis T 6 SS is very wide, with a maximum of 21 proteins encoded in an adjacent cluster of genes. Furthermore, it has three major components of Multimeric: the baseplate (TssEFGK), transmembrane core (TssJLM), tail and sheath complex (Hcp, VgrG and TssBC) 5 . Intriguingly, T 6 SS shares structural homology with phage tails. Moreover, VgrG 1 is structurally like the T 4 phage (gp 27)3-(gp 5)3 puncturing. The compound of the spike is organized as a needle-like $ -helix and is sited at the tip of the machinery of the shooting phage 6 The dual hemolysin co-regulated protein 1 and valine-glycine repeat protein G 1 (Hcp 1/VgrG 1) approach has been suggested to act as a spike wherein the long tail constitutes Hcp 1 and the penetrating tip is VgrG 1. Similar to the tail and tip used by phages to inject the host cell with their DNA, together, each of these proteins crosses the target membrane 7 . Furthermore, several VgrG proteins contain C-terminal extensions which have an effector function, such as the VgrG-1 actin crosslinking domain (ACD). VgrG-1 or its ACD domain is translocated to cross-link cell actin into the host cell cytosol following the diffusion of bacteria into macrophage cell lines, affecting the subsequent phagocytic process 8 . P. aeruginosa is a gram-negative bacillus pathogen associated with Cystic Fibrosis (CF) and affects immunocompromised patients 9 Typically, P. aeruginosa genomes have sizes of approximately 6 and 7 Mb and it has the lowest AT content (33%) by 5,570 Open Reading Frames (ORFs). This genome helps P. aeruginosa survive and withstand the effects of several antimicrobial substances in different environments 10 Interestingly, several bacterium proteins are measured as hypothetical proteins because their biological and structural roles remain unknown. Therefore, bioinformatics methods could play a key role in predicting and studying the structure, biological functions and protein-protein interactions of these hypothetical proteins. Accordingly, this study aimed to assign the hypothetical protein PA 2373 structural and biological functions using in silico analysis. Subcellular localization, physiochemical properties and secondary structure were predicted; additionally, conserved domain, family and superfamily were identified and protein-protein interactions were analyzed. Homology modelling techniques were used to produce a quality model of PA 2373 MATERIALS AND METHODS Study area: The current work was carried out at the pathogen biology Department, Harbin Medical University, from November, 2020 to April, 2021 Sequence assembly: The hypothetical protein (PA 2373) sequence information was obtained through the NCBI database. In a FASTA format, the sequence was taken and then presented for in silico characterization to several prediction servers (Table 1). Similarity searches were carried out with the NCBI Protein Database and Swiss Prot to identify proteins that may have structural similarities to uncharacterized proteins using the “BLAST p tool of the BLAST software Table 1: Tools used for the in-silico characterization of hypothetical protein PA 2373 Server name Purpose BLAST Prot BLAST MUSCLE Similarity search multiple sequence alignment ProtParam PSORTb Physicochemical characterization CELLO SOSUIGram N TMHMM CCTOP Topology prediction Motif Motif discovery Pfam Family relationship identification Superfamily Superfamily search InterPro Functional classification PSIPRED Secondary structure prediction HHpred Tertiary structure prediction STRING Interaction network analysis PROCHECK ERRAT Structure verification 263

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Int. J. Pharmacol., 17 (5): 262-270, 2021 Alignment of sequences and study of phylogeny: Multiple sequence alignments were achieved using the EBI MUSCLE server 11 . Phylogenetic analysis was performed using Phylogeny.fr 12 . Analysis of physicochemical properties: Physical and chemical features such as amino acid composition, predictable half-life, the total number of negatively charged residues (Asp +Glu), the total number of positively charged residues (Arg+Lys), aliphatic index, instability index and the grand average of hydropathicity (GRAVY) predictions were determined using the ProtParam tool of ExPASy 13 Subcellular localization: The CELLO was used to predict the subcellular localization 14 . Upshots were also verified through subcellular localization predictions gained from SOSUIGramN 15 and PSLpred 16 TMHMM 17 and HMMTOP 18 Conserved domain and family identification: The conserved domains on the Conserved Domains Database (CDD), available on the NCBI webpage has been used for research 19 . Two domain search methods, InterProScan 20 and Pfam 21 were also used to confirm the outcomes. The protein motif search was performed using the MOTIF search tool (Genome Net, the Institute for Chemical Research, Kyoto University, Japan) 22 and SUPERFAMILY 23 . The COILS server was used to classify the coiled-coil conformation into the protein 24 . The PFP-FunDSeqE server was used to recognize protein folding patterns 25 . The virulence activity of HPs was predicted using VICMpred 26 Prediction of secondary structure: A PSI blast-based secondary structure prediction (PSIPRED) was implemented to investigate the structure of the protein. The Self-Optimized Prediction Method with Alignment (SOPMA), an online tool was also applied to predict the secondary protein structure 27 Prediction of the three-dimensional structure: The HHpred server predicted the three-dimensional structure 28 . At The Max Planck Institute for Developmental Biology, Tubingen. The process used the pairwise comparison profile of Hidden Markov Models (HMMs). For advanced precision, the 3 D structure was predicted based on the best score template. The homology-modelled protein validated by the expected three-dimensional model evaluated using PROCHECK, Ramachandran plots 29 , ERRAT 30 and ProSA web 31 . The ProB is the server that used the homology-modelled hypothetical protein to classify structurally related protein-binding sites 32 The homology-modelled protein was superimposed with the UCSF Chimera 1.10 33 RESULTS AND DISCUSSION Sequence similarity data: Homology with the other VgrG proteins were identified in the BLAST (BLASTp search) against non-redundant protein sequence which showed homology with another type VI secretion system tip protein VgrG proteins in the same genus: Pseudomonas , Pseudomonas aeruginosa , Pseudomonas fluorescens with sequence identity (100 and 99.8%) respectively through score 1367 and E-value 0.0. Table 2. Furthermore, Table 3 showed the homology with Type VI secretion system in the different genus of bacteria, Aeromonas hydrophila , Dickeya dadantii , Vibrio cholerae 01 and Vibrio cholerae 0395, with sequence identity (34.56, 34.40, 37.11, 36.93, 33.99 and 35.34%) respectively through scores ( 348,342, 341, 316 and 345) and E value Ie-109, Table 2: Similar protein obtained from non-redundant UniProt KB/swiss prot sequences Protein ID Protein name Organism Identity (%) Score E-value WP̲003114515.1 Type VI secretion system tip protein VgrG Pseudomonas 100.0 1367 0.0 MBI 9132181.1 Type VI secretion system tip protein VgrG Pseudomonas aeruginosa 99.8 1367 0.0 MBG 7402737.1 Type VI secretion system tip protein VgrG Pseudomonas aeruginosa 99.8 1367 0.0 WP̲134302382.1 Type VI secretion system tip protein VgrG Pseudomonas aeruginosa 99.8 1367 0.0 WP̲114230990.1 Type VI secretion system tip protein VgrG protein VgrG Pseudomonas aeruginosa 99.8 1367 0.0 WP̲003122692.1 VgrG Pseudomonas fluorescens 99.8 1367 0.0 Table 3: Similar protein obtained from UniProt database Sequence ID Protein name Organism Identity (%) Score E-value K 7 WKL 8.1 Type VI secretion system spike protein VgrG 1 Aeromonas hydrophila 34.56 348 1 e-109 A 0 KJB 0.1 Type VI secretion system spike protein VgrG 1 Aeromonas hydrophila 34.40 348 6 e-109 E 0 SAL 0.1 Putative type VI secretion system protein VgrGA Dickeya dadantii 37.11 342 8 e-108 E 0 SIS 4.1 Putative type VI secretion system protein VgrGB Dickeya dadantii 36.93 341 1 e-107 Q 9 KS 45.1 Actin cross-linking toxin VgrG 1 Vibrio cholerae 01 33.99 316 1 e-93 A 0 A 0 H 3 AIG 7.1 Actin cross-linking toxin VgrG 1 Vibrio cholerae O 395 35.34 345 8 e-90 264

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Int. J. Pharmacol., 17 (5): 262-270, 2021 Fig. 1: Phylogenetic trees of different VgrG proteins Fig. 2: Coil depicts the heptads corresponding to the residue windows 14 (green), 21(blue) and 28 (red) 61-109, 8 e-108, Ie-107, Ie-93 and 8 e-90) in the Swiss Prot databases. Hypothetical protein (PA 2373) FASTA sequences and annotated homologous proteins were systematized. To validate the homology between the proteins, a phylogenetic analysis was also performed. Based on the alignment and BLAST results, a phylogenetic tree was constructed, which provided a similar concept of protein, as shown in Fig. 1 Physicochemical features: The protein contained 668 amino acids and the molecular weight measured was 7877.95 Da and the theoretical pI was 5.207, representing that the protein was negatively charged. Among the most abundant charged residues, the whole number of positively charged residues (Arg+Lys) was 12 and the whole number of negatively charged residues was 13. The determined index of instability classifies the protein as stable. The measured protein half-life was 7.2 “hrs” in mammalian reticulocytes ( in vitro ), >20 hrs in yeast ( in vivo ) and >10 hrs in Escherichia coli ( in vivo ). The aliphatic index was 71.39, which indicates the stability of the protein in a high-temperature range. The GRAVY value was -0.335. A negative GRAVY value shows that the protein is nonpolar. The molecular protein formula was defined as C 356 H 539 N 95 O 102 S 3 Subcellular localization: The hypothetical protein (2373) subcellular localization was expected to be in the extracellular space. The absence of transmembrane helices predicted by THMM and HMMTOP besides enhances the final result of extracellular protein 15-18 . Functional annotation and virulence prediction: The conserved domain search tool showed two domains in this hypothetical protein sequence, VI̲Rhs̲Vgr (accession no TIGR 03361) and 5 superfamilies (accession no cl 33691). The Pfam server predicted the Phage̲GPD at 29‒353 amino acid residues with an e-value of 4.9 e-82, phage base V at 357-583 with an e-value of 3.1 e-13 and Gp 5 C at 560-646 amino acid residues with an e-value of 0.0031. The Inter-ProScan server predicted the type VI secretion system, RhsGE-related Vgr protein family subset. Phage GPD family subset, Phage̲GPDPhage̲base̲V, Gp 5̲C, and DUF 3540 domains were also predicted using the MOTIF server. Fold pattern predicted by the PFP-FunDSeqE tool shown the presence of conA-like lectin/glucanases; fold inside the protein sequence. The x-axis of the diagram shows the position in the protein of amino acid number (starting at the N-terminus) and the y-axis represents the coiled-coil whereas ʻWindowʼ refers to the width of the amino acid in Fig. 2 265 WP_003114515 MBI 9132181 MBG 7402737 WP_114230990 WP_134302382 WP_003122692 0 0 0 0.5 Position in the protein of amino acid number 0 100 200 300 400 500 600 700 1.0 0.8 0.6 0.4 0.2 0.0 Coiled coil Coils output for unknown Window = 14 Window = 21 Window = 28

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Int. J. Pharmacol., 17 (5): 262-270, 2021 Superfamily analyses identified the presence of phage tail proteins and the phage fibre protein superfamily. To predict the bacterial virulence factor of PA 2373, we used the VICMpred bioinformatics tool. PA 2373 includes a virulent element that may offer clues for future drug design as a treatment objective. The characteristics of HP PA 2373 from Pseudomonas aeruginosa PA 01 were investigated and studied for the first time. The recent finding was agreed with Wiehlmann L et al 34 who made the report that HPs are attractive therapeutic targets since they are involved in important pathways such as (cell wall integrity e and maintaining genome). Analysis of the secondary structure: The study using the secondary structure prediction SOPMA tool showed the alpha helix, beta-turn, extended strand and random protein coil proportions as 20.96, 6.8, 28.1 and 44.01%, respectively Analysis of the three-dimensional structure: 3 D structure prediction was accomplished using the HHpred server with the highest scoring template for 100 percent identification (PDB ID: 4 UHV), Fig. 3 and 4. The UHV is a trimetric fold crystal structure that separates two major fragments assembly of the protein, the head and the spike bound by a neck centred on a cord 29-31 . This unique molecular structure is identical to the T 4 bacteriophage (gp 27)3-(gp 5)3 complex puncturing-device machinery used by the virus to inject its DNA into the host cell 34 . The energy minimization server Modrefiner was used for the refined prediction of homology models. For both the energy aspects and geometries, the ProSA web helped evaluate the energy-minimized structures by accessing the Z-score protein structure, representing the overall quality of the model, Fig. 4. It was helpful to verify whether the input structure was within the range of scores typically seen for similar-sized native proteins. The overall model quality Z-score was -6.57, suggesting a similarity between the template and query structure. The Ramachandran plot revealed that 71.9% of the residues were located in the most favourable regions, where the distribution of N and R angle in the model within the limits are shown as illustrated in Fig. 5. The ERRAT server predicted an overall model quality factor of 58.0813, which indicates a good model. The homology-modelled protein was superimposed with the UCSF Chimera 1.10 is presented in Fig. 6. Analysis of protein-protein interaction: The STRING 10.0 tool was used to establish potential protein functional interaction networks 35,36 . The partners of functional listed with scores Fig. 3: Predicted three-dimensional hypothetical protein structure Fig. 4: Predicted functional regions of selected hypothetical protein by using ProBis server Highly conserved residues are shown in red and the least conserved regions are shown in blue were; PA 2369 (0.938), PA 2370 (0.934), PA 2367 (0.928), PA 2366 (0.915), ClpV 1 (0.910), PA 2365 (0.909), PA 2371 (0.908), PA 0088 (0.900), IcmF 1 (0.900), PA 1660 (0.899). PA 2369, PA 2370, PA 2367, PA 2365, PA 0088 and PA 1660 are hypothetical 266 Variable Conserved

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Int. J. Pharmacol., 17 (5): 262-270, 2021 Fig. 5: Ramachandran plot of modelled structure validated by PROCHECK program Fig. 6: Homology modelled proteins are superimposed with the template of (PDB ID: 4 uhv) by using UCSF chimera-1.10 267 180 135 90 45 0 -45 -90 -135 P si (d eg re es ) Phi (degrees) -180 -135 -90 -45 0 45 90 135 180 4 uhv

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Int. J. Pharmacol., 17 (5): 262-270, 2021 Fig. 7: A string network analysis of the hypothetical protein is identified as PA 2373 proteins. PA 2366 is an uricase, ClpV 1 is a protein, which is required for secretion of hcp 1 probably by providing an energy source for its translocation, PA 2371 is a ClpA/B-type protease and IcmF 1 as shown in Fig. 7. CONCLUSION The detection of protein functions is crucial to the understanding of biological processes. Therefore, this study aimed to define the biological and structural role of PA 2373, a hypothetical protein from P. aeruginosa , via in silico analysis. The hypothetical protein that was identified revealed some characteristics, including extracellular protein, Vgr protein and type VI secretion system, containing two domains. These hypothetical protein characteristics provide basic information about P. aeruginosa . The findings of this study will help determine mechanisms of virulence, drug resistance and pathogenesis of P. aeruginosa infections through extended in vitro experiments to innovate treatment strategies for these infections subsequently. SIGNIFICANCE STATEMENT The current research is aimed at describing the structure and function annotation of HPs which have an antibioticresistant activity that can help find new targets to improve P. aeruginosa treatment and investigation. Hypothetical proteins in P. aeruginosa have been predicted using several structural and functional annotation informatics servers ACKNOWLEDGMENT We thank our professors and support from the Department of Microbiology, Harbin Medical University, Harbin, China. Taif University Researchers Supporting Project Number (TURSP-2020/140), Taif University, Taif, Saudi Arabia 268 PA 2367 clpV 1 PA 2371 PA 2369 PA 2373 PA 2370 PA 0088 PA 1660 PA 2366 PA 2365 icmF 1

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Family, Protein, Pathogenesis, Toxin, Biological function, Treatment strategies, Pathogenic bacteria, Hidden Markov Model, Molecular weight, Drug resistance, Physicochemical properties, Pseudomonas aeruginosa, P. aeruginosa, Amino acid composition, Phylogenetic tree, Molecular mechanism, Ramachandran plot, Phylogenetic analysis, Homology modelling, Immunocompromised patient, Bacterial pathogenesis, Cystic fibrosis, Therapeutic target, Superfamilies, Gram-negative bacillus, In silico analysis, Physiochemical properties, Virulence factor, Amino acid sequence, Secondary structure, Subcellular localization, Three-dimensional structure, Sequence information, Multiple sequence alignment, Family identification, Sequence alignment, Functional annotation, Virulence, NCBI database, Hypothetical protein, Bioinformatics methods, Secondary Structure Prediction, Extracellular protein, Procheck, Superfamily, Protein sequence, Sequence similarity, Pathogen survival, Open reading frame, Enzyme, Host cell, UCSF Chimera, Motif, Protein-protein interaction network, Homologous proteins, Protein-protein interaction, Bacterial virulence factor, Functional domain, Secretion system, Physical and chemical features, Virulence activity, FASTA format, Bioinformatics Tool, Protein families, HHpred server, Type VI secretion system, Conserved domain, Sequence similarities, ProSA web, Swiss Prot.