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Talukdar S, Mal S, Kundu P. Physico-chemical features and functional relevance of tomato rhomboid proteases. Int J Biol Macromol 2024; 272:132681. [PMID: 38806088 DOI: 10.1016/j.ijbiomac.2024.132681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
In plants, regulated intramembrane proteolysis (RIP) is crucial for proper growth, development, and stress management. Rhomboid proteases (RPs) residing in the membrane play a vital role in orchestrating RIP. Although RPs can be found in most sequenced genomes, tomato rhomboids (SlRPs) have not yet been studied. Using alternative and comprehensive strategies, we found ten SlRPs encoded in the tomato genome. These SlRPs possess signature motifs and transmembrane domains, showing structural similarity to other members of the RP family. Also, SlRPs are genetically related to other known RPs of the Solanaceae family. Seven of the SlRPs retain serine-histidine catalytic dyads, making them proteolytically active, while three iRhoms lack the dyad and other structural motifs. Although SlRPs could have functional redundancy, their distribution and expression pattern indicate tissue specificity and responsiveness to specific external stimuli. The presence of development and stress-response-related cis-elements in the promoters of SlRPs supports this view. Furthermore, our strategically designed substrate-reporter assay shows that SlRPs have proteolytic activity similar to that of known RPs. This study provides a detailed understanding of all SlRPs and their physico-chemical features, shedding light on their involvement in physiological processes.
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Affiliation(s)
- Sushmita Talukdar
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Sayan Mal
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Pallob Kundu
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India.
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Mei KC, Thota N, Wei PS, Yi B, Bonacquisti EE, Nguyen J. Calreticulin P-domain-derived "Eat-me" peptides for enhancing liposomal uptake in dendritic cells. Int J Pharm 2024; 653:123844. [PMID: 38272193 PMCID: PMC10994729 DOI: 10.1016/j.ijpharm.2024.123844] [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: 07/07/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
Discovering new ligands for enhanced drug uptake and delivery has been the core interest of the drug delivery field. This study capitalizes on the natural "eat-me" signal of calreticulin (CRT), proposing a novel strategy for functionalizing liposomes to improve cellular uptake. CRT is presented on the surfaces of apoptotic cells, and it plays a crucial role in immunogenic cell death (ICD). This is because it is essential for antigen uptake via low-density lipoprotein (LDL) receptor-mediated phagocytosis. Inspired by this mechanism, we interrogated CRT's "eat-me" feature using CRT-derived peptides to functionalize liposomes. We studied liposomal formulation stability, properties, cellular uptake, toxicity, and intracellular trafficking in dendritic cells. We identified key peptide fragments of CRT, specifically from the hydrophilic P-domain, that are compatible with liposomal formulations. Contrary to the more hydrophobic N-domain peptides, the P-domain peptides induced significantly higher liposomal uptake in DC2.4 dendritic cells than cationic DOTAP and anionic DPPG liposomes without inducing toxicity. The P-domain-derived peptides led to enhanced liposomal uptake into DC2.4 dendritic cells compared to the standard DPPC liposomes. The uptake can be partially blocked by the receptor-associated protein (RAP). Upon internalization, P-domain-peptide-decorated liposomes showed higher co-localization with lysosomes compared to the standard DPPC liposomes. Our findings illuminate CRT's operational role and identify P-domain peptides as promising agents for developing biomimetic drug delivery systems that can potentially replicate CRT's "eat-me" function.
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Affiliation(s)
- Kuo-Ching Mei
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 29599, USA; Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY 13790, USA.
| | - Nagasri Thota
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY 13790, USA
| | - Pu-Sheng Wei
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY 13790, USA
| | - Bofang Yi
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY 13790, USA
| | - Emily E Bonacquisti
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 29599, USA
| | - Juliane Nguyen
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 29599, USA.
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Debroy B, Chowdhury S, Pal K. Designing a novel and combinatorial multi-antigenic epitope-based vaccine "MarVax" against Marburg virus-a reverse vaccinology and immunoinformatics approach. J Genet Eng Biotechnol 2023; 21:143. [PMID: 38012426 PMCID: PMC10681968 DOI: 10.1186/s43141-023-00575-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
CONTEXT Marburg virus (MARV) is a member of the Filoviridae family and causes Marburg virus disease (MVD) among humans and primates. With fatality rates going up to 88%, there is currently no commercialized cure or vaccine to combat the infection. The National Institute of Allergy and Infectious Diseases (NIAID) classified MARV as priority pathogen A, which presages the need for a vaccine candidate which can provide stable, long-term adaptive immunity. The surface glycoprotein (GP) and fusion protein (FP) mediate the adherence, fusion, and entry of the virus into the host cell via the TIM-I receptor. Being important antigenic determinants, studies reveal that GP and FP are prone to evolutionary mutations, underscoring the requirement of a vaccine construct capable of eliciting a robust and sustained immune response. In this computational study, a reverse vaccinology approach was employed to design a combinatorial vaccine from conserved and antigenic epitopes of essential viral proteins of MARV, namely GP, VP24, VP30, VP35, and VP40 along with an endogenous protein large polymerase (L). METHODS Epitopes for T-cell and B-cell were predicted using TepiTool and ElliPro, respectively. The surface-exposed TLRs like TLR2, TLR4, and TLR5 were used to screen high-binding affinity epitopes using the protein-peptide docking platform MdockPeP. The best binding epitopes were selected and assembled with linkers to design a recombinant multi-epitope vaccine construct which was then modeled in Robetta. The in silico biophysical and biochemical analyses of the recombinant vaccine were performed. The docking and MD simulation of the vaccine using WebGro and CABS-Flex against TLRs support the stable binding of vaccine candidates. A virtual immune simulation to check the immediate and long-term immunogenicity was carried out using the C-ImmSim server. RESULTS The biochemical characteristics and docking studies with MD simulation establish the recombinant protein vaccine construct MarVax as a stable, antigenic, and potent vaccine molecule. Immune simulation studies reveal 1-year passive immunity which needs to be validated by in vivo studies.
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Affiliation(s)
- Bishal Debroy
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Sribas Chowdhury
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Kuntal Pal
- Cancer Biology Laboratory, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India.
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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Herrera-Ong LR. Strategic construction of mRNA vaccine derived from conserved and experimentally validated epitopes of avian influenza type A virus: a reverse vaccinology approach. Clin Exp Vaccine Res 2023; 12:156-171. [PMID: 37214143 PMCID: PMC10193103 DOI: 10.7774/cevr.2023.12.2.156] [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: 01/22/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose The development of vaccines that confer protection against multiple avian influenza A (AIA) virus strains is necessary to prevent the emergence of highly infectious strains that may result in more severe outbreaks. Thus, this study applied reverse vaccinology approach in strategically constructing messenger RNA (mRNA) vaccine construct against avian influenza A (mVAIA) to induce cross-protection while targeting diverse AIA virulence factors. Materials and Methods Immunoinformatics tools and databases were utilized to identify conserved experimentally validated AIA epitopes. CD8+ epitopes were docked with dominant chicken major histocompatibility complexes (MHCs) to evaluate complex formation. Conserved epitopes were adjoined in the optimized mVAIA sequence for efficient expression in Gallus gallus. Signal sequence for targeted secretory expression was included. Physicochemical properties, antigenicity, toxicity, and potential cross-reactivity were assessed. The tertiary structure of its protein sequence was modeled and validated in silico to investigate the accessibility of adjoined B-cell epitope. Potential immune responses were also simulated in C-ImmSim. Results Eighteen experimentally validated epitopes were found conserved (Shannon index <2.0) in the study. These include one B-cell (SLLTEVETPIRNEWGCR) and 17 CD8+ epitopes, adjoined in a single mRNA construct. The CD8+ epitopes docked favorably with MHC peptide-binding groove, which were further supported by the acceptable ΔGbind (-28.45 to -40.59 kJ/mol) and Kd (<1.00) values. The incorporated Sec/SPI (secretory/signal peptidase I) cleavage site was also recognized with a high probability (0.964814). Adjoined B-cell epitope was found within the disordered and accessible regions of the vaccine. Immune simulation results projected cytokine production, lymphocyte activation, and memory cell generation after the 1st dose of mVAIA. Conclusion Results suggest that mVAIA possesses stability, safety, and immunogenicity. In vitro and in vivo confirmation in subsequent studies are anticipated.
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Affiliation(s)
- Leana Rich Herrera-Ong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Metro Manila, Philippines
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Tiwari K, Singh G, Singh SK. Purification and Structural Characterization of N-Terminal 190 Amino Acid Deleted Essential Mammalian Protein; Transcription Termination Factor 1. ACS OMEGA 2022; 7:45165-45173. [PMID: 36530226 PMCID: PMC9753541 DOI: 10.1021/acsomega.2c05603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The mammalian transcription termination factor 1 (TTF1) is an essential protein that plays diverse cellular physiological functions like transcription regulation (both initiation and termination), replication fork blockage, chromatin remodeling, and DNA damage repair. Hence, understanding the structure and mechanism conferred by its variable conformations is important. However, so far, almost nothing is known about the structure of either the full-length protein or any of its domains in isolation. Since the full-length protein even after multiple attempts could not be purified in soluble form, we have codon optimized, expressed, and purified the N-terminal 190 amino acid deleted TTF1 (ΔN190TTF1) protein. In this study, we characterized this essential protein by studying its homogeneity, molecular size, and secondary structure using tools like dynamic light scattering (DLS), circular dichroism (CD) spectroscopy, Raman spectroscopy, and atomic force microscopy (AFM). By CD spectroscopy and DLS, we confirmed that the purified protein is homogeneous and soluble. CD spectroscopy also revealed that ΔN190TTF1 is a helical protein, which was further established by analysis of Raman spectra and amide I region deconvolution studies. The DLS study estimated the size of a single protein molecule to be 17.2 nm (in aqueous solution). Our structural and biophysical characterization of this essential protein will open avenues toward solving the structure to atomic resolution and will also encourage researchers to investigate the mechanism behind its diverse functions attributed to its various domains.
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Mollusc Crystallins: Physical and Chemical Properties and Phylogenetic Analysis. DIVERSITY 2022. [DOI: 10.3390/d14100827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The purpose of the present study was to perform bioinformatic analysis of crystallin diversity in aquatic molluscs based on the sequences in the NCBI Protein database. The objectives were as follows: (1) analysis of some physical and chemical properties of mollusc crystallins, (2) comparison of mollusc crystallins with zebrafish and cubomedusa Tripedalia cystophora crystallins, and (3) determination of the most probable candidates for the role of gastropod eye crystallins. The calculated average GRAVY values revealed that the majority of the seven crystallin groups, except for μ- and ζ-crystallins, were hydrophilic proteins. The predominant predicted secondary structures of the crystallins in most cases were α-helices and coils. The highest values of refractive index increment (dn/dc) were typical for crystallins of aquatic organisms with known lens protein composition (zebrafish, cubomedusa, and octopuses) and for S-crystallin of Pomacea canaliculata. The evolutionary relationships between the studied crystallins, obtained from multiple sequence alignments using Clustal Omega and MUSCLE, and the normalized conservation index, calculated by Mirny, showed that the most conservative proteins were Ω-crystallins but the most diverse were S-crystallins. The phylogenetic analysis of crystallin was generally consistent with modern mollusc taxonomy. Thus, α- and S-, and, possibly, J1A-crystallins, can be assumed to be the most likely candidates for the role of gastropod lens crystallins.
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Dey S, Shahrear S, Afroj Zinnia M, Tajwar A, Islam ABMMK. Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity. Bioinform Biol Insights 2022; 16:11779322221115535. [PMID: 35958299 PMCID: PMC9358594 DOI: 10.1177/11779322221115535] [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: 04/01/2022] [Accepted: 06/11/2022] [Indexed: 11/25/2022] Open
Abstract
Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.
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Affiliation(s)
- Supantha Dey
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Ahnaf Tajwar
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Bakshi A, Rai U. In silico analyses of leptin and leptin receptor of spotted snakehead Channa punctata. PLoS One 2022; 17:e0270881. [PMID: 35797380 PMCID: PMC9262212 DOI: 10.1371/journal.pone.0270881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
The present study, in addition to molecular characterization of leptin (lepa) and its receptor (lepr) of spotted snakehead Channa punctata, is focussed on physicochemical, structural, evolutionary and selection pressure analyses which are poorly elucidated in teleosts in spite of that existence of these genes is well reported in several fish species. The putative full-length Lep and Lepr of C. punctata showed conserved structural and functional domains, especially the residues responsible for structural integrity and signal transduction. Conversely, residues predicted essential for Lep-Lepr interaction displayed divergence between teleosts and tetrapods. Impact of substitutions/deletions predicted using protein variation effect analyser tool highlighted species specificity in ligand-receptor interaction. Physicochemical properties of ligand and receptor predicted for the first time in vertebrates revealed high aliphatic and instability indices for both Lepa and Lepr, indicating thermostability of proteins but their instability under ex vivo conditions. Positive grand average of hydropathy score of Lepa suggests its hydrophobic nature conjecturing existence of leptin binding proteins in C. punctata. In addition to disulphide bonding, a novel posttranslational modification (S-126 phosphorylation) was predicted in Lepa of C. punctata. In Lepr, disulphide bond formation and N-linked glycosylation near WSXWS motif in ECD, and phosphorylation at tyrosine residues in ICD were predicted. Leptin and its receptor sequence of C. punctata cladded with its homolog from C. striata and C. argus of order Anabantiformes. Leptin system of Anabantiformes was phylogenetically closer to that of Pleuronectiformes, Scombriformes and Perciformes. Selection pressure analysis showed higher incidence of negative selection in teleostean leptin genes indicating limited adaptation in their structure and function. However, evidence of pervasive and episodic diversifying selection laid a foundation of co-evolution of Lepa and Lepr in teleosts.
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Affiliation(s)
- Amrita Bakshi
- Department of Zoology, University of Delhi, Delhi, India
| | - Umesh Rai
- Department of Zoology, University of Delhi, Delhi, India
- * E-mail:
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Choi Y, Han SW, Kim JS, Jang Y, Shin JS. Biochemical characterization and synthetic application of aromatic L-amino acid decarboxylase from Bacillus atrophaeus. Appl Microbiol Biotechnol 2021; 105:2775-2785. [PMID: 33713143 DOI: 10.1007/s00253-021-11122-3] [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: 04/29/2020] [Revised: 01/04/2021] [Accepted: 01/16/2021] [Indexed: 12/29/2022]
Abstract
Aromatic L-amino acid decarboxylases (AADCs) are ubiquitously found in higher organisms owing to their physiological role in the synthesis of neurotransmitters and alkaloids. However, bacterial AADC has not attracted much attention because of its rather limited availability and narrow substrate range. Here, we examined the biochemical properties of AADC from Bacillus atrophaeus (AADC-BA) and assessed the synthetic feasibility of the enzyme for the preparation of monoamine neurotransmitters. AADC-BA was expressed in Escherichia coli BL21(DE3) and the purified enzyme showed a specific activity of 2.6 ± 0.4 U/mg for 10 mM L-phenylalanine (L-Phe) at 37 °C. AADC-BA showed optimal pH and temperature ranges at 7-8 and 37-45 °C, respectively. The KM and kcat values for L-Phe were 7.2 mM and 7.4 s-1, respectively, at pH 7.0 and 37 °C. Comparison of the kinetic constants at different temperatures revealed that the temperature dependency of the enzyme was mainly determined by catalytic turnover rather than substrate binding. AADC-BA showed a broad substrate scope for various aromatic amino acids, including L-Phe, L-tryptophan (610% relative to L-Phe), L-tyrosine (12%), 3,4-dihydroxyphenyl-L-alanine (24%), 5-hydroxy-L-tryptophan (L-HTP, 71%), 4-chloro-L-phenylalanine (520%), and 4-nitro-L-phenylalanine (450%). Homology modeling and docking simulations were carried out and were consistent with the observed substrate specificity. To demonstrate the synthetic potential of AADC-BA, we carried out the production of serotonin by decarboxylation of L-HTP. The reaction yield of serotonin reached 98% after 1 h at the reaction conditions of 50 mM L-HTP and 4 U/mL AADC-BA. Moreover, we carried out preparative-scale decarboxylation of L-Phe (100 mM in 40-mL reaction mixture) and isolated the resulting 2-phenylethylamine (51% recovery yield). We expect that the broad substrate specificity of AADC-BA can be exploited to produce various aromatic biogenic amines. KEY POINTS: • AADC-BA showed broad substrate specificity for various aromatic amino acids. • The substrate specificity was elucidated by in silico structural modeling. • The synthetic potential of AADC-BA was demonstrated for the production of biogenic amines.
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Affiliation(s)
- Yeri Choi
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jun-Sung Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
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Bhagwat P, Amobonye A, Singh S, Pillai S. A comparative analysis of GH18 chitinases and their isoforms from Beauveria bassiana: An in-silico approach. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
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Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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Koludarov I, Aird SD. Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure. PeerJ 2019; 7:e6154. [PMID: 30755823 PMCID: PMC6368836 DOI: 10.7717/peerj.6154] [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: 09/26/2018] [Accepted: 11/25/2018] [Indexed: 01/28/2023] Open
Abstract
NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
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Affiliation(s)
- Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, Japan
| | - Steven D Aird
- Ecology and Evolution Unit and Division of Faculty Affairs, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, Japan
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Ojha R, Khatoon N, Prajapati VK. Conglomeration of novel Culex quinquefasciatus salivary proteins to contrive multi-epitope subunit vaccine against infections caused by blood imbibing transmitter. Int J Biol Macromol 2018; 118:834-843. [DOI: 10.1016/j.ijbiomac.2018.06.112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/18/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022]
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Heuts J, Varypataki EM, van der Maaden K, Romeijn S, Drijfhout JW, van Scheltinga AT, Ossendorp F, Jiskoot W. Cationic Liposomes: A Flexible Vaccine Delivery System for Physicochemically Diverse Antigenic Peptides. Pharm Res 2018; 35:207. [PMID: 30209623 PMCID: PMC6156754 DOI: 10.1007/s11095-018-2490-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/03/2018] [Indexed: 12/30/2022]
Abstract
PURPOSE Personalized peptide-based cancer vaccines will be composed of multiple patient specific synthetic long peptides (SLPs) which may have various physicochemical properties. To formulate such SLPs, a flexible vaccine delivery system is required. We studied whether cationic liposomes are suitable for this purpose. METHODS Fifteen SIINFEKL T cell epitope-containing SLPs, widely differing in hydrophobicity and isoelectric point, were separately loaded in cationic liposomes via the dehydration-rehydration method. Particle size and polydispersity index (PDI) were measured via dynamic light scattering (DLS), and zeta potential with laser Doppler electrophoresis. Peptide loading was fluorescently determined and the immunogenicity of the formulated peptides was assessed in co-cultures of dendritic cells (DCs) and CD8+ T-cells in vitro. RESULTS All SLPs were loaded in cationic liposomes by using three different loading method variants, depending on the SLP characteristics. The fifteen liposomal formulations had a comparable size (< 200 nm), PDI (< 0.3) and zeta potential (22-30 mV). Cationic liposomes efficiently delivered the SLPs to DCs that subsequently activated SIINFEKL-specific CD8+ T-cells, indicating improved immunological activity of the SLPs. CONCLUSION Cationic liposomes can accommodate a wide range of different SLPs and are therefore a potential delivery platform for personalized cancer vaccines.
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Affiliation(s)
- Jeroen Heuts
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Eleni Maria Varypataki
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Koen van der Maaden
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Stefan Romeijn
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Anton Terwisscha van Scheltinga
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Centre, Leiden, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Wim Jiskoot
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands.
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15
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Aarthy M, Kumar D, Giri R, Singh SK. E7 oncoprotein of human papillomavirus: Structural dynamics and inhibitor screening study. Gene 2018. [DOI: 10.1016/j.gene.2018.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Ono H, Ogasawara O, Okubo K, Bono H. RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. Sci Data 2017; 4:170105. [PMID: 28850115 PMCID: PMC5574374 DOI: 10.1038/sdata.2017.105] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 06/29/2017] [Indexed: 12/28/2022] Open
Abstract
Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.
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Affiliation(s)
- Hiromasa Ono
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Osamu Ogasawara
- Center for Information Biology, National Institute of Genetics, Research Organization for Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Kosaku Okubo
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
- Center for Information Biology, National Institute of Genetics, Research Organization for Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Hidemasa Bono
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
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17
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Zhang Q, Li J, Xie H, Xue H, Wang Y. A network-based pathway-expanding approach for pathway analysis. BMC Bioinformatics 2016; 17:536. [PMID: 28155638 PMCID: PMC5259956 DOI: 10.1186/s12859-016-1333-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Pathway analysis combining multiple types of high-throughput data, such as genomics and proteomics, has become the first choice to gain insights into the pathogenesis of complex diseases. Currently, several pathway analysis methods have been developed to study complex diseases. However, these methods did not take into account the interaction between internal and external genes of the pathway and between pathways. Hence, these approaches still face some challenges. Here, we propose a network-based pathway-expanding approach that takes the topological structures of biological networks into account. Results First, two weighted gene-gene interaction networks (tumor and normal) are constructed integrating protein-protein interaction(PPI) information, gene expression data and pathway databases. Then, they are used to identify significant pathways through testing the difference of topological structures of expanded pathways in the two weighted networks. The proposed method is employed to analyze two breast cancer data. As a result, the top 15 pathways identified using the proposed method are supported by biological knowledge from the published literatures and other methods. In addition, the proposed method is also compared with other methods, such as GSEA and SPIA, and estimated using the classification performance of the top 15 expanded pathways. Conclusions A novel network-based pathway-expanding approach is proposed to avoid the limitations of existing pathway analysis approaches. Experimental results indicate that the proposed method can accurately and reliably identify significant pathways which are related to the corresponding disease. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1333-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaosheng Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China.,College of Science, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China.
| | - Haozhe Xie
- School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China
| | - Hanqing Xue
- School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China
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18
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Elguoshy A, Magdeldin S, Xu B, Hirao Y, Zhang Y, Kinoshita N, Takisawa Y, Nameta M, Yamamoto K, El-Refy A, El-Fiky F, Yamamoto T. Why are they missing? : Bioinformatics characterization of missing human proteins. J Proteomics 2016; 149:7-14. [PMID: 27535355 DOI: 10.1016/j.jprot.2016.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/17/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
NeXtProt is a web-based protein knowledge platform that supports research on human proteins. NeXtProt (release 2015-04-28) lists 20,060 proteins, among them, 3373 canonical proteins (16.8%) lack credible experimental evidence at protein level (PE2:PE5). Therefore, they are considered as "missing proteins". A comprehensive bioinformatic workflow has been proposed to analyze these "missing" proteins. The aims of current study were to analyze physicochemical properties, existence and distribution of the tryptic cleavage sites, and to pinpoint the signature peptides of the missing proteins. Our findings showed that 23.7% of missing proteins were hydrophobic proteins possessing transmembrane domains (TMD). Also, forty missing entries generate tryptic peptides were either out of mass detection range (>30aa) or mapped to different proteins (<9aa). Additionally, 21% of missing entries didn't generate any unique tryptic peptides. In silico endopeptidase combination strategy increased the possibility of missing proteins identification. Coherently, using both mature protein database and signal peptidome database could be a promising option to identify some missing proteins by targeting their unique N-terminal tryptic peptide from mature protein database and or C-terminus tryptic peptide from signal peptidome database. In conclusion, Identification of missing protein requires additional consideration during sample preparation, extraction, digestion and data analysis to increase its incidence of identification.
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Affiliation(s)
- Amr Elguoshy
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Sameh Magdeldin
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Bo Xu
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ying Zhang
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Naohiko Kinoshita
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yusuke Takisawa
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Masaaki Nameta
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ali El-Refy
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Fawzy El-Fiky
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan.
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19
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Magdeldin S, Hirao Y, El Guoshy A, Xu B, Zhang Y, Fujinaka H, Yamamoto K, Yates JR, Yamamoto T. Comprehensive data analysis of human ureter proteome. Data Brief 2016; 6:853-7. [PMID: 26937461 PMCID: PMC4749945 DOI: 10.1016/j.dib.2016.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 12/04/2022] Open
Abstract
Comprehensive human ureter proteome dataset was generated from OFFGel fractionated ureter samples. Our result showed that among 2217 non-redundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, Cytoscape GO annotation was examined on the final ureter dataset to better understand proteins molecular function, biological processes, and cellular component. The ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery.
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Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt; Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, CA 92037, United States
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Amr El Guoshy
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Bo Xu
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Ying Zhang
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, CA 92037, United States
| | - Tadashi Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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20
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Magdeldin S, Hirao Y, Elguoshy A, Xu B, Zhang Y, Fujinaka H, Yamamoto K, Yates JR, Yamamoto T. A proteomic glimpse into human ureter proteome. Proteomics 2015; 16:80-4. [PMID: 26442468 PMCID: PMC4737284 DOI: 10.1002/pmic.201500214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/31/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
Abstract
Urine has evolved as one of the most important biofluids in clinical proteomics due to its noninvasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620).
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Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismaïlia, Egypt.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Bo Xu
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Ying Zhang
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Tadashi Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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21
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Magdeldin S, Blaser RE, Yamamoto T, Yates JR. Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio). J Proteome Res 2014; 14:943-52. [PMID: 25398274 PMCID: PMC4324451 DOI: 10.1021/pr500998e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The
purpose of this study is to determine the behavioral and proteomic
consequences of shock-induced stress in zebrafish (Danio rerio) as a vertebrate model. Here we describe the behavioral effects
of exposure to predictable and unpredictable electric shock, together
with quantitative tandem mass tag isobaric labeling workflow to detect
altered protein candidates in response to shock exposure. Behavioral
results demonstrate a hyperactivity response to electric shock and
a suppression of activity to a stimulus predicting shock. On the basis
of the quantitative changes in protein abundance following shock exposure,
eight proteins were significantly up-regulated (HADHB, hspa8, hspa5,
actb1, mych4, atp2a1, zgc:86709, and zgc:86725). These proteins contribute
crucially in catalytic activities, stress response, cation transport,
and motor activities. This behavioral proteomic driven study clearly
showed that besides the rapid induction of heat shock proteins, other
catalytic enzymes and cation transporters were rapidly elevated as
a mechanism to counteract oxidative stress conditions resulting from
elevated fear/anxiety levels.
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Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University , 1-757 Asahimachi-dori, Niigata 951-8510, Japan
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22
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Magdeldin S, Moresco JJ, Yamamoto T, Yates JR. Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC-MS/MS. J Proteome Res 2014; 13:3826-36. [PMID: 25040086 PMCID: PMC4123945 DOI: 10.1021/pr500530e] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Indexed: 01/09/2023]
Abstract
Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples.
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Affiliation(s)
- Sameh Magdeldin
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
- Department
of Structural Pathology, Institute of Nephrology, Graduate School
of Medical and Dental Sciences, Niigata
University, 1-757 Asahimachi-dori, Niigata 951-8510, Japan
- Department
of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - James J. Moresco
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
| | - Tadashi Yamamoto
- Department
of Structural Pathology, Institute of Nephrology, Graduate School
of Medical and Dental Sciences, Niigata
University, 1-757 Asahimachi-dori, Niigata 951-8510, Japan
| | - John R. Yates
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
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23
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New Proteomic Insights on the Role of NPR-A in Regulating Self-Renewal of Embryonic Stem Cells. Stem Cell Rev Rep 2014; 10:561-72. [DOI: 10.1007/s12015-014-9517-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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