Structural and Functional Annotation of Conserved Virulent Hypothetical Proteins in Chlamydia Trachomatis: An In-Silico Approach

Author(s): Muhammad Naveed*, Muhammad Zubair Mehboob, Aadil Hussain, Khadija Ikram, Attha Talat, Nadia Zeeshan.

Journal Name: Current Bioinformatics

Volume 14 , Issue 4 , 2019

Become EABM
Become Reviewer

Graphical Abstract:


Background: Though after a start of genome sequencing most of the protein sequences are deposited in databases, some proteins remain to be unannotated and functionally uncharacterized. Chlamydia trachomatis L2C is a gram-negative pathogen bacterium involved in causing severe disorders like lymphogranuloma venereum, nongonococcal urethritis, and cervicitis.

Objectives: Analyzing and annotating the hypothetical proteins can help to understand its pathogenicity and therapeutic hotspots. Its genome encodes a total of 221 hypothetical proteins and out of these, 14 hypothetical proteins are declared as virulent by virulence prediction server (VirulentPred).

Methods: In this study, the functional and structural analysis was carried out by conserve domain finding servers, protein function annotators and physiochemical properties predictors. Proteinprotein interactions studies revealed the involvement of these virulent HPs in a number of pathways, which would be of interest for drug designers.

Results: Classifier tool was used to classify the virulent hypothetical proteins into enzymes, membrane protein, transporter and regulatory protein groups.

Conclusion: Our study would help to understand the mechanisms of pathogenesis and new potential therapeutic targets for a couple of diseases caused by C. trachomatis.

Keywords: Nongonococcal urethritis, virulent hypothetical proteins, elementary bodies, chlamydia trachomatis, pathogenicity, enzymes.

Lubec G, Afjehi-Sadat L, Yang JW, John JPP. Searching for hypothetical proteins: theory and practice based upon original data and literature. Prog Neurobiol 2005; 77(1-2): 90-127.
Bidkar A. In-silico Structural and Functional analysis of Hypothetical proteins of Leptospira Interrogans. Biochem Pharmacol 2014; 3(136): 2167-0501.1000136.
Sharma P, Patil K, Sarang D, Shinde P. In silico structure modeling and characterization of hypothetical proteins present in human fetal brain. Intl J Adv Bioinformatics Comput Biol 2013; pp. 22-30.
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999; 96(8): 4285-8.
Brown MP, Grundy WN, Lin D, et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000; 97(1): 262-7.
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998; 95(25): 14863-8.
Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000; 18(12): 1257-61.
Bharat Siva Varma P, Adimulam YB, Kodukula S. In silico functional annotation of a hypothetical protein from Staphylococcus aureus. J Infect Public Health 2015; 8(6): 526-32.
Budai I. Chlamydia trachomatis: milestones in clinical and microbiological diagnostics in the last hundred years: a review. Acta Microbiol Immunol Hung 2007; 54(1): 5-22.
Abraham S, Toutous-Trellu L, Pechère M, et al. Increased incidence of sexually transmitted infections in Geneva, Switzer-land. Dermatology (Basel) 2006; 212(1): 41-6.
Yuan Y, Zhang Y-X, Watkins NG, Caldwell HD. Nucleotide and deduced amino acid sequences for the four variable domains of the major outer membrane proteins of the 15 Chlamydia trachomatis serovars. Infect Immun 1989; 57(4): 1040-9.
Ward H, Martin I, Macdonald N, et al. Lymphogranuloma venereum in the United kingdom. Clin Infect Dis 2007; 44(1): 26-32.
Ingalls RR, Rice PA, Qureshi N, Takayama K, Lin JS, Golenbock DT. The inflammatory cytokine response to Chlamydia trachomatis infection is endotoxin mediated. Infect Immun 1995; 63(8): 3125-30.
Somboonna N, Wan R, Ojcius DM, et al. Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lympho-granuloma venereum (L(2)) and D lineages. MBio 2011; 2(3): e00045-11.
Vadhan-Raj S, Murray LJ, Bueso-Ramos C, et al. Stimulation of megakaryocyte and platelet production by a single dose of recombinant human thrombopoietin in patients with cancer. Ann Intern Med 1997; 126(9): 673-81.
Moulder JW. Interaction of chlamydiae and host cells in vitro. Microbiol Rev 1991; 55(1): 143-90.
Choroszy-Król IC, Frej-Mądrzak M, Jama-Kmiecik A, Bober T, Jolanta Sarowska J. Characteristics of the Chlamydia trachomatis species - immunopathology and infections. Adv Clin Exp Med 2012; 21(6): 799-808.
Nans A, Ford C, Hayward RD. Host-pathogen reorganisation during host cell entry by Chlamydia trachomatis. Microbes Infect 2015; 17(11-12): 727-31.
Liu C, Zhang H, Shi W, Lei A. Bond formations between two nucleophiles: transition metal catalyzed oxidative cross-coupling reactions. Chem Rev 2011; 111(3): 1780-824.
Li Z, Chen C, Chen D, Wu Y, Zhong Y, Zhong G. Characterization of fifty putative inclusion membrane proteins encoded in the Chlamydia trachomatis genome. Infect Immun 2008; 76(6): 2746-57.
Stephens RS. The cellular paradigm of chlamydial pathogenesis. Trends Microbiol 2003; 11(1): 44-51.
Enany S. Structural and functional analysis of hypothetical and conserved proteins of Clostridium tetani. J Infect Public Health 2014; 7(4): 296-307.
Shahbaaz M, Hassan MI, Ahmad F. Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PLoS One 2013; 8(12): e84263.
Barragan-Osorio L, Giraldo G, Almeciga-Diaz CJ, Aliev G, Barreto GE, Gonzalez J. Computational Analysis and Functional Prediction of Ubiquitin Hypothetical Protein: A Possible Target in Parkinson Disease. Cent Nerv Syst Agents Med Chem 2015; 16(1): 4-11.
Coordinators NR. Database resources of the national center for biotechnology information. Nucleic Acids Res 2013; 41: D8-D20.
Garg A, Gupta D. VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics 2008; 9(1): 62.
Walker JM. The proteomics protocols handbook 2005.
Horton P, Park K-J, Obayashi T, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res 2007; 35(Suppl. 2): W585-7.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215(3): 403-10.
Marchler-Bauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res 2015; 43: D222-6.
Finn RD, Coggill P, Eberhardt RY, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44: D279-85.
Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015; 43: 447-52.
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44(D1): D457-62.
Zou KH, Warfield SK, Fielding JR, et al. Statistical validation based on parametric receiver operating characteristic analysis of continuous classification data. Acad Radiol 2003; 10(12): 1359-68.
Swets J, Dawes R, Monahan J. Better Decisions through Science Every day, important and complex yes-or-no diagnostic decisions are made throughout medicine, industry and society. sci American J 2000; 283(4): 70-5.
Eng J. ROC analysis: web-based calculator for ROC curves 2006.
Naveed M, Malik SM, Ashraf NM, Bilal M. In Silico Structural and Functional Characterization of Hypothetical Protein of Vaccinia Virus. J Biohem Biotechnol Biomaterials 2016; 1(1): 28-35.
Chen C, Chen D, Sharma J, et al. The hypothetical protein CT813 is localized in the Chlamydia trachomatis inclusion membrane and is immunogenic in women urogenitally infected with C. trachomatis. Infect Immun 2006; 74(8): 4826-40.
Luo J, Liu G, Zhong Y, et al. Characterization of hypothetical proteins Cpn0146, 0147, 0284 & 0285 that are predicted to be in the Chlamydia pneumoniae inclusion membrane. BMC Microbiol 2007; 7(1): 38.
de Jesús De Haro-Cruz M, Deleón-Rodriguez I, Escobedo-Guerra MR, et al. Genotyping of Chlamydia trachomatis from endocervical specimens of infertile Mexican women. Enferm Infecc Microbiol Clin 2011; 29(2): 102-8.
Grossman L, Yeung AT. The UvrABC endonuclease system of Escherichia coli--a view from Baltimore. Mutat Res 1990; 236(2-3): 213-21.
Verhoeven EE, van Kesteren M, Moolenaar GF, Visse R, Goosen N. Catalytic sites for 3′ and 5′ incision of Escherichia coli nucleotide excision repair are both located in UvrC. J Biol Chem 2000; 275(7): 5120-3.
Piekarowicz A, Kłyz A, Kwiatek A, Stein DC. Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. Mol Microbiol 2001; 41(5): 1199-210.
Kaspar S, Bott M. The sensor kinase CitA (DpiB) of Escherichia coli functions as a high-affinity citrate receptor. Arch Microbiol 2002; 177(4): 313-21.
Urbauer JL, Cowley AB, Broussard HP, Niedermaier HT, Bieber Urbauer RJ. Solution structure and properties of AlgH from Pseudomonas aeruginosa. Proteins 2015; 83(6): 1137-50.
Tanzer RJ, Hatch TP. Characterization of outer membrane proteins in Chlamydia trachomatis LGV serovar L2. J Bacteriol 2001; 183(8): 2686-90.
Everett KD, Hatch TP. Sequence analysis and lipid modification of the cysteine-rich envelope proteins of Chlamydia psittaci 6BC. J Bacteriol 1991; 173(12): 3821-30.
Allen JE, Cerrone MC, Beatty PR, Stephens RS. Cysteine-rich outer membrane proteins of Chlamydia trachomatis display compensatory sequence changes between biovariants. Mol Microbiol 1990; 4(9): 1543-50.
Jones RB, Bruins SC, Newhall WJV. Comparison of reticulate and elementary body antigens in detection of antibodies against Chlamydia trachomatis by an enzyme-linked immunosorbent assay. J Clin Microbiol 1983; 17(3): 466-71.
Stephens RS, Kalman S, Lammel C, et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 1998; 282(5389): 754-9.
Vieira OV, Botelho RJ, Grinstein S. Phagosome maturation: aging gracefully. Biochem J 2002; 366(Pt 3): 689-704.
Fields KA, Fischer E, Hackstadt T. Inhibition of fusion of Chlamydia trachomatis inclusions at 32 degrees C correlates with restricted export of IncA. Infect Immun 2002; 70(7): 3816-23.
Damiani MT, Gambarte Tudela J, Capmany A. Targeting eukaryotic Rab proteins: a smart strategy for chlamydial survival and replication. Cell Microbiol 2014; 16(9): 1329-38.
Rzomp KA, Scholtes LD, Briggs BJ, Whittaker GR, Scidmore MA. Rab GTPases are recruited to chlamydial inclusions in both a species-dependent and species-independent manner. Infect Immun 2003; 71(10): 5855-70.
Garmory HS, Titball RW. ATP-binding cassette transporters are targets for the development of antibacterial vaccines and therapies. Infect Immun 2004; 72(12): 6757-63.
Hirano T. SMC proteins and chromosome mechanics: from bacteria to humans. Philos Trans R Soc Lond B Biol Sci 2005; 360(1455): 507-14.
Singh A, Bhagavat R, Vijayan M, Chandra N. A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes. Tuberculosis 2016; 99: 109-19.
Jensen RB, Shapiro L. Cell-cycle-regulated expression and subcellular localization of the Caulobacter crescentus SMC chromosome structural protein. J Bacteriol 2003; 185(10): 3068-75.
Jacob AI, Köhrer C, Davies BW. RajBhandary UL, Walker GC. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 2013; 49(3): 427-38.
Arai R, Murayama K, Uchikubo-Kamo T, et al. Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8. J Struct Biol 2009; 168(3): 575-81.
Kassebaum NJ, Bertozzi-Villa A, Coggeshall MS, et al. Global, regional, and national levels and causes of maternal mortality during 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 2014; 384(9947): 980-1004.
Rosario CJ, Tan M. The early gene product EUO is a transcriptional repressor that selectively regulates promoters of Chlamydia late genes. Mol Microbiol 2012; 84(6): 1097-107.
Akers RL. Social learning and social structure: A general theory of crime and deviance 2011.
Wichlan DG, Hatch TP. Identification of an early-stage gene of Chlamydia psittaci 6BC. J Bacteriol 1993; 175(10): 2936-42.
Zhang Z. A flexible new technique for camera calibration. Pattern Analysis and Machine Intelligence. IEEE Transactions on 2000; 22(11): 1330-4.
Tong S, Li Y, Rivailler P, et al. A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci USA 2012; 109(11): 4269-74.
Belland RJ, Zhong G, Crane DD, et al. Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis. Proc Natl Acad Sci USA 2003; 100(14): 8478-83.

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2019
Page: [344 - 352]
Pages: 9
DOI: 10.2174/1574893613666181107111259
Price: $58

Article Metrics

PDF: 42