Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects

References

• Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25–29.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37:W202–W208.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in bipolymers. Proceeding of the second International Conference on Intelligent Systems for Molecular Biology August 1994, 28–36.
   Google Scholar
• Bairoch A, Boeckmann B. 1994. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res. 22:3578–3580.
   PubMed Web of Science ®Google Scholar
• Baloğlu MC, Negre-Zakharov F, Öktem HA, Yücel AM. 2011. Molecular cloning, characterization, and expression analysis of a gene encoding a Ran binding protein (RanBP) in Cucumis melo L. Turk J Biol. 35: 387–397.
   Web of Science ®Google Scholar
• Bjellqvist B, Basse B, Olsen E, Celis JE. 1994. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis. 15:529–539.
   PubMed Web of Science ®Google Scholar
• Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F, Sanchez JC, Frutiger S, Hochstrasser D. 1993. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis. 14:1023–1031.
   PubMed Web of Science ®Google Scholar
• Blankenship RE. 2013. Molecular mechanisms of photosynthesis. John Wiley & Sons, Wiley-Blackwell.
   Google Scholar
• Bordoli L, Schwede T. 2012. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Methods Mol Biol. 857:107–136.
   PubMedGoogle Scholar
• Brandt U, Trumpower B. 1994. The protonmotive Q cycle in mitochondria and bacteria. Crit Rev Biochem Mol Biol 29:165–197.
   PubMed Web of Science ®Google Scholar
• Brasseur R. 1988. Calculation of the three-dimensional structure of Saccharomyces cerevisiae cytochrome b inserted in a lipid matrix. J Biol Chem. 263:12571–12575.
   PubMed Web of Science ®Google Scholar
• Castresana J. 2001. Cytochrome b phylogeny and the taxonomy of great apes and mammals. Mol Biol Evol. 18:465–471.
   PubMed Web of Science ®Google Scholar
• Combet C, Blanchet C, Geourjon C, Deleage G. 2000. NPS@: network protein sequence analysis. Trends Biochem Sci. 25:147–150.
   PubMed Web of Science ®Google Scholar
• Cramer W, Black M, Widger W, Girvin M. 1987. Structure and function of photosynthetic cytochrome bc1 and b6f complexes. In: Barber J, editor. The light reactions. Amsterdam: Elsevier Science Publishers B.V; vol.8, p. 447–493.
   Google Scholar
• Crofts A, Hacker B, Barquera B, Yun CH, Gennis R. 1992. Structure and function of the bc-complex of Rhodobacter sphaeroides. BBA-Bioenergetics. 1101:162–165.
   Google Scholar
• Crofts AR, Hong S, Ugulava N, Barquera B, Gennis R, Guergova-Kuras M, Berry EA. 1999. Pathways for proton release during ubihydroquinone oxidation by the bc(1) complex. Proc Natl Acad Sci USA. 96:10021–10026.
   PubMed Web of Science ®Google Scholar
• Crofts AR, Robinson HH, Andrews K, Van Doren S, Berry E. 1987. Catalytic sites for reduction and oxidation of quinones. In: Papa S, Chance B and Ernster L, editors. Cytochrome systems: molecular biology and bioenergetics. New York: Plenum Press; p. 617–624.
   Google Scholar
• Crofts A, Wang Z, Chen Y, Mahalingham S, Yun C. 1990. Function, steady-state turnover, and structure of the ubiquinol:cytochrome c2 oxidoreductase of Rhodobacter sphaeroides. In: Lenaz G, Barnabei O, Rabbi A and Battino M, editors. Highlights in ubiquinone research. London: Taylor and Francis; p. 98–103.
   Google Scholar
• Darabi M, Farhadi-Nejad H. 2013. Study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) protein in Rosaceae by bioinformatics tools. Caryologia. 66:351–359.
   Web of Science ®Google Scholar
• Darabi M, Seddigh S. 2015. Bioinformatic characterization of aspartic protease (AP) enzyme in seed plants. Plant Syst Evol. 301:2399–2417.
   Web of Science ®Google Scholar
• Darabi M, Seddigh S, Abarshahr M 2017. Structural, functional, and phylogenetic analysis of the cytochrome P450 (CYP) enzyme in seed plants by bioinformatics tools. Caryologia. DOI: 10.1080/00087114.2016.1274866.
   Web of Science ®Google Scholar
• Darabi M, Masoudi-Nejad A, Nemat-Zadeh G. 2012. Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae. Mol Biol Rep. 39:8925–8935.
   PubMed Web of Science ®Google Scholar
• Degli Esposti M. 1989. Prediction and comparison of the haem-binding sites in membrane haemoproteins. BBA-Bioenergetics. 977:249–265.
   Google Scholar
• Degli Esposti M, Crimi M. 1990. The membrane proteins that interact with quinones have common structural features. In: Lenaz G, Barnabei O, Rabbi A and Battino M, editors. Highlights in Ubiquinone research. London: Taylor and Francis; p. 166–169.
   Google Scholar
• Degli Esposti M, De Vries S, Crimi M, Ghelli A, Patarnello T, Meyer A. 1993. Mitochondrial cytochrome b: evolution and structure of the protein. BBA-Bioenergetics. 1143:243–271.
   Google Scholar
• De Vries S, Marres CA. 1987. The mitochondrial respiratory chain of yeast. Structure and biosynthesis and the role in cellular metabolism. BBA-Bioenergetics. 895:205–239.
   Google Scholar
• Dutton P. 1986. Energy transduction in anoxygenic photosynthesis. In: Staehelin LA and Arntzen CJ, editors. Photosynthesis III, photosynthetic membranes and light harvesting systems. Berlin Heidelberg: Springer; vol. 19, p. 197–237.
   Google Scholar
• Farias IP, Ortí G, Sampaio I, Schneider H, Meyer A. 2001. The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes. J Mol Evol. 53:89–103.
   PubMed Web of Science ®Google Scholar
• Gao X, Wen X, Esser L, Quinn B, Yu L, Yu CA, Xia D. 2003. Structural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site. Biochemistry. 42:9067–9080.
   PubMed Web of Science ®Google Scholar
• Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. In: Walker JM, editor. The proteomics protocols handbook. Humana Press; p. 571–607.
   Google Scholar
• Geourjon C, Deleage G. 1995. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci. 11:681–684.
   PubMedGoogle Scholar
• Guruprasad K, Reddy BB, Pandit MW. 1990. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4:155–161.
   PubMedGoogle Scholar
• Hauska G, Hurt E, Gabellini N, Lockau W. 1983. Comparative aspects of quinol-cytochrome c/plastocyanin oxidoreductases. BBA-Bioenergetics. 726:97–133.
   Google Scholar
• Hauska G, Nitschke W, Herrmann R. 1988. Amino acid identities in the three redox center-carrying polypeptides of cytochrome bc1/b6f complexes. J Bioenerg Biomembr. 20:211–228.
   PubMed Web of Science ®Google Scholar
• Howell N. 1989. Evolutionary conservation of protein regions in the protonmotive cytochromeb and their possible roles in redox catalysis. J Mol Evol. 29:157–169.
   PubMed Web of Science ®Google Scholar
• Ikai A. 1980. Thermostability and aliphatic index of globular proteins. J Biochem. 88:1895–1898.
   PubMed Web of Science ®Google Scholar
• Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of the cytochromeb gene of mammals. J Mol Evol. 32:128–144.
   PubMed Web of Science ®Google Scholar
• Jagow Gv, Walter S. 1980. b-Type cytochromes. Annu Rev Biochem. 49:281–314.
   PubMed Web of Science ®Google Scholar
• Kelley LA, Sternberg MJ. 2009. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 4:363–371.
   PubMed Web of Science ®Google Scholar
• Kent RJ, Norris, DE. 2005. Identification of mammalian blood meals in mosquitoes by a multiplexed polymerase chain reaction targeting cytochrome B. Am J Trop Med Hyg. 73:336–342.
   PubMedGoogle Scholar
• Kirstein F, Gray J. 1996. A molecular marker for the identification of the zoonotic reservoirs of Lyme borreliosis by analysis of the blood meal in its European vector Ixodes ricinus. Appl Environ Microb. 62: 4060–4065.
   PubMed Web of Science ®Google Scholar
• Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA. 86:6196–6200.
   PubMed Web of Science ®Google Scholar
• Kumazawa Y, Nishida M. 2000. Molecular phylogeny of Osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Mol Biol Evol. 17:1869–1878.
   PubMed Web of Science ®Google Scholar
• Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157:105–132.
   PubMed Web of Science ®Google Scholar
• Laskay ÜA, Burg J, Kaleta EJ, Vilcins IME, Telford III SR, Barbour AG, Wysocki VH. 2012. Development of a host blood meal database: de novo sequencing of hemoglobin from nine small mammals using mass spectrometry. Biol Chem. 393:195–201.
   PubMed Web of Science ®Google Scholar
• Lee JH, Hassan H, Hill G, Cupp EW, Higazi TB, Mitchell CJ, Godsey MS and Unnasch TR. 2002. Identification of mosquito avian-derived blood meals by polymerase chain reaction-heteroduplex analysis. Am J Trop Med Hyg. 66:599–604.
   PubMed Web of Science ®Google Scholar
• Lee D, Redfern O, Orengo C. 2007. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol. 8:995–1005.
   PubMed Web of Science ®Google Scholar
• Mahler H, Perlman P. 1985. The Enzymes of Biological Membranes. In: Martonosl AN, editor. New York: Plenum Press; p. 195–234
   Google Scholar
• Maiti R, Van Domselaar GH, Zhang H, Wishart DS. 2004. SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 32:W590–W594.
   PubMed Web of Science ®Google Scholar
• Moller S, Croning MD, Apweiler R. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics. 17:646–653.
   PubMed Web of Science ®Google Scholar
• Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB. 2003. Classification schemes for protein structure and function. Nat Rev Genet. 4:508–519.
   PubMed Web of Science ®Google Scholar
• Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 8:785–786.
   PubMed Web of Science ®Google Scholar
• Pettersson E, Bensch S, Ander M, Chirico J, Sigvald R, Ignell R. 2013. Molecular identification of bloodmeals and species composition in Culicoides biting midges. Med Vet Entomol. 27:104–112.
   PubMed Web of Science ®Google Scholar
• Rogers S, Wells R, Rechsteiner M. 1986. Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis. Science. 234:364–368.
   PubMed Web of Science ®Google Scholar
• Santiago-Alarcon D, Havelka P, Pineda E, Segelbacher G, Schaefer HM. 2013. Urban forests as hubs for novel zoonosis: blood meal analysis, seasonal variation in Culicoides (Diptera: Ceratopogonidae) vectors, and avian haemosporidians. Parasitology. 140:1799–1810.
   PubMed Web of Science ®Google Scholar
• Saraste M. 1984. Location of haem-binding sites in the mitochondrial cytochrome b. FEBS Lett. 166:367–372.
   PubMed Web of Science ®Google Scholar
• Schwartz AS, Yu J, Gardenour KR, Finley RL Jr, Ideker T. 2009. Cost-effective strategies for completing the interactome. Nat Methods. 6:55–61.
   PubMed Web of Science ®Google Scholar
• Seddigh S, Darabi M. 2014. Comprehensive analysis of beta-galactosidase protein in plants based on Arabidopsis thaliana. Turk J Biol. 38:140–150.
   Web of Science ®Google Scholar
• Seddigh S, Darabi M. 2015. Structural and phylogenetic analysis of α-glucosidase protein in insects. Biologia. 70:812–825.
   Web of Science ®Google Scholar
• Seddigh S, Darabi M. 2016. Proteomics comparison of aspartic protease enzyme in insects. Turk J Biol. 40:69–83.
   Web of Science ®Google Scholar
• Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D. 2002. ProDom: automated clustering of homologous domains. Brief Bioinformatics. 3:246–251.
   PubMedGoogle Scholar
• Söding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics. 21:951–960.
   PubMed Web of Science ®Google Scholar
• Steuber S, Abdel-Rady A, Clausen PH. 2005. PCR-RFLP analysis: a promising technique for host species identification of blood meals from tsetse flies (Diptera: Glossinidae). Parasitol Res. 97:247–254.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP. 2015. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43:D447–D452.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Tian H, White S, Yu L, Yu CA. 1999. Evidence for the head domain movement of the rieske iron-sulfur protein in electron transfer reaction of the cytochrome bc1 Complex. J Biol Chem. 274:7146–7152.
   PubMed Web of Science ®Google Scholar
• Trumpower BL. 1990. Cytochrome bc1 complexes of microorganisms. Microbiol Rev. 54:101–129.
   PubMedGoogle Scholar
• Trumpower BL, Gennis RB. 1994. Energy transduction by cytochrome complexes in mitochondrial and bacterial respiration: the enzymology of coupling electron transfer reactions to transmembrane proton translocation. Annu Rev Biochem. 63:675–716.
   PubMed Web of Science ®Google Scholar
• Vihinen M. 2001. Bioinformatics in proteomics. Biomol Eng. 18:241–248.
   PubMedGoogle Scholar
• Widget W, Cramer W. 1991. Cell culture and somatic cell, genetics of plants. New York: Academic Press; p. 149–176.
   Google Scholar
• Widger WR, Cramer W, Herrmann R, Trebst A. 1984. Sequence homology and structural similarity between cytochrome b of mitochondrial complex III and the chloroplast b6-f complex: position of the cytochrome b hemes in the membrane. Proc Natl Acad Sci USA. 81:674–678.
   PubMed Web of Science ®Google Scholar
• Wodecka B, Rymaszewska A, Skotarczak B. 2014. Host and pathogen DNA identification in blood meals of nymphal Ixodes ricinus ticks from forest parks and rural forests of Poland. Exp Appl Acarol. 62:543–555.
   PubMed Web of Science ®Google Scholar
• Wojcik J, Schächter V. 2000. Proteomic databases and software on the web. Brief Bioinformatics. 1:250–259.
   PubMedGoogle Scholar
• Xu J, Zhang Y. 2010. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics. 26:889–895.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH. 1998. Electron transfer by domain movement in cytochrome bc1. Nature. 392:677–684.
   PubMed Web of Science ®Google Scholar
• Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 490:556–560.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Skolnick J. 2004. Scoring function for automated assessment of protein structure template quality. Proteins. 57:702–710.
   PubMed Web of Science ®Google Scholar
• Zhao L, Pridgeon JW, Becnel JJ, Clark GG, Linthicum KJ. 2009. Mitochondrial gene cytochrome b developmental and environmental expression in Aedes aegypti (Diptera: Culicidae). J Med Entomol. 46:1361–1369.
   PubMed Web of Science ®Google Scholar
• Zhen Y, Hoganson CW, Babcock GT, Ferguson-Miller S. 1999. Definition of the Interaction Domain for Cytochrome con Cytochrome c Oxidase I. Biochemical, spectral, and kinetic characterization of surface mutants in subunit ii of Rhodobacter sphaeroides cytochrome aa 3. J Biol Chem. 274:38032–38041.
   PubMed Web of Science ®Google Scholar