• Logo
  • SBMUJournals

Bioinformatics Evaluation of Plant Chlorophyllase, the Key Enzyme in Chlorophyll Degradation

Ebrahim Sharafi, Ali Dehestani, Jamshid Farmani, Ali Pakdin Parizi
1302

Views

PDF

Abstract


Background and Objective: Chlorophyllase catalyzes the hydrolysis of chlorophylls to chlorophyllide and phytol. Recently, several applications including removal of chlorophylls from vegetable oils, use in laundry detergents and production of chlorophyllides have been described for chlorophyllase. However, there is little information about the biochemical characteristics of chlorophyllases.

Material and Methods: 35 chlorophyllase protein sequences were obtained from the National Centre for Biotechnology Information database. All of the sequences were analyzed using bioinformatics tools for their conserved domain, phylogenetic relationships and biochemical characteristics.

Results and Conclusion: The overall domain architecture of chlorophyllases consisted of the esterases/lipases superfamily domain over their full length and the alpha/beta hydrolase family domain over the middle part of their sequences. Plant chlorophyllases could be classified into 4 clades. Molecular weight and pI of the chlorophyllases ranged 32.65-37.77 kDa and 4.80-8.97, respectively. The most stable chlorophyllase is probably obtained from Malus domestica. Chlorophyllases form Solanum pennellii, Triticum aestivum, Triticum urartu, Arabidopsis lyrata, Pachira macrocarpa, Prunus mume and Malus domestica were predicted to be soluble upon overexpression in Escherichia coli, Beta vulgaris and Chenopodium album chlorophyllases were predicted to form no disulfide bond. Chlorophyllases from Jatropha curcas, Amborella trichopod, Setaria italica, Piper betle, Triticum urartu and Arabidopsis thaliana were predicted to be in non-N-glycosylated form.

Conflict of interest: The authors declare no conflict of interest.


Keywords

Bioinformatics, Biochemical characteristics, Chlorophyllase, Phylogenetic

References

Hörtensteiner S. Kräutler B. Chlorophyll breakdown in higher plants. BBA. 2011: 1807: 977-988.

Lee GC. Chepyshko H., Chen HH. Chu CC. Chou YF. Akoh CC. Shaw JF. Genes and biochemical characterization of three novel chlorophyllase isozymes from Brassica oleracea. J. Agric. Food Chem. 2010: 58: 8651–8657.

Kariola T. Brader G. Li J. Palva ET. Chlorophyllase1, a damage control enzyme affects the balance between defense pathways in plants. Plant Cell. 2005: 17: 282–2949.

Yi Y. Kermasha S. Hocine L. Neufeld R. Encapsulation of chlorophyllase in hydrophobically modified hydrogel. J Mol Catal B-Enzym. 2002: 20: 319–325.

Bitar M. Karboune S. Bisakowski B. Kermasha S. Chlorophyllase biocatalysis in an aqueous/miscible organic medium containing canola oil. J. Am. Oil Chem.Soc. 2004: 81: 927–932.

Samaha H. Kermasha S. Biocatalysis of chlorophyllase in ternary micellar systems using Pheophytins as substrates. J Chem Tech Biotechnol. 1997: 68: 315–323.

Yi Y. Kermasha S. Neufeld RJ. Matrix physicochemical properties affect activity of entrapped chlorophyllase. J Chem Technol Biotechnol. 2005: 80: 1395–1402.

Yi Y. Kermasha S. Neufeld RJ. Characterization of Sol-Gel Entrapped Chlorophyllase. Biotechnol. Bioeng. 2006: 95: 840-849.

Arkus K. Cahoon EB. Jez JM. Mechanistic analysis of wheat chlorophyllase. Arch Biochem Biophys. 2005: 438: 146–155.

Chou YL. Ko CY. Yen CC. Chen LC. Shaw LF. A Novel Recombinant Chlorophyllase1 from Chlamydomonas reinhardtii for the Production of Chlorophyllide Derivatives. J. Agric. Food Chem. 2015: 63: 9496−9503.

Tsuchiya T. Ohta H. Okawa K. Iwamatsu A. Shimada H. Masuda T. Takamiya K. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Proc. Natl. Acad. Sci. U.S.A. 1999: 96: 15362–15367.

Chen M. Yang J. Liu C. Lin K. Yang, C. Molecular, structural, and phylogenetic characterization of two chlorophyllase isoforms in

Pachira macrocarpa. Plant Syst Evol. 2014: 300: 633–643.

Chou YL. Lee CC. Yen LF. Chen LC. Shaw LF. A Novel Recombinant Chlorophyllase from Cyanobacterium Cyanothece sp. ATCC 51142 for the Production of Bacteriochlorophyllide a. Biotechnol Appl Biochem. 2015: 10: 1002-1017.

Khalyfa A. Kermasha S. Khamessan A. Marsota P. Alli I. Purification and Characterization of Chlorophyllase from Alga (Phaeodactylum tricornutum) by Preparative Isoelectric Focusing. Biosci. Biotechnol. Biochem. 1993: 57: 433-437.

Tsuchiya T. Oht H. Masuda T. Mikami B. Kita N Shioi Y. Takamiya K. Purification and characterization of two isozymes of chlorophyllase from mature leaves of Chenopodium album. Plant Cell Physiol. 1997: 38: 1026–1031.

See-Kiong N. Limsoon W. Accomplishments and challenges in bioinformatics. IT Professional.2004: 6: 44- 50.

Marchler-Bauer A. Derbyshire MK. Gonzales NR. Lu S. Chitsaz F. Geer LY. Geer R C. He J. Gwadz M. Hurwitz DI. Lanczycki CJ. Lu F. Marchler GH. Song JS. Thanki N. Wang Z. Yamashita RA. Zhang D. Zheng C. Bryant SH. "CDD: NCBI's conserved domain database". Nucleic Acids Res. 2015: 43: 222-226.

Thompson JD. Higgins DG. Gibson TJ. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994: 22: 4673–4680.

Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1978: 4: 406–425.

Gasteiger E, Hoogland C. Gattiker A. Duvaud S. Protein identification and analysis tools on the ExPASyserver. In: The Proteomics Protocols Handbook, J. M. Walker, (Ed.), Humana Press, New Jersey (USA). 2005: 571–607.

Magnan C N. Randall A. Baldi P. SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics. 2009: 25: 2200–2207.

Cheng J. Saigo H. Baldi P. Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matchin. Proteins. 2006: 62: 617–629.

Gupta R. Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac. Symp. Biocomput. 2002: 7: 310–322.

Shemer TA. Smadar HS. Belausov E. Lovat N. Krokhin O. Spicer V. Standing KG. Goldschmidt EE. Eyal Y. Citrus chlorophyllase dynamics at ethylene-induced fruit color-break: a study of chlorophyllase expression posttranslational processing kinetics, and in situ intracellular localization. Plant Physiology. 2008: 148: 108–118.

Marcussen T. Sandve SR. Heier L. Spannag M. Pfeifer M. Jakobsen KS. Wulff BB. Steuernagel B. Mayer KF. Olsen OA. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014: 345: 263-294.

Albert V A. Barbazuk WB. Pamphilis CW. Der JP. Leebens-Mack J. Ma H. Palmer J D. Rounsley S. Sankoff D. Schuster SC. Soltis DE. Soltis PS. Wessler SR. Wing RA. Chamala S. Chanderbali AS. Chang TH. Determann R. Lan T. Arikit S. Axtell MJ. Ayyampalayam S. Burnette JM. Chamala S. De Paoli E. Estill JC. Farrell NP. Harkess A. Jiao Y. Leebens-Mack J. Liu K. Mei W. Meyers BC. Shahid S. Wafula E. Walts B. The Amborella genome and the evolution of flowering plants. Science. 2013: 342: 616- 629.

Hu TT. Pattyn P. Bakker EG. Cao J. Cheng JF. Clark RM. Fahlgren N. Fawcett JA. Grimwood J. Gundlach H. Haberer G. Hollister JD. Ossowski S. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 2011: 43: 476–481.

Theologis A, Ecker JR. Palm CJ. Federspiel NA. Kaul S. White O. Alonso J. Altafi H. Araujo R. Bowman CL. Brooks SY. Buehler E. Chan A. Chao Q. Chen H. Cheuk RF. Chin CW. Chung MK. Conn L. Conway AB. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000: 6814: 816-820.

Dohm JC. Minoche A. Holtgräwe D. Capella-Gutiérrez S. Zakrzewski F. Tafer H. Rupp O. Rosleff Sörensen T. Stracke R. Reinhardt R. Goesmann A. Kraft T. Schulz B. Stadler F. Schmidt T. Gabaldón T. Lehrach H. Weisshaar B. Himmelbauer H. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014: 7484: 546-549.

Chalhoub B. Denoeud F. Liu S. Parkin IA. Tang H. Wang X. Chiquet J. Belcram H. Tong C. Samans B. Corréa M. Da Silva C. Just J. Falentin C. Koh CS., Le Clainche I. Bernard M. Bento P. Noel B. Labadie K. Alberti A. Charles M. Arnaud D. Guo H. Daviaud C. Alamery S. Jabbari K. Zhao M. Edger PP. Chelaifa H. Tack D. Lassalle G. Mestiri I. Schnel N. Le Paslier MC. Fan G. Renault V. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oil seed genome. Science. 2014: 345: 950-953.

Long-Fang O. Chen B. Chin-Hong L. Swati M. Kelkarc C. Shawa F. Transgenic broccoli (Brassica oleracea var. italica) with antisense chlorophyllase (BoCLH1) delays postharvest yellowing. Plant Sci. 2008: 174: 25-31.

Azoulay-Shemer T. Harpaz-Saad S. Cohen-Peer R. Mett1 A. Spicer V. Lovat N. Krokhin O. Brand A. Gidoni D. Standing K. Goldschmidt E. Eyal Y. Dual N- and C-terminal processing of citrus chlorophyllase precursor within the plastid membranes leads to the mature enzyme. Plant Cell Physiol. 2011: 52: 70-83.

Jacob-Wilk D. Holland D. Goldschmidt EE. Riov J. Eyal Y. Chlorophyll breakdown by chlorophyllase: isolation and functional expression of the Chlase1 gene from ethylene-treated Citrus fruit and its regulation during development. Plant J. 1999: 20: 653-661.

Azuma RK, Kurata H. Shimokawa K. Adachi M. BAB47176. 2001.

Li Z. Zhang Z. Yan P. Huang S. Fei Z. Lin K. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics. 2011: 12: 1-11.

Yan H. Ge W. Cheng Y. AEO19902. 2011.

Okazawa A. Tang L. Fukusaki EI. Kobayashi A. AAP44978. 2003.

Zhang L. Zhang C. Wu P. Chen Y. Li M. Jiang H. Wu G. Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress. Plos one. 2014: 5: 1-9.

Wang N. Yue Z. Liang D. Ma F. Genome-wide identification of members in the YTH domain-containing RNA-binding protein family in apple and expression analysis of their responsiveness to senescence and abiotic stresses. Gene. 2014: 538: 292-305.

Young ND. Debellé F. Oldroyd GE. Geurts R. Cannon SB. Udvardi MK. Benedito VA. Mayer KF. Gouzy J. Schoof H. Van de Peer Y. Proost S. Cook DR. Meyers BC. Spannagl M. Cheung F. De Mita S. Krishnakumar V. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011: 480: 520-524.

Rambo T. Preston R. Yu Y. Currie J. Saski C. Kim R. Collura R. Thompson R. Simmons J. Yang T. Nah G. Pate A. Thurmond S. Henry D. Oates R. Palmer M. Pries G. Gibson J. Anderson H. Manjiri J. Crane L. Dale J. In-depth view of structure, activity, and evolution of rice chromosome 10. Science. 2003: 5625: 1566-1569.

Fang Y. Wu H. Zhang T. Yang M. Yin Y. Pan L. Yu X. Zhang X. Hu S. Mssallem IS. Yu J. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. Plos one. 2012: 5:1-12.

Reid KE. Liao N. ACN40275. 2009.

Parkash J. Sood A. Sharma M. Sanjeeta S. Manjula M. Dutt S. AHZ35334. 2014.

Gupta S. Kumar N. Gupta S M. Sane AP. Nath P. AAP92160. 2005.

Tuskan, G. A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, R. P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G. L., Cooper, D., 2006. The genome of black cottonwood,

Populus trichocarpa (Torr. & Gray). Science. 313, 1596-1604.

Zhang Q. Chen W. Sun L. Zhao F. Huang B. Yang W. Tao Y. Jia W. Yuan Z. Fan G. Xing Z. Han C. Pan H. Zhong X. Shi W. Liang X. Du D. Sun F. The genome of Prunus mume. Nat. Commun. 2012: 1318: 1-8.

Zhang H. Wei L. Miao H. Zhang T. Wang C. Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics. 2012: 13: 2-10.

Bennetzen, J. L., Schmutz, J., 2012. Reference genome sequence of the model plant Setaria. Nat. Biotechnol. 30, 555-561.

Spyropoulou EA. Haring MA. Schuurink RC. Expression of Terpenoids, a glandular trichome-specific transcription factor from tomato that activates the terpene synthase 5 promoter. Plant Mol Biol. 2014: 3: 345-357.

Almeida J. Quadrana L. Asís R. Setta N. Godoy F. Bermúdez L. Otaiza SN. Corrêa D. Silva JV. Fernie AR. Carrari F. Rossi M. Genetic dissection of vitamin E biosynthesis in tomato. J. Exp. Bot. 2011: 11: 3781–3798.

Xu X. Pan S. Cheng S. Zhang B. Mu D. Genome sequence and analysis of the tuber crop potato. Nature. 2011: 475:189–195.

Pranjali HG. Krishna KG. Singh VP. Arora A. AHJ14565. 2013.

Ling HQ, Zhao S, Liu D. Wang J. Sun H. Zhang C. Fan H. Li D. Dong L. Tao Y. Gao, C. Wu H. Li Y. Cui Y. Guo X. Zheng S. Wang B. Yu K. Liang Q. Yang W. Lou X. Chen J. Feng M. Jian J. Zhang X. Luo G. Jiang Y. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature. 2013: 7443: 87-90.

Venturini L, Ferrarini A, Zenoni S, Tornielli GB, Fasoli M, Dal Santo S, Minio A, Buson G, Tononi P, Zago ED. Zamperin G. Bellin D. Pezzotti M. Delledonne M. De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genomics. 2013: 14: 1-13.

Schnable PS. Ware D. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009: 5956: 1112-1115.

Shioi Y. Sasa T. Purification of solubilized chlorophyllase from

Chlorella protorhecoides. Method Enzymol. 1986: 123: 421–427.

Trebitsh T. Goldschmidt EE. RiovJ. Ethylene induces de novo synthesis of chlorophyllase, a chlorophyll degrading enzyme, in Citrus fruit peel. Proc. Natl. Acad. Sci. U.S.A. 1993: 90: 9441–9445.

Von Heijne G, Abrahmsén L. Species-specific variation in signal peptide design: implications for protein secretion in foreign hosts. FEBS. 1989: 244: 439–446.

Holmquist M. Alpha/Beta- hydrolase fold enzymes: structures, functions and mechanisms. Curr Protein Pept Sc. 2000: 1: 209-235.

Ikai A. Thermostability and aliphatic index of globular proteins. J Biochem. 1980: 88: 1895-1898.

Bommarius S. Riebel BR. Biocatalysis. 1974: Wiley-VCH, Weinheim (Germany).

Kyte J. Doolittle RF. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982: 157:105-132.

Manzur M. Muñoz R. Lucero A. Ayub M. Alvarez S. Ciuffo G. Production of recombinant enzymes of wide use for research. Electron. J. Biotechnol. 2006: 9: 3-16.

Diaz A. Tomba E. Lennarson R. Rex R. Bagajewicz M. Harrison R. Prediction of Protein Solubility in Escherichia coli Using Logistic Regression. Biotechnol. Bioeng. 2009: 9999: 3-20.

Idicula-Thomas S. Balaji, PV. Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli. Protein Sci. 2005: 14: 582–592.

Bertone P. Kluger Y. Lan N. Zheng D. Goh C. Echols N. Shawn M. Milburn D. Xiao R. Ma L. Wunderlich Z. Acton T. Gaetano T. Gerstein M. SPINE: An integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res. 2001: 29: 2884–2898.

Luan CH. Qiu S. Finley JB. Carson M. Gray RJ. Huang W. Johnson D. Tsao J. Reboul J. Vaglio P. Hill DE. Vidal M. Delucas LJ. Luo M. Hight- throughput expression of C.elegansproteins. Genome Res. 2004: 14: 2102–2110.

Goh CS. Lan N. Douglas SM. Wu B. Echols N. Smith A. Milburn D. Montelione GT. Zhao H. Gerstein M. Mining the structural genomics pipeline: identification of protein properties that affect high throughput experimental analysis. J. Mol. Biol. 2004: 336: 115–130.

Bulleid N. Ellgaard L. Multiple ways to make disulfides. Trends Biochem. Sci. 2011: 36: 485-492.

Easton R. Glycosylation of proteins structure, function and analysis. Life Science- Technical Bulletin ISSUE N°4. 2011.

Daly R. Hearn MTW. Expression of heterologous proteins in Pichia pastoris: a useful experimental tool in protein engineering and production. J. Mol. Recogn. 2005: 18: 119–138.

Sola RJ. Griebenow K. Effects of glycosylation on the stability of protein pharmaceuticals. J Pharm Sci.2009: 98: 1223–1245.

Hamilton SR. Gerngross TU. Glycosylation engineering in yeast: the advent of fully humanized yeast. Curr Opin Biotechnol. 2007: 18: 387–392.

Terpstra w. Identification of chlorophyllase as a glycoprotein. Febs letters. 1981: 126: 231-235.




DOI: https://doi.org/10.22037/afb.v4i3.14396

Refbacks

  • There are currently no refbacks.