Three-dimensional structure modeling of a protease from lactic acid bacteria Leuconostoc mesenteroides K7 using automated protein homology analysis
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Abstract. Hidayat H, Haryadi W, Raharjo TJ. 2020. Three-dimensional structure modeling of a protease from lactic acid bacteria Leuconostoc mesenteroides K7 using automated protein homology analysis. Biodiversitas 21: 3156-3162. This study aimed to characterize the protease encoding gene of Leuconostoc mesenteroides K7 isolated from Kelengkeng (Dimocarpus longan) fruit as well as to predict the structure of the protein using in silico approach. Gene characterization was performed using PCR employs primers designed based on protease gene of other Leuconostoc species, followed by cloning and sequencing of the PCR product. Protein structural modeling was targeted to the deduced amino acid sequence of the gene employ multiple sequence alignment and SWISS-Model online software. As a result, the sequence of the PCR product contains an open reading frame with a size of 1,140 bp, which can be translated into 379 amino acids. The amino acid sequence shares 98.60% identity with protease from Leuconostoc suionicum (AP017935.1). Three conserved sequences of QTDA, INPGNSGGPL, and FAIP are known as the signature from the Serine endoprotease DegS family are detected. The three-dimensional modeling structure application shows that the protein share similarity of 37.62% to Protease Do-like I chloroplastic that belong to serine protease.
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References
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Sánchez-González M, Alagón A, Rodríguez-Sotrés R, López-Munguía A. (1999) Proteolytic processing of dextransucrase of Leuconostoc mesenteroides. FEMS Microbiol. Lett. 181 (1): 25–30. DOI: 10.1111/j.1574-6968.1999.tb08822.x.
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
Suberu Y, Akande I, Samuel T, Lawal A, Olaniran A. 2019. Cloning, expression, purification and characterisation of serine alkaline protease from Bacillus subtilis RD7. Biocatal. Agric. Biotechnol. 20, 101264. DOI: 10.1016/j.bcab.2019.101264.
Savijoki K, Ingmer H, Varmanen P. 2006. Proteolytic systems of lactic acid bacteria. Appl. Microbiol Biotechnol., 71(4):394-406. DOI: 10.1007/s00253-006-0427-1.
Tokita F, Hosono A. 1975. Production and Some Properties of the Intracellular Protease of Leuconostoc citrovorum. Jap. J. Zootech. Sci., 47 (5): 277-282.
Watanabe K, Hayano K. 1994. Estimate of the Source of Soil Protease In Upland Fields. Biol. Fertil Soils. 18, 341-346. DOI: 10.1007/BF00570638.
Anbu P. 2013. Characterization of solvent stable, extracellular protease from Bacillus koreensis (BK-P21A). Int. J. Biol. Macromol. 56, 162–168. DOI: 10.1016/j.ijbiomac.2013.02.014.
Ali N, Ullah N, Qasim M, Rahman H, Khan SN, Sadig A. 2016. Molecular characterization and growth optimization of halo-tolerant protease producing Bacillus subtilis Strain BLK-1.5 isolated from salt mines of Karak, Pakistan. Extremophiles 20, 395–402. DOI: 10.1007/s00792-016-0830-1.
Argüello-Morales M, Sánchez-González M, Canedo M, Quirasco M, Farrés A, López-Munguía A. 2005. Proteolytic modification of Leuconostoc mesenteroides B-512F dextransucrase. Antonie Van Leeuwenhoek 87(2):131-41. DOI: 10.1007/s10482-004-2042-4.
Asgher M, Bashir F, Iqbal HM. 2018. Protease-based crosslinked enzyme aggregates with improved catalytic stability, silver removal, dehairing potentials. Int. J. Biol. Macromol. 118, 1247–1256. DOI: 10.1016/j.ijbiomac.2018.06.107.
Bach H-J, Errampalli D, Leung KT, Lee H, Hartmann A, Trevors JT, Munch JC. 1999. Specific Detection Of The Gene For The Extracellular Neutral Protease Of Bacillus cereus by PCR and Blot Hybridization. Appl. Environ. Microbiol. 65 (7): 3226–3228.
Banerjee G, Ray AK. 2017. Impact of microbial proteases on biotechnological industries. Biotechnol. Genet. Eng. Rev. 33, 119–143. DOI: 10.1080/02648725.2017.1408256.
Bell PJ, Sunna A, Gibbs MD, Curach NC, Nevalainen H, Bergquist PL. 2002. Prospecting for novel lipase gene using PCR. Microbiology 148, 2283–2291. DOI: 10.1099/00221287-148-8-2283.
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. 2014. SWISS-MODEL: Modelling protein tertiary and uaternary structure using evolutionary information. Nucleic Acids Res. 42, 252–258. DOI: 10.1093/nar/gku340.
Di Cera E. 2009. Critical Review: Serine Proteases. IUBMB Life 61(5): 510–515. DOI: 10.1002/iub.186
Hidayat H, Haryadi W, Matsjeh S, Raharjo TJ. 2019. Molecular identification 16s rRNA gene of active proteolytic lactic acid bacteria (LAB) isolated from kelengkeng (Dimocarpus longan) fruit. Biodiversitas 20 (8): 2222-2228. DOI: 10.13057/biodiv/d200816
Hidayat H. 2020. Karakterisasi Gen dan Modeling Protease Bakteri Asam Laktat (BAL) Hasil Isolasi Dari Buah Kelengkeng (Dimocarpus longan). Disertasi. Universitas Gadjah Mada, Yogyakarta. Gene Characterization And Protease Modeling Of Lactic Acid Bacteria (LAB) Isolated From Kelengkeng (Dimocarpus Longan) Fruit. Dissertation. Universitas Gadjah Mada, Yogyakarta.
Hou J, Han D, Zhou Y, Li Y, Cui H-L. 2020. Identification and characterization of the gene encoding an extracellular protease from haloarchaeon, Halococcus salifodinae. Microbiol. Res. 236, 126468. DOI: 10.1016/j.micres.2020.126468.
Jeong YJ, Baek SC, Kim H. 2018. Cloning and characterization of a novel intracellular serine protease (IspK) from Bacillus megaterium with a potential additive for detergents. Int. J. Biol. Macromol.108: 808-816. DOI: 10.1016/j.ijbiomac.2017.10.173.
Ji Z-L, Peng S, Chen L-L, Liu Y, Yan C, Zhu F. 2020. Identification and characterization of a serine protease from Bacillus licheniformis W10: A potential antifungal agent. Int. J. Biol. Macromol. 145: 594-603. DOI: 10.1016/j.ijbiomac.2019.12.216.
Kaur I, Kocher GS, Gupta VK. 2012. Molecular Cloning and Nucleotide Sequence of the Gene for an Alkaline Protease from Bacillus circulans MTCC 7906. Indian J. Microbiol. 52(4): 630–637. DOI: 10.1007/s12088-012-0297-4.
Liu M, Bayjanov JR, Renckens B, Nauta A, Siezen RJ. 2010. The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics. 11:36. DOI: 10.1186/1471-2164-11-36
Madala PK, Tyndall JDA, Nall T, Fairlie DP. 2010. Proteases Universally Recognize Beta Strands In Their Active Sites. Chemical Rev. 110 (6): PR1-PR31. DOI: 10.1021/cr900368a.
Matkawala F, Nighojkar S, Kumar A, Nighojkar A. 2019. A novel thiol-dependent serine protease from Neocosmospora sp. N1. Heliyon 5 (8): e02246. DOI: 10.1016/j.heliyon.2019.e02246.
Nataningtyas DR, Raharjo TJ, Astuti E. 2019. Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium Alcaligenes sp. JG3 Using Automated Protein Homology Analysis. Indo. J. Chem. 19 (3): 565-574. DOI: 10.22146/ijc.34152.
Poliana J, MacCabe AP. 2007. Industrial Enzymes; Structure, Function, and Applications. Dordrecht. Springer. 1, 174.
Razzaq A, Shamsi S, Ali A, Ali Q, Sajjad M, Malik A, Ashraf M. 2019. Microbial Proteases Applications, Front. Bioeng. Biotechnol., 7: article no. 110. DOI: 10.3389/fbioe.2019.00110.
Sánchez-González M, Alagón A, Rodríguez-Sotrés R, López-Munguía A. (1999) Proteolytic processing of dextransucrase of Leuconostoc mesenteroides. FEMS Microbiol. Lett. 181 (1): 25–30. DOI: 10.1111/j.1574-6968.1999.tb08822.x.
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
Suberu Y, Akande I, Samuel T, Lawal A, Olaniran A. 2019. Cloning, expression, purification and characterisation of serine alkaline protease from Bacillus subtilis RD7. Biocatal. Agric. Biotechnol. 20, 101264. DOI: 10.1016/j.bcab.2019.101264.
Savijoki K, Ingmer H, Varmanen P. 2006. Proteolytic systems of lactic acid bacteria. Appl. Microbiol Biotechnol., 71(4):394-406. DOI: 10.1007/s00253-006-0427-1.
Tokita F, Hosono A. 1975. Production and Some Properties of the Intracellular Protease of Leuconostoc citrovorum. Jap. J. Zootech. Sci., 47 (5): 277-282.
Watanabe K, Hayano K. 1994. Estimate of the Source of Soil Protease In Upland Fields. Biol. Fertil Soils. 18, 341-346. DOI: 10.1007/BF00570638.
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