Genomic and functional characterization of halophilic sp. LC4: A novel protease producer for valorization of soy sauce cake waste

Arahal DR (2014) Chap. 6 – Whole-genome analyses: average nucleotide identity. Methods Microbiol 41:103–122. https://doi.org/10.1016/bs.mim.2014.07.002

Article  Google Scholar 

Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134. https://doi.org/10.4056/sigs.531120

Article  PubMed  PubMed Central  Google Scholar 

Baldwin RL (2007) Energetics of protein folding. J Mol Biol 371(2):283–301. https://doi.org/10.1016/j.jmb.2007.05.078

Article  CAS  PubMed  Google Scholar 

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahni N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cezairliyan B, Ausubel FM (2017) Investment in secreted enzymes during nutrient-limited growth is utility dependent. Proc Natl Acad Sci 114(37):E7796–E7802. https://doi.org/10.1073/pnas.1708580114

Article  CAS  PubMed  PubMed Central  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. Proteom Protoc Handb 571–607. https://doi.org/10.1385/1592598900

Gupta RS, Kanter-Eivin DA (2023) AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of > 700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 73(5):1–22. https://doi.org/10.1099/ijsem.0.005844

Article  CAS  Google Scholar 

Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinform 29(8):1072–1075. https://doi.org/10.1093/bioinformatics/btt086

Article  CAS  Google Scholar 

Hew MQ, Lim C, Gooi HH, Lim IKJ, An H, Chong CS, Lam MQ, Ee KY (2024) Integrating in Silico analysis and submerged fermentation to liberate antioxidant peptide from soy sauce cake with halophilic Virgibacillus sp. CD6. J Food Meas Charact 18:7418–7430. https://doi.org/10.1007/s11694-024-02737-x

Article  Google Scholar 

Huang J, Xu Q, Liu Z, Jain N, Tyagi M, Wei DQ, Hong L (2021) Controlling the substrate specificity of an enzyme through structural flexibility by varying the salt-bridge density. Mol 26(18):5693. https://doi.org/10.3390/molecules26185693

Article  CAS  Google Scholar 

Ikai A (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88(6):1895–1898

CAS  PubMed  Google Scholar 

Izzi G, Campanile M, Vecchio PD, Graziano G (2024) On the stabilizing effect of aspartate and glutamate and its counteraction by common denaturants. Int J Mol Sci 25(17):9630. https://doi.org/10.3390/ijms25179360

Article  CAS  Google Scholar 

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(5114). https://doi.org/10.1038/s41467-018-07641-9

Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinform 30(9):1236–1240. https://doi.org/10.1093/bioinformatics/btu031

Article  CAS  Google Scholar 

Kanso S, Greene AC, Patel BKC (2002) Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 52(3):869–874. https://doi.org/10.1099/00207713-52-3-869

Article  CAS  PubMed  Google Scholar 

Khadka DB, Pahadi T, Aryal S, Karki DB (2024) Partial purification and characterization of protease extracted from kimena. Heliyon 10(5):e27173. https://doi.org/10.1016/j.heliyon.2024.e27173

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lam MQ, Nik Mut NN, Thevarajoo S, Chen SJ, Selvaratnam C, Hussin H, Jamaluddin H, Chong CS (2018) Characterization of detergent compatible protease from halophilic Virgibacillus sp. CD6. 3 Biotech 8(2):104. https://doi.org/10.1007/s13205-018-1133-2

Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM, McQueen-Mason SJ, Bruce NC, Chong CS (2020) Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter. Genomics 112(1):952–960. https://doi.org/10.1016/j.ygeno.2019.06.011

Article  CAS  PubMed  Google Scholar 

Lam MQ, Chen SJ, Goh KM, Manan FA, Yahya A, Shamsir MS, Chong CS (2021) Genome sequence of an uncharted halophilic bacterium Robertkochia Marina with Deciphering its phosphate-solubilizing ability. Braz J Microbiol 51:251–256. https://doi.org/10.1007/s42770-020-00401-2

Article  CAS  Google Scholar 

Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Tech Bact Syst. Wiley, Chichester, pp 115–175

Google Scholar 

Lim JY, Chai TT, Lam MQ, Ng WJ, Ee KY (2022) In Silico enzymatic hydrolysis of soy sauce cake glycinin G4 to reveal the bioactive peptides as potential food ingredients. J Food Meas Charact 16:3477–3487. https://doi.org/10.1007/s11694-022-01433-y

Article  Google Scholar 

Lim IKJ, Chong CS, Chong EZH, Lam MQ, Ee KY (2024) Advances in employing omics and bioinformatics to reveal the potential of halophilic bacteria for biodegrading proteinaceous high-salt food waste. Asia-Pac J Mol Biol Biotechnol 32(4):88–96. https://doi.org/10.35118/apjmbb.2024.032.4.10

Article  Google Scholar 

Majeed T, Lee CC, Orts WJ, Tabassum R, Shah TA, Jardan YA, Dawoud TM, Bourhia M (2024) Characterization of a thermostable protease from Bacillus subtilis BSP strain. BMC Biotechnol 24(29). https://doi.org/10.1186/s12896-024-00870-5

Maret W (2013) Inhibitory zinc sites in enzymes. Biometals 26(2):197–204. https://doi.org/10.1007/s10534-013-9613-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mokashe N, Chaudhari B, Patil U (2018) Operative utility of salt-stable proteases of halophilic and halotolerant bacteria in the biotechnology sector. Int J Biol Macromol 117:493–522. https://doi.org/10.1016/j.ijbiomac.2018.05.217

Article  CAS  PubMed  Google Scholar 

Moreno MDL, Pérez D, García MT, Mellado E (2013) Halophilic bacteria as a source of novel hydrolytic enzymes. Life 3(1):38–51. https://doi.org/10.3390/life3010038

Article  CAS  Google Scholar 

Nagai T, Tanoue Y, Kai N, Suzuki N (2012) In-vitro antioxidative activity and antihypertensive activity of soy sauce cake derived from the manufacturing of Japanese style fermented soy sauce. Food Nutr Sci 3(8):1118–1127. https://doi.org/10.4236/fns.2012.38147

Article  CAS  Google Scholar 

Nayek A, Gupta PSS, Banerjee S, Mondal B, Bandyopadhyay AK (2014) Salt-bridge energetics in halophilic proteins. PLoS ONE 9(4):e93862. https://doi.org/10.1371/journal.pone.0093862

Article  PubMed  PubMed Central  Google Scholar 

Ohyama T, Fujii K, Ohtsuka T, Sueyoshi K, Ohtake N (2020) The effect of application of soy sauce cake on lettuce plants cultivated in a pot. Bull Facul Agric Niigata Univ 72:13–22

CAS  Google Scholar 

Patel S, Gupta RS (2020) A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 70(1). https://doi.org/10.1099/ijsem.0.003775

Quyoom S (2014) An overview of Inhibition of enzymatic activity by heavy metal ions. Chem Sci Rev Lett 3(11):381–387. https://chesci.com/wp-content/uploads/2016/10/V3i11_7_CS252044062.pdf [pdf]

Google Scholar 

Richter M, Rosselló-Móra R, Glöckner FO, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinform 32(6):929–931. https://doi.org/10.1093/bioinformatics/btv681

Article  CAS  Google Scholar 

Ryšlavá H, Doubnerová V, Kavan D, Vaněk O (2013) Effect of posttranslational modifications on enzyme function and assembly. J Proteom 92:80–109. https://doi.org/10.1016/j.jprot.2013.03.025

Article  CAS  Google Scholar 

Sari RWW, Jamarun N, Arief, Pazla R, Yanti G, Ikhlas Z (2022) Nutritional analysis of mangrove leaves (Rhizophora apiculata) soaking with lime water for ruminant feed. Int Conf Sust Anim Res Environ 1020(2022):012010. https://doi.org/10.1088/1755-1315/1020/1/012010

Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinform 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153

Article  CAS  Google Scholar 

Shimoyama Y (2022) COGclassifier: a tool for classifying prokaryote protein sequences into COG functional category. https://github.com/moshi4/COGclassifier

Smith AC, Hussey MA (2005) Gram stain protocols. American Society for Microbiology. https://asm.org/getattachment/5c95a063-326b-4b2f-98ce-001de9a5ece3/gram-stain-protocol-2886.pdf

Teufel F, Armenteros JJA, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H (2022) SignalP 6.0 predicts all five types of signal peptides using protein Language models. Nat Biotechnol 40:1023–1025.

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