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Physicochemical Characterization and Comparative Analysis of Ribulose 1,5 Biphosphate Carboxylase-Oxygenase Like Proteins (RLP) from Halophilic Chromohalobacter salexigens BKL 5 and Non-Halophilic Counterparts Using in Silico Approaches

1Chemical Study Program, Faculty of Science, Institute Technology of Sumatera, Jl Terusan Ryacudu, WayHui, Lampung Selatan, 35365, Lampung, Indonesia

2Post Graduate Program of Biotechnology, Post Graduate Program, Universitas Gadjah Mada, Jl Teknika Utara, Catur Tunggal, Sleman, 55281, Yogyakarta, Indonesia

3Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl Fauna No 2, Karang gayam, Catur tunggal, Sleman, 55281, Yogyakarta, Indonesia

4 Department of Agriculture Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Karang malang, Catur Tunggal, Sleman, 55281, Yogyakarta, Indonesia

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Received: 2 Nov 2023; Revised: 4 Mar 2024; Accepted: 1 Apr 2024; Published: 30 Apr 2024.
Open Access Copyright 2024 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

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Abstract

This study is intended to analyze and compare halophilic RuBisCo-like proteins (RLP) with non-halophilic homologs using computational analysis approaches. The data used were protein sequences from NCBI and protein sequences from clonned and expressed RuBisCo-like proteins Chromohalobacter salexigens BKL 5 from our previous study. The analysis was in the form of Principal Component Analysis (PCA) and Partial Least Square (PLS). The tools used were Origin Lab Full Version 2019 and Metaboanalyst 5.0. The parameters tested were isoelectric point (pI), negative charge (acidic amino acids), aliphatic index, and GRAVY index using the ProtParam tool from Expasy. Calculations analysis showed that the amino acid residues in halophilic RuBisCo-like proteins that differ significantly from their homologs were glutamic acid and alanine, while the variables that could be observed as differentiating were negative charge and aliphatic index. Analysis shows that some parameters obtained from the program can be used as discriminants to differentiate halophilic and non-halophilic RuBisCo-like proteins.

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Keywords: halophilic; metaboanalyst 5.0; Chromohalobacter salexigens BKL5; RuBisCo-like Protein; Partial Least Square
Funding: Institute of Technology of Sumatera

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  1. Gabriel Zamith Leal Dalmaso, Davis Ferreira, Alane Beatriz Vermelho, Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications, Marine Drugs, 13, 4, (2015), 1925-1965 https://doi.org/10.3390/md13041925
  2. Bassam Oudh Aljohny, Halophilic Bacterium - A Review of New Studies, Biosciences Biotechnology Research Asia, 12, 3, (2015), 2061-2069 http://dx.doi.org/10.13005/bbra/1874
  3. Bhramar Dutta, Rajib Bandopadhyay, Biotechnological potentials of halophilic microorganisms and their impact on mankind, Beni-Suef University Journal of Basic and Applied Sciences, 11, (2022), 75 https://doi.org/10.1186/s43088-022-00252-w
  4. Guangya Zhang, Huihua Ge, Protein Hypersaline Adaptation: Insight from Amino Acids with Machine Learning Algorithms, The Protein Journal, 32, (2013), 239-245 https://doi.org/10.1007/s10930-013-9484-3
  5. Yan-Huey Chen, Chia-Wei Lu, Yuan-Tay Shyu, Shih-Shun Lin, Revealing the Saline Adaptation Strategies of the Halophilic Bacterium Halomonas beimenensis through High-throughput Omics and Transposon Mutagenesis Approaches, Scientific Reports, 7, (2017), 13037 https://doi.org/10.1038/s41598-017-13450-9
  6. Aharon Oren, Halophilic microbial communities and their environments, Current Opinion in Biotechnology, 33, (2015), 119-124 https://doi.org/10.1016/j.copbio.2015.02.005
  7. Nina Gunde-Cimerman, Ana Plemenitaš, Aharon Oren, Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations, FEMS Microbiology Reviews, 42, 3, (2018), 353-375 https://doi.org/10.1093/femsre/fuy009
  8. Qin Wang, Yanchao Wang, Xiaoming Jiang, Lei Ma, Zhaojie Li, Yaoguang Chang, Yuming Wang, Changhu Xue, Amino Acid Profiling with Chemometric Analysis as a Feasible Tool for the Discrimination of Marine-Derived Peptide Powders, Foods, 10, 6, (2021), 1294 https://doi.org/10.3390/foods10061294
  9. Mukhammad Asy’ari, Pingkan Aditiawati, Akhmaloka, Rukman Hertadi, Structural Analysis of Halophilic Lipases Isolated from Bledug Kuwu Mud Crater, Purwodadi-Grobogan, Indonesia: A Structural Bioinformatics Study, Procedia Chemistry, 16, (2015), 392-399 https://doi.org/10.1016/j.proche.2015.12.069
  10. Muhammad Saifur Rohman, Irfan Dwidya Prijambada, Yohanna Anisa Indriyani, Heri Hendrosatriyo, Identification of Protease Producing Halophilic Bacteria from Bledug KuwuMud Volcano, Indonesian Journal of Biotechnology, 17, 1, (2012), 35-41 https://doi.org/10.22146/ijbiotech.15995
  11. Pabulo Henrique Rampelotto, Extremophiles and Extreme Environments, Life, 3, 3, (2013), 482-485 https://doi.org/10.3390/life3030482
  12. James Charlesworth, Brendan P. Burns, Extremophilic adaptations and biotechnological applications in diverse environments, AIMS Microbiology, 2, 3, (2016), 251-261 https://doi.org/10.3934/microbiol.2016.3.251
  13. Thomas E. Hanson, F. Robert Tabita, A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress, Proceedings of the National Academy of Sciences, 98, 8, (2001), 4397-4402 https://doi.org/10.1073/pnas.081610398
  14. Suk Min Kim, Hyun Seung Lim, Sun Bok Lee, Discovery of a RuBisCO-like Protein that Functions as an Oxygenase in the Novel D-Hamamelose Pathway, Biotechnology and Bioprocess Engineering, 23, (2018), 490-499 https://doi.org/10.1007/s12257-018-0305-6
  15. John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli, Demis Hassabis, Highly accurate protein structure prediction with AlphaFold, Nature, 596, 7873, (2021), 583-589 https://doi.org/10.1038/s41586-021-03819-2
  16. Gurjeet Kaur, Manisha Prajapat, Harvinder Singh, Phulen sarma, Sanjay kumar Bhadada, Nishant Shekhar, Saurabh Sharma, Shweta Sinha, Subodh kumar, Ajay Prakash, Bikash Medhi, Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions, Scientific Reports, 13, (2023), 9337 https://doi.org/10.1038/s41598-023-35599-2
  17. Clara Carolina Silva De Oliveira, Gabriel Rodrigues Coutinho Pereira, Jamile Yvis Santos De Alcantara, Deborah Antunes, Ernesto Raul Caffarena, Joelma Freire De Mesquita, In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine, PLoS ONE, 14, 4, (2019), e0215508 https://doi.org/10.1371/journal.pone.0215508
  18. Dipok Kumer Shill, Shafina Jahan, Mohammad Mamun Alam, Md Belayet Hasan Limon, Muntasir Alam, Mohammed Ziaur Rahman, Mustafizur Rahman, S-Adenosyl-l-Homocysteine Exhibits Potential Antiviral Activity Against Dengue Virus Serotype-3 (DENV-3) in Bangladesh: A Viroinformatics-Based Approach, Bioinformatics and Biology Insights, 17, (2023), https://doi.org/10.1177/11779322231158249
  19. Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, Amos Bairoch, ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Research, 31, 13, (2003), 3784-3788 https://doi.org/10.1093/nar/gkg563
  20. Amritpreet Kaur, Pratap Kumar Pati, Aparna Maitra Pati, Avinash Kaur Nagpal, Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches, PLoS ONE, 15, 9, (2020), e0239836 https://doi.org/10.1371/journal.pone.0239836
  21. William L. Trimble, Le T. Phung, Folker Meyer, Simon Silver, Jack A. Gilbert, Draft Genome Sequence of Achromobacter piechaudii Strain HLE, Journal of Bacteriology, 194, 22, (2012), 6355-6355 https://doi.org/10.1128/jb.01660-12
  22. Yoshiyuki Ohtsubo, Fumito Maruyama, Hisayuki Mitsui, Yuji Nagata, Masataka Tsuda, Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader, Journal of Bacteriology, 194, 24, (2012), 6970-6971 https://doi.org/10.1128/jb.01848-12
  23. Mirjam Arnold, Olivia Richard, Corinne Gurtner, Heiko Nathues, Alexander Grahofer, A case report: Actinobaculum suis infection associated with formation of pyogranuloma, epididymitis and azoospermia in a boar, BMC Veterinary Research, 17, 1, (2021), 6 https://doi.org/10.1186/s12917-020-02680-1
  24. Wriddhiman Ghosh, Ashish George, Atima Agarwal, Praveen Raj, Masrure Alam, Prosenjit Pyne, Sujoy Kumar Das Gupta, Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis, Journal of Bacteriology, 193, 19, (2011), 5553-5554 https://doi.org/10.1128/jb.05781-11
  25. Julian Parkhill, Mohammed Sebaihia, Andrew Preston, Lee D. Murphy, Nicholas Thomson, David E. Harris, Matthew T. G. Holden, Carol M. Churcher, Stephen D. Bentley, Karen L. Mungall, Ana M. Cerdeño-Tárraga, Louise Temple, Keith James, Barbara Harris, Michael A. Quail, Mark Achtman, Rebecca Atkin, Steven Baker, David Basham, Nathalie Bason, Inna Cherevach, Tracey Chillingworth, Matthew Collins, Anne Cronin, Paul Davis, Jonathan Doggett, Theresa Feltwell, Arlette Goble, Nancy Hamlin, Heidi Hauser, Simon Holroyd, Kay Jagels, Sampsa Leather, Sharon Moule, Halina Norberczak, Susan O'Neil, Doug Ormond, Claire Price, Ester Rabbinowitsch, Simon Rutter, Mandy Sanders, David Saunders, Katherine Seeger, Sarah Sharp, Mark Simmonds, Jason Skelton, Robert Squares, Steven Squares, Kim Stevens, Louise Unwin, Sally Whitehead, Bart G. Barrell, Duncan J. Maskell, Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica, Nature Genetics, 35, 1, (2003), 32-40 https://doi.org/10.1038/ng1227
  26. Johannes F. Imhoff, Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna–Matthews–Olson protein) gene sequences, International Journal of Systematic and Evolutionary Microbiology, 53, 4, (2003), 941-951 https://doi.org/10.1099/ijs.0.02403-0
  27. Thomas Weissgerber, Renate Zigann, David Bruce, Yun-juan Chang, John C. Detter, Cliff Han, Loren Hauser, Cynthia D. Jeffries, Miriam Land, A. Christine Munk, Roxanne Tapia, Christiane Dahl, Complete genome sequence of Allochromatium vinosum DSM 180T, Standards in Genomic Sciences, 5, 3, (2011), 311-330 https://doi.org/10.4056/sigs.2335270
  28. Jaewoo Yoon, Kyoko Adachi, Sanghwa Park, Hiroaki Kasai, Akira Yokota, Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov, International Journal of Systematic and Evolutionary Microbiology, 61, 10, (2011), 2342-2347 https://doi.org/10.1099/ijs.0.027573-0
  29. Yanbing Lin, Haoxin Fan, Xiuli Hao, Laurel Johnstone, Yao Hu, Gehong Wei, Hend A. Alwathnani, Gejiao Wang, Christopher Rensing, Draft Genome Sequence of Halomonas sp. Strain HAL1, a Moderately Halophilic Arsenite-Oxidizing Bacterium Isolated from Gold-Mine Soil, Journal of Bacteriology, 194, 1, (2012), 199-200 https://doi.org/10.1128/jb.06359-11
  30. Lionel Frangeul, Philippe Quillardet, Anne-Marie Castets, Jean-François Humbert, Hans C. P. Matthijs, Diego Cortez, Andrew Tolonen, Cheng-Cai Zhang, Simonetta Gribaldo, Jan-Christoph Kehr, Yvonne Zilliges, Nadine Ziemert, Sven Becker, Emmanuel Talla, Amel Latifi, Alain Billault, Anthony Lepelletier, Elke Dittmann, Christiane Bouchier, Nicole Tandeau de Marsac, Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium, BMC Genomics, 9, 1, (2008), 274 https://doi.org/10.1186/1471-2164-9-274
  31. Andrea I. Moreno Switt, Alexis D. Andrus, Matthew L. Ranieri, Renato H. Orsi, Reid Ivy, Henk C. den Bakker, Nicole H. Martin, Martin Wiedmann, Kathryn J. Boor, Genomic comparison of sporeforming bacilli isolated from milk, BMC Genomics, 15, 1, (2014), 26 https://doi.org/10.1186/1471-2164-15-26
  32. M. Julia Althabegoiti, Luis Lozano, Gonzalo Torres-Tejerizo, Ernesto Ormeño-Orrillo, Marco A. Rogel, Víctor González, Esperanza Martínez-Romero, Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris, Journal of Bacteriology, 194, 23, (2012), 6651-6652 https://doi.org/10.1128/jb.01785-12
  33. Meijie Li, Tongtong Zhu, Rumeng Yang, Zhaobao Wang, Min Liu, Jianming Yang, Carotenoids synthesis affects the salt tolerance mechanism of Rhodopseudomonas palustris, Frontiers in Microbiology, 14, (2023), 1292937 https://doi.org/10.3389/fmicb.2023.1292937
  34. Xiaofeng Dai, Xiaochong Shi, Xin Gao, Jingli Liu, Xiao-Hua Zhang, Roseivivaxmarinus sp. nov., isolated from deep water, International Journal of Systematic and Evolutionary Microbiology, 64, Pt_8, (2014), 2540-2544 https://doi.org/10.1099/ijs.0.062760-0
  35. Joseph Hair, Abdullah Alamer, Partial Least Squares Structural Equation Modeling (PLS-SEM) in second language and education research: Guidelines using an applied example, Research Methods in Applied Linguistics, 1, 3, (2022), 100027 https://doi.org/10.1016/j.rmal.2022.100027
  36. Jasmine Chong, David S. Wishart, Jianguo Xia, Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis, Current Protocols in Bioinformatics, 68, 1, (2019), e86 https://doi.org/10.1002/cpbi.86
  37. Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, John H. Morris, Thomas E. Ferrin, UCSF ChimeraX: Meeting modern challenges in visualization and analysis, Protein Science, 27, 1, (2018), 14-25 https://doi.org/10.1002/pro.3235
  38. Óscar Álvarez, Juan Luis Fernández-Martínez, Celia Fernández-Brillet, Ana Cernea, Zulima Fernández-Muñiz, Andrzej Kloczkowski, Principal component analysis in protein tertiary structure prediction, Journal of Bioinformatics and Computational Biology, 16, 02, (2018), 1850005 https://doi.org/10.1142/S0219720018500051
  39. Cristina Sotomayor-Vivas, Enrique Hernández-Lemus, Rodrigo Dorantes-Gilardi, Linking protein structural and functional change to mutation using amino acid networks, PLoS ONE, 17, 1, (2022), e0261829 https://doi.org/10.1371/journal.pone.0261829
  40. Anindya S. Panja, Smarajit Maiti, Bidyut Bandyopadhyay, Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges, Scientific Reports, 10, (2020), 1822 https://doi.org/10.1038/s41598-020-58825-7
  41. Tobias J. Erb, Jan Zarzycki, A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme, Current Opinion in Biotechnology, 49, (2018), 100-107 https://doi.org/10.1016/j.copbio.2017.07.017
  42. Hiroki Ashida, Yohtaro Saito, Toshihiro Nakano, Nicole Tandeau de Marsac, Agnieszka Sekowska, Antoine Danchin, Akiho Yokota, RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO, Journal of Experimental Botany, 59, 7, (2008), 1543-1554 https://doi.org/10.1093/jxb/ern104
  43. Moshe Mevarech, Felix Frolow, Lisa M. Gloss, Halophilic enzymes: proteins with a grain of salt, Biophysical Chemistry, 86, 2, (2000), 155-164 https://doi.org/10.1016/S0301-4622(00)00126-5
  44. Christopher J. Reed, Hunter Lewis, Eric Trejo, Vern Winston, Caryn Evilia, Protein Adaptations in Archaeal Extremophiles, Archaea, 2013, (2013), 373275 https://doi.org/10.1155/2013/373275
  45. Guangya Zhang, Ge huihua, Lin Yi, Stability of halophilic proteins: From dipeptide attributes to discrimination classifier, International Journal of Biological Macromolecules, 53, (2013), 1-6 https://doi.org/10.1016/j.ijbiomac.2012.10.031
  46. Ram Karan, Melinda D. Capes, Shiladitya DasSarma, Function and biotechnology of extremophilic enzymes in low water activity, Aquatic Biosystems, 8, (2012), 4 https://doi.org/10.1186/2046-9063-8-4
  47. K. Linda Britton, Patrick J. Baker, Martin Fisher, Sergey Ruzheinikov, D. James Gilmour, María-José Bonete, Juan Ferrer, Carmen Pire, Julia Esclapez, David W. Rice, Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei, Proceedings of the National Academy of Sciences, 103, 13, (2006), 4846-4851 https://doi.org/10.1073/pnas.0508854103
  48. Akira Nomoto, Suguru Nishinami, Kentaro Shiraki, Solubility Parameters of Amino Acids on Liquid–Liquid Phase Separation and Aggregation of Proteins, Frontiers in Cell and Developmental Biology, 9, (2021), https://doi.org/10.3389/fcell.2021.691052
  49. Renganathan Senthil, Singaravelu Usha, Konda Mani Saravanan, Importance of fluctuating amino acid residues in folding and binding of proteins, Avicenna Journal of Medical Biotechnology, 11, 4, (2019), 339-343
  50. Lea Weinisch, Steffen Kühner, Robin Roth, Maria Grimm, Tamara Roth, Daili J. A. Netz, Antonio J. Pierik, Sabine Filker, Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum, PLoS Biology, 16, 1, (2018), e2003892 https://doi.org/10.1371/journal.pbio.2003892
  51. C. Brininger, S. Spradlin, L. Cobani, C. Evilia, The more adaptive to change, the more likely you are to survive: Protein adaptation in extremophiles, Seminars in Cell & Developmental Biology, 84, (2018), 158-169 https://doi.org/10.1016/j.semcdb.2017.12.016
  52. Dixita Chettri, Ashwani Kumar Verma, Lija Sarkar, Anil Kumar Verma, Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation, Extremophiles, 25, (2021), 203-219 https://doi.org/10.1007/s00792-021-01225-0
  53. Pu Ge, Gen Luo, Yi Luo, Wei Huang, Hongbin Xie, Jingwen Chen, Jingping Qu, Molecular understanding of the interaction of amino acids with sulfuric acid in the presence of water and the atmospheric implication, Chemosphere, 210, (2018), 215-223 https://doi.org/10.1016/j.chemosphere.2018.07.014
  54. Atsushi Ikai, Thermostability and Aliphatic Index of Globular Proteins, The Journal of Biochemistry, 88, 6, (1980), 1895-1898 https://doi.org/10.1093/oxfordjournals.jbchem.a133168
  55. Qingzhen Hou, Raphaël Bourgeas, Fabrizio Pucci, Marianne Rooman, Computational analysis of the amino acid interactions that promote or decrease protein solubility, Scientific Reports, 8, (2018), 14661 https://doi.org/10.1038/s41598-018-32988-w
  56. Xiangyi Jiang, Ji Yu, Zhongxia Zhou, Jacob Kongsted, Yuning Song, Christophe Pannecouque, Erik De Clercq, Dongwei Kang, Vasanthanathan Poongavanam, Xinyong Liu, Peng Zhan, Molecular design opportunities presented by solvent-exposed regions of target proteins, Medicinal Research Reviews, 39, 6, (2019), 2194-2238 https://doi.org/10.1002/med.21581
  57. Alessandro Siglioccolo, Alessandro Paiardini, Maria Piscitelli, Stefano Pascarella, Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface, BMC Structural Biology, 11, (2011), 50 https://doi.org/10.1186/1472-6807-11-50
  58. David March, Valentino Bianco, Giancarlo Franzese, Protein Unfolding and Aggregation near a Hydrophobic Interface, Polymers, 13, 1, (2021), 156 https://doi.org/10.3390/polym13010156

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