Academic Journal
A novel urease gene structure of Sporosarcina pasteurii with double operons.
| Τίτλος: | A novel urease gene structure of Sporosarcina pasteurii with double operons. |
|---|---|
| Συγγραφείς: | Pei D; College of Sciences, National University of Defense Technology, Changsha, Hunan, China. 397141499@qq.com.; China Astronaut Research and Training Center, Beijing, China. 397141499@qq.com., Liu Z; Academy of Chemical Defense, Academy of Military Science, Beijing, China., Hu B; College of Sciences, National University of Defense Technology, Changsha, Hunan, China. |
| Πηγή: | Molecular genetics and genomics : MGG [Mol Genet Genomics] 2025 Feb 22; Vol. 300 (1), pp. 25. Date of Electronic Publication: 2025 Feb 22. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101093320 Publication Model: Electronic Cited Medium: Internet ISSN: 1617-4623 (Electronic) Linking ISSN: 16174623 NLM ISO Abbreviation: Mol Genet Genomics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Berlin : Springer-Verlag, c2001- |
| Ιατρικοί όροι (MeSH): | Urease*/genetics , Urease*/metabolism , Sporosarcina*/genetics , Sporosarcina*/enzymology , Sporosarcina*/growth & development , Operon*/genetics , Bacterial Proteins*/genetics, Calcium Carbonate/metabolism ; Promoter Regions, Genetic ; Gene Expression Regulation, Bacterial ; Transcription Initiation Site |
| Περίληψη: | Microbially induced calcium carbonate precipitation (MICP) had emerged as an important biomineralization process with wide-ranging applications in construction, environmental remediation, and space exploration. Sporosarcina pasteurii (S. pasteurii) was a key bacterium in MICP due to its efficient urease activity, yet the regulation of its urease genes remains poorly understood, limiting its practical applications. This study aimed to elucidate the structure and expression regulation mechanism of urease genes in S. pasteurii to enhance its mineralization potential. We compared the growth and urease gene expression of S. pasteurii under three different culture conditions using transcriptome sequencing. Operon, Transcription Start Site (TSS) and Transcription Termination Site (TTS) were predicted based on the distribution of reads on the genome using Rockhopper online analysis software. The 700 bp sequence upstream of the TTS was extracted and promoter prediction was performed by Time-Delay Neural Network (TDNN) method. Finally, we verified the prediction results by RT-PCR. Our results revealed, for the first time, a double operon structure of S. pasteurii urease, with operon 1 containing ureA, ureB, ureC, ureE, and ureF genes, and operon 2 containing ureG and ureD genes. This discovery provides crucial insights into the regulation of urease expression in S. pasteurii, paving the way for more efficient and controllable mineralization applications. The findings of this study not only advanced our understanding of urease gene regulation but also opened new avenues for optimizing S. pasteurii-based biomineralization technologies. (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.) |
| Competing Interests: | Declarations. Competing interests: The authors had declared that no competing interests exist. |
| References: | Akada JK, Shirai M, Takeuchi H, Tsuda M, Nakazawa TJ (2000) Identification of the urease operon in Helicobacter pylori and its control by mRNA decay in response to pH. Mol Microbiol 36(5):1071–1084. (PMID: 10.1046/j.1365-2958.2000.01918.x10844692) Anbu P, Kang CH, Shin YJ, So JSJS (2016) Formations of calcium carbonate minerals by bacteria and its multiple applications. Springerplus 5(1):1–26. (PMID: 10.1186/s40064-016-1869-2) Bergdale TE, Pinkelman RJ, Hughes SR, Zambelli B, Ciurli S, Bang SS (2012) Engineered biosealant strains producing inorganic and organic biopolymers. J Biotechnol 161(3):181–189. (PMID: 10.1016/j.jbiotec.2012.07.00122789480) Castro-Alonso MJ, Montaez-Hernandez LE, Sanchez-Muoz MA, Franco M, Balagurusamy N (2019) Microbially induced calcium carbonate precipitation (MICP) and its potential in bioconcrete: microbiological and molecular concepts. Front Mater 6:126. (PMID: 10.3389/fmats.2019.00126) Cruz-Ramos H, Glaser P, Wray LV, Fisher SH (1997) The Bacillus subtilis ureABC operon. J Bacteriol 179(10):3371–3373. (PMID: 10.1128/jb.179.10.3371-3373.19979150240179123) Di P, Zhi-Ming L, Bi-Ru HU, Wen-Jian WU (2020) Progress on mineralization mechanism and application research of Sporosarcina pasteurii. Prog Biochem Biophys 47(6):467–482. Di P, Liu Zhi-Ming Hu, Wen-Jian B-R (2021) Transcriptome analyses reveal the utilization of nitrogen sources and related metabolic mechanisms of Sporosarcina pasteurii. PLoS One 16(2):e0246818. (PMID: 10.1371/journal.pone.0246818) Dikshit R, Dey A, Gupta N et al (2021) Space bricks: From LSS to machinable structures via MICP. Ceramics Int 47(10):47. (PMID: 10.1016/j.ceramint.2020.07.309) Ednie-Brown P (2013) Biomason and the speculative engagements of biotechnical architecture. Archit Design 83(1):84–91. (PMID: 10.1002/ad.1529) Ernst FD, Kuipers EJ, Heijens A, Sarwari R, Stoof J, Penn CW et al (2005) The nickel-responsive regulator NikR controls activation and repression of gene transcription in Helicobacter pylori. Infect Immun 73(11):7252. (PMID: 10.1128/IAI.73.11.7252-7258.2005162395201273850) Ferris FG, Stehmeier LG, Kantzas A, Mourits FM (1996) Bacteriogenic mineral plugging. J Canadian Petrol Technol 35(08):56–61. Gerald-F G, Steven C, Nichols WA (1988) Characterization of the genes encoding urease activity of Klebsiella pneumoniae. FEMS Microbiol Lett 50(2–3):131–135. Goss TJ, Bender RA (1995) The nitrogen assimilation control protein, NAC, is a DNA binding transcription activator in Klebsiella aerogenes. J Bacteriol 177(12):3546. (PMID: 10.1128/jb.177.12.3546-3555.19957768865177061) Huang SC, Burne RA, Chen YY (2014) The pH-dependent expression of the urease operon in streptococcus salivarius is mediated by CodY. Appl Environ Microbiol 80(17):5386–93. (PMID: 10.1128/AEM.00755-14249517854136106) Jonkers HM (2007) Self healing concrete: a biological approach. Jonkers HM, Thijssen A, Muyzer G, Copuroglu O, Schlangen E (2010) Application of bacteria as self-healing agent for the development of sustainable concrete. Ecol Eng 36(2):230–5. (PMID: 10.1016/j.ecoleng.2008.12.036) Kim SD, Spizizen J (1985) Molecular cloning and expression of Bacillus pasteurii urease gene in Escherichia coli. Microbiol Biotechnol Lett 13(3):297–302. (PMID: 10.4014/kjmb.1407.07006) Kim JK, Mulrooney SB, Hausinger RP (2005) Biosynthesis of active Bacillus subtilis urease in the absence of known urease accessory proteins. J Bacteriol 187(20):7150–7154. (PMID: 10.1128/JB.187.20.7150-7154.2005161995861251626) Kobayashi YJG (2011) Regulation of Bacillus subtilis glutamine synthetase gene expression by the product of the glnR gene. Development 25(23):2540–53. Larson M (2010) Professor uses bacteria to make ecofriendly bricks. Archit Rec 265(1):1–1. Liang L, Heveran C, Liu R, Gill RT, Cook SM (2018) Rational control of calcium carbonate precipitation by engineered Escherichia coli. ACS Synthet Biol 7(11):24987–2506. (PMID: 10.1021/acssynbio.8b00194) Ma L, Pang AP, Luo Y, Lu X, Lin F (2020) Beneficial factors for biomineralization by ureolytic bacterium Sporosarcina pasteurii. Microb Cell Factor. Macaluso A, Best EA, Bender RA (1990) Role of the nac gene product in the nitrogen regulation of some NTR-regulated operons of Klebsiella aerogenes. J Bacteriol 172(12):7249–7255. (PMID: 10.1128/jb.172.12.7249-7255.19901979323210849) McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B (2013) Computational analysis of bacterial RNA-Seq data. Nucleic acids Res 41(14):e140–e140. (PMID: 10.1093/nar/gkt444237166383737546) Mobley HLT, Garner RM, Bauerfeind P (1995) Helicobacter pylori nickel-transport gene nixA: synthesis of catalytically active urease in Escherichia coli independent of growth conditions. Mol Microbiol 16(1):97–109. (PMID: 10.1111/j.1365-2958.1995.tb02395.x7651142) Molle V, Nakaura Y, Shivers RP, Yamaguchi H, Losick R, Fujita Y, Sonenshein AL (2003) Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 185(6):1911–1922. (PMID: 10.1128/JB.185.6.1911-1922.200312618455150151) Nicholson EB, Concaugh EA, Foxall PA, Island MD, Mobley HL (1993) Proteus mirabilis urease: transcriptional regulation by UreR. J Bacteriol 175(2):465–473. (PMID: 10.1128/jb.175.2.465-473.19937678244196161) Okyay TO, Rodrigues DF (2014) Optimized carbonate micro-particle production by Sporosarcina pasteurii using response surface methodology. Ecol Eng 62:168–174. (PMID: 10.1016/j.ecoleng.2013.10.024) Pflock M, Kennard S, Delany I, Scarlato V, Beier D (2005) Acid-induced activation of the urease promoters is mediated directly by the ArsRS two-component system of Helicobacter pylori. Infect immun 73(10):6437. (PMID: 10.1128/IAI.73.10.6437-6445.2005161773151230922) Ramachandran SK, Ramakrishnan V, Bang SS (2001) Remediation of concrete using microorganisms. Mater J 98(1):3–9. Randall DG (2018) Urine: the liquid gold of wastewater. J Environ Chem Eng 6(5):2627–2635. (PMID: 10.1016/j.jece.2018.04.012) Rincón CM, García C (2006) A modified Christensen’s urea and CLSI broth microdilution method for testing susceptibilities of six Malassezia species to voriconazole, itraconazole, and ketoconazole. J Clin Microbiol 44(9):3429–3431. (PMID: 10.1128/JCM.00989-06169542931594707) Sonenshein AL (2005) CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr Opin Microbiol 8(2):203–207. (PMID: 10.1016/j.mib.2005.01.00115802253) Stocks-Fischer S, Galinat JK, Bang SS (1999) Microbiological precipitation of CaCO3. Soil Biol Biochem 31(11):1563–1571. (PMID: 10.1016/S0038-0717(99)00082-6) Tingting Z, Dittrich M (2016) Carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review. Front Bioeng Biotechn 4:4. Van Paassen LA, Harkes MP, Van Zwieten GA, Van der Zon WH, Van der Star WR, Van Loosdrecht MC (2009) Scale up of BioGrout: a biological ground reinforcement method. In Proceedings of the 17th International Conference on Soil Mechanics and Geotechnical Engineering (Volumes 1, 2, 3 and 4) (pp. 2328-2333). IOS Press. Wang RX, Qian CX (2008) Restoration of defects on the surface of cement-based materials by microbiologically precipitated CaCO<sub>3</sub>. J Chinese Ceram Soc 04:37–44. Wang RX, Qian CX, Wang JY, Cheng L (2008) Different treated methods of microbiologically deposited CaCO<sub>3</sub> layer on hardened cement paste surface. J Chinese Ceram Soc 36(10):1378–1384. Wedel A (1995) The bacterial enhancer-binding protein NtrC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. Genes Dev 9(16):2042–2052. (PMID: 10.1101/gad.9.16.20427649482) Whiffin VS (2004) Microbial CaCO<sub>3</sub> precipitation for the production of biocement. Wray LV, Ferson AE, Fisher SH (1997) Expression of the Bacillus subtilis ureABC operon is controlled by multiple regulatory factors including CodY, GlnR, TnrA, and Spo0H. J Bacteriol 179(17):5494–5501. (PMID: 10.1128/jb.179.17.5494-5501.19979287005179421) Wu WQ, Zheng XB, Liu YC, Tang K, Zhu HQ (2011) Biophysics. Operon prediction based on an iterative self-learning algorithm 38(7):642–651. |
| Contributed Indexing: | Keywords: Sporosarcina pasteurii urease; Double operons; Gene structure; MICP |
| Substance Nomenclature: | EC 3.5.1.5 (Urease) 0 (Bacterial Proteins) H0G9379FGK (Calcium Carbonate) |
| SCR Organism: | Sporosarcina pasteurii |
| Entry Date(s): | Date Created: 20250222 Date Completed: 20250509 Latest Revision: 20250509 |
| Update Code: | 20260130 |
| DOI: | 10.1007/s00438-025-02236-8 |
| PMID: | 39985601 |
| Βάση Δεδομένων: | MEDLINE |
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