Abstract
Glutamine synthetase is an essential enzyme in ammonium assimilation and glutamine biosynthesis. The Haloferax mediterranei genome has two other glnA-type genes (glnA2 and glnA3) in addition to the glutamine synthetase gene glnA. To determine whether the glnA2 and glnA3 genes can replace glnA in nitrogen metabolism, we generated deletion mutants of glnA. The glnA deletion mutants could not be generated in a medium without glutamine, and thus, glnA is an essential gene in H. mediterranei. The glnA deletion mutant was achieved by adding 40 mM glutamine to the selective medium. This conditional HM26-ΔglnA mutant was characterised with different approaches in the presence of distinct nitrogen sources and nitrogen starvation. Transcriptomic analysis was performed to compare the expression profiles of the strains HM26-ΔglnA and HM26 under different growth conditions. The glnA deletion did not affect the expression of glnA2, glnA3 and nitrogen assimilation genes under nitrogen starvation. Moreover, the results showed that glnA, glnA2 and glnA3 were not expressed under the same conditions. These results indicated that glnA is an essential gene for H. mediterranei and, therefore, glnA2 and glnA3 cannot replace glnA in the conditions analysed.
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References
Allers T, Ngo HP, Mevarech M, Lloyd RG (2004) Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl Environ Microbiol 70:943–953. https://doi.org/10.1128/aem.70.2.943-953.2004
Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, Alber BE, Fuchs G (2010) Autotrophic carbon fixation in archaea. Nat Rev Microbiol 8:447–546. https://doi.org/10.1038/nrmicro2365
Bitan-Banin G, Ortenberg R, Mevarech M (2003) Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J Bacteriol 85:772–778. https://doi.org/10.1128/aem.70.2.943-953.2004
Bonete MJ, Martínez-Espinosa RM, Pire C, Zafrilla B, Richardson DJ (2008) Nitrogen metabolism in haloarchaea. Saline Syst 4:9. https://doi.org/10.1186/1746-1448-4-9
Brown JR, Masuchi Y, Robb FT, Doolittle WF (1994) Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J Mol Evol 38:566–576. https://doi.org/10.1007/bf00175876
Chant J, Hui I, De Jong-Wong D, Shimmin L, Dennis PP (1986) The protein synthesizing machinery of the Archaebacterium Halobacterium cutirubrum: molecular characterization. Sys Appl Microbiol 7(1):106–114. https://doi.org/10.1016/S0723-2020(86)80132-1
Chavez S, Lucena JM, Reyes JC, Florencio FJ, Candau P (1999) The presence of glutamate dehydrogenase is a selective advantage for the cyanobacterium Synechocystis sp. strain PCC 6803 under nonexponential growth conditions. J Bacteriol 181(3):808–813
Cline SW, Lam WL, Charlebois RL, Schalkwyk LC, Doolittle WF (1989) Transformation methods for halophilic archaebacteria. Can J Microbiol 35(1):148–152. https://doi.org/10.1139/m89-022
Cohen-Kupiec R, Marx CJ, Leigh JA (1999) Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis. J Bacteriol 181(1):56–261
Cupp JR, McAlister-Henn L (1993) Kinetic analysis of NAD+-isocitrate dehydrogenase with altered isocitrate binding sites: contribution of IDH1 and IDH2 subunits to regulation and catalysis. Biochemistry 32(36):9323–9328. https://doi.org/10.1021/bi00087a010
Domínguez-Martín MA, Díez J, García-Fernández JM (2016) Physiological studies of glutamine synthetases I and III from Synechococcus sp. WH7803 reveal differential regulation. Front Microbiol 7:969. https://doi.org/10.3389/fmicb.2016.00969
Eisenberg D, Gill HS, Pfluegl GMU, Rotstein SH (2000) Structure-function relationships of glutamine synthetases. Biochim Biophys Acta 1477(1–2):122–145. https://doi.org/10.1016/s0167-4838(99)00270-8
Esclapez J, Pire C, Camacho M, Bautista V, Martínez-Espinosa RM, Zafrilla B, Vegara A, Alcaraz LA, Bonete MJ (2015) Transcriptional profiles of Haloferax mediterranei based on nitrogen availability. J Biotechnol 193:100–107. https://doi.org/10.1016/j.jbiotec.2014.11.018
Fernandez R, Rodriguez F, Gonzalez J, Ruiz F (1986) Accumulation of poly(beta-hydroxybutyrate) by Halobacteria. Appl Environ Microbiol 51:214–216
Fisher SH (1989) Glutamate synthesis in Streptomyces coelicolor. J Bacteriol 171(5):2372–2377. https://doi.org/10.1128/jb.171.5.2372-2377.1989
Han J, Hou J, Zhang F, AiG LiM, Cai S, Liu H, Wang L, Wang Z, Zhang S, Cai L, Zhao D, Zhou J, Xiang H (2013) Multiple propionyl coenzyme A-supplying pathways for production of the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in Haloferax mediterranei. Appl Environ Microbiol 79(9):2922–2931. https://doi.org/10.1128/aem.03915-12
Harth G, Maslesa-Galic S, Tullius MV, Horwitz MA (2005) All four Mycobacterium tuberculosis glnA genes encode glutamine synthetase activities but only GlnA1 is abundantly expressed and essential for bacterial homeostasis. Mol Microbiol 58(4):1157–1172. https://doi.org/10.1111/j.1365-2958.2005.04899.x
Hechler T, Pfeifer F (2013) Anaerobiosis inhibits gas vesicle formation in halophilic Archaea. Mol Microbiol 71(1):132–145. https://doi.org/10.1111/j.1365-2958.2008.06517.x
van Heeswijk WC, Westerhoff HV, Boogerd FC (2013) Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 77(4):628–695. https://doi.org/10.1128/MMBR.00025-13
Herrmann U, Soppa J (2002) Cell cycle-dependent expression of an essential SMC-like protein and dynamic chromosome localization in the archaeon Halobacterium salinarum. Mol Microbiol 46(2):395–409. https://doi.org/10.1046/j.1365-2958.2002.03181.x
Hildenbrand C, Stock T, Lange C, Rother M, Soppa J (2011) Genome copy numbers and gene conversion in methanogenic archaea. J Bacteriol 193(3):734–743. https://doi.org/10.1128/jb.01016-10
Jantzer K, Zerulla K, Soppa J (2011) Phenotyping in the archaea: optimization of growth parameters and analysis of mutants of Haloferax volcanii. FEMS Microbiol Lett 322(2):123–130. https://doi.org/10.1111/j.1574-6968.2011.02341.x
Kappler U, Histon WM, McEwan AG (2002) Control of dimethylsulfoxide reductase expression in Rhodobacter capsulatus: the role of carbon metabolites and the response regulators DorR and RegA. Microbiology 148(Pt 2):605–614. https://doi.org/10.1099/00221287-148-2-605
Kim JN, Méndez-García C, Geier RR, Iakiviak M, Chang J, Cann I, Mackie RI (2017) Metabolic networks for nitrogen utilization in Prevotella ruminicola23. Sci Rep 7:7851. https://doi.org/10.1038/2Fs41598-017-08463-3
Kyrpides NC, Ouzounis CA (1999) Transcription in archaea. Proc Natl Acad Sci USA 96(15):8545–8550. https://doi.org/10.1073/pnas.96.15.8545
Lange C, Zerrulla K, Breuert S, Soppa J (2011) Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii. Mol Microbiol 80(3):666–677. https://doi.org/10.1111/j.1365-2958.2011.07600.x
Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, Van der Oos J, Rice DW, Rafferty JB (2001) Crystal structure ofthe Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J 20(5):990–997. https://doi.org/10.1093/emboj/20.5.990
Li X, Liu T, Wu Y, Zhao G, Zhou Z (2010) Derepressive effect of NH4+ on hydrogen production by deleting the glnA1 gene in Rhodobacter sphaeroides. Biotechnol Bioeng 106(4):564–572. https://doi.org/10.1002/bit.22722
Mackwan RR, Carver GT, Drake JW, Grogan DW (2007) An unusual pattern of spontaneous mutations recovered in the halophilic archaeon Haloferax volcanii. Genetics 176(1):697–702. https://doi.org/10.1534/genetics.106.069666
Martínez-Espinosa RM, Esclapez J, Bautista V, Bonete MJ (2006) An octameric prokaryotic glutamine synthetase from the haloarchaeon Haloferax mediterranei. FEMS Microbiol Lett 264(1):110-116. https://doi.org/10.1111/j.1574-6968.2006.00434.x
Muro-Pastor MI, Reyes JC, Florencio FJ (2005) Ammonium assimilation in cyanobacteria. Photosynth Res 83(2):135–150. https://doi.org/10.1007/s11120-004-2082-7
Napoli A, Van der Oost J, Sensen CW, Charlebois RL, Rossi M, Ciaramella M (1999) An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. J Bacteriol 181(5):1474–1480
Nystrdm T, Neidhardt FC (1992) Cloning, mapping and nucleotide sequencing of a gene encoding a universal stress protein in Escherichia coli. Mol Microbiol 6(21):3187–3198. https://doi.org/10.1111/j.1365-2958.1992.tb01774.x
Pedro-Roig L, Camacho M (1834) Bonete MJ (2013) Regulation of ammonium assimilation in Haloferax mediterranei: interaction between glutamine synthetase and two GlnK proteins. Biochim Biophys Acta 1:16–23. https://doi.org/10.1016/j.bbapap.2012.10.006
Pedro-Roig L, Camacho M, Bonete MJ (2011) In vitro proof of direct regulation of glutamine synthetase by GlnK proteins in the extreme halophilic archaeon Haloferax mediterranei. Biochem Soc Trans 39(1):259–262. https://doi.org/10.1042/bst0390259
Pedro-Roig L, Lange C, Bonete MJ, Soppa J, Maupin-Furlow J (2013) Nitrogen regulation of protein–protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea. MicrobiologyOpen 2(5):826–840. https://doi.org/10.1002/mbo3.120
Peeters E, Charlier D (2010) The Lrp family of transcription regulators in Archaea. Archaea. https://doi.org/10.1155/2010/750457
Pire C, Martínez-Espinosa RM, Pérez-Pomares F, Esclapez J, Bonete MJ (2014) Ferredoxin-dependent glutamate synthase: involvement in ammonium assimilation in Haloferax mediterranei. Extremophiles 18(1):147–159. https://doi.org/10.1007/s00792-013-0606-9
Reitzer L (2003) Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 57:155–176. https://doi.org/10.1146/annurev.micro.57.030502.090820
Reyes JC, Florencio F (1994) A mutant lacking the glutamine synthetase gene (glnA) is impaired in the regulation of the nitrate assimilation system in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 176(24):7516–7523. https://doi.org/10.1128/jb.176.24.7516-7523.1994
Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormezana A (1980) Behaviour of mixed populations of halophilic bacteria in continuous cultures. Can J Microbiol 26(11):1259–1263. https://doi.org/10.1139/m80-210
Soppa J (2011) Ploidy and gene conversion in Archaea. Biochem Soc Trans 39(1):150–154. https://doi.org/10.1042/bst0390150
Soppa J (2013) Evolutionary advantages of polyploidy in halophilic archaea. Biochem Soc Trans 41(1):339–343. https://doi.org/10.1042/bst20120315
Sorek R, Lawrence CM, Wiedenheft B (2013) CRISPR-mediated adaptive immune systems in Bacteria and Archaea. Annu Rev Biochem 82:237–266. https://doi.org/10.1146/annurev-biochem-072911-172315
Todd JD, Curson AR, Nikolaidou-Katsaraidou N, Brearley CA, Watmough NJ, Chan Y, Page PC, Sun L, Johnston AW (2010) Molecular dissection of bacterial acrylate catabolism: unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production. Environ Microbiol 12(2):327–343. https://doi.org/10.1111/j.1462-2920.2009.02071.x
Tomita T, Miyazaki T, Miyazaki J, Kuzuyama T, Nishiyama M (2010) Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus. Microbiology 156(12):3801–3813. https://doi.org/10.1099/mic.0.042721-0
Van-Thuoc D, Huu-Phong T, Thi-Binh N, Thi-Tho N, Minh-Lam D, Quillaguamán J (2012) Polyester production by halophilic and halotolerant bacterial strains obtained from mangrove soil samples located in Northern Vietnam. MicrobiologyOpen 1(4):395–406. https://doi.org/10.1002/mbo3.44
Vegara A (2017) Glutamina sintetasas recombinantes de Haloferax mediterranei. Dissertation, University of Alicante (Spain)
Woods DR, Reid SJ (1993) Recent developments on the regulation and structure of glutamine synthetase enzymes from selected bacterial groups. FEMS Microbiol Rev 11(4):273–284. https://doi.org/10.1111/j.1574-6976.1993.tb00001.x
Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J (2014) DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival. PLoS ONE 9(4):e94819. https://doi.org/10.1371/journal.pone.0094819
Zerulla K, Soppa J (2014) Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 274(5):1–8. https://doi.org/10.3389/fmicb.2014.00274
Acknowledgements
We thank Jörg Soppa for the useful comments on and assistance with this work. This work was funded by MICINN Grant Number BIO2013-42921P (to MJB), Generalitat Valenciana Grant Number ACIF/2018/200 (to GP) and Universidad de Alicante (VIGROB-016).
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GP and VB designed and characterised the mutants; AV, JE, and MC prepared the array samples and performed the data collection; VHR, MCM and JE analysed the microarray data; GP and VHR wrote the paper; JE, VB, MC and MJB conducted the review and editing; MJB provided funding, project administration, and resources. All authors read and approved the final manuscript.
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Rodríguez-Herrero, V., Payá, G., Bautista, V. et al. Essentiality of the glnA gene in Haloferax mediterranei: gene conversion and transcriptional analysis. Extremophiles 24, 433–446 (2020). https://doi.org/10.1007/s00792-020-01169-x
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DOI: https://doi.org/10.1007/s00792-020-01169-x