Abstract
Halophilic archaea belong to the third domain of life, which live and survive in a highly salty environment. Nitrate assimilation is one of the main processes of the N-cycle, allowing the use of NO3 −, NO2 − and/or NH4 + as N source for growth. This pathway in general termed “Assimilatory nitrate pathway or assimilatory nitrate reduction” includes not only assimilatory nitrate reduction but also the assimilation of nitrite and ammonium. In the assimilatory nitrate reduction, NO3 − is finally reduced to NH4 + by two sequential reactions catalysed by a ferredoxin-dependent nitrate reductase (Nas; EC 1.6.6.2) and a ferredoxin-dependent nitrite reductase (Nir; EC 1.7.7.1). The glutamine synthetase/glutamate synthase pathway (GS-GOGAT; EC 6.3.1.2, EC 1.4.7.1, respectively) or l-glutamate dehydrogenase (GDH; EC 1.4.1.2) are responsible for incorporating NH4 + into carbon skeletons. This chapter reviews current knowledge on nitrogen metabolism in haloarchaea with emphasis on assimilatory nitrate reduction, proteins involved and its regulation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adul Rahman RN, Jongsareejit B, Fujiwara S, Imanaka T (1997) Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl Environ Microbiol 63:2472–2476
Alcántara-Hernández RJ, Valenzuela-Encinas C, Zavala-Díaz de la Serna FJ, Rodriguez-Revilla J, Dendooven L, Marsch R (2009) Haloarchaeal assimilatory nitrate-reducing communities from a saline alkaline soil. FEMS Microbiol Lett 298(1):56–66
Andrade SL, Einsle O (2007) The Amt/Mep/Rh family of ammonium transport proteins. Mol Membr Biol 24:357–365
Andrade SL, Dickmanns A, Ficner R, Einsle O (2005) Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc Natl Acad Sci U S A 102:14994–14999
Asker D, Ohta Y (2002) Production of canthaxanthin by Haloferax alexandrines under non-aseptic conditions and a simple, rapid method for its extraction. Appl Microbiol Biotechnol 58:743–750
Bauernfeind JC (1981) Natural food colors. In: Bauernfeind JC, Stewart GF, Schweigert BS, Hawthorn J (eds) Carotenoids as colorants and vitamin A precursors. Technological and nutritional applications. Academic Press, New York, pp 1–45. ISBN:978-0-12-082850-0
Beckers G, Nolden L, Burkovski A (2001) Glutamate synthase of Corynebacterium glutamicum is not essential for glutamate synthesis and is regulated by the nitrogen status. Microbiology 147(11):2961–2970
Beinert H (2000) Iron–sulfur proteins: ancient structures, still full of surprises. J Biol Inorg Chem 5:2–15
Belitsky BR, Wray LV, Fisher SH, Bohannon DE, Sonenshein AL (2000) Role of TnrA in nitrogen source-dependent repression of bacillus subtilis glutamate synthase gene expression. J Bacteriol 182(21):5939–5947
Bonete MJ, Camacho ML, Cadenas E (1986) Purification and some properties of NAD + -dependent glutamate dehydrogenase from Halobacterium halobium. Int J Biochem 18:785–789
Bonete MJ, Camacho ML, Cadenas E (1987) A new glutamate dehydrogenase from Halobacterium halobium with different coenzyme specificity. Int J Biochem 19:1149–1155
Bonete MJ, Perez-Pomares F, Ferrer J, Camacho ML (1996) NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids. Biochim Biophys Acta 1289(1):14–24
Bonete MJ, Martínez-Espinosa RM, Pire C, Zafrilla B, Richardson DJ (2008) Nitrogen metabolism in haloarchaea. Saline Syst 4:9. doi:10.1186/1746-1448-4-9
Bowsher CG, Lacey AE, Hanke GT, Clarkson DT, Saker LR, Stulen I, Emes MJ (2007) The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis. J Exp Bot 58(5):1109–1118
Brown JR, Masuchi Y, Robb FT, Doolittle WF (1994) Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J Mol Evol 38(6):566–576
Campbell WH, Kinghorn JR (1990) Functional domains of assimilatory nitrate reductase and nitrite reductases. Trends Biochem Sci 15:315–319
Carpenter KLH, van der Veen C, Hird R, Dennis IF, Ding T, Mitchinson MJ (1997) The carotenoids: β-carotene, canthaxanthin and zeaxanthin inhibit macrophage-mediated LDL oxidation. FEBS Lett 401:262–266
Chai W, Stewart V (1998) NasR, a novel RNA-binding protein, mediates nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader in vitro. J Mol Biol 283:339–351
Chávez 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
Chew BP, Park JS, Wong MW, Wong TSA (1999) Comparison of the anticancer activities of dietary β-carotene, canthaxanthin and astaxanthin in mice in vivo. Anticancer Res 19:1849–1853
Díaz S, Pérez-Pomares F, Pire C, Ferrer J, Bonete MJ (2006) Gene cloning, heterologous overexpression and optimized refolding of the NAD-glutamate dehydrogenase from Haloferax mediterranei. Extremophiles 10(2):105–115
Dixon R, Kahn D (2004) Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol 2(8):621–631
Edge R, McGarvey DJ, Truscott TG (1997) The carotenoids as antioxidants – a review. J Photochem Photobiol B Biol 41:189–200
Ehlers C, Grabbe R, Veit K, Schmitz RA (2002) Characterization of GlnK1 from Methanosarcina mazei Strain Gö1: complementation of an Escherichia coli glnK Mutant Strain by GlnK1. J Bacteriol 184:1028–1040
Ehlers C, Weidenbach K, Veit K, Forchhammer K, Schmitz RA (2005) Unique mechanistic features of post-translational regulation of glutamine synthetase activity in Methanosarcina mazei strain Gö1 in response to nitrogen availability. Mol Microbiol 55:1841–1854
Esclapez J, Bravo-Barrales G, Bautista V, Pire C, Camacho M, Bonete MJ (2014) Effects of nitrogen sources on the nitrate assimilation in Haloferax mediterranei: growth kinetics and transcriptomic analysis. FEMS Microbiol Lett 350:168–174
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
Fang CJ, Ku KL, Lee MH, Su NW (2010) Influence of nutritive factors on C50 carotenoids production by Haloferax mediterranei ATCC 33500 with two-stage cultivation. Bioresour Technol 101(16):6487–6493
Feng J, Liu B, Zhang Z, Ren Y, Li Y, Gan F, Huang Y, Chen X, Shen P, Wang L, Tang B, Tang XF (2012) The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. PLoS One 7(7), e41621
Fernández E, Galvan A, Quesada A (1998) Nitrogen assimilation and its regulation. In: The molecular biology of chloroplast and mitochondria in Chlamydomonas. Kluwer Academic Publishers, The Netherlands, pp 637–659
Ferrer J, Pérez-Pomares F, Bonete MJ (1996) NADP-glutamate dehydrogenase from the halophilic archaeon Haloferax mediterranei: enzyme purification, N-terminal sequence and stability. FEMS Microbiol Lett 141(1):59–63
Forchhammer K (2008) P(II) signal transducers: novel functional and structural insights. Trends Microbiol 16(2):65–72
Forchhammer K (2010) The network of PII signalling protein interactions in unicellular cyanobacteria. Adv Exp Med Biol 675:71–90. Chap 5. doi:10.1007/978-1-4419-1528-3_5
Forde BG, Lea PJ (2007) Glutamate in plants: metabolism, regulation, and signalling. J Exp Bot 58(9):2339–2358
Frolow F, Harel M, Sussman JL, Mevarech M, Shoham M (1996) Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat Struct Biol 3(5):452–458
Geiger B, Mevarech M, Werber MM (1978) Immunochemical characterization of ferredoxin from Halobacterium of the Dead Sea. Eur J Biochem 84(2):449–455
Heinrich A, Maheswaran M, Ruppert U, Forchhammer K (2004) The Synechococcus elongates PII signal transduction protein controls arginine synthesis by complex formation with N-acetyl-l-glutamate kinase. Mol Microbiol 52:1303–1314
Helfmann S, Lü W, Litz C, Andrade SLA (2010) Cooperative binding of MgATP and MgADP in the trimeric PII protein GlnK2 from Archaeoglobus fulgidus. J Mol Biol 402:165–177
Helling RB (1994) Why does Escherichia coli have two primary pathways for synthesis of glutamate? J Bacteriol 176:4664–4668
Hochman A, Nissany A, Amizur M (1988) Nitrate reduction and assimilation by a moderately halophilic, halotolerant bacterium Ba1. Biochim Biophys Acta 965(1):82–89
Ingoldsby LM, Geoghegan KF, Hayden BM, Engel PC (2005) The discovery of four distinct glutamate dehydrogenase genes in a strain of Halobacterium salinarum. Gene 349:237–244
Javelle A, Severi E, Thornton J, Merrick M (2004) Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB–GlnK complex formation. J Biol Chem 279:8530–8538
Jiang P, Mayo AE, Ninfa AJ (2007) Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC 2.7.7.49): kinetic characterization of regulation by PII, PII-UMP, glutamine, and α-ketoglutarate. Biochemistry 46:4133–4146
Kameya M, Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y (2007) A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium Hydrogenobacter thermophilus TK-6. J Bacteriol 189(7):2805–2812
Khademi S, Stroud RM (2006) The Amt/MEP/Rh family: structure of AmtB and the mechanism of ammonia gas conduction. Physiology (Bethesda) 21:419–429
Kumada Y, Benson DR, Hillemann D, Hosted TJ, Rochefort DA, Thompson CJ, Wohlleben W, Tateno Y (1993) Evolution of the glutamine synthetase gene, one of the oldest existing and functioning genes. Proc Natl Acad Sci USA 90:3009–3013
Labboun S, Tercé-Laforgue T, Roscher A, Bedu M, Restivo FM, Velanis CN et al (2009) Resolving the role of plant glutamate dehydrogenase. I. In vivo real time nuclear magnetic resonance spectroscopy experiments. Plant Cell Physiol 50:1761–1773
Leigh JA, Dodsworth JA (2007) Nitrogen regulation in bacteria and archaea. Annu Rev Microbiol 61:349–377
Lin JT, Stewart V (1998) Nitrate assimilation by bacteria. Adv Microb Physiol 39:330–379
Litz C, Helfmann S, Gerhardt S, Andrade SLA (2011) Structure of GlnK1, a signaling protein from Archaeoglobus fulgidus. Acta Crystallogr 67:178–181
Lledó B, Marhuenda-Egea FC, Martínez-Espinosa RM, Bonete MJ (2005) Identification and transcriptional analysis of nitrate assimilation genes in the halophilic archaeon Haloferax mediterranei. Gene 361:80–88
Luque-Almagro VM, Gates AJ, Moreno-Vivián C, Ferguson SJ, Richardson DJ, Roldán MD (2011) Bacterial nitrate assimilation: gene distribution and regulation. Biochem Soc Trans 39:1838–1843
Manitz B, Holldorf AW (1993) Purification and properties of glutamine synthetase from the archaebacterium Halobacterium salinarium. Arch Microbiol 159:90–97
Martínez-Espinosa RM, Marhuenda-Egea FC, Bonete MJ (2001a) Assimilatory nitrate reductase from the haloarchaeon Haloferax mediterranei: purification and characterisation. FEMS Microbiol Lett 204(2):381–385
Martínez-Espinosa RM, Marhuenda-Egea FC, Bonete MJ (2001b) Purification and characterisation of a possible assimilatory nitrite reductase from the halophile archaeon Haloferax mediterranei. FEMS Microbiol Lett 196(2):113–118
Martínez-Espinosa RM, Marhuenda-Egea FC, Donaire A, Bonete MJ (2003) NMR studies of a ferredoxin from Haloferax mediterranei and its physiological role in nitrate assimilatory pathway. Biochim Biophys Acta 1623(1):47–51
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
Martínez-Espinosa RM, Lledó B, Marhuenda-Egea FC, Bonete MJ (2007) The effect of ammonium on assimilatory nitrate reduction in the haloarchaeon Haloferax mediterranei. Extremophiles 11(6):759–767
Martínez-Espinosa RM, Lledó B, Marhuenda-Egea FC, Díaz S, Bonete MJ (2009) NO3 −/NO2 − assimilation in halophilic archaea: physiological analysis, nasA and nasD expressions. Extremophiles 13:785–792
McCarty GW, Bremner J (1992) Regulation of assimilatory nitrate reductase activity in soil by microbial assimilation of ammonium. Proc Natl Acad Sci USA 89:453–456
Mehta BJ, Obraztsova IN, Cerda-Olmedo E (2003) Mutants and intersexual heterokaryons of Blakeslea trispora for production of beta-carotene and lycopene. Appl Environ Microbiol 69:4043–4048
Miflin BJ (2002) The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops. J Exp Bot 53(370):979–987
Miller A, Fan X, Shen Q, Smith SJ (2008) Amino acids and nitrate as signals for the regulation of nitrogen acquisition. J Exp Bot 59:111–119
Moir W, Wood NJ (2001) Nitrate and nitrite transport in bacteria. Cell Mol Life Sci 58:215–224
Moreno-Vivián C, Flores E (2007) Nitrate assimilation in Bacteria. In: Bothe H, Ferguson SF, Newton WE (eds) Biology of the nitrogen cycle. Elsevier BV, Amsterdam, pp 263–282
Nesbo CL, L’Haridon S, Stetter KO, Doolittle WF (2001) Phylogenetic analyses of two ‘archaeal’ genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol 18(3):362–375
Ninfa AJ, Jiang P (2005) PII signal transduction proteins: sensors of [alpha]-ketoglutarate that regulate nitrogen metabolism. Curr Opin Microbiol 8:168–173
Olaizola M (2000) Commercial production of astaxanthin from Haematococcus pluvialis using 25,000-liter outdoor photobioreactors. J Appl Phycol 12:499–506
Palanca C, Pedro-Roig L, Llácer JL, Camacho M, Bonete MJ, Rubio V (2014) The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations. FEBS J 281:3299–3314
Palozza P, Maggiano N, Calviello G, Lanza P, Piccioni E, Ranelletti FO, Bartoli GM (1998) Canthaxanthin induces apoptosis in human cancer cell lines. Carcinogenesis 19:373–376
Pantoja O (2012) High affinity ammonium transporters: molecular mechanism of action. Front Plant Sci 3:34. doi:10.3389/fpls.2012.00034
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 39:259–262
Pedro-Roig L, Camacho M, Bonete MJ (2013a) Haloferax mediterranei GlnK proteins are post-translationally modified by uridylylation. Proteomics 13:1371–1374
Pedro-Roig L, Camacho M, Bonete MJ (2013b) Regulation of ammonium assimilation in Haloferax mediterranei: Interaction between glutamine synthetase and two GlnK proteins. Biochim Biophys Acta 1834:16–23
Pedro-Roig L, Lange C, Bonete MJ, Soppa J, Maupin-Furlow J (2013c) 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
Pérez-Pomares F, Ferrer J, Camacho M, Pire C, Llorca F, Bonete MJ (1999) Amino acid residues implied in the catalytic mechanism of NAD-dependent glutamate dehydrogenase from Halobacterium salinarum. Biochim Biophys Acta 1426:513–525
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
Radin JW (1977) Amino acid interactions in the regulation of nitrate reductase induction in cotton root tips. Plant Physiol 60:467–469
Raja R, Hemaiswarya S, Rengasamy R (2007) Exploitation of Dunaliella for betacarotene production. Appl Microbiol Biotechnol 74:517–523
Reitzer L (2003) Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 57:155–176
Reyes JC, Florencio FJ (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 176:7516–7523
Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ (2001) Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 58(2):165–178
Robertson DL, Alberte RS (1996) Isolation and characterization of glutamine synthetase from the marine diatom Skeletonema costatum. Plant Physiol 111(4):1169–1175
Santero E, Hervás AB, Canosa I, Govantes F (2012) Glutamate dehydrogenases: enzymology, physiological role and biotechnological relevance; Chapter 12. In: Canuto RA (ed) Dehydrogenases. InTech, under CC BY 3.0 license. doi:10.5772/2903. ISBN 978-953-307-019-3
Schulz AA, Collett HJ, Reid SJ (2001) Nitrogen and carbon regulation of glutamine synthetase and glutamate synthase in Corynebacterium glutamicum ATCC 13032. FEMS Microbiol Lett 205(2):361–367
Shapiro BM (1969) The glutamine synthetase deadenylylating enzyme system from Escherichia coli. Resolution into two components, specific nucleotide stimulation, and cofactor requirements. Biochemistry 8(2):659–670
Smith EL, Austen BM, Blumenthal KM, Nyc JF (1975) Glutamate dehydrogenase. In: Boyer PD (ed) The enzymes, vol 11, 3rd edn. Academic Press, New York, pp 293–367
Sugimori D, Ichimata T, Ikeda A, Nakamura S (2000) Purification and characterization of a ferredoxin from Haloarcula japonica strain TR-1. Biometals 13(1):23–28
Tomita T, Miyazaki T, Miyazaki J, Kuzuyama T, Nishiyama M (2010) Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus. Microbiology 156:3801–3813
Tomita T, Kuzuyama T, Nishiyama M (2011) Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase. J Biol Chem 286:37406–37413
Vanoni MA, Curti B (1999) Glutamate synthase: a complex iron-sulfur flavoprotein. Cell Mol Life Sci 55:617–638
Vanoni MA, Curti B (2005) Structure and function studies on the ironsulfur flavoenzyme glutamate synthase: an unexpectedly complex self-regulated enzyme. Arch Biochem Biophys 433(1):193–211
Wanner C, Soppa J (1999) Genetic Identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii. Genetics 152(4):1417–1428
Wood NJ, Alizadeh T, Richardson DJ, Ferguson SJ, Moir JW (2002) Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol Microbiol 44(1):157–170
Zafrilla B, Martínez-Espinosa RM, Bonete MJ, Butt JN, Richardson DJ, Gates AJ (2011) A haloarchaeal ferredoxin electron donor that plays an essential role in nitrate assimilation. Biochem Soc Trans 39(6):1844–1848
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Esclapez, J. et al. (2016). Recent Advances in the Nitrogen Metabolism in Haloarchaea and Its Biotechnological Applications. In: Rampelotto, P. (eds) Biotechnology of Extremophiles:. Grand Challenges in Biology and Biotechnology, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-319-13521-2_9
Download citation
DOI: https://doi.org/10.1007/978-3-319-13521-2_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-13520-5
Online ISBN: 978-3-319-13521-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)