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• W2893506532 abstract "Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNAIle. As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research. Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNAIle. As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research. Polyamines (Fig. 1) are a relatively overlooked component of the bacterial and archaeal metabolomes. This is due to several factors, including the patchwork phylogenetic distribution of any specific polyamine, the nontrivial problem of their detection and quantification, and the dearth of knowledge in bacteria about any molecular mechanisms that polyamines are involved in. Consequently, the terms “enigmatic” and “mysterious” occasionally decorate the titles of polyamine papers, yet the polyamine spermidine was almost certainly present in the last universal common ancestor of life (LUCA), 2The abbreviations used are: LUCAlast universal common ancestor of lifeDHSdeoxyhypusine synthaseSAMS-adenosylmethionine. because LUCA likely encoded spermidine synthase (1Weiss M.C. Sousa F.L. Mrnjavac N. Neukirchen S. Roettger M. Nelson-Sathi S. Martin W.F. The physiology and habitat of the last universal common ancestor.Nat. Microbiol. 2016; 1 (27562259)1611610.1038/nmicrobiol.2016.116Crossref PubMed Scopus (504) Google Scholar). The extent to which polyamine functions are selected for by evolution can be inferred from the fact that two entirely independent biosynthetic pathways exist for spermidine production; similarly, two distinct, independent pathways exist for homospermidine biosynthesis, and polyamine biosynthetic enzyme arginine decarboxylase has convergently evolved from four different protein folds (2Michael A.J. Biosynthesis of polyamines and polyamine-containing molecules.Biochem. J. 2016; 473 (27470594): 2315-232910.1042/BCJ20160185Crossref PubMed Scopus (97) Google Scholar). This minireview will discuss polyamine function in archaea and bacteria but will not discuss production of agmatine, putrescine, or cadaverine by acid-inducible basic amino acid decarboxylases (2Michael A.J. Biosynthesis of polyamines and polyamine-containing molecules.Biochem. J. 2016; 473 (27470594): 2315-232910.1042/BCJ20160185Crossref PubMed Scopus (97) Google Scholar, 3Kanjee U. Gutsche I. Ramachandran S. Houry W.A. The enzymatic activities of the Escherichia coli basic aliphatic amino acid decarboxylases exhibit a pH zone of inhibition.Biochemistry. 2011; 50 (21957966): 9388-939810.1021/bi201161kCrossref PubMed Scopus (51) Google Scholar) or the agmatine deiminase system that takes up exogenous agmatine and exports putrescine (4Griswold A.R. Jameson-Lee M. Burne R.A. Regulation and physiologic significance of the agmatine deiminase system of Streptococcus mutans UA159.J. Bacteriol. 2006; 188 (16428386): 834-84110.1128/JB.188.3.834-841.2006Crossref PubMed Scopus (102) Google Scholar). It will not, for the most part, cover inferred functions of polyamines determined from observations of in vitro biochemical behaviors of polyamines in binding RNA and DNA and other macromolecules. To highlight the phylogenetically narrow scope of current published polyamine function studies in bacteria, the host phylum of the various bacterial species discussed is indicated. last universal common ancestor of life deoxyhypusine synthase S-adenosylmethionine. Archaea (Archaebacteria) were formerly viewed as extremophile bacteria until they were unveiled as the third domain of life by Woese and Fox (5Woese C.R. Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms.Proc. Natl. Acad. Sci. U.S.A. 1977; 74 (270744): 5088-509010.1073/pnas.74.11.5088Crossref PubMed Scopus (2438) Google Scholar). They differ from bacteria in having isoprene lipids conjugated by ether bonds to glycerol-1-phosphate in their membranes, they lack peptidoglycan in their cell walls, and their informational proteins (e.g. those involved in transcription and translation) are more similar to eukaryotes than to bacteria (6Spang A. Caceres E.F. Ettema T.J.G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.Science. 2017; 357 (28798101)eaaf388310.1126/science.aaf3883Crossref PubMed Scopus (162) Google Scholar). Recently, culture-independent sequencing approaches have greatly expanded the known phylogenetic diversity of archaea, with many new phylum-level lineages being discovered in diverse habitats (6Spang A. Caceres E.F. Ettema T.J.G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.Science. 2017; 357 (28798101)eaaf388310.1126/science.aaf3883Crossref PubMed Scopus (162) Google Scholar, 7Adam P.S. Borrel G. Brochier-Armanet C. Gribaldo S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.ISME J. 2017; 11 (28777382): 2407-242510.1038/ismej.2017.122Crossref PubMed Scopus (213) Google Scholar8Castelle C.J. Banfield J.F. Major new microbial groups expand diversity and alter our understanding of the tree of life.Cell. 2018; 172 (29522741): 1181-119710.1016/j.cell.2018.02.016Abstract Full Text Full Text PDF PubMed Scopus (269) Google Scholar). The lifestyles of archaea (e.g. hyperthermophiles, methanogens, and halophiles) do not necessarily reflect phylogeny but have been a useful descriptor before specific molecular phylogenetic attributions were possible. The distribution of individual polyamines (Fig. 1) among archaeal groups is distinctive. Some of the earliest observations about polyamines in archaea were that they are absent in halophiles (9Chen K.Y. Martynowicz H. Lack of detectable polyamines in an extremely halophilic bacterium.Biochem. Biophys. Res. Commun. 1984; 124 (6388576): 423-42910.1016/0006-291X(84)91570-5Crossref PubMed Scopus (16) Google Scholar, 10Kamekura M. Bardocz S. Anderson P. Wallace R. Kushner D.J. Polyamines in moderately and extremely halophilic bacteria.Biochim. Biophys. Acta. 1986; 880: 204-20810.1016/0304-4165(86)90081-4Crossref Scopus (13) Google Scholar11Hamana K. Kamekura M. Onishi H. Akazawa T. Matsuzaki S. Polyamines in photosynthetic and extreme-halophilic archaebacteria.J. Biochem. 1985; 97 (3928615): 1653-165810.1093/oxfordjournals.jbchem.a135223Crossref PubMed Scopus (32) Google Scholar). It was also noted that the halophile Halobacterium halobium was unable to take up exogenous putrescine (9Chen K.Y. Martynowicz H. Lack of detectable polyamines in an extremely halophilic bacterium.Biochem. Biophys. Res. Commun. 1984; 124 (6388576): 423-42910.1016/0006-291X(84)91570-5Crossref PubMed Scopus (16) Google Scholar), but cell extracts of H. halobium and Halococcus morrhuae were able to produce agmatine from added arginine (11Hamana K. Kamekura M. Onishi H. Akazawa T. Matsuzaki S. Polyamines in photosynthetic and extreme-halophilic archaebacteria.J. Biochem. 1985; 97 (3928615): 1653-165810.1093/oxfordjournals.jbchem.a135223Crossref PubMed Scopus (32) Google Scholar). Polyamines can be described by the number of methylene carbons between amine groups (e.g. putrescine is represented by [4] and spermidine by [34]). Analysis of diverse hyperthermophilic, acidophilic, and thermoacidophilic archaea found a variety of linear polyamines, including norspermidine [33], spermidine [34], homospermidine [44], norspermine [333], spermine [343], thermospermine [334], caldopentamine [3333], homocaldopentamine [3334], thermopentamine [3343], and caldohexamine [33333], and quarternary branched pentaamine N4-bis(aminopropyl)spermidine (12Hamana K. Tanaka T. Hosoya R. Niitsu M. Itoh T. Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta.J. Gen. Appl. Microbiol. 2003; 49 (14673752): 287-29310.2323/jgam.49.287Crossref PubMed Scopus (31) Google Scholar) (Fig. 1). Some methanogens contain only homospermidine and putrescine, the majority contain only spermidine, and some contain both homospermidine and spermidine (13Scherer P. Kneifel H. Distribution of polyamines in methanogenic bacteria.J. Bacteriol. 1983; 154 (6406430): 1315-1322Crossref PubMed Google Scholar). This diversity of polyamine structures and phylogenetic distribution suggests lifestyle-related functions for different polyamines. However, some core conserved functions of polyamines in archaea can be discerned. A common feature of archaea is the presence of the polyamine-derived deoxyhypusine/hypusine modification of translation elongation factor aIF5A (14Bartig D. Schumann H. Klink F. The unique posttranslational modification leading to deoxyhypusine or hypusine is a general feature of the archaebacterial kingdom.Syst. Appl. Microbiol. 1990; 13: 112-11610.1016/S0723-2020(11)80156-6Crossref Scopus (37) Google Scholar). In eukaryotes, the aminobutyl moiety of spermidine is transferred by deoxyhypusine synthase (DHS) to a single lysine residue in eIF5A to form deoxyhypusine, which, after hydroxylation by deoxyhypusine hydroxylase, forms the hypusine post-translational modification (15Park M.H. Cooper H.L. Folk J.E. Identification of hypusine, an unusual amino acid, in a protein from human lymphocytes and of spermidine as its biosynthetic precursor.Proc. Natl. Acad. Sci. U.S.A. 1981; 78 (6789324): 2869-287310.1073/pnas.78.5.2869Crossref PubMed Scopus (188) Google Scholar, 16Cooper H.L. Park M.H. Folk J.E. Safer B. Braverman R. Identification of the hypusine-containing protein hy+ as translation initiation factor eIF-4D.Proc. Natl. Acad. Sci. U.S.A. 1983; 80 (6403941): 1854-185710.1073/pnas.80.7.1854Crossref PubMed Scopus (155) Google Scholar17Park J.H. Aravind L. Wolff E.C. Kaevel J. Kim Y.S. Park M.H. Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme.Proc. Natl. Acad. Sci. U.S.A. 2006; 103 (16371467): 51-5610.1073/pnas.0509348102Crossref PubMed Scopus (117) Google Scholar). Hypusine modification of eIF5A is required for translation of mRNAs encoding polyproline tracts that would otherwise cause ribosome stalling and translational arrest (18Gutierrez E. Shin B.S. Woolstenhulme C.J. Kim J.R. Saini P. Buskirk A.R. Dever T.E. eIF5A promotes translation of polyproline motifs.Mol. Cell. 2013; 51 (23727016): 35-4510.1016/j.molcel.2013.04.021Abstract Full Text Full Text PDF PubMed Scopus (293) Google Scholar). DHS is essential for growth of eukaryotes as phylogenetically distant as budding yeast (19Sasaki K. Abid M.R. Miyazaki M. Deoxyhypusine synthase gene is essential for cell viability in the yeast Saccharomyces cerevisiae.FEBS Lett. 1996; 384 (8612813): 151-15410.1016/0014-5793(96)00310-9Crossref PubMed Scopus (111) Google Scholar), mouse (20Nishimura K. Lee S.B. Park J.H. Park M.H. Essential role of eIF5A-1 and deoxyhypusine synthase in mouse embryonic development.Amino Acids. 2012; 42 (21850436): 703-71010.1007/s00726-011-0986-zCrossref PubMed Scopus (74) Google Scholar), and trypanosamatid parasites (21Nguyen S. Jones D.C. Wyllie S. Fairlamb A.H. Phillips M.A. Allosteric activation of trypanosomatid deoxyhypusine synthase by a catalytically dead paralog.J. Biol. Chem. 2013; 288 (23525104): 15256-1526710.1074/jbc.M113.461137Abstract Full Text Full Text PDF PubMed Scopus (36) Google Scholar, 22Chawla B. Jhingran A. Singh S. Tyagi N. Park M.H. Srinivasan N. Roberts S.C. Madhubala R. Identification and characterization of a novel deoxyhypusine synthase in Leishmania donovani.J. Biol. Chem. 2010; 285 (19880510): 453-46310.1074/jbc.M109.048850Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar). Diverse archaea have been shown to contain either deoxyhypusine- or hypusine-modified aIF5A (14Bartig D. Schumann H. Klink F. The unique posttranslational modification leading to deoxyhypusine or hypusine is a general feature of the archaebacterial kingdom.Syst. Appl. Microbiol. 1990; 13: 112-11610.1016/S0723-2020(11)80156-6Crossref Scopus (37) Google Scholar, 23Schumann H. Klink F. Archaebacterial protein contains hypusinme a unique amino acid characteristic for eukaryotic translation initiation factor 4D.Syst. Appl. Microbiol. 1989; 11: 103-10710.1016/S0723-2020(89)80047-5Crossref Scopus (18) Google Scholar, 24Bartig D. Lemkemeier K. Frank J. Lottspeich F. Klink F. The archaebacterial hypusine-containing protein: structural features suggest common ancestry with eukaryotic translation initiation factor 5A.Eur. J. Biochem. 1992; 204 (1541288): 751-75810.1111/j.1432-1033.1992.tb16690.xCrossref PubMed Scopus (59) Google Scholar). Analysis of archaeal genomes by BLASTP indicates that all archaea are likely to encode DHS. Inhibition of the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius DHS by N1-guanyl-1,7-diaminoheptane led to cell cycle arrest (25Jansson B.P. Malandrin L. Johansson H.E. Cell cycle arrest in archaea by the hypusination inhibitor N1-guanyl-1,7-diaminoheptane.J. Bacteriol. 2000; 182 (10648545): 1158-116110.1128/JB.182.4.1158-1161.2000Crossref PubMed Scopus (55) Google Scholar). Although deoxyhypusine formation in eukaryotes depends on spermidine as an aminobutyl group donor (15Park M.H. Cooper H.L. Folk J.E. Identification of hypusine, an unusual amino acid, in a protein from human lymphocytes and of spermidine as its biosynthetic precursor.Proc. Natl. Acad. Sci. U.S.A. 1981; 78 (6789324): 2869-287310.1073/pnas.78.5.2869Crossref PubMed Scopus (188) Google Scholar), and this is likely to apply to most archaea (Fig. 2), the mechanism of deoxyhypusine formation in halophiles does not depend on spermidine. Halophiles do not accumulate either spermidine or putrescine; however, they do accumulate agmatine. An agmatinase-like gene (agmatinase converts agmatine to putrescine) is necessary for deoxyhypusine formation in Haloferax volcanii, and only deoxyhypusine, and not hypusine, is detected in aIF5A (26Prunetti L. Graf M. Blaby I.K. Peil L. Makkay A.M. Starosta A.L. Papke R.T. Oshima T. Wilson D.N. de Crécy-Lagard V. Deciphering the translation initiation factor 5A modification pathway in halophilic archaea.Archaea. 2016; 2016 (28053595)7316725Crossref PubMed Scopus (14) Google Scholar). The H. volcanii agmatinase-like gene is essential for growth even though putrescine and spermidine are not accumulated. It was suggested that the aminobutyl moiety of deoxyhypusine in H. volcanii might be derived from putrescine or from agmatine that is transferred to aIF5A and the guanidino group subsequently released to form deoxyhypusine by the action of the agmatinase-like enzyme. Currently, it is not certain whether putrescine is required for growth of halophiles, and, as mentioned above, the halophile H. halobium was unable to take up exogenous putrescine (9Chen K.Y. Martynowicz H. Lack of detectable polyamines in an extremely halophilic bacterium.Biochem. Biophys. Res. Commun. 1984; 124 (6388576): 423-42910.1016/0006-291X(84)91570-5Crossref PubMed Scopus (16) Google Scholar). In contrast, the recombinant DHS of the hyperthermophilic euryarchaeote Thermococcus kodakarensis transfers the aminobutyl group of spermidine to T. kodakarensis aIF5A to form deoxyhypusinated aIF5A (26Prunetti L. Graf M. Blaby I.K. Peil L. Makkay A.M. Starosta A.L. Papke R.T. Oshima T. Wilson D.N. de Crécy-Lagard V. Deciphering the translation initiation factor 5A modification pathway in halophilic archaea.Archaea. 2016; 2016 (28053595)7316725Crossref PubMed Scopus (14) Google Scholar) (Fig. 2). Although spermidine is required for deoxyhypusine formation in T. kodakarensis (26Prunetti L. Graf M. Blaby I.K. Peil L. Makkay A.M. Starosta A.L. Papke R.T. Oshima T. Wilson D.N. de Crécy-Lagard V. Deciphering the translation initiation factor 5A modification pathway in halophilic archaea.Archaea. 2016; 2016 (28053595)7316725Crossref PubMed Scopus (14) Google Scholar), putrescine is not required for growth because spermidine is synthesized from agmatine via aminopropylagmatine rather than putrescine (27Morimoto N. Fukuda W. Nakajima N. Masuda T. Terui Y. Kanai T. Oshima T. Imanaka T. Fujiwara S. Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis.J. Bacteriol. 2010; 192 (20675472): 4991-500110.1128/JB.00279-10Crossref PubMed Scopus (42) Google Scholar). Some methanogens, in particular the Methanosarcinaceae, accumulate only homospermidine rather than spermidine (13Scherer P. Kneifel H. Distribution of polyamines in methanogenic bacteria.J. Bacteriol. 1983; 154 (6406430): 1315-1322Crossref PubMed Google Scholar). Homospermidine contains two aminobutyl groups, and the human DHS can use homospermidine to donate an aminobutyl group to eIF5A (28Park J.H. Wolff E.C. Folk J.E. Park M.H. Reversal of the deoxyhypusine synthesis reaction: generation of spermidine or homospermidine from deoxyhypusine by deoxyhypusine synthase.J. Biol. Chem. 2003; 278 (12788913): 32683-3269110.1074/jbc.M304247200Abstract Full Text Full Text PDF PubMed Scopus (45) Google Scholar). Intriguingly, homospermidine-accumulating members of the Methanosarcinaceae are capable of nitrogen fixation (29Chien Y.T. Auerbuch V. Brabban A.D. Zinder S.H. Analysis of genes encoding an alternative nitrogenase in the archaeon Methanosarcina barkeri 227.J. Bacteriol. 2000; 182 (10809706): 3247-325310.1128/JB.182.11.3247-3253.2000Crossref PubMed Scopus (26) Google Scholar), and recently homospermidine biosynthesis was shown to be essential for normal diazotrophic (nitrogen-fixing) growth of the filamentous cyanobacterium Anabaena (30Burnat M. Li B. Kim S.H. Michael A.J. Flores E. Homospermidine biosynthesis in the cyanobacterium Anabaena requires a deoxyhypusine synthase homologue and is essential for normal diazotrophic growth.Mol. Microbiol. 2018; 109 (29923645): 763-78010.1111/mmi.14006Crossref PubMed Scopus (14) Google Scholar). Spermidine is therefore dispensable for growth in archaeal halophiles and some methanogens. In most but not all archaea, agmatine is transferred to tRNAIle to form the covalent modification known as agmatidine (2-agmatinylcytidine) on the cytidine of the anticodon CAT (31Mandal D. Köhrer C. Su D. Russell S.P. Krivos K. Castleberry C.M. Blum P. Limbach P.A. Söll D. RajBhandary U.L. Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine.Proc. Natl. Acad. Sci. U.S.A. 2010; 107 (20133752): 2872-287710.1073/pnas.0914869107Crossref PubMed Scopus (96) Google Scholar, 32Ikeuchi Y. Kimura S. Numata T. Nakamura D. Yokogawa T. Ogata T. Wada T. Suzuki T. Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.Nat. Chem. Biol. 2010; 6 (20139989): 277-28210.1038/nchembio.323Crossref PubMed Scopus (102) Google Scholar) (Fig. 2). This modification, performed by the enzyme TiaS, is required for the discrimination of isoleucine and methionine codons and is essential for growth. The enzyme TiaS is also essential for growth (33Blaby I.K. Phillips G. Blaby-Haas C.E. Gulig K.S. El Yacoubi B. de Crécy-Lagard V. Towards a systems approach in the genetic analysis of archaea: accelerating mutant construction and phenotypic analysis in Haloferax volcanii.Archaea. 2010; 2010 (21234384)426239Crossref PubMed Scopus (15) Google Scholar). A few archaeal species, including Candidatus Korarchaeum cryptofilum OPF8 and Nanoarchaeum equitans do not encode a TiaS homologue and instead encode tRNAIle genes with TAT anticodons (34Suzuki T. Numata T. Convergent evolution of AUA decoding in bacteria and archaea.RNA Biol. 2014; 11 (25629511): 1586-159610.4161/15476286.2014.992281Crossref PubMed Scopus (22) Google Scholar). In the vast majority of archaea, it is likely that agmatine, specifically, will be necessary for growth due to the need for the agmatidine modification of tRNAIle. The role of agmatine in agmatinylation explains why agmatine but not putrescine is essential for growth of T. kodakarensis (35Fukuda W. Morimoto N. Imanaka T. Fujiwara S. Agmatine is essential for the cell growth of Thermococcus kodakaraensis.FEMS Microbiol. Lett. 2008; 287 (18702616): 113-12010.1111/j.1574-6968.2008.01303.xCrossref PubMed Scopus (45) Google Scholar) and why agmatine is the only polyamine accumulated in some extreme halophiles (36Hamana K. Hamana H. Itoh T. Ubiquitous occurrence of agmatine as the major polyamine within extremely halophilic archaebacteria.J. Gen. Appl. Microbiol. 1995; 41: 153-15810.2323/jgam.41.153Crossref Scopus (9) Google Scholar). An equivalent modification of tRNAIle in bacteria is achieved by covalent attachment of lysine (37Muramatsu T. Yokoyama S. Horie N. Matsuda A. Ueda T. Yamaizumi Z. Kuchino Y. Nishimura S. Miyazawa T. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli.J. Biol. Chem. 1988; 263 (3132458): 9261-9267Abstract Full Text PDF PubMed Google Scholar) by the enzyme TilS (38Soma A. Ikeuchi Y. Kanemasa S. Kobayashi K. Ogasawara N. Ote T. Kato J. Watanabe K. Sekine Y. Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.Mol. Cell. 2003; 12 (14527414): 689-69810.1016/S1097-2765(03)00346-0Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar), a nonhomologous equivalent of TiaS that has arisen by convergent evolution (34Suzuki T. Numata T. Convergent evolution of AUA decoding in bacteria and archaea.RNA Biol. 2014; 11 (25629511): 1586-159610.4161/15476286.2014.992281Crossref PubMed Scopus (22) Google Scholar). Due to the role of agmatine in agmatinylation of tRNAIle, provision of agmatine by arginine decarboxylase is particularly important in archaea. A pyruvoyl-dependent arginine decarboxylase is present in Euryarchaeota (39Graham D.E. Xu H. White R.H. Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis.J. Biol. Chem. 2002; 277 (11980912): 23500-2350710.1074/jbc.M203467200Abstract Full Text Full Text PDF PubMed Scopus (44) Google Scholar), but this gene has been lost in Crenarchaeota, and instead a SAM decarboxylase paralogue has evolved to decarboxylate arginine (40Giles T.N. Graham D.E. Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme.J. Biol. Chem. 2008; 283 (18650422): 25829-2583810.1074/jbc.M802674200Abstract Full Text Full Text PDF PubMed Scopus (25) Google Scholar). The covalent incorporation of agmatine into agmatidine in tRNAIle, and the aminobutyl group of spermidine or homospermidine into deoxyhypusine in aIF5A means that agmatine and spermidine/homospermidine are independently essential for growth in most archaea. The diverse roles of polyamines in archaea are best exemplified by the difference in polyamine content between hyperthermophiles and halophiles. Disruption of the gene encoding the agmatine aminopropyltransferase of the hyperthermophile T. kodakarensis (27Morimoto N. Fukuda W. Nakajima N. Masuda T. Terui Y. Kanai T. Oshima T. Imanaka T. Fujiwara S. Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis.J. Bacteriol. 2010; 192 (20675472): 4991-500110.1128/JB.00279-10Crossref PubMed Scopus (42) Google Scholar) resulted in depletion of spermidine and branched-chain polyamines (N4-aminopropylspermidine and N4-bis(aminopropyl)spermidine, originally misassigned as spermine and N4-aminopropylspermidine) and severe growth defects at 85 °C, and even more so at 93 °C, that could be slightly reversed at 85 °C but not at 93 °C by supplying spermidine. If only the branched-chain polyamines are eliminated by deletion of the branched-chain aminopropyltransferase BspA, growth at 93 °C is abolished, but some growth can be restored by provision of 1 mm N4-bis(aminopropyl)spermidine (41Okada K. Hidese R. Fukuda W. Niitsu M. Takao K. Horai Y. Umezawa N. Higuchi T. Oshima T. Yoshikawa Y. Imanaka T. Fujiwara S. Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles.J. Bacteriol. 2014; 196 (24610711): 1866-187610.1128/JB.01515-14Crossref PubMed Scopus (32) Google Scholar). These findings establish the essential role of branched polyamines in high-temperature growth of T. kodakarensis. In vitro biochemical studies indicate that both linear long-chain polyamines and branched polyamines induce structural changes to DNA that are proposed to facilitate growth at extreme temperatures (42Nishio T. Yoshikawa Y. Fukuda W. Umezawa N. Higuchi T. Fujiwara S. Imanaka T. Yoshikawa K. Branched-chain polyamine found in hyperthermophiles induces unique temperature-dependent structural changes in genome-size DNA.Chemphyschem. 2018; 19 (29931720): 2299-230410.1002/cphc.201800396Crossref PubMed Scopus (15) Google Scholar, 43Terui Y. Ohnuma M. Hiraga K. Kawashima E. Oshima T. Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus.Biochem. J. 2005; 388 (15673283): 427-43310.1042/BJ20041778Crossref PubMed Scopus (85) Google Scholar). In notable contrast to the exotic polyamine content of hyperthermophiles that, in addition to branched polyamines, can contain long linear chain polyamines, such as caldohexamine featuring five aminopropyl group additions (12Hamana K. Tanaka T. Hosoya R. Niitsu M. Itoh T. Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta.J. Gen. Appl. Microbiol. 2003; 49 (14673752): 287-29310.2323/jgam.49.287Crossref PubMed Scopus (31) Google Scholar), halophilic archaea contain only agmatine. The genes encoding the spermidine biosynthetic enzymes SAM decarboxylase and spermidine synthase have been lost from halophiles. Archaeal halophiles grow in up to 3 mm external NaCl by using a salt-in strategy, accumulating in their cytosol millimolar quantities of KCl (44Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity.Saline Systems. 2008; 4 (18412960): 210.1186/1746-1448-4-2Crossref PubMed Scopus (567) Google Scholar). An interesting question then is whether polyamines have been lost from halophiles because they are not capable of performing their usual functions in high KCl or whether high KCl renders the noncovalent function of polyamines superfluous. Certainly, halophiles have evolved to supply an aminobutyl group for deoxyhypusine formation without the participation of spermidine or homospermidine (26Prunetti L. Graf M. Blaby I.K. Peil L. Makkay A.M. Starosta A.L. Papke R.T. Oshima T. Wilson D.N. de Crécy-Lagard V. Deciphering the translation initiation factor 5A modification pathway in halophilic archaea.Archaea. 2016; 2016 (28053595)7316725Crossref PubMed Scopus (14) Google Scholar). In conclusion, agmatine and agmatidine formation are essential for growth in most but not all archaea, and agmatine is required for spermidine biosynthesis (Fig. 2). Agmatine or possibly putrescine is required for the essential deoxyhypusine modification of aIF5A in halophiles. Spermidine or homospermidine are essential in most archaea except halop" @default.
• W2893506532 created "2018-10-05" @default.
• W2893506532 creator A5075919961 @default.
• W2893506532 date "2018-11-01" @default.
• W2893506532 modified "2023-10-13" @default.
• W2893506532 title "Polyamine function in archaea and bacteria" @default.
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