Evolution and Multiplicity of Arginine Decarboxylases in Polyamine Biosynthesis and Essential Role in Bacillus subtilis Biofilm Formation

Abstract

Arginine decarboxylases (ADCs; EC 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. Biosynthetic alanine racemase fold (AR-fold) ADC is widespread in bacteria and plants. We report the discovery and characterization of an ancestral form of the AR-fold ADC in the bacterial Chloroflexi and Bacteroidetes phyla. The ancestral AR-fold ADC lacks a large insertion found in Escherichia coli and plant AR-fold ADC and is more similar to the lysine biosynthetic enzyme meso-diaminopimelate decarboxylase, from which it has evolved. An E. coli acid-inducible ADC belonging to the aspartate aminotransferase fold (AAT-fold) is involved in acid resistance but not polyamine biosynthesis. We report here that the acid-inducible AAT-fold ADC has evolved from a shorter, ancestral biosynthetic AAT-fold ADC by fusion of a response regulator receiver domain protein to the N terminus. Ancestral biosynthetic AAT-fold ADC appears to be limited to firmicute bacteria. The phylogenetic distribution of different forms of ADC distinguishes bacteria from archaea, euryarchaeota from crenarchaeota, double-membraned from single-membraned bacteria, and firmicutes from actinobacteria. Our findings extend to eight the different enzyme forms carrying out the activity described by EC 4.1.1.19. ADC gene clustering reveals that polyamine biosynthesis employs diverse and exchangeable synthetic modules. We show that in Bacillus subtilis, ADC and polyamines are essential for biofilm formation, and this appears to be an ancient, evolutionarily conserved function of polyamines in bacteria. Also of relevance to human health, we found that arginine decarboxylation is the dominant pathway for polyamine biosynthesis in human gut microbiota. Arginine decarboxylases (ADCs; EC 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. Biosynthetic alanine racemase fold (AR-fold) ADC is widespread in bacteria and plants. We report the discovery and characterization of an ancestral form of the AR-fold ADC in the bacterial Chloroflexi and Bacteroidetes phyla. The ancestral AR-fold ADC lacks a large insertion found in Escherichia coli and plant AR-fold ADC and is more similar to the lysine biosynthetic enzyme meso-diaminopimelate decarboxylase, from which it has evolved. An E. coli acid-inducible ADC belonging to the aspartate aminotransferase fold (AAT-fold) is involved in acid resistance but not polyamine biosynthesis. We report here that the acid-inducible AAT-fold ADC has evolved from a shorter, ancestral biosynthetic AAT-fold ADC by fusion of a response regulator receiver domain protein to the N terminus. Ancestral biosynthetic AAT-fold ADC appears to be limited to firmicute bacteria. The phylogenetic distribution of different forms of ADC distinguishes bacteria from archaea, euryarchaeota from crenarchaeota, double-membraned from single-membraned bacteria, and firmicutes from actinobacteria. Our findings extend to eight the different enzyme forms carrying out the activity described by EC 4.1.1.19. ADC gene clustering reveals that polyamine biosynthesis employs diverse and exchangeable synthetic modules. We show that in Bacillus subtilis, ADC and polyamines are essential for biofilm formation, and this appears to be an ancient, evolutionarily conserved function of polyamines in bacteria. Also of relevance to human health, we found that arginine decarboxylation is the dominant pathway for polyamine biosynthesis in human gut microbiota. IntroductionThe evolution of central metabolic pathways was one of the key biochemical developments in the early stages of primordial life (1Caetano-Anollés G. Yafremava L.S. Gee H. Caetano-Anollés D. Kim H.S. Mittenthal J.E. Int. J. Biochem. Cell Biol. 2009; 41: 285-297Crossref PubMed Scopus (87) Google Scholar). Metabolic pathways evolve through mechanisms such as gene duplication followed by neofunctionalization of one of the copies to produce a new enzyme with an altered substrate preference (2Ohno S. Evolution by Gene Duplication. Springer-Verlag, New York1970Crossref Google Scholar, 3Serres M.H. Kerr A.R. McCormack T.J. Riley M. Biol. Direct. 2009; 4: 46Crossref PubMed Scopus (41) Google Scholar, 4Innan H. Kondrashov F. Nat. Rev. Genet. 2010; 11: 97-108Crossref PubMed Scopus (825) Google Scholar). Other mechanisms involved in the evolution of metabolic pathways include gene fusions, which can be fusion of two paralogous genes to achieve gene elongation. An example is the formation of eukaryotic S-adenosylmethionine decarboxylase (AdoMetDC), 5The abbreviations used are: AdoMetDCS-adenosylmethionine decarboxylaseAAT-foldaspartate aminotransferase foldADCarginine decarboxylaseAIHagmatine iminohydrolaseAR-foldalanine racemase foldAUHagmatine ureohydrolaseCANSDCcarboxy(nor)spermidine decarboxylaseDAPDCmeso-diaminopimelate decarboxylaseLDClysine decarboxylaseL/ODClysine/ornithine decarboxylaseNCPAHN-carbamoylputrescine amidohydrolaseODCornithine decarboxylasePLPpyridoxal 5′-phosphatepylADCpyruvoyl-dependent arginine decarboxylaseRECreceiver domainaaamino acidsCHES2-(cyclohexylamino)ethanesulfonic acid. a polyamine biosynthetic enzyme, by fusion of two prokaryotic AdoMetDC genes (5Toms A.V. Kinsland C. McCloskey D.E. Pegg A.E. Ealick S.E. J. Biol. Chem. 2004; 279: 33837-33846Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar). Gene fusions may bring together different protein functional modules such as regulatory and enzymatic components and are often generated independently in different lineages by fusion of open reading frames within operons (6Yanai I. Wolf Y.I. Koonin E.V. Genome. Biol. 2002; 3 (research0024)Google Scholar). New steps in metabolic pathways can be recruited from preexisting pathways in the same cell (the “patchwork” model of pathway evolution) (7Jensen R.A. Annu. Rev. Microbiol. 1976; 30: 409-425Crossref PubMed Scopus (815) Google Scholar) or from other organisms by horizontal or endosymbiotic gene transfer. Convergent evolution of the same enzymatic activity in different organisms by completely different, evolutionarily unrelated proteins (recently described as non-homologous isofunctional enzymes) (8Omelchenko M.V. Galperin M.Y. Wolf Y.I. Koonin E.V. Biol. Direct. 2010; 5: 31Crossref PubMed Scopus (100) Google Scholar) is a result of independent biochemical invention (9Galperin M.Y. Walker D.R. Koonin E.V. Genome Res. 1998; 8: 779-790Crossref PubMed Scopus (191) Google Scholar).The biosynthesis of polyamines is an excellent model for studying processes of metabolic pathway evolution. Polyamines are small organic polycations, usually linear di-, tri-, and tetra-amines, that are found in almost all cells. Synthesis of polyamines is achieved through biosynthetic modules: a diamine is produced directly or indirectly from an amino acid, and a triamine is produced from the diamine by the addition of an aminopropyl or aminobutyl group. Tetra-amines are produced from triamines by aminopropyl or more rarely by aminobutyl group addition. The modular nature of polyamine biosynthesis facilitates horizontal and endosymbiotic transfer (10Shaw F.L. Elliott K.A. Kinch L.N. Fuell C. Phillips M.A. Michael A.J. J. Biol. Chem. 2010; 285: 14711-14723Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar).By far, in all three domains of life, the most common diamine is putrescine (1,4-diaminobutane), which can be used to form spermidine (by aminopropyl addition) or sym-homospermidine (by aminobutyl addition). Almost all eukaryotes synthesize putrescine directly from ornithine by the action of ornithine decarboxylase (ODC). However, plants possess an additional, indirect pathway for putrescine biosynthesis from arginine, through the action of arginine decarboxylase (ADC) (11Fuell C. Elliott K.A. Hanfrey C.C. Franceschetti M. Michael A.J. Plant Physiol. Biochem. 2010; 48: 513-520Crossref PubMed Scopus (136) Google Scholar). It is unclear which bacteria use the ADC route to synthesize putrescine, and the relative importance of the ODC and ADC routes in bacterial polyamine biosynthesis is also unclear. The product of ADC, agmatine, may be converted directly to putrescine by agmatine ureohydrolase (AUH) (12Satishchandran C. Boyle S.M. J. Bacteriol. 1986; 165: 843-848Crossref PubMed Scopus (54) Google Scholar) or indirectly via N-carbamoylputrescine by agmatine deiminase/iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NCPAH) (13Nakada PubMed Scopus Google are four protein fold an The alanine racemase fold (AR-fold) of the eukaryotic ODC from human and M.A. Phillips M.A. J. Biol. PubMed Scopus Google Scholar, Phillips M.A. PubMed Scopus Google decarboxylase from J. Michael A.J. D. Phillips M.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google meso-diaminopimelate decarboxylase from and G. H. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar, J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, D. J. J. H. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google and decarboxylase and ADC J. Michael A.J. D.R. Phillips M.A. J. Biol. Chem. 2010; 285: Full Text Full Text PDF PubMed Scopus Google Scholar). The AR-fold ADC is the other of the AR-fold amino acid decarboxylases J. Michael A.J. D. Phillips M.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google to a large insertion relative to other of the ADC of Escherichia which is not involved in polyamine to the aspartate aminotransferase fold which also the E. coli and biosynthetic ODC and also bacterial acid-inducible lysine ADC is in M. and most of the euryarchaeota D.E. H. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google and most of the possess an ADC that has evolved from the AdoMetDC D.E. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). An not involved in polyamine is in D.E. J. Bacteriol. PubMed Scopus Google Scholar). large such as possess an AR-fold ADC that and has evolved from an AR-fold ODC J. Pegg A.E. Phillips M.A. J. Biol. Chem. 2004; 279: Full Text Full Text PDF PubMed Scopus Google Scholar, Phillips M.A. PubMed Scopus Google Scholar). the form of ADC enzyme in bacteria, ADC is by the polyamines are primordial of life, it has to eukaryotes and archaea, spermidine is for formation, which is essential for cell in eukaryotes and M. PubMed Scopus Google Scholar, J. Bacteriol. PubMed Scopus Google Scholar). in archaea, it was that agmatine is for an essential of a in a produce the for the D. C. D. D. 2010; PubMed Scopus Google Scholar, S. D. Nat. Chem. Biol. 2010; PubMed Scopus Google Scholar). of that the of spermidine is in formation for in the H. PubMed Scopus Google Scholar, M.H. H. PubMed Scopus Google Scholar) and in Pegg A.E. Biochem. J. PubMed Scopus Google Scholar, M. A.R. J. J. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). are also that polyamines function independently of formation M.H. Biochem. J. PubMed Scopus Google Scholar, G. M.H. C. J. Biol. Chem. 2010; 285: Full Text Full Text PDF PubMed Scopus Google Scholar). The essential for spermidine and agmatine in and formation, other of polyamines in eukaryotes and bacteria, which and a more model for of However, of E. coli is by polyamine H. J. Bacteriol. 2009; PubMed Scopus (54) Google Scholar). and of all polyamines or of in a of of M.A. J. Bacteriol. PubMed Scopus Google Scholar, J. D.E. J. Phillips M.A. Michael A.J. J. Biol. Chem. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). polyamine of (13Nakada PubMed Scopus Google Scholar) and of (10Shaw F.L. Elliott K.A. Kinch L.N. Fuell C. Phillips M.A. Michael A.J. J. Biol. Chem. 2010; 285: 14711-14723Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar). polyamine of and polyamine in biofilm M.A. J. Bacteriol. PubMed Scopus Google Scholar, J. D.E. J. Phillips M.A. Michael A.J. J. Biol. Chem. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). formation is a key polyamines are independently of or formation, in two of we that an ancestral form of the AR-fold ADC in of the Chloroflexi and phyla. The ancestral AR-fold ADC lacks the insertion of the AR-fold which is found in most of the double-membraned bacteria. We also show that the firmicute AAT-fold biosynthetic ADC is an ancestral form of the acid-inducible ADC found in E. coli and lacks the domain for We found that the domain of the acid-inducible AAT-fold ADC is from a response regulator protein receiver domain that has to the N of a biosynthetic AAT-fold The Bacillus biosynthetic AAT-fold ADC is to be essential for biofilm formation, that polyamines are involved in biofilm formation in single-membraned as as bacteria. that a in biofilm formation may be an function of polyamines in bacteria. We the phylogenetic distribution of the different ADC and show that is a double-membraned and single-membraned and single-membraned bacteria and we show that the ADC route for putrescine biosynthesis is the dominant pathway for polyamine formation in the human gut decarboxylation for polyamine biosynthesis has to from However, arginine decarboxylation in and plants a model for the processes metabolic pathway evolution. mechanisms involved in pathway evolution are gene duplication and gene The AR-fold of amino acid decarboxylases most evolved by gene duplication from the in the lysine biosynthetic of the AR-fold the is to the product of J. Michael A.J. D. Phillips M.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, M. J. Bacteriol. PubMed Scopus Google Scholar). of the AR-fold is involved in the polyamine pathway from a diamine to a triamine or The AR-fold decarboxylase a to arginine decarboxylation for putrescine biosynthesis. the it was that ADC was within the AR-fold decarboxylase it is the other is to a large The of the insertion is conserved prokaryotic but the amino acid of the insertion is conserved in a for the insertion the insertion domain in the AR-fold ADC has to be a that is for the AR-fold ADC a a the of the AR-fold decarboxylase J. Michael A.J. D.R. Phillips M.A. J. Biol. Chem. 2010; 285: Full Text Full Text PDF PubMed Scopus Google Scholar). The form of AR-fold ADC in the Chloroflexi and Bacteroidetes lacks the domain insertion and an ancestral form of AR-fold It is the same as and may a form and the AR-fold The is the domain and the AR-fold decarboxylases are with two from the the domain of one and the domain of the The of the insertion is the in the enzyme an insertion not enzymatic The ODC enzyme can be this same and the and domains can be and a functional ODC enzyme can be in from the two domains M. D. Phillips M.A. PubMed Scopus Google Scholar). We not the ADC the was widespread in bacteria and was by the form or the form ADC early in bacterial evolution. The Chloroflexi and are not to be was not a widespread of the form ADC, was horizontal transfer of the form ADC the two phyla. It appears that the form ADC is in all plants and that this is a of endosymbiotic gene transfer from the of the the of the AAT-fold amino acid decarboxylases and in the acid-inducible ADC, gene fusion was a key in the evolution of The most is that the biosynthetic AAT-fold ADC, found in such as subtilis, C. and S. was the ancestral form of the acid-inducible AAT-fold ADC S. the form AAT-fold ADC is a S. J. Biochem. PubMed Scopus Google Scholar). response regulator receiver domain protein was to the N of the biosynthetic AAT-fold ADC, the domain of the acid-inducible AAT-fold The domain is for formation of of the acid-inducible ADC to the of the domain in the J. S. 2009; 48: PubMed Scopus Google Scholar). the E. coli acid-inducible ADC, which has the formation is for enzyme activity in the with the domain of the and of enzymatic the of the domain is to formation and J. S. 2009; 48: PubMed Scopus Google Scholar). the form is and the is The domain can be to be as a response the of the receiver domain in the acid-inducible AAT-fold ADC acid to the domain the ADC the AR-fold and AAT-fold are also the two the and the are four different protein and two different the activity EC are three forms of the AR-fold the ancestral form described the form with and the ADC which has evolved from the AR-fold ODC J. Pegg A.E. Phillips M.A. J. Biol. Chem. 2004; 279: Full Text Full Text PDF PubMed Scopus Google Scholar, Phillips M.A. PubMed Scopus Google Scholar). are two forms of the AAT-fold ADC, the firmicute biosynthetic ADC and the E. coli acid-inducible are biosynthetic and acid-inducible forms of the D.E. H. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar, D.E. J. Bacteriol. PubMed Scopus Google Scholar, D.E. Ealick S.E. 11: Full Text Full Text PDF PubMed Scopus (31) Google Scholar) and the one form of the are four protein and eight different enzyme forms by the EC 4.1.1.19. is a form of described isofunctional (8Omelchenko M.V. Galperin M.Y. Wolf Y.I. Koonin E.V. Biol. Direct. 2010; 5: 31Crossref PubMed Scopus (100) Google carrying out the same but from different The of ADC forms the importance of arginine decarboxylation and polyamine biosynthesis for life different enzymatic for arginine decarboxylation independently gene the or are found in prokaryotic gene a that has for gene and operons is a for the genes of the to be in the biochemical as S. A.R. Biol. 2010; PubMed Scopus Google Scholar, Biol. 2009; PubMed Scopus (31) Google Scholar). the gene is a for the to be the of the that is in the gene is the of polyamine biosynthesis. are ADC but form of involved in polyamine biosynthesis can be with agmatine ureohydrolase or with agmatine and N-carbamoylputrescine as of a putrescine biosynthetic The may also include the or the for the spermidine biosynthetic of the a that is an (10Shaw F.L. Elliott K.A. Kinch L.N. Fuell C. Phillips M.A. Michael A.J. J. Biol. Chem. 2010; 285: 14711-14723Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar).The phylogenetic distribution of the different forms of ADC a the and form AR-fold are limited to double-membraned bacteria for two the genes by horizontal transfer. Biosynthetic AAT-fold ADC is limited to the not ADC for one ADC is the ADC of the it is found in bacterial as and the ADC is found in the for the of the of life the or in the Chloroflexi Biol. Direct. PubMed Scopus Google of bacteria and Biol. PubMed Scopus Google or to for a of life but with the prokaryotic bacteria and Wolf Y.I. Koonin E.V. J. Biol. 2009; 8: PubMed Scopus Google Scholar). The phylogenetic distribution of the different ADC forms the of bacteria, archaea, and for eukaryotes not possess a polyamine biosynthetic bacteria are from single-membraned bacteria by different ADC single-membraned bacteria, are from The are from and the are from bacteria. use and use The route for putrescine is of limited phylogenetic distribution in in a and of arginine is the dominant of polyamine biosynthesis in bacteria and of the ADC pathway for polyamine biosynthesis in bacteria is by the human gut ADC is the route for polyamine biosynthesis the most common gut human the ODC pathway for polyamine of ADC activity of the gut polyamines are found in almost all bacteria, it is not the for polyamines We that ADC polyamines are essential for biofilm in the single-membraned It is that polyamines are for biofilm in the double-membraned bacteria and However, in the polyamine biosynthetic putrescine and not spermidine biofilm formation, in but not spermidine was subtilis, spermidine is to biofilm of spermidine is to in E. coli S. S. Biochem. PubMed Scopus Google it is to that in biofilm formation is spermidine and is by a regulatory I. Microbiol. 2010; PubMed Scopus Google Scholar). IntroductionThe evolution of central metabolic pathways was one of the key biochemical developments in the early stages of primordial life (1Caetano-Anollés G. Yafremava L.S. Gee H. Caetano-Anollés D. Kim H.S. Mittenthal J.E. Int. J. Biochem. Cell Biol. 2009; 41: 285-297Crossref PubMed Scopus (87) Google Scholar). Metabolic pathways evolve through mechanisms such as gene duplication followed by neofunctionalization of one of the copies to produce a new enzyme with an altered substrate preference (2Ohno S. Evolution by Gene Duplication. Springer-Verlag, New York1970Crossref Google Scholar, 3Serres M.H. Kerr A.R. McCormack T.J. Riley M. Biol. Direct. 2009; 4: 46Crossref PubMed Scopus (41) Google Scholar, 4Innan H. Kondrashov F. Nat. Rev. Genet. 2010; 11: 97-108Crossref PubMed Scopus (825) Google Scholar). Other mechanisms involved in the evolution of metabolic pathways include gene fusions, which can be fusion of two paralogous genes to achieve gene elongation. An example is the formation of eukaryotic S-adenosylmethionine decarboxylase (AdoMetDC), 5The abbreviations used are: AdoMetDCS-adenosylmethionine decarboxylaseAAT-foldaspartate aminotransferase foldADCarginine decarboxylaseAIHagmatine iminohydrolaseAR-foldalanine racemase foldAUHagmatine ureohydrolaseCANSDCcarboxy(nor)spermidine decarboxylaseDAPDCmeso-diaminopimelate decarboxylaseLDClysine decarboxylaseL/ODClysine/ornithine decarboxylaseNCPAHN-carbamoylputrescine amidohydrolaseODCornithine decarboxylasePLPpyridoxal 5′-phosphatepylADCpyruvoyl-dependent arginine decarboxylaseRECreceiver domainaaamino acidsCHES2-(cyclohexylamino)ethanesulfonic acid. a polyamine biosynthetic enzyme, by fusion of two prokaryotic AdoMetDC genes (5Toms A.V. Kinsland C. McCloskey D.E. Pegg A.E. Ealick S.E. J. Biol. Chem. 2004; 279: 33837-33846Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar). Gene fusions may bring together different protein functional modules such as regulatory and enzymatic components and are often generated independently in different lineages by fusion of open reading frames within operons (6Yanai I. Wolf Y.I. Koonin E.V. Genome. Biol. 2002; 3 (research0024)Google Scholar). New steps in metabolic pathways can be recruited from preexisting pathways in the same cell (the “patchwork” model of pathway evolution) (7Jensen R.A. Annu. Rev. Microbiol. 1976; 30: 409-425Crossref PubMed Scopus (815) Google Scholar) or from other organisms by horizontal or endosymbiotic gene transfer. Convergent evolution of the same enzymatic activity in different organisms by completely different, evolutionarily unrelated proteins (recently described as non-homologous isofunctional enzymes) (8Omelchenko M.V. Galperin M.Y. Wolf Y.I. Koonin E.V. Biol. Direct. 2010; 5: 31Crossref PubMed Scopus (100) Google Scholar) is a result of independent biochemical invention (9Galperin M.Y. Walker D.R. Koonin E.V. Genome Res. 1998; 8: 779-790Crossref PubMed Scopus (191) Google Scholar).The biosynthesis of polyamines is an excellent model for studying processes of metabolic pathway evolution. Polyamines are small organic polycations, usually linear di-, tri-, and tetra-amines, that are found in almost all cells. Synthesis of polyamines is achieved through biosynthetic modules: a diamine is produced directly or indirectly from an amino acid, and a triamine is produced from the diamine by the addition of an aminopropyl or aminobutyl group. Tetra-amines are produced from triamines by aminopropyl or more rarely by aminobutyl group addition. The modular nature of polyamine biosynthesis facilitates horizontal and endosymbiotic transfer (10Shaw F.L. Elliott K.A. Kinch L.N. Fuell C. Phillips M.A. Michael A.J. J. Biol. Chem. 2010; 285: 14711-14723Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar).By far, in all three domains of life, the most common diamine is putrescine (1,4-diaminobutane), which can be used to form spermidine (by aminopropyl addition) or sym-homospermidine (by aminobutyl addition). Almost all eukaryotes synthesize putrescine directly from ornithine by the action of ornithine decarboxylase (ODC). However, plants possess an additional, indirect pathway for putrescine biosynthesis from arginine, through the action of arginine decarboxylase (ADC) (11Fuell C. Elliott K.A. Hanfrey C.C. Franceschetti M. Michael A.J. Plant Physiol. Biochem. 2010; 48: 513-520Crossref PubMed Scopus (136) Google Scholar). It is unclear which bacteria use the ADC route to synthesize putrescine, and the relative importance of the ODC and ADC routes in bacterial polyamine biosynthesis is also unclear. The product of ADC, agmatine, may be converted directly to putrescine by agmatine ureohydrolase (AUH) (12Satishchandran C. Boyle S.M. J. Bacteriol. 1986; 165: 843-848Crossref PubMed Scopus (54) Google Scholar) or indirectly via N-carbamoylputrescine by agmatine deiminase/iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NCPAH) (13Nakada PubMed Scopus Google are four protein fold an The alanine racemase fold (AR-fold) of the eukaryotic ODC from human and M.A. Phillips M.A. J. Biol. PubMed Scopus Google Scholar, Phillips M.A. PubMed Scopus Google decarboxylase from J. Michael A.J. D. Phillips M.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google meso-diaminopimelate decarboxylase from and G. H. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar, J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, D. J. J. H. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google and decarboxylase and ADC J. Michael A.J. D.R. Phillips M.A. J. Biol. Chem. 2010; 285: Full Text Full Text PDF PubMed Scopus Google Scholar). The AR-fold ADC is the other of the AR-fold amino acid decarboxylases J. Michael A.J. D. Phillips M.A. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google to a large insertion relative to other of the ADC of Escherichia which is not involved in polyamine to the aspartate aminotransferase fold which also the E. coli and biosynthetic ODC and also bacterial acid-inducible lysine ADC is in M. and most of the euryarchaeota D.E. H. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google and most of the possess an ADC that has evolved from the AdoMetDC D.E. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). An not involved in polyamine is in D.E. J. Bacteriol. PubMed Scopus Google Scholar). large such as possess an AR-fold ADC that and has evolved from an AR-fold ODC J. Pegg A.E. Phillips M.A. J. Biol. Chem. 2004; 279: Full Text Full Text PDF PubMed Scopus Google Scholar, Phillips M.A. PubMed Scopus Google Scholar). the form of ADC enzyme in bacteria, ADC is by the polyamines are primordial of life, it has to eukaryotes and archaea, spermidine is for formation, which is essential for cell in eukaryotes and M. PubMed Scopus Google Scholar, J. Bacteriol. PubMed Scopus Google Scholar). in archaea, it was that agmatine is for an essential of a in a produce the for the D. C. D. D. 2010; PubMed Scopus Google Scholar, S. D. Nat. Chem. Biol. 2010; PubMed Scopus Google Scholar). of that the of spermidine is in formation for in the H. PubMed Scopus Google Scholar, M.H. H. PubMed Scopus Google Scholar) and in Pegg A.E. Biochem. J. PubMed Scopus Google Scholar, M. A.R. J. J. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). are also that polyamines function independently of formation M.H. Biochem. J. PubMed Scopus Google Scholar, G. M.H. C. J. Biol. Chem. 2010; 285: Full Text Full Text PDF PubMed Scopus Google Scholar). The essential for spermidine and agmatine in and formation, other of polyamines in eukaryotes and bacteria, which and a more model for of However, of E. coli is by polyamine H. J. Bacteriol. 2009; PubMed Scopus (54) Google Scholar). and of all polyamines or of in a of of M.A. J. Bacteriol. PubMed Scopus Google Scholar, J. D.E. J. Phillips M.A. Michael A.J. J. Biol. Chem. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). polyamine of (13Nakada PubMed Scopus Google Scholar) and of (10Shaw F.L. Elliott K.A. Kinch L.N. Fuell C. Phillips M.A. Michael A.J. J. Biol. Chem. 2010; 285: 14711-14723Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar). polyamine of and polyamine in biofilm M.A. J. Bacteriol. PubMed Scopus Google Scholar, J. D.E. J. Phillips M.A. Michael A.J. J. Biol. Chem. 2009; Full Text Full Text PDF PubMed Scopus Google Scholar). formation is a key polyamines are independently of or formation, in two of we that an ancestral form of the AR-fold ADC in of the Chloroflexi and phyla. The ancestral AR-fold ADC lacks the insertion of the AR-fold which is found in most of the double-membraned bacteria. We also show that the firmicute AAT-fold biosynthetic ADC is an ancestral form of the acid-inducible ADC found in E. coli and lacks the domain for We found that the domain of the acid-inducible AAT-fold ADC is from a response regulator protein receiver domain that has to the N of a biosynthetic AAT-fold The Bacillus biosynthetic AAT-fold ADC is to be essential for biofilm formation, that polyamines are involved in biofilm formation in single-membraned as as bacteria. that a in biofilm formation may be an function of polyamines in bacteria. We the phylogenetic distribution of the different ADC and show that is a double-membraned and single-membraned and single-membraned bacteria and we show that the ADC route for putrescine biosynthesis is the dominant pathway for polyamine formation in the human gut microbiota.