Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution

Gallagher, Connor

Marsh, Andrew

Millard, Andrew D.

Scanlan, David J.

Taylor, Paul C.

English

Millard, A

Scanlan, DJ

Gallagher, C

Marsh, A

Taylor, PC

White Rose Research Online

Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Warwick Research Archives Portal Repository

http://wrap.warwick.ac.uk           Original citation: Millard, Andrew D, Scanlan, David J. , Gallagher, Connor, Marsh, A. (Andrew) and Taylor, Paul C.. (2014) Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation. Molecular BioSystems, Volume 10 (Number 3). pp. 380-383. ISSN 1742-206X  Permanent WRAP url: http://wrap.warwick.ac.uk/58891                Copyright and reuse: The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions.  Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners.  To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.  Copies of full items can be used for personal research or study, educational, or not-for  profit purposes without prior permission or charge.  Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way.  A note on versions: The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher’s version.  Please see the ‘permanent WRAP url’ above for details on accessing the published version and note that access may require a subscription.  For more information, please contact the WRAP Team at: publications@warwick.ac.uk  Journal Name Cite this: DOI: 10.1039/c0xx00000x www.rsc.org/xxxxxx Dynamic Article Links ► ARTICLE TYPE  This journal is © The Royal Society of Chemistry [year] [journal], [year], [vol], 00–00 | 1 Unexpected Evolutionary Proximity of Eukaryotic and Cyanobacterial Enzymes responsible for Biosynthesis of Retinoic Acid and its Oxidation  Andrew Millard, a David J. Scanlan,*a Connor Gallagher,b Andrew Marshb and Paul C. Taylor*b Received (in XXX, XXX) Xth XXXXXXXXX 20XX, Accepted Xth XXXXXXXXX 20XX DOI: 10.1039/b000000x 5 Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in 10 evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution. Retinoic acid (RA) is the main biologically active form of Vitamin A1 and controls key development processes in the animal kingdom.2 Indeed, RA signalling has been considered to be a 15 distinctive feature of animals3 with phylogenetic analyses pushing the evolutionary origins of retinoid biosynthesis ever earlier through the chordate4 and bilaterian5 lineages. RA is also medically important. Both RA and analogues are used as therapeutic drugs;6 RA can be a harmful teratogen in other 20 circumstances.7  Given its animal “heritage”, it is surprising that RA, its biosynthetic precursor retinaldehyde and oxidised catabolites of RA have recently been discovered in cyanobacteria,8 since animals and cyanobacteria are, in standard models, linked only at 25 the very beginning of evolutionary history.9 Research has focused little on the possibility that RA is a signalling molecule in cyanobacteria, with more emphasis on its seemingly aggressive teratogenic effects on other organisms during cyanobacterial blooms in, for example, eutrophic lakes in China.10 30  Our interests in sensory processes in cyanobacteria11 and eukaryotic signalling molecules12 led us to consider the possibility that there were hitherto unnoticed links between RA signalling in the animal kingdom and in cyanobacteria. Since lateral gene transfer between cyanobacteria and animals has been 35 implied previously,13 we reasoned it unwise to assume that RA signalling had evolved independently in these apparently utterly diverse lineages. Herein we extend to cyanobacteria phylogenetic analyses of the distinctive enzymes responsible for retinoid biosynthesis in animals and conclude that assumptions about 40 separate evolution of RA pathways should be re-evaluated.  In vertebrates, retinoic acid 3 is biosynthesised from dietary retinal 2 (or dietary beta-carotene 1 via retinal 2).3 There are two enzymes that are highly characteristic of retinoid biosynthesis and catabolism and that have been the subjects of detailed 45 phylogenetic analysis in eukaryotes, namely the aldehyde dehydrogenase (ALDH) that catalyses dehydrogenation of retinal 2 to form RA5,14 and the cytochrome P450 that further transforms, or catabolises, RA.15 Our study sought, very simply, to extend these phylogenetic analyses to prokaryotes. 50   In 2011 Sobreira et al. published their phylogenetic analysis of ALDH enzymes in eukaryotes, which included a range of organisms from across the evolutionary spectrum.14 We submitted the protein sequence of human ALDH1A1 55 (EAW62544) to NCBI BLASTp16 using standard settings but including only prokaryotes. Intriguingly, the closest alignments from all bacteria and archaea were with aldehyde dehydrogenases from cyanobacteria and from planctomycetes. We therefore added representative examples of these classes to the eukaryotic 60 dataset used by Sobreira et al.14 ALDH sequences were aligned in MUSCLE and viewed in MEGA5 (see Supplementary Information). Phylogeny was inferred by Maximum Likelihood using the Jones-Taylor-Thornton (JTT) model with 1000 bootstrap replicates. Our unrooted phylogenetic tree including 65 cyanobacterial and planctomycete orthologs is shown in Figure 1.  According to Sobreira et al., ALDH1a and ALDH2 enzymes fall into a common clade, in which the former specifically do and the latter specifically do not process retinaldehyde.14 Our research  2 | Journal Name, [year], [vol], 00–00 This journal is © The Royal Society of Chemistry [year] suggests that the bacterial orthologs should be considered phylogenetically as part of the same clade and that animal ALDH1a/2 enzymes are more closely related in evolutionary terms to these bacterial ALDHs than they are to their closest paralogs in the same animals, ALDH1L and ALDH8 5 dehydrogenases (Fig. 1).  The next biosynthetic step is the oxidation of RA by cytochrome P450 enzymes known as CYP26 in animals6 and CYP120 in cyanobacteria.17,18 A 2009 phylogenetic analysis of CYP26s by Albalat and Canestro gave an early clue that RA 10 pathways may be ‘ancient elements of animal genomes, already present in the last common ancestor of bilaterians’.5 Once again, we first verified that we could reproduce Albalat and Canestro’s tree using our methods. We then used NCBI BLASTp against the prokaryotic proteome to identify non-eukaryotic orthologs and, 15 once again, found the best matches to be in cyanobacteria (though not planctomycetes).  Figure 2 presents our expanded phylogenetic tree for metazoan CYP26, plant CYP707 and cyanobacterial CYP120 orthologs. Animal CYP51 and CYP4v2 paralogs were added and the tree 20 was rooted on human CYP4v2 as in the literature.5 Again, the cyanobacterial CYP120s fall clearly within the clade including animal CYP26s and plant CYP707s  The two phylogenetic trees presented here are together strong evidence that the retinoic acid biosynthetic pathway outlined in 25 Scheme 1 did not evolve separately in eukaryotes and prokaryotes. Rather the occurrence of two enzymes in the same pathway that both have structural and functional analogies across cyanobacteria and metazoans is more easily explained by a hitherto unsuspected lateral transfer of the corresponding genes.19 30 Lateral gene transfer from cyanobacteria to animals has precedent; Aravind et al. have concluded that WD40 domains in metazoans most likely arose through such an event.13,20  Structural, spectroscopic and analytical studies show that CYP120A1 from Synechocystis and metazoan CYP26s are 35 strikingly similar. They have both been shown to catalyse reactions of RA and to oxidise it at the 4- and 18- positions (oxidation at the 2-position has also been proposed in the cyanobacterium).6,17,21,22 Furthermore, there are conserved tryptophan and phenylalanine residues believed to occupy 40 important positions in the binding site. Indeed, Alder et al. have observed that ‘despite the huge evolutionary distance' vertebrate and cyanobacterial retinoic acid hydroxylases are similar.18 Our proposal of lateral gene transfer may resolve this conundrum.  To our knowledge there are no structural or mechanistic 45 studies on the bacterial ALDH enzymes included in our phylogenetic analysis and the few annotations as “retinal dehydrogenase” appear to be from homology only. Therefore, we undertook a detailed study of the active site motif identified by Sobreira et al. as being characteristic of the catalytic site of these 50 enzymes in vertebrates, GQCC, which is found at amino acids 299-302 of human ALDH1A1.14  The GQCC motif is found in many of the eukaryotic ALDH1 and ALDH2 enzymes in our study and in none of the ALDH8 and ALDH1L proteins. Strikingly the same motif is present in all of 55 the bacteria we investigated, as indicated in Figure 1. This conserved motif at the catalytic site lends further support to our proposal that the similarities between animal and bacterial ALDHs are unlikely to have arisen through independent, convergent evolution. 60    ALDH8A1 H. sapiens  ALDH8B1 C. elegans  ALDH1L1 D. melanogaster  ALDH1L1 H. sapiens  ALDH1L S. purpuratus  ALDH1L1 C. elegans  ALDH2b S. purpuratus *ALDH9B2 C. elegans *ALDH2 L. gigantea *ALDH2 C. teleta *ALDH2 Capitella sp. *ALDH1A10 D. melanogaster *ALDH2 B. floridae *ALDH2 N. vectensis *ALDH1B1 H. sapiens *ALDH1B1 M. musculus *ALDH1B1 R. norvegicus *ALDH2 H. sapiens *ALDH2 M. musculus *ALDH2 R. norvegicus *G. obscuriglobus (ZP 02730696) *Singulosphaera (ZP 09565902) *B. marina (ZP 01091754) *P. staleyi (YP 003370928) *Rhodopirellula (NP 869285) *Rhodopirellula (EGF24028) *P. maris (ZP 01851832) *P. limnophilus (YP 003629897) *Singulosphaera (ZP 09568612) *Isosphaera (YP 004178423) *P. brasiliensis (YP 004269788) *Cyanothece sp. (YP 002379008 PCC 7424) *Cyanothece sp. (YP 003890169 PCC 7822) *Lyngbya sp. (ZP 01618896 PCC 8106) *M. chthonoplastes (ZP 05023575 PCC 7420) *Cyanothece sp. (YP 001804643 ATCC 51142) *Cyanothece sp. (ZP 01726360 CCY0110) *Crocosphaera (ZP 00518574 WH 8501) *Crocosphaera (EHJ10116 WH 0003) *Cyanothece sp. (YP 003137302 PCC 8802) *T. erythraeum (YP 722268 IMS101) *M. producta (ZP 08426871 3L) *ALDH1a N. vectensis *ALDH1b N. vectensis  ALDH1c C. teleta  ALDH1c L. gigantea *ALDH1e B. floridae  ALDH1f B. floridae *ALDH1b B. floridae  ALDH1c B. floridae  ALDH1d B. floridae  ALDH1a C. teleta  ALDH1A1/2/3A Capitella sp.  ALDH1b C. teleta *ALDH1a L. gigantea *ALDH1b L. gigantea  ALDH1M1 D. melanogaster *ALDH1A1/2/3A D. Pulex  ALDH1A4 R. norvegicus  ALDH1A7 M. musculus *ALDH1A1 R. norvegicus *ALDH1A1 M. musculus *ALDH1A1 H. sapiens *ALDH1A2 R. norvegicus *ALDH1A2 H. sapiens *ALDH1A2 H. sapiens *ALDH1A3 R. norvegicus *ALDH1A3 M. musculus *ALDH1A3 H. sapiens  ALDH1a C. savignyi  ALDH1a C. intestinalis  ALDH1b C. intestinalis  ALDH1c C. intestinalis  ALDH1b C. savignyi999999899998996099969999989193998299999999995691999983999858999998988366818393898585796463985095 Fig. 1 Phylogenetic tree of aldehyde dehydrogenase (ALDH) enzymes from representative metazoans, cyanobacteria and planctomycetes. Proteins analysed previously in Ref. 14 are shown in teal (ALDH8), orange (ALDH1L), blue 65 (ALDH1) and pink (ALDH2). Cyanobacterial and planctomycete proteins added in this study are shown in cyan. Proteins with active site motif GQCC are indicated with an asterisk. In Fig. S1 (ESI) branches present in less than 50% of bootstrap replicates are collapsed.  This journal is © The Royal Society of Chemistry [year] Journal Name, [year], [vol], 00–00 | 3  CYP26B1 H. sapiens CYP26B1 M. musculus CYP26B1 D. rerio CYP26C1 D. rerio CYP26C1 H. sapeins CYP26C1 M. musculus Pred. CYP26A1 C. intestinalis Pred. CYP26A1 S. purpuratus CYP26A1 D. rerio CYP26A1 H. sapiens CYP26A1 M. musculus XP 002588109.1 B. floridae XP 002588110.1 B. floridae XP 002588109.1 B. floridae XP 002588112.1 B. floridae CYP26 Capitella sp. CYP26 Capitella sp. (2) CYP26 Capitella sp. (4) CYP26 Capitella sp. (3) ABA 8-hydroxylase 4 A. thaliana ABA 8-hydroxylase C. sinensis ABA 8-hydroxylase M. truncatula ABA 8-hydroxylase N. plumbaginifolia ABA 8-hydroxylase S. tuberosum CYP P. pacifica SIR-1 CYP Cyanobium sp. PCC 7001 CYP P. marinus str. MIT 9313 CYP P. marinus str. MIT 9303 CYP Synechococcus sp. RS9916 CYP Synechococcus sp. WH 8016 CYP Synechococcus sp. WH 8102 CYP Synechococcus sp. RCC307 CYP Synechococcus sp. CC9605 Putative CYP120 S. aurantiaca DW4/3-1 CYP H. aurantiacus DSM 785 CYP N. punctiforme PCC 73102 CYP M. chthonoplastes PCC 7420 CYP Cyanothece sp. PCC 7822 CYP Cyanothece sp. ATCC 51142 CYP Synechococcus sp. PCC 7335 CYP A. marina MBIC11017 CYP Acaryochloris sp. CCMEE 5410 CYP Synechococcus sp. PCC 7335 CYP N. spumigena CCY9414 ABA 8-hydroxylase Fischerella sp. JSC-11 CYP M. chthonoplastes PCC 7420 Putative CYP120 Oscillatoria sp. PCC 6506 ABA 8-hydroxylase M. vaginatus FGP-2 CYP Cyanothece sp. PCC 7425 CYP Lyngbya sp. PCC 8106 CYP M. producta 3L CYP120 M. aeruginosa PCC 7806 CYP M. aeruginosa NIES-843 CYP Cyanothece sp. PCC 7424 CYP Cyanothece sp. CCY0110 CYP Synechococcus sp. PCC 7002 CYP Synechocystis sp. PCC 6803 CYP A. marina MBIC11017 CYP T. erythraeum IMS101 CYP51 Capitella sp. CYP51 H. sapiens CYP4v2 H. sapiens CYP4v2 M. musculus100100946210010010010010010010010010082100939998899083747454555150645653515150859987797478 Figure 2. Phylogenetic tree of cytochrome P450 (CYP) enzymes from representative metazoans, plants and cyanobacteria. Proteins analysed previously in Ref. 5 are shown in pink (metazoan CYP26), orange (metazoan CYP51 & CYP4v2) and green (plant CYP707). Cyanobacterial proteins added in this study are shown in 5 cyan. In Fig. S2 (ESI) branches present in less than 50% of bootstrap replicates are collapsed.  Conclusions Maximum likelihood phylogenetic analyses, across all kingdoms, of both ALDH1a/2 aldehyde dehydrogenases and cytochrome 10 P450 enzymes known to oxidise retinoic acid show surprising evolutionary proximities between animal and cyanobacterial proteins (and also planctomycetes in the case of ALDHs). We believe the simplest explanation consistent with these data, and with literature observations on the structures and functions of the 15 enzymes, to be a lateral gene transfer event between the bacteria and animals. Given the importance of retinoic acid biosynthesis to developmental biology and in medicine, our observations suggest that detailed research of the pathway in cyanobacteria could have 20 an impact on human healthcare,2 as well as understanding of important ecosystems.10 Further studies of the evolutionary links between such apparently distant species may also be revealing. Notes and references a School of Life Sciences, University of Warwick, Coventry, CV4 7AL, 25 UK. b Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK. Fax: 44 24 76524112; Tel: 44 24 76524375; E-mail: p.c.taylor@warwick.ac.uk † Electronic Supplementary Information (ESI) available: Methods. 30 Accession numbers for proteins added in this study. Full names of organisms added in this study. Full page versions of Figs. 1, 2, S1 & S2. See DOI: 10.1039/b000000x/  1 J. Gutierrez-Mazariegos, M. Theodosiou, F. Campo-Paysaa, M. 35 Schubert, Semin. Cell Dev. Biol., 2011, 22, 603. 2 M. Theodosiou, V. Laudet and M. Schubert, Cell Mol. Life Sci., 2010, 67, 1423. 3 R. Blomhoff and H. K. Blomhoff, J. Neurobiol., 2006, 66, 606. 4 M. S. Simoes-Costa, A. P. Azambuja and J. Xavier-Neto, J. Exp. 40 Zool. (Mol. Dev. Evol.), 2008, 310B, 54. 5 R. Albalat and C. Canestro, Chem. Biol. Interact., 2009, 178, 188. 6 V. C. O. Njar, L. Gediya, P. Purushottamachar, P. Chopra, T. S. Vasaitis, A. Khandelwal, J. Mehta, C. Huynh, A. Belosay and J. Patel, Bioorg. Med. Chem., 2006, 14, 4323. 45 7 S.V. Bryant and D. M. Gardiner, Dev. Biol., 1992, 152, 1. 8 X-Q. Wu, J-Q. Jiang, Y. Wan, J. P. Giesy and J-Y. Hu, Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 9477. 9 F. D. Ciccarelli, T. Doerks, C. von Mering, C. J. Creevey, B. Snel and P. Bork, Science, 2006, 311, 1283. 50 10 X-Q. Wu, J-Q. Jiang and J-Y. Hu, Environ. Sci. Technol., 2013, 47, 807. 11 D. J. Scanlan, M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen and F. Partensky, Microbiol. Mol. Biol. Rev., 2009, 73, 249. 55 12 S. J. Dilly, M. J. Bell, A. J. Clark, A. Marsh, R. M. Napier, M. J. Sergeant, A. J. Thompson and P. C. Taylor, Chem. Commun., 2007, 2808. 13 L. Aravind, L. M. Iyer, V. Anantharaman. Natural History of Sensor Domains in Bacterial Signalling Systems in 'Sensory Mechanisms in 60 Bacteria: Molecular Aspects of Signal Recognition', eds. Spiro S and Dixon R, Caister, UK, 2010. 14 T. J. P. Sobreira, F. Marlétaz, M. Simoes-Costa, D. Schechtman, A. C. Pereira, F. Brunet, S. Sweeney, A. Pani, J. Aronowicz, C. J. Lowe, B. Davidson, V. Laudet, M. Bronner, P. S. L. de Oliveira, M. 65 Schubert and J. Xavier-Neto, Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 226. 15 A. R. Topletz, J. E. Thatcher, A. Zelter, J. D. Lutz, S. Taya, W. L. Nelson, N. Isoherranen, Biochem. Pharm., 2012, 83, 149. 16 S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. 70 Miller W and  D. J. Lipman, Nucleic Acids Res., 1997, 25, 3389. 17 K. Kühnel, N. Ke, M. J. Cryle, S. G. Sligar, M. A. Schuler and I. Schlichting, Biochemistry, 2008, 47, 6552. 18 A. Alder, P. Bigler, D. le Werck-Reichhart and S. Al-Babili, FEBS Journal, 2009, 276, 5416. 75 19 M. A. Ragan and R. G. Beiko, Phil. Trans. R. Soc. B. 2009, 364, 2241. 20 C. P. Ponting, L. Aravind, J. Schultz, P. Bork and E. V. Koonin, J. Mol. Biol., 1999, 289, 729. 21 M. S. Gomaa, S. W. Yee, C. E. Milbourne, M. C. Barbera, C. Simons 80 and A. Brancale, J. Enzyme Inhib. Med. Chem., 2006, 21, 361. 22 K. Kaya, F. Shiraishi, H. Uchida and T. Sano, Biochim. Biophys. Acta, 2011, 1810, 414. 23 A. L. Lamb and M. E. Newcomer, Biochemistry, 1999, 38, 6003.  85 

Andrew Millard

David J. Scanlan

Connor Gallagher

Andrew Marsh

Paul C. Taylor

Crossref

Molecular BioSystems

http://wrap.warwick.ac.uk/58891/1/WRAP_Scanlan_8871765-lf-080814-taylor_retinoic_acid_revised_dec13.pdf

Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Abstract

Similar works

Full text

Available Versions

White Rose Research Online

White Rose Research Online

Warwick Research Archives Portal Repository

Crossref