Molecular Machines Encoded by Bacterially-Derived Multi-Domain Gene Fusions That Potentially Synthesize, N-Methylate and Transfer Long Chain Polyamines in Diatoms
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 585 (2011) 2627–2634 journal homepage: www.FEBSLetters.org Hypothesis Molecular machines encoded by bacterially-derived multi-domain gene fusions that potentially synthesize, N-methylate and transfer long chain polyamines in diatoms Anthony J. Michael Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA article info abstract Article history: Silica glass formation in diatoms requires the biosynthesis of unusual, very long chain polyamines Received 20 July 2011 (LCPA) composed of iterated aminopropyl units. Diatoms processively synthesize LCPA, N-methylate Accepted 21 July 2011 the amine groups and transfer concatenated, N-dimethylated aminopropyl groups to silaffin pro- Available online 4 August 2011 teins. Here I show that diatom genomes possess signal peptide-containing gene fusions of bacteri- ally-derived polyamine biosynthetic enzymes S-adenosylmethionine decarboxylase (AdoMetDC) Edited by Miguel De la Rosa and an aminopropyltransferase, sometimes fused to a eukaryotic histone N-methyltransferase domain, that potentially synthesize and N-methylate LCPA. Fusions of similar, alternatively Keywords: configured domains but with a catalytically dead AdoMetDC and in one case a Tudor domain, may Diatom Biosilica glass N-dimethylate and transfer multiple aminopropyl unit polyamines onto silaffin proteins. Long chain polyamine biosynthesis Ó 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. N-methylation Aminopropyltransferase 1. Introduction Polyamines are small organic polycations found in almost all cells and are essential for growth and cell proliferation in eukary- Diatoms are ubiquitous, aquatic single-celled eukaryotic organ- otes. In normal eukaryotic polyamine metabolism (Fig. 1A), the isms responsible for 20% of planetary photosynthetic activity, triamine spermidine is formed by transfer of an aminopropyl group equal to all terrestrial rainforests combined [1]. Their highly elab- to the diamine putrescine (1,4-diaminobutane). The aminopropyl orate, biosilica glass cell wall is constructed from monosilicic acid group is derived from decarboxylated S-adenosylmethionine (Si(OH)4) by a biomineralization process initiated by highly modi- formed by S-adenosylmethionine decarboxylase (AdoMetDC) fied proteins known as silaffins [2–5] and by very long chain linear [14]. Transfer of the aminopropyl group to putrescine is performed polyamines (LCPA) (Fig. 1A) that may be N-methylated on second- by the aminopropyltransferase spermidine synthase [15]. The ary and primary amines [6–10]. In some species, proteins called tetramines spermine and thermospermine are formed from sper- cingulins form an organic matrix that acts as a template to guide midine by transfer of another aminopropyl group to the N8 (amin- silicification [11]. Silaffin proteins are modified by dimethylation obutyl) or N1 (aminopropyl) ends of spermidine, respectively, by of some lysine residues and by transfer of multiple aminopropyl the aminopropyltransferases spermine [16] and thermospermine unit polyamines to other lysine e-amino groups. Transferred poly- synthase [17]. At the beginning of the pathway (Fig. 1A), putrescine amine moieties may be dimethylated on primary and secondary is formed from ornithine by the action of ornithine decarboxylase amine groups. The LCPA may be composed of as many as 20 ami- (ODC) [18]. In eukaryotic cells, spermidine levels are highly regu- nopropyl units [12], the chain length and degree of methylation lated at the level of biosynthesis, catabolism, uptake and export of primary and secondary amine groups dependent on species. In [19]. The key biosynthetic enzymes ODC and AdoMetDC are the diatom Thalassiosira pseudonana, LCPA may contain putrescine, negatively regulated in response to polyamine levels by sensitive spermidine or 1,3-diaminopropane as well as the multiple post-transcriptional feedback systems that include programmed aminopropyl repeat units [7,13]. ribosomal frameshifting and ribosome stalling [20,21]. These pow- erful homeostatic systems adjust spermidine concentrations to the level required by the physiological state of the cell. Synthesis of Abbreviations: LCPA, long chain polyamine; ODC, ornithine decarboxylase; LCPA therefore must not disrupt spermidine homeostasis and LCPA AdoMet, S-adenosylmethionine; AdoMetDC, S-adenosylmethionine decarboxylase; MTA, methylthioadenosine must be sequestered from the normal cellular binding sites of E-mail address: [email protected] polyamines. The pathway for LCPA biosynthesis, polyamine 0014-5793/$36.00 Ó 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. doi:10.1016/j.febslet.2011.07.038 2628 A.J. Michael / FEBS Letters 585 (2011) 2627–2634 O ornithine H2N OH S-adenosylmethionine NH2 N N HO OH ornithine O decarboxylase H2N N SH NH N O OH 2 H2N putrescine NH2 S-adenosylmethionine decarboxylase spermidine synthase NH2 N HO N H2NN OH H spermidine H2N N SH N O decarboxylated NH2 thermospermine S-adenosylmethionine synthase NH2 H2N NN H H thermospermine S-adenosylmethionine N N HO Silica deposition vesicle OH O H2N N SH N O OH aminopropyltransferase/ S-adenosylmethionine decarboxylase NH2 fusion domain for successive aminopropyl SET domain group transfer methyltransferase n = up to 20 NH2 H2N N NN H {}H present in some N N HO OH long chain polyamines O H2N N S N O OH S-adenosylhomocysteine NH2 Fig. 1A. Polyamine and LCPA biosynthesis in diatoms. modification of silaffins, and methylation of primary and second- perturbation of normal polyamine homeostasis. Here I show that ary amines has remained enigmatic. In particular, it is unclear the genomes of T. pseudonana, Phaeodactylum tricornutum and how multiple aminopropyl units could be sequentially transferred Fragilariopsis cylindrus encode one set of molecular machines that to the growing polyamine chain of LCPA. It is unlikely that LCPA potentially perform the tasks of iterative addition of multiple biosynthesis is similar to normal polyamine biosynthesis where aminopropyl groups to form LCPA, by supplying their own decar- each aminopropyl group transfer is achieved by different amino- boxylated S-adenosylmethionine and concommitent or subsequent propyltransferase enzymes, otherwise there would need to be up N-methylation of the LCPA. Another set of fusion proteins could to 20 different successive aminopropyltransferases. It is also not perform aminopropyl group transfer to lysine residues of silaffins, clear how multiple amino groups in a single LCPA chain could be and processive N-dimethylation of amine groups. The molecular methylated. LCPA synthesis would require a relatively large supply machines are derived from bacterial polyamine biosynthetic of decarboxylated S-adenosylmethionine, and a mechanism would enzyme fusions and chromatin protein modification and binding have to be in place to prevent physiologically damaging domains. A.J. Michael / FEBS Letters 585 (2011) 2627–2634 2629 2. Materials and methods Formation of the triamine spermidine from putrescine in eukaryotes requires AdoMetDC and the aminopropyltransferase 2.1. Sequence and phylogenetic analysis spermidine synthase (Fig. 1A). Typical eukaryotic AdoMetDC orthologues are present in the three diatom genomes (Table S1), The diatom genomes were analysed using the US Department of and in T. pseudonana and P. tricornutum AdoMetDC mRNAs, for Energy Joint Genome Institute Genome Portal (http://genome.jgi- which mRNA sequences with long 50 leader sequences are avail- psf.org/). BLASTP of diatom proteins in the NCBI non-redundant able, an upstream open reading frame encoding peptides of 29 protein sequences yielded only very partial proteins (e.g., 70–90 and 26 amino acids, respectively, is present in the mRNA 50 region. a.a. instead of 750–950 a.a., using a Thermotoga maritima Ado- The upstream ORFs likely encode ribosome-stalling peptides anal- MetDC sequence to screen the diatom proteins). Phylogenetic anal- ogous to plant and mammalian AdoMetDC mRNAs [21], as part of a ysis was performed as previously described [22]. Alignments were polyamine-responsive autoregulatory negative feedback system. performed with ClustalW in ClustalX [23] and trees were made Typical spermidine synthase orthologues are present in each of with PAUP⁄ [24]. Signal peptides were analysed using the SignalP the three diatom genomes, and in T. pseudonana, the spermidine server http://www.cbs.dtu.dk/services/SignalP/ taking into consid- synthase paralogue ThaSDS1 has been shown [26] to be functional. eration both the result from the neural network analysis and Hid- There are three spermidine synthase paralogues in F. cylindrus, and den Markov models. All aminopropyltransferase fusions were two each in P. tricornutum and T. pseudonana (shown below in identified by TBLASTN and BLASTP usuing the DoE JGI database Fig. 3). Uniquely for spermidine synthase orthologues, the F.cylin- for each diatom species, and additional domains in the fusion pro- drusFraSDS3 and the T. pseudonana ThaSDS2 proteins have ac- teins were identified by BLASTP or PSIBLAST using the NCBI server quired signal peptides. It is possible that one of the spermidine (http://blast.ncbi.nlm.nih.gov/Blast.cgi). synthase paralogues encodes the related aminopropyltransferase spermine synthase. Each of the three sequenced diatom genomes 3. Results