Evolution and Multifarious Horizontal Transfer of an Alternative Biosynthetic Pathway for the Alternative Polyamine sym-Homospermidine

Abstract

Polyamines are small flexible organic polycations found in almost all cells. They likely existed in the last universal common ancestor of all extant life, and yet relatively little is understood about their biological function, especially in bacteria and archaea. Unlike eukaryotes, where the predominant polyamine is spermidine, bacteria may contain instead an alternative polyamine, sym-homospermidine. We demonstrate that homospermidine synthase (HSS) has evolved vertically, primarily in the ␣-Proteobacteria, but enzymatically active, diverse HSS orthologues have spread by horizontal gene transfer to other bacteria, bacteriophage, archaea, eukaryotes, and viruses. By expressing diverse HSS orthologues in Escherichia coli, we demonstrate in vivo the production of co-products diaminopropane and N 1 -aminobutylcadaverine, in addition to sym-homospermidine. We show that sym-homospermidine is required for normal growth of the ␣-proteobacterium Rhizobium leguminosarum. However, sym-homospermidine can be replaced, for growth restoration, by the structural analogues spermidine and sym-norspermidine, suggesting that the symmetrical or unsymmetrical form and carbon backbone length are not critical for polyamine function in growth. We found that the HSS enzyme evolved from the alternative spermidine biosynthetic pathway enzyme carboxyspermidine dehydrogenase. The structure of HSS is related to lysine metabolic enzymes, and HSS and carboxyspermidine dehydrogenase evolved from the aspartate family of pathways. Finally, we show that other bacterial phyla such as Cyanobacteria and some ␣-Proteobacteria synthesize sym-homospermidine by an HSS-independent pathway, very probably based on deoxyhypusine synthase orthologues, similar to the alternative homospermidine synthase found in some plants. Thus, bacteria can contain alternative biosynthetic pathways for both spermidine and sym-norspermidine and distinct alternative pathways for sym-homospermidine.Polyamines are primordial, small flexible organic polycations found in almost all cells of bacteria, archaea, and eukaryotes (1). In bacteria and archaea, the key polyamines (see Fig. 1A) are the triamines spermidine, sym-norspermidine, and sym-homospermidine (referred to herein as norspermidine and homospermidine), and occasionally more than one triamine can be found in the same cell. In eukaryotes, which contain spermidine (and in some plants, yeasts, and animals, the tetraamine spermine), polyamines are required for growth, cell proliferation, and normal cellular physiology. Polyamine biosynthesis is essential in the fungi Saccharomyces cerevisiae (2), Schizosaccharomyces pombe (3), Aspergillus nidulans (4), and Ustilago maydis (5), the kinetoplastid parasites Trypanosoma brucei (6) and Leishmania donovani (7), and the diplomonad parasite Giardia lamblia (8). In mouse, polyamines are essential for early embryo development (9, 10), and they are also essential for seed development in the flowering plant Arabidopsis thaliana (11).The universal distribution of polyamines suggests that...

Alternative Spermidine Biosynthetic Route Is Critical for Growth of Campylobacter jejuni and Is the Dominant Polyamine Pathway in Human Gut Microbiota

“…The ability of sym-homospermidine to replace spermidine in C. jejuni, and of N 1 -aminopropylcadaverine to replace spermidine in E. coli, indicates that the exact structure of the polyamine is not critical. Indeed, in most species in the bacterial phyla Chlorobi and Chloroflexi, in filamentous Cyanobacteria, and in many ␣-proteobacteria, symhomospermidine is the only polyamine present (6). Although sym-homospermidine and N 1 -aminopropylcadaverine are one carbon longer than spermidine, they are flexible linear chains and can bend, whereas sym-norspermidine, which is one carbon shorter than spermidine, is unlikely to stretch.…”

“…The Pseudomonas aeruginosa PAO1 N-carbamoylputrescine amidohydrolase gene deletion produced a leaky biosynthetic phenotype, and it was consequently found that acetylputrescine amidohydrolase, which has a very similar substrate to N-carbamoylputrescine (26), is induced in the gene deletion mutant and allows bypass of the metabolic block. The CANSDH/ CASDH enzyme is related to homospermidine synthase, lysine 6-dehydrogenase, saccharopine dehydrogenase, and aspartate dehydrogenase (6). There may be a dehydrogenase in C. jejuni that can serendipitously substitute the activity of the missing CASDH.…”

New aspect of plant–rhizobia interaction: Alkaloid biosynthesis in Crotalaria depends on nodulation

“…In homospermidine-producing bacteria, a bacterial HSS (EC 2.5.1.44) catalyzes the formation of homospermidine from two molecules of putrescine in an NAD + -dependent reaction (33,34). Despite the similar reaction mechanism, bacterial HSS and plant-derived HSS are not related with respect to the degree of sequence identity (12,35) and to their predicted 3D structure (24). Both the presence of introns at conserved positions in the genomic DNA encoding the HSS identified in C. spectabilis, and the ability of this enzyme to catalyze the formation of homospermidine from spermidine and putrescine, establishes that the identified HSS is not of bacterial, but of plant, origin.…”

“…A central question in our study has been which partner of the symbiosis provides homospermidine for PA biosynthesis: the microsymbiont or the plant. In many bacterial phyla, homospermidine is found to replace spermidine, which is the prevalent triamine in other bacteria and in eukaryotes (24). Indeed, homospermidine has been found repeatedly in nodules of fabaceous plants and in the associated rhizobia (31,32).…”

“…The same would be true if only the first pathway-specific intermediate (i.e., homospermidine) was provided by the microsymbiont. Of note, homospermidine is the predominant polyamine in many α-proteobacteria, including Bradyrhizobium (24).…”