Homospermidine synthase, the first pathway-specific enzyme of pyrrolizidine alkaloid biosynthesis, evolved from deoxyhypusine synthase

Ober, Dietrich; Hartmann, Thomas

doi:10.1073/pnas.96.26.14777

Cited by 165 publications

(161 citation statements)

References 37 publications

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“…DHS is also capable of producing homospermidine from spermidine as a side reaction in the absence of eIF5A(Lys) and presence of putrescine and may be responsible for the presence of homospermidine within cells lacking HSS (39,(41)(42)(43). DHS and HSS employ the same enzymatic mechanism, and the residues defining the active-site tunnel and the NAD binding site are highly conserved.…”

Section: Structure Of Gc 7 -Inhibited Deoxyhypusine Synthasementioning

confidence: 99%

A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme·NAD·Inhibitor Ternary Complex

Umland

Wolff

Park

et al. 2004

Journal of Biological Chemistry

109

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Deoxyhypusine synthase catalyzes the first step in the two-step post-translational synthesis of hypusine, which is uniquely present in eukaryotic initiation factor 5A (eIF5A). Deoxyhypusine synthase and eIF5A are conserved throughout the eukaryotic kingdom, and both are essential for cell proliferation and survival. A previous study (Liao, D. I., Wolff, E. C., Park, M. H., and Davies, D. R. (1998) Structure 6, 23-32) of human deoxyhypusine synthase revealed four active sites of the homotetrameric enzyme located within deep tunnels. These Form I crystals were obtained under conditions of acidic pH and high ionic strength and likely contain an inactive enzyme. Each active-site entrance is blocked by a ball-and-chain motif composed of a region of extended structure capped by a two-turn ␣-helix. We report here at 2.2 Å a new Form II crystal of the deoxyhypusine synthase:NAD holoenzyme grown at low ionic strength and pH 8.0, near the optimal pH for enzymatic activity. The ball-and-chain motif could not be detected in the electron density, suggesting that it swings freely and thus it no longer obstructs the active-site entrance. The deoxyhypusine synthase competitive inhibitor N 1 -guanyl-1,7-diaminoheptane (GC 7 )is observed bound within the putative active site of the enzyme in the new crystal form (Form II) after exposure to the inhibitor. This first structure of a deoxyhypusine synthase⅐NAD⅐inhibitor ternary complex under physiological conditions now provides a structural context to discuss the results of previous biochemical investigations of the deoxyhypusine synthase reaction mechanism. This structure also provides a basis for the development of improved inhibitors and antiproliferative agents.Deoxyhypusine synthase (DHS) 1 catalyzes the first of two steps in the post-translational modification of a single lysine residue of the precursor eukaryotic initiation factor 5A (eIF5A(Lys)) to the unique amino acid hypusine (N ⑀ -(4-aminobutyl-2-hydroxyl)lysine) (1). DHS converts lysine to deoxyhypusine (N ⑀ -(4-aminobutyl)lysine) by a NAD-dependent transfer of the butylamine moiety of spermidine. In the second step of the modification, deoxyhypusine hydroxylase catalyzes the hydroxylation of deoxyhypusine, yielding hypusine. A highly interesting aspect of this post-translational modification is the extreme specificity of it. The only known endogenous occurrence of hypusine is a single modified lysine in the mature form of eIF5A. The importance of this post-translational modification is underscored by the conservation of DHS and eIF5A in all eukaryotes and archaea (2-4) and the requirement of active DHS and eIF5A for cell proliferation. eIF5A(Lys) is likely modified directly following translation, as there is little or no accumulation of eIF5A(Lys) in cultured cells (1). Specific inhibitors of DHS or deoxyhypusine hydroxylase result in cellular growth arrest and alter tumor cell proliferation and differentiation (5-9). Furthermore, the hypusine residue of eIF5A has been reported to be critical for in vitro RNA binding (...

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Section: Structure Of Gc 7 -Inhibited Deoxyhypusine Synthasementioning

confidence: 99%

A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme·NAD·Inhibitor Ternary Complex

Umland

Wolff

Park

et al. 2004

Journal of Biological Chemistry

109

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“…In contrast is the homospermidine synthesized in some plants and which is used as the precursor for pyrrolizidine alkaloid production (36). The plant homospermidine synthase is derived from deoxyhypusine synthase, an enzyme that transfers an aminobutyl group from spermidine to a unique lysine residue in translation initiation factor eIF5A (40,41) and that is unrelated to the bacterial HSS enzyme described above. The plant homospermidine synthase has an absolute requirement for spermidine as a substrate, and an aminobutyl group from spermidine is transferred to a molecule of putrescine to form homospermidine (42).…”

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confidence: 99%

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

Shaw

Elliott

Kinch

et al. 2010

Journal of Biological Chemistry

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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...

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

Irmer

Podzun

Langel

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Infection of legume hosts by rhizobial bacteria results in the formation of a specialized organ, the nodule, in which atmospheric nitrogen is reduced to ammonia. Nodulation requires the reprogramming of the plant cell, allowing the microsymbiont to enter the plant tissue in a highly controlled manner. We have found that, in Crotalaria (Fabaceae), this reprogramming is associated with the biosynthesis of pyrrolizidine alkaloids (PAs). These compounds are part of the plant’s chemical defense against herbivores and cannot be regarded as being functionally involved in the symbiosis. PAs in Crotalaria are detectable only when the plants form nodules after infection with their rhizobial partner. The identification of a plant-derived sequence encoding homospermidine synthase (HSS), the first pathway-specific enzyme of PA biosynthesis, suggests that the plant and not the microbiont is the producer of PAs. Transcripts of HSS are detectable exclusively in the nodules, the tissue with the highest concentration of PAs, indicating that PA biosynthesis is restricted to the nodules and that the nodules are the source from which the alkaloids are transported to the above ground parts of the plant. The link between nodulation and the biosynthesis of nitrogen-containing alkaloids in Crotalaria highlights a further facet of the effect of symbiosis with rhizobia on the ecologically important trait of the plant’s chemical defense.

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Homospermidine synthase, the first pathway-specific enzyme of pyrrolizidine alkaloid biosynthesis, evolved from deoxyhypusine synthase

Cited by 165 publications

References 37 publications

A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme·NAD·Inhibitor Ternary Complex

A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme·NAD·Inhibitor Ternary Complex

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

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

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