Antizyme regulates the degradation of ornithine decarboxylase in fission yeast Schizosaccharomyces pombe. Study in the spe2 knockout strains

The combination of ultraviolet mutagenesis and PPX1 overexpression synergistically enhanced S-adenosyl-L-methionine synthesis in industrial Saccharomyces cerevisiae

S-adenosyl-L-methionine (SAM) is the only injectable drug among the hepatoprotective and choleretic drugs, which has remarkable efficacy and is favored by hepatopaths. The demand for SAM is constantly increasing in clinical settings. Therefore, many efforts have been made to increase SAM biosynthesis from L-methionine and ATP in Saccharomyces cerevisiae. This study aimed to construct a stable and high-accumulating SAM industrial strain through successive ultraviolet irradiation (UV) mutations coupled with three resistant (ethionine, nystatin, and cordycepin, respectively) screening procedures and metabolic engineering strategies. Following multiple UV mutagenesis, a higher production mutant strain ZJT15-33 was successfully obtained. In addition, the recombinant strain spe2△-PPX1 was derived from ZJT15-33 by deleting the SPE2 and overexpressing the PPX1, resulting in a 2.5-fold enhanced ATP accumulation, which promoted the synthesis of 2.41 g/L SAM in the shake-flask, representing an 11.4-fold enhancement over the original strain (0.21 g/L). Furthermore, 11.65 g/L SAM was accumulated with 113 mg/g DCW SAM content in a 5-L fermenter at 96 h, marking a 36.57 % increase compared to strain ZJT15-33 (8.53 g/L). These results indicated that UV mutagenesis combined with PPX1 overexpression could effectively improve SAM synthesis in S. cerevisiae, providing a feasible approach for developing highly SAM industrial production.

A link between urease and polyamine metabolism in Cryptococcus neoformans

The urease enzyme of Cryptococcus neoformans is linked to different metabolic pathways within the yeast cell, several of which are involved in polyamine metabolism. Cryptococcal biogenic amine production is, however, largely unexplored and is yet to be investigated in relation to urease. The aim of this study was therefore to explore and compare polyamine metabolism in wild-type, urease-negative and urease-reconstituted strains of C. neoformans. Mass spectrometry analysis showed that agmatine and spermidine were the major extra- and intracellular polyamines of C. neoformans and significant differences were observed between 26 and 37 °C. In addition, compared to the wild-type, the relative percentages of extracellular putrescine and spermidine were found to be lower and agmatine higher in cultures of the urease-deficient mutant. The inverse was true for intracellular spermidine and agmatine. Cyclohexylamine was a more potent polyamine inhibitor compared to DL-α-difluoromethylornithine and inhibitory effects were more pronounced at 37 °C than at 26 °C. At both temperatures, the urease-deficient mutant was less susceptible to cyclohexylamine treatment compared to the wild-type. For both inhibitors, growth inhibition was alleviated with polyamine supplementation. This study has provided novel insight into the polyamine metabolism of C. neoformans, highlighting the involvement of urease in biogenic amine production.

Different polyamine pathways from bacteria have replaced eukaryotic spermidine biosynthesis in ciliates Tetrahymena thermophila and Paramecium tetaurelia

The polyamine spermidine is absolutely required for growth and cell proliferation in eukaryotes, due to its role in post-translational modification of essential translation elongation factor eIF5A, mediated by deoxyhypusine synthase. We have found that free-living ciliates Tetrahymena and Paramecium lost the eukaryotic genes encoding spermidine biosynthesis: S-adenosylmethionine decarboxylase (AdoMetDC) and spermidine synthase (SpdSyn). In Tetrahymena, they were replaced by a gene encoding a fusion protein of bacterial AdoMetDC and SpdSyn, present as three copies. In Paramecium, a bacterial homospermidine synthase replaced the eukaryotic genes. Individual AdoMetDC-SpdSyn fusion protein paralogues from Tetrahymena exhibit undetectable AdoMetDC activity; however, when two paralogous fusion proteins are mixed, AdoMetDC activity is restored and spermidine is synthesized. Structural modelling indicates a functional active site is reconstituted by sharing critical residues from two defective protomers across the heteromer interface. Paramecium was found to accumulate homospermidine, suggesting it replaces spermidine for growth. To test this concept, a budding yeast spermidine auxotrophic strain was found to grow almost normally with homospermidine instead of spermidine. Biosynthesis of spermidine analogue aminopropylcadaverine, but not exogenously provided norspermidine, correlated with some growth. Finally, we found that diverse single-celled eukaryotic parasites and multicellular metazoan Schistosoma worms have lost the spermidine biosynthetic pathway but retain deoxyhypusine synthase.

Polyamine metabolism in fungi with emphasis on phytopathogenic species

Polyamines are essential metabolites present in all living organisms, and this subject has attracted the attention of researchers worldwide interested in defining their mode of action in the variable cell functions in which they are involved, from growth to development and differentiation. Although the mechanism of polyamine synthesis is almost universal, different biological groups show interesting differences in this aspect that require to be further analyzed. For these studies, fungi represent interesting models because of their characteristics and facility of analysis. During the last decades fungi have contributed to the understanding of polyamine metabolism. The use of specific inhibitors and the isolation of mutants have allowed the manipulation of the pathway providing information on its regulation. During host-fungus interaction polyamine metabolism suffers striking changes in response to infection, which requires examination. Additionally the role of polyamine transporter is getting importance because of its role in polyamine regulation. In this paper we analyze the metabolism of polyamines in fungi, and the difference of this process with other biological groups. Of particular importance is the difference of polyamine biosynthesis between fungi and plants, which makes this process an attractive target for the control of phytopathogenic fungi.

Evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine

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 alpha-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 alpha-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 alpha-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.

Cloning and sequence analysis of ornithine decarboxylase gene fragments from theAscomycota

Ornithine decarboxylase (ODC; EC 4.1.1.17) catalyzes the initial step in the biosynthesis of polyamines, the conversion of ornithine to putrescine. Based on the most conserved regions of fungal ODCs, we designed and synthesized oligonucleotides to amplify homologous fragments of three important plant pathogenic Pyrenomycete fungi (Ascomycota), Magnaporthe grisea, Colletotrichum lindemuthianum and Fusarium solani, and one insect pathogenic fungus Metarhizium anisopliae. Cloning and sequencing of the amplified fragments revealed homologies of between 37 to 88% with other fungal ODCs. The predicted peptide sequences were compared by Clustal analysis and conserved sequences corresponding to the substrate and cofactor binding sites were identified. Comparative analyses of the ODC fragments isolated in this study, revealed high homology between them (68.3-81.1%) and also with other Pyrenomycetes such as Neurospora crassa (order Sordariales; 68.6-72.9%) and Fusarium graminearum (order Hypocreales; 70.8-88.1%). Data obtained in this work revealed that these fungi constitute a compact group separated from other eukaryotic ODCs.

Analysis of the transcriptional regulation of YlODC gene from the dimorphic fungus Yarrowia lipolytica

Polyamines are small polycations essential for cell growth. Ornithine decarboxylase (ODC), the first enzyme of the polyamine synthesis pathway, is one of the most regulated enzymes of eukaryotes. In the present report, the transcriptional regulation of the gene encoding ODC from the dimorphic fungus Yarrowia lipolytica (YlODC) was analyzed. To this end we made a transcriptional fusion of its promoter with the ORF of the beta-glucuronidase gene from Escherichia coli, and analyzed the effect of polyamines and the dimorphic transition on the rate of transcription. The results obtained show that there exists a weak but reproducible transcriptional regulation of YlODC under the analyzed conditions. Our data suggest that gene transcription is down-regulated by putrescine, and stimulated by spermidine. It is suggested that the simultaneous operation of transcriptional and post-translational regulatory mechanisms endows the cell with a more efficient mechanism to control the physiological processes that depend on polyamines.

Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation

The protein antizyme is a negative regulator of intracellular polyamine levels. Ribosomes synthesizing antizyme start in one ORF and at the codon 5′ adjacent to its stop codon, shift +1 to a second and partially overlapping ORF which encodes most of the protein. The ribosomal frameshifting is a sensor and effector of an autoregulatory circuit which is conserved in animals, fungi and protists. Stimulatory signals encoded 5′ and 3′ of the shift site act to program the frameshifting. Despite overall conservation, many individual branches have evolved specific features surrounding the frameshift site. Among these are RNA pseudoknots, RNA stem-loops, conserved primary RNA sequences, nascent peptide sequences and branch-specific ‘shifty’ codons.

Novel antizyme gene in Danio rerio expressed in brain and retina

The synthesis of the protein antizyme requires a +1 ribosomal frameshift event. The frameshifting serves as a regulatory sensor. Antizyme homologs have been identified in diverse organisms ranging from yeast to human and characterized in a disparate subset. Most vertebrates have multiple antizyme paralogs. Here we present identification in the zebrafish Danio rerio of a heretofore unknown member of the antizyme gene family. This novel antizyme does not correspond to any of the known orthologous groups in vertebrates and unlike most other antizymes is preferentially expressed in the retinal ganglion cell layer of the eye. In addition to the retina, it is also expressed in the brain and somites.

BUD2, encoding an S-adenosylmethionine decarboxylase, is required for Arabidopsis growth and development

Polyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushy and dwarf mutant, bud2, which results from the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases (SAMDCs) necessary for the formation of the indispensable intermediate in the polyamine biosynthetic pathway. The bud2 plant has enlarged vascular systems in inflorescences, roots, and petioles, and an altered homeostasis of polyamines. The double mutant of bud2 and samdc1, a knockdown mutant of another SAMDC member, is embryo lethal, demonstrating that SAMDCs are essential for plant embryogenesis. Our results suggest that polyamines are required for the normal growth and development of higher plants.

Studies on the regulation of ornithine decarboxylase in yeast: effect of deletion in the MEU1 gene

Methylthioadenosine is formed during the biosynthesis of spermidine and of spermine and is metabolized by methylthioadenosine phosphorylase, an enzyme missing in several tumor cell lines. In Saccharomyces cerevisiae, this enzyme is coded by the MEU1 gene. We have now studied the effect of the meu1 deletion on polyamine metabolism in yeast. We found that the effects of the meu1Delta mutation mostly depend on the stage of cell growth. As the cell density increases, there is a marked fall in the level of ornithine decarboxylase (ODC) in the MEU1(+) cells, which we show is caused by an antizyme-requiring degradation system. In contrast, there is only a small decrease in the ODC level in the meu1Delta cells. The meu1Delta cells have a higher putrescine and a lower spermidine level than MEU1(+) cells, suggesting that the decreased spermidine level in the meu1Delta cultures is responsible for the greater apparent stability of ODC in the meu1Delta cells. The lower spermidine level in the meu1Delta cells probably results from an inhibition of spermidine synthase by the methylthioadenosine that presumably accumulates in these mutants. In both MEU1(+) and the meu1Delta cultures, the ODC levels were markedly decreased by the addition of spermidine to the media, and thus our results contradict the postulation of Subhi et al. [Subhi, A. L., et al. (2003) J. Biol. Chem. 278, 49868-49873] of a novel regulatory pathway in meu1Delta cells in which ODC is not responsive to spermidine.

Polyamine metabolism during the germination of Sclerotinia sclerotiorum ascospores and its relation with host infection

• Polyamine biosynthesis inhibitors were used to study polyamine metabolism during the germination of Sclerotinia sclerotiorum ascospores, and to evaluate the potential of polyamine biosynthesis inhibition for the control of ascospore-borne diseases in plants. • The effects of inhibitors on ascospore germination, free polyamine levels, ornithine decarboxylase activity and development of disease symptoms on tobacco (Nicotiana tabacum) leaf discs inoculated with ascospores were determined. • α-Difluoromethylornithine inhibited ornithine decarboxylase and decreased free spermidine levels, but had no effect on ascospore germination. Both, the spermidine synthase inhibitor cyclohexylamine and the S-adenosyl-methionine decarboxylase inhibitor methylglyoxal bis-[guanyl hydrazone] decreased free spermidine levels, but only the latter inhibited ascospore germination, at concentrations of 5 mm or higher. Lesion development on leaf discs was reduced by cyclohexylamine and methylglyoxal bis-[guanyl hydrazone], but not by α-difluoromethylornithine. In the absence of inhibitors, dormant ascospores contained higher polyamine levels than mycelium. • Ascospore germination did not depend on ornithine decarboxylase activity and inhibitors of this enzyme will probably have a limited potential for the control of ascospore-borne plant diseases. On the contrary, spermidine synthase and S-adenosyl-methionine decarboxylase could be more suitable targets for fungicidal action. The relative insensitivity of ascospore germination to polyamine biosynthesis inhibitors may be caused by their high polyamine content.

Ubiquitin-independent mechanisms of mouse ornithine decarboxylase degradation are conserved between mammalian and fungal cells

The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway in mammalian cells. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1). Mouse ODC (mODC) that is expressed in the yeast Saccharomyces cerevisiae is also rapidly degraded by the proteasome of that organism. We have now carried out in vivo and in vitro studies to determine whether S. cerevisiae proteasomes recognize mODC degradation signals. Mutations of mODC that stabilized the protein in animal cells also did so in the fungus. Moreover, the mODC degradation signal was able to destabilize a GFP or Ura3 reporter in GFP-mODC and Ura3-mODC fusion proteins. Co-expression of AZ1 accelerated mODC degradation 2-3-fold in yeast cells. The degradation of both mODC and the endogenous yeast ODC (yODC) was unaffected in S. cerevisiae mutants with various defects in ubiquitin metabolism, and ubiquitinylated forms of mODC were not detected in yeast cells. In addition, recombinant mODC was degraded in an ATP-dependent manner by affinity-purified yeast 26 S proteasomes in the absence of ubiquitin. Degradation by purified yeast proteasomes was sensitive to mutations that stabilized mODC in vivo, but was not accelerated by recombinant AZ1. These studies demonstrate that cell constituents required for mODC degradation are conserved between animals and fungi, and that both mammalian and fungal ODC are subject to proteasome-mediated proteolysis by ubiquitin-independent mechanisms.

Regulation of ornithine decarboxylase by antizymes and antizyme inhibitor in zebrafish (Danio rerio)

Mammalian polyamine synthesis is regulated by a unique feedback mechanism. When cellular polyamine levels increase, antizyme, an ornithine decarboxylase (ODC) inhibitory protein, is induced by polyamine-dependent translational frameshifting. Antizyme not only inhibits ODC, a key enzyme in polyamine synthesis, it also targets the enzyme degradation by the 26S proteasome. Furthermore, it suppresses cellular uptake of polyamines. Previously, we isolated two zebrafish antizymes with different expressions and activities. This suggested that a common feedback mechanism of polyamine metabolism might operate in mammals and zebrafish (Danio rerio). In the present study, cDNAs of zebrafish ODC and antizyme inhibitor, another regulatory protein that inhibits antizyme action, were cloned. The presence of ODC and antizyme inhibitor mRNAs was confirmed by Northern blotting in embryos and adult fish, as well as in a zebrafish-derived cell line (BRF41). The activity of the ODC cDNA expression product was inhibited by short and long zebrafish antizymes, and recombinant zebrafish antizyme inhibitor reversed this inhibition. In the BRF41 cells, the ODC half-life was considerably longer than that of mammalian ODC but shorter than that of Schizosaccharomyces pombe. Spermidine elicited a rapid decay of ODC activity and ODC protein in a protein synthesis-dependent manner.

Ornithine decarboxylase encoded by chlorella virus PBCV-1

Sequence analysis of the 330-kb genome of chlorella virus PBCV-1 revealed an open reading frame, A207R, which encodes a protein with 37-41% amino acid identity to ornithine decarboxylase (ODC) from many eukaryotic organisms. The a207r gene was cloned and the protein was expressed as a His-A207R fusion protein in Escherichia coli. The recombinant protein catalyzes pyridoxal 5'-phosphate-dependent decarboxylation of ornithine to putrescine, the first step in the polyamine biosynthetic pathway. The enzyme has a pH optimum of 9.0 and a temperature optimum of 42 degrees C, and it requires dithiothreitol for maximal activity. The enzyme has a K(m) for ornithine of 0.78 mM and a specific activity of 100 micromol/min/mg protein. PBCV-1 ODC is quite sensitive to the competitive inhibitor L-arginine and the irreversible inhibitor difluoromethylarginine but it is less sensitive to the irreversible inhibitor difluoromethylornithine. The a207r gene is expressed both early and late in PBCV-1 infection and is highly conserved among the chlorella viruses. The 42-kDa PBCV-1 ODC (372 amino acids) is the smallest ODC in the databases and, to our knowledge, is the first virus-encoded ODC.

Absolute requirement of spermidine for growth and cell cycle progression of fission yeast (Schizosaccharomyces pombe)

Schizosaccharomyces pombe cells that cannot synthesize spermidine or spermine because of a deletion-insertion in the gene coding for S-adenosylmethionine decarboxylase (Deltaspe2) have an absolute requirement for spermidine for growth. Flow cytometry studies show that in the absence of spermidine an overall delay of the cell cycle progression occurs with some accumulation of cells in the G(1) phase; as little as 10(-6) M spermidine is sufficient to maintain normal cell cycle distribution and normal growth. Morphologically some of the spermidine-deprived cells become spherical at an early stage with little evidence of cell division. On further incubation in the spermidine-deprived medium, growth occurs in most of the cells, not by cell division but rather by cell elongation, with an abnormal distribution of the actin cytoskeleton, DNA (4', 6-diamidino-2-phenylindole staining), and calcofluor-staining moieties. More prolonged incubation in the spermidine-deficient medium leads to profound morphological changes including nuclear degeneration.

Degradation of ornithine decarboxylase in Saccharomyces cerevisiae is ubiquitin independent

Ornithine decarboxylase (ODC), the first rate-limiting enzyme in the polyamine biosynthesis is one of the most rapidly degraded proteins in eukaryotic cells. Mammalian ODC is a notable exception to the widely accepted dogma that ubiquitination is always required for targeting a protein to degradation by the 26S proteasome. However, while it is well established that in mammalian cells degradation of ODC is ubiquitin independent, the requirement of ubiquitination for degradation of ODC in yeast cells remained undetermined. We have investigated ODC degradation in three mutant strains of Saccharomyces cerevisiae in which ubiquitin-dependent protein degradation activity is severely compromised. While yeast ODC was rapidly degraded in all these mutant strains the degradation of N-end rule substrates was inhibited. A mutant mouse ODC that fails to interact with Az was rapidly degraded in yeast cells but was stable in mammalian cells suggesting that interaction with a mammalian Az like yeast protein is not necessary for the degradation of ODC in yeast cells. Deletion analysis revealed that sequences from its unique N-terminus are involved in targeting yeast ODC to rapid degradation in yeast cells.

Recoding: translational bifurcations in gene expression

During the expression of a certain genes standard decoding is over-ridden in a site or mRNA specific manner. This recoding occurs in response to special signals in mRNA and probably occurs in all organisms. This review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria.

Effect of spermidine on the in vivo degradation of ornithine decarboxylase in Saccharomyces cerevisiae

As part of our studies on the regulation of polyamine biosynthesis in Saccharomyces cerevisiae, we have investigated the effect of spermidine on the degradation of ornithine decarboxylase in this organism. We have found that in S. cerevisiae, as in other eukaryotic cells, the rate of degradation of ornithine decarboxylase, measured either enzymatically or immunologically, is increased by the addition of spermidine to a yeast culture. It is noteworthy that this effect of added spermidine is found even when the experiments are conducted with strains in which the ornithine decarboxylase is overexpressed several hundred-fold more than the wild-type level. The effect of added spermidine in the overexpressed SPE1 strains is best seen in spe2 mutants in which the initial intracellular spermidine is very low or absent. Experiments with cycloheximide show that new protein synthesis is required to effect the breakdown of the ornithine decarboxylase. These results indicate that S. cerevisiae contains an antizyme-like mechanism for the control of the level of ornithine decarboxylase by spermidine, even though, as contrasted with other eukaryotic cells, no specific antizyme homologue has been detected either in in vitro experiments or in the S. cerevisiae genome.