The ornithine decarboxylase gene of Caenorhabditis elegans: cloning, mapping and mutagenesis

SIN-3 transcriptional coregulator maintains mitochondrial homeostasis and polyamine flux

Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays a role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals revealed a mitochondria stress signature and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.

Polyamine-independent Expression of Caenorhabditis elegans Antizyme

Degradation of ornithine decarboxylase, the rate-limiting enzyme of polyamine biosynthesis, is promoted by the protein antizyme. Expression of antizyme is positively regulated by rising polyamine concentrations that induce a +1 translational frameshift required for production of the full-length protein. Antizyme itself is negatively regulated by the antizyme inhibitor. In our study, the regulation of Caenorhabditis elegans antizyme was investigated, and the antizyme inhibitor was identified. By applying a novel GFP-based method to monitor antizyme frameshifting in vivo, we show that the induction of translational frameshifting also occurs under stressful conditions. Interestingly, during starvation, the initiation of frameshifting was independent of polyamine concentrations. Because frameshifting was also prevalent in a polyamine auxotroph double mutant, a polyamine-independent regulation of antizyme frameshifting is suggested. Polyamine-independent induction of antizyme expression was found to be negatively regulated by the peptide transporter PEPT-1, as well as the target of rapamycin, but not by the daf-2 insulin signaling pathway. Stress-dependent expression of C. elegans antizyme occurred morely slowly than expression in response to increased polyamine levels, pointing to a more general reaction to unfavorable conditions and a diversion away from proliferation and reproduction toward conservation of energy. Interestingly, antizyme expression was found to drastically increase in aging individuals in a postreproductive manner. Although knockdown of antizyme did not affect the lifespan of C. elegans, knockdown of the antizyme inhibitor led to a significant reduction in lifespan. This is most likely caused by an increase in antizyme-mediated degradation of ornithine decarboxylase-1 and a resulting reduction in cellular polyamine levels.

Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation

Massive water loss is a serious challenge for terrestrial animals, which usually has fatal consequences. However, some organisms have developed means to survive this stress by entering an ametabolic state called anhydrobiosis. The molecular and cellular mechanisms underlying this phenomenon are poorly understood. We recently showed that Caenorhabditis elegans dauer larva, an arrested stage specialized for survival in adverse conditions, is resistant to severe desiccation. However, this requires a preconditioning step at a mild desiccative environment to prepare the organism for harsher desiccation conditions. A systems approach was used to identify factors that are activated during this preconditioning. Using microarray analysis, proteomics, and bioinformatics, genes, proteins, and biochemical pathways that are upregulated during this process were identified. These pathways were validated via reverse genetics by testing the desiccation tolerances of mutants. These data show that the desiccation response is activated by hygrosensation (sensing the desiccative environment) via head neurons. This leads to elimination of reactive oxygen species and xenobiotics, expression of heat shock and intrinsically disordered proteins, polyamine utilization, and induction of fatty acid desaturation pathway. Remarkably, this response is specific and involves a small number of functional pathways, which represent the generic toolkit for anhydrobiosis in plants and animals.

Filarial parasites possess an antizyme but lack a functional ornithine decarboxylase

In eukaryotes, the key player in polyamine metabolism is the ornithine decarboxylase (ODC) that catalyses the first and rate limiting step in cellular polyamine synthesis. The half life of ODC is strictly regulated by the antizyme (AZ), which promotes its degradation. Older reports on the polyamine situation in filarial parasites indicate a lack of ornithine decarboxylation activity and an increased uptake of polyamines. Our in silico analysis of the Brugia malayi genome revealed only an ODC-like protein that lacks essential residues. Consequently, the recombinant protein had no enzymatic ODC activity. Furthermore, only ODC-like genes were found in the available draft genomes of other filarial parasites. In this ODC-free scenario, we set out to investigate the AZ of O. volvulus (OvAZ). The expression of the recombinant protein allowed us to analyse the localization of OvAZ in different O. volvulus stages as well as to identify it as target for the human humoral immune response. Strong immunostaining was observed in the outer zone of the uterine epithelium as well as in the uterus lumen around the periphery of the developing parasite, indicating a potential role of the OvAZ in the control of polyamine levels during embryonic development. By employing a novel in vivo method using Caenorhabditis elegans, we postulate that the OvAZ enters the secretory pathway. Even though the ODCs are absent in filarial parasites, OvAZ has the ability to bind to various ODCs, thereby demonstrating the functionality of the conserved AZ-binding domains. Finally, pull-down assays show an interaction between B. malayi AZ and the B. malayi ODC-like protein, indicating that the B. malayi ODC-like protein might function as an AZI. Taken together, our results suggest that filarial species do not possess the ODC while retaining the ODC-regulatory proteins AZ and AZI. It is tempting to speculate that both proteins are retained for the regulation of polyamine transport systems.

Molecular and biochemical characterisation of ornithine decarboxylases in the sheep abomasal nematode parasites Teladorsagia circumcincta and Haemonchus contortus

Full length cDNA encoding ornithine decarboxylases (ODC; EC 4.1.1.17) were cloned from the sheep abomasal nematode parasites Teladorsagia circumcincta (TcODC) and Haemonchus contortus (HcODC). The TcODC (1272 bp) and HcODC cDNA (1266 bp) encoded 424 and 422 amino acid proteins respectively. The predicted TcODC amino acid sequence showed 87% identity with HcODC and 65% and 64% with Caenorhabditis elegans and Caenorhabditis briggsae ODC respectively. All binding sites and active regions were completely conserved in both proteins. Soluble N-terminal His-tagged ODC proteins were expressed in Escherichia coli strain BL21, purified and characterised. The recombinant TcODC and HcODC had very similar kinetic properties: K(m) ornithine was 0.2-0.25 mM, optimum [PLP] was 0.3 mM and the pH optima were pH 8. No enzyme activity was detected when arginine was used as substrate. One millimolar difluoromethylornithine (DFMO) completely inhibited TcODC and HcODC activity, whereas 2 mM agmatine did not inhibit activity. The present study showed that ODC is a separate enzyme from arginine decarboxylase and strictly uses ornithine as substrate.

Caenorhabditis elegans P5B-type ATPase CATP-5 operates in polyamine transport and is crucial for norspermidine-mediated suppression of RNA interference

Physiological polyamines are required in various biological processes. In the current study, we used norspermidine, a structural analog of the natural polyamine spermidine, to investigate polyamine uptake in the model organism Caenorhabditis elegans. Norspermidine was found to have two remarkable effects: it is toxic for the nematode, without affecting its food, Escherichia coli; and it hampers RNA interference. By characterizing a norspermidine-resistant C. elegans mutant strain that has been isolated in a genetic screen, we demonstrate that both effects, as well as the uptake of a fluorescent polyamine-conjugate, depend on the transporter protein CATP-5, a novel P(5B)-type ATPase. To our knowledge, CATP-5 represents the first P(5)-type ATPase that is associated with the plasma membrane, being expressed in the apical membrane of intestinal cells and the excretory cell. Moreover, genetic interaction studies using C. elegans polyamine synthesis mutants indicate that CATP-5 has a function redundant to polyamine synthesis and link reduced polyamine levels to retarded postembryonic development, reduced brood size, shortened life span, and small body size. We suggest that CATP-5 represents a crucial component of the pharmacologically important polyamine transport system, the molecular nature of which has not been identified so far in metazoa.

Evolution of pharyngeal behaviors and neuronal functions in free-living soil nematodes

To explore the use of Caenorhabditis elegans and related nematodes for studying behavioral evolution, we conducted a comparative study of pharyngeal behaviors and neuronal regulation in free-living soil nematodes. The pharynx is divided into three parts: corpus, isthmus and terminal bulb,and pharyngeal behaviors consist of stereotyped patterns of two motions:pumping and peristalsis. Based on an outgroup species, Teratocephalus lirellus, the ancestral pattern of pharyngeal behaviors consisted of corpus pumping, isthmus peristalsis and terminal bulb pumping, each occurring independently. Whereas corpus pumping remained largely conserved, isthmus and terminal bulb behaviors evolved extensively from the ancestral pattern in the four major free-living soil nematode families. In the Rhabditidae family,which includes Caenorhabditis elegans, the anterior isthmus switched from peristalsis to pumping, and anterior isthmus and terminal bulb pumping became coupled to corpus pumping. In the Diplogasteridae family, the terminal bulb switched from pumping to peristalsis, and isthmus and terminal bulb became coupled for peristalsis. In the Cephalobidae family, isthmus peristalsis and terminal bulb pumping became coupled. And in the Panagrolaimidae family, the posterior isthmus switched from peristalsis to pumping. Along with these behavioral changes, we also found differences in the neuronal regulation of isthmus and terminal bulb behaviors. M2, a neuron that has no detectable function in C. elegans, stimulated anterior isthmus peristalsis in the Panagrolaimidae. Further, M4 was an important excitatory neuron in each family, but its exact downstream function varied between stimulation of posterior isthmus peristalsis in the Rhabditidae,isthmus/terminal bulb peristalsis in the Diplogasteridae, isthmus peristalsis and terminal bulb pumping in the Cephalobidae, and posterior isthmus/terminal bulb pumping in the Panagrolaimidae. In the Rhabditidae family, although M4 normally has no effect on the terminal bulb, we found that M4 can stimulate the terminal bulb in C. elegans if the Ca2+-activated K+ channel SLO-1 is inactivated. C. elegans slo-1 mutants have generally increased neurotransmission, and in slo-1 mutants we found novel electropharyngeogram signals and increased pumping rates that suggested activation of M4-terminal bulb synapses. Thus, we suggest that the lack of M4-terminal bulb stimulations in C. elegans and the Rhabditidae family evolved by changes in synaptic transmission. Altogether, we found behavioral and neuronal differences in the isthmus and terminal bulb of free-living soil nematodes, and we examined potential underlying mechanisms of one aspect of M4 evolution. Our results suggest the utility of Caenorhabditis elegans and related nematodes for studying behavioral evolution.

Cloning, expression, characterisation and three-dimensional structure determination of Caenorhabditis elegans spermidine synthase

The polyamine synthesis enzyme spermidine synthase (SPDS) has been cloned from the model nematode Caenorhabditis elegans. Biochemical characterisation of the recombinantly expressed protein revealed a high degree of similarity to other eukaryotic SPDS with the exception of a low affinity towards the substrate decarboxylated S-adenosylmethionine (Km = 110 microM) and a less pronounced feedback inhibition by the second reaction product 5'-methylthioadenosine (IC50 = 430 microM). The C. elegans protein that carries a nematode-specific insertion of 27 amino acids close to its N-terminus was crystallized, leading to the first X-ray structure of a dimeric eukaryotic SPDS.

Genetic approaches to the cellular functions of polyamines in mammals

The polyamines putrescine, spermidine and spermine are organic cations shown to participate in a bewildering number of cellular reactions, yet their exact functions in intermediary metabolism and specific interactions with cellular components remain largely elusive. Pharmacological interventions have demonstrated convincingly that a steady supply of these compounds is a prerequisite for cell proliferation to occur. The last decade has witnessed the appearance of a substantial number of studies, in which genetic engineering of polyamine metabolism in transgenic rodents has been employed to unravel their cellular functions. Transgenic activation of polyamine biosynthesis through an overexpression of their biosynthetic enzymes has assigned specific roles for these compounds in spermatogenesis, skin physiology, promotion of tumorigenesis and organ hypertrophy as well as neuronal protection. Transgenic activation of polyamine catabolism not only profoundly disturbs polyamine homeostasis in most tissues, but also creates a complex phenotype affecting skin, female fertility, fat depots, pancreatic integrity and regenerative growth. Transgenic expression of ornithine decarboxylase antizyme has suggested that this unique protein may act as a general tumor suppressor. Homozygous deficiency of the key biosynthetic enzymes of the polyamines, ornithine and S-adenosylmethionine decarboxylase, as achieved through targeted disruption of their genes, is not compatible with murine embryogenesis. Finally, the first reports of human diseases apparently caused by mutations or rearrangements of the genes involved in polyamine metabolism have appeared.

Functional GATA- and initiator-like-elements exhibit a similar arrangement in the promoters of Caenorhabditis elegans polyamine synthesis enzymes

Polyamines are essential cell constituents involved in growth processes. In Caenorhabditis elegans the polyamine synthetic pathway consists of three enzymes, ornithine decarboxylase (ODC), S-adenosylmethionine decarboxylase (AdoMetDC) and spermidine synthase. Their gene expression pattern was determined in C. elegans by microinjection of green fluorescent protein (GFP) reporter gene constructs. All transgenic animals exhibited GFP expression in their intestinal cells. For the AdoMetDC promoter, fluorescence was additionally observed in dopaminergic neurons, while the ODC promoter also drives a male-specific GFP expression in the distal part of the reproductive system. The minimal promoter regions for intestine-specific expression of the AdoMetDC and spermidine synthase genes were determined by deletion mutants. Using the Seqcomp and Family Relation programs, a similar arrangement of putative cis-regulatory elements within these regions and also within the respective regions of the orthologous Caenorhabditis briggsae genes were found. The functional conservation of the latter was confirmed by heterologous transformation experiments. Moreover, the involvement of putative GATA- and initiator-(Inr)-like-elements in gene expression was determined by mutagenesis studies. RNase protection assay revealed that the Inr-like-element does not represent the main transcriptional start site, at least of C. elegans spermidine synthase. In conclusion, a similar minimal promoter architecture was found for C. elegans as well as C. briggsae AdoMetDC and spermidine synthase, two genes that participate in the same metabolic pathway.

Developmental effect of polyamine depletion in Caenorhabditis elegans

Ornithine decarboxylase (ODC) catalyses the conversion of ornithine to putrescine, an obligate precursor to the polyamines spermidine and spermine. We reported previously that homozygous odc-1 (pc13) worms have no detectable ODC activity. Despite their inability to make polyamines, these mutant worms appear normal, but with a slight reduction in total brood size, when grown in complex medium that presumably contains polyamines. We now show that when ODC-deficient worms are transferred to polyamine-free medium, they show a strong phenotype. odc-1 worms have two different fates, depending upon the developmental stage at which polyamines are removed. If the polyamines are removed at the L1 larval stage, the mutant animals develop into adult hermaphrodites that produce very few or no eggs. In contrast, if mutant larvae at the later L4 stage of development are transferred to polyamine-deficient medium, they develop and lay eggs normally. However, approx. 90% of the eggs yield embryos that, although well differentiated, arrest at early stage 3. Either maternal or zygotic expression of ODC provides partial rescue of embryonic lethality. Supplementing deficient medium with the polyamine spermidine allows ODC-deficient worms to develop as on complex medium. Together, these findings suggest that ODC activity is most critically required during oogenesis and embryogenesis and, furthermore, that exogenous polyamines can override the requirement for ODC activity.

Arginine decarboxylase (polyamine synthesis) mutants of Arabidopsis thaliana exhibit altered root growth

Putrescine and polyamines are produced by two alternative pathways in plants. One pathway starts with the enzyme arginine decarboxylase; the other with ornithine decarboxylase. The authors developed an in vivo screening strategy to identify mutants with low levels of arginine decarboxylase activity. The screen requires both a primary screen of the M2 generation and a secondary screen of the M3 generation. The method used was to screen 15,000 EMS-mutagenized M2 seedlings for low levels of arginine decarboxylase (ADC) activity and identified seven mutants that fall into two complementation groups. These mutants have from 20% to 50% of wild-type enzyme activity. Morphological alterations common among the mutants include increased levels of lateral root branching. The authors obtained a double mutant combining the alleles with the lowest activities from the two complementation groups; this has lower ADC enzyme activity and putrescine levels than either of the single mutants. The double mutant has highly kinked roots that form a tight cluster; it also has narrower leaves, sepals, and petals than either single mutant or wild-type, and delayed flowering. These results suggest there may be more than one ADC gene in Arabidopsis, and that ADC and polyamine levels play roles in root meristem function and in lateral growth of leaf-homolog organs.

Haemonchus contortus: cloning and functional expression of a cDNA encoding ornithine decarboxylase and development of a screen for inhibitors

Polyamines (PA) are essential for viability and replication of all cells; organisms either synthesize PA or acquire them from the environment. How nematodes that parasitize the gut satisfy their PA requirement has not been resolved. The primary regulatory enzyme in PA biosynthesis in most animals is ornithine decarboxylase (ODC). This enzyme has recently been characterized in free-living nematodes and in the parasitic species. Haemonchus contortus. Nematode and mammalian ODC are reported to differ in subcellular localization, kinetics, and sensitivity to inhibitors. We cloned an H. contortus cDNA that encodes a full-length ODC (sequence data from this article have been deposited with the GenBank Data Library under Accession Nos. AF016538 and AF016891). This cDNA was functionally expressed in strains of Escherichia coli and Saccharomyces cerevisiae that lack ODC and are dependent upon exogenous PA for survival. Expression of nematode ODC reversed the PA-dependence phenotype of both microorganisms. The complemented yeast strain was used to develop a nutrient-dependent viability screen for selective inhibitors of nematode ODC. The antiprotozoal drug stilbamidine isethionate was identified as active in this screen, but biochemical characterization revealed that this compound did not inhibit ODC. Instead, like other cationic diamidines, stilbamidine probably inhibits yeast S-adenosylmethionine decarboxylase. Nonetheless, the activity in the screen of the known ODC inhibitor difluoromethylornithine (DFMO) validates the concept that specific recombinant microorganisms can serve as the basis for extremely selective and facile screens.

Onchocerca volvulus: immunohistochemical and immunoelectron microscopical distribution of a polyamine oxidizing enzyme

We studied the distribution of a polyamine oxidizing enzyme (PAO) in Onchocerca volvulus and other nematode parasites by immunohistochemistry and electron microscopy with immunogold technique using a polyclonal antiserum raised against purified PAO from Ascaris suum. In adult O. volvulus the protein was localized in the outer zone and the area of the basal labyrinth of the hypodermis and occasionally in the outer zone of the uterine epithelium. Further, the fluid in the body cavity was strongly stained. No specific labelling was observed in the cuticle, muscles, epithelia of intestine, ovaries, testis and vas deferens or in sperm, oocytes and embryos. Third-stage larvae of O. volvulus in Simulium soubrense showed strong staining; the same was observed in Anisakis sp. larvae, where the inner and outer zone of the hypodermis were strongly labelled. All mature, intact and dead microfilariae in nodules, skin and lymph nodes were well stained and it was possible to show that the cytoplasm of the hypodermal cells, but not the mitochondria, nuclei or other organelles of muscle cells, was preferentially labelled by immunogold particles. Investigation of adult A. suum presented specific labelling of the hypodermis, but the basal labyrinth was more strongly marked than the outer zone.

An abnormal ketamine response in mutants defective in the ryanodine receptor gene ryr-1 (unc-68) of Caenorhabditis elegans

To characterize excitation-contraction coupling in Caenorhabditis elegans, we applied two approaches. First, we isolated a mutant having abnormal responses to ketamine, an anesthetic in vertebrates. The novel mutation unc-68(kh30) (isolated as kra-1(kh30)), exhibited strict ketamine-dependent convulsions followed by paralysis. Second, we cloned the C. elegans ryanodine receptor gene ryr-1 that is located near the center of chromosome V. ryr-1 consists of 46 exons, which encode a predicted protein of 5071 amino acid residues that is homologous to Drosophila and vertebrate ryanodine receptors. ryr-1 promoter/lacZ plasmids were expressed in body-wall and pharyngeal muscles. Non-muscle cell expression may be seen with a truncated promoter. In addition, we show that the unc-68/kra-1(kh30) mutation is a Ser1444 Asn substitution at a putative protein kinase C phosphorylation site in ryr-1, and that unc-68(e540) contains a splice acceptor mutation that creates a premature stop codon in the ryr-1 gene. We confirmed that unc-68(e540) is a mutation in ryr-1 by injecting the complete ryr-1 gene into unc-68(e540) animals and recovering wild-type progeny. Results presented here will be useful in studying the structure and function of ryanodine receptors in excitation-contraction coupling and in understanding the evolution of ryanodine receptor tissue specificity.

gutfeeling, a Drosophila gene encoding an antizyme-like protein, is required for late differentiation of neurons and muscles

The gutfeeling (guf) gene was uncovered in a genetic screen for genes that are required for proper development of the embryonic peripheral nervous system. Mutations in guf cause defects in growth cone guidance and fasciculation and loss of expression of several neuronal markers in the embryonic peripheral and central nervous systems. guf is required for terminal differentiation of neuronal cells. Mutations in guf also affect the development of muscles in the embryo. In the absence or guf activity, myoblasts are formed properly, but myoblast fusion and further differentiation of muscle fibers is severely impaired. The guf gene was cloned and found to encode a 21-kD protein with a significant sequence similarity to the mammalian ornithine decarboxylase antizyme (OAZ). In mammals, OAZ plays a key regulatory role in the polyamine biosynthetic pathway through its binding to, and inhibition of, ornithine decarboxylase (ODC), the first enzyme in the pathway. The elaborate regulation of ODC activity in mammals still lacks a defined developmental role and little is known about the involvement of polyamines in cellular differentiation. GUF is the first antizyme-like protein identified in invertebrates. We discuss its possible developmental roles in light of this homology.

Panagrellus redivivus ornithine decarboxylase: structure of the gene, expression in Escherichia coli and characterization of the recombinant protein

A southern blot analysis of the Panagrellus redivivus ornithine decarboxylase (ODC) gene suggests that it is a single-copy gene that resides on a genomic 3.2 kb EcoRI fragment. Phage clones possessing ODC gene sequences were isolated from a genomic EMBL-4 library and purified. The phage DNA inserts were analysed and a 3.2 kb EcoRI fragment containing the entire ODC gene was isolated. The nucleotide sequence analysis of this fragment reveals that the gene is interrupted by two introns of 47 and 49 bp. In the 5' non-translated region of the gene, putative AP1, VPE2 and c-Myc binding sites were identified. The ODC cDNA was expressed in a bacterial system as a His-fusion protein and the enzyme was purified by Ni(2+)-chelating affinity chromatography. The subunit molecular mass, as deduced from the cDNA and shown by SDS/PAGE, is 47.1 kDa. On the basis of gel filtration analyses it is shown that the active enzyme is a dimer. The specific enzyme activity was determined to be 4.2 mumol CO2/min/mg protein. The enzyme is dependent on pyridoxal 5-phosphate as a cofactor, and the presence of dithioerythritol or other thiol-reducing agents is essential for maximal activity. The Km value for L-ornithine was determined as 44 microM. The Ki values for putrescine, alpha-diffluoromethylornithine, alpha-hydrazino-ornithine and alpha-methylornithine were calculated as 51, 34, 0.34 and 42 microM respectively.