S-adenosylmethionine Enzymes Research Articles

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC50 values from 6 to 50 μM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC50 values from 12 to 341 μM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC50 values from 3.5 to 39 μM. Overall, 32 inhibitors encompassing 11 chemotypes had IC50 values < 50 μM and 5 inhibitors in 4 chemotypes had IC50 values < 10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.

Dietary-derived vitamin B12 protects Caenorhabditis elegans from thiol-reducing agents

BackgroundOne-carbon metabolism, which includes the folate and methionine cycles, involves the transfer of methyl groups which are then utilised as a part of multiple physiological processes including redox defence. During the methionine cycle, the vitamin B12-dependent enzyme methionine synthetase converts homocysteine to methionine. The enzyme S-adenosylmethionine (SAM) synthetase then uses methionine in the production of the reactive methyl carrier SAM. SAM-binding methyltransferases then utilise SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids.ResultsWe describe a novel SAM methyltransferase, RIPS-1, which was the single gene identified from forward genetic screens in Caenorhabditis elegans looking for resistance to lethal concentrations of the thiol-reducing agent dithiothreitol (DTT). As well as RIPS-1 mutation, we show that in wild-type worms, DTT toxicity can be overcome by modulating vitamin B12 levels, either by using growth media and/or bacterial food that provide higher levels of vitamin B12 or by vitamin B12 supplementation. We show that active methionine synthetase is required for vitamin B12-mediated DTT resistance in wild types but is not required for resistance resulting from RIPS-1 mutation and that susceptibility to DTT is partially suppressed by methionine supplementation. A targeted RNAi modifier screen identified the mitochondrial enzyme methylmalonyl-CoA epimerase as a strong genetic enhancer of DTT resistance in a RIPS-1 mutant. We show that RIPS-1 is expressed in the intestinal and hypodermal tissues of the nematode and that treating with DTT, β-mercaptoethanol, or hydrogen sulfide induces RIPS-1 expression. We demonstrate that RIPS-1 expression is controlled by the hypoxia-inducible factor pathway and that homologues of RIPS-1 are found in a small subset of eukaryotes and bacteria, many of which can adapt to fluctuations in environmental oxygen levels.ConclusionsThis work highlights the central importance of dietary vitamin B12 in normal metabolic processes in C. elegans, defines a new role for this vitamin in countering reductive stress, and identifies RIPS-1 as a novel methyltransferase in the methionine cycle.

Down-regulation of PvSAMS impairs S-adenosyl-L-methionine and lignin biosynthesis, and improves cell wall digestibility in switchgrass.

S-adenosyl- l-methionine (SAM) is the methyl donor involved in the biosynthesis of guaiacyl (G) and syringyl (S) lignins in vascular plants. SAM is synthesized from methionine through the catalysis of the enzyme S-adenosylmethionine synthase (SAMS). However, the detailed function of SAMS in lignin biosynthesis has not been widely investigated in plants, particularly in monocot species. In this study, we identified PvSAMS genes from switchgrass (Panicum virgatum L.), an important dual-purpose fodder and biofuel crop, and generated numerous transgenic switchgrass lines through PvSAMS RNA interference technology. Down-regulation of PvSAMS reduced the contents of SAM, G-lignins, and S-lignins in the transgenic switchgrass. The methionine and glucoside derivatives of caffeoyl alcohol were found to accumulate in the transgenic plants. Moreover, down-regulation of PvSAMS in switchgrass resulted in brownish stems associated with reduced lignin content and improved cell wall digestibility. Furthermore, transcriptomic analysis revealed that most sulfur deficiency-responsive genes were differentially expressed in the transgenic switchgrass, leading to a significant increase in total sulfur content; thus implying an important role of SAMS in the methionine cycle, lignin biosynthesis, and sulfur assimilation. Taken together, our results suggest that SAMS is a valuable target in lignin manipulation, and that manipulation of PvSAMS can simultaneously regulate the biosynthesis of SAM and methylated monolignols in switchgrass.

Mechanisms of bacterial degradation of arsenic

Arsenic is a toxic metalloid that exists in two major forms (arsenate and arsenite). The anthropogenic activities of man are its major source in the environment. Bacteria have developed resistance against arsenic by using detoxification mechanisms such as oxidation of arsenite to arsenate with the aid of an enzyme arsenite oxidase and in the process gain energy, reduction of arsenate to arsenite through phosphate transporters by a reductase enzyme arsenate reductase and methylation of arsenite with the enzyme S-adenosylmethionine methyltransferases (SAM). The ars operon which mediates the extrusion of arsenic out of bacterial contains a three and five gene operon that assist bacterial with arsenic resistance respectively. Keywords: Arsenic, Arsenate, Arsenite, Arsenate reductase, Arsenite oxidase, Phosphate transporters, Bioremediation.

A quick freeze shows an enzyme's secrets

Enzymology Organic radicals are chemically useful in enzymatic reactions but are often hard to observe, owing to their short lifetimes. Dong et al. used rapid freeze-quench methods to trap two intermediates formed by a noncanonical radical S-adenosylmethionine (SAM) enzyme: a fragmented SAM molecule

Synthesis and evaluation of analogs of 5′-(((Z)-4-amino-2-butenyl)methylamino)-5′-deoxyadenosine (MDL 73811, or AbeAdo) – An inhibitor of S-adenosylmethionine decarboxylase with antitrypanosomal activity

We describe our efforts to improve the pharmacokinetic properties of a mechanism-based suicide inhibitor of the polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC), essential for the survival of the eukaryotic parasite Trypanosoma brucei responsible for Human African Trypanosomiasis (HAT). The lead compound, 5′-(((Z)-4-amino-2-butenyl)methylamino)-5′-deoxyadenosine (1, also known as MDL 73811, or AbeAdo), has curative efficacy at a low dosage in a hemolymphatic model of HAT but displayed no demonstrable effect in a mouse model of the CNS stage of HAT due to poor blood–brain barrier permeation. Therefore, we prepared and evaluated an extensive set of analogs with modifications in the aminobutenyl side chain, the 5′-amine, the ribose, and the purine fragments. Although we gained valuable structure–activity insights from this comprehensive dataset, we did not gain traction on improving the prospects for CNS penetration while retaining the potent antiparasitic activity and metabolic stability of the lead compound 1.

Plasmodium AdoMetDC/ODC bifunctional enzyme is essential for male sexual stage development and mosquito transmission.

ABSTRACTPolyamines are positively-charged organic molecules that are important for cellular growth and division. Polyamines and their synthesizing enzymes are particularly abundant in rapidly proliferating eukaryotic cells such as parasitic protozoa and cancer cells. Polyamine biosynthesis inhibitors, such as Elfornithine, are now being considered for cancer prevention and have been used effectively against Trypanosoma brucei. Inhibitors of polyamine biosynthesis have caused growth arrest of Plasmodium falciparum blood stages in vitro, but in P. berghei only partial inhibition has been observed. While polyamine biosynthesis enzymes are characterized and conserved in Plasmodium spp., little is known on the biological roles of these enzymes inside malaria parasite hosts. The bifunctional polyamine biosynthesis enzyme S-adenosyl methionine decarboxylase/ornithine decarboxylase (AdoMetDC/ODC) was targeted for deletion in P. yoelii. Deletion of AdoMetDC/ODC significantly reduced blood stage parasitemia but Anopheles transmission was completely blocked. We showed that male gametocytogenesis and male gamete exflagellation were abolished and consequently no ookinetes or oocyst sporozoites could be generated from adometdc/odc(–) parasites. Supplementation of putrescine and spermidine did not rescue the defective phenotypes of male gametocytes and gametes of the knockout parasites. These results highlight the crucial role of polyamine homeostasis in the development and functions of Plasmodium erythrocytic stages in the blood and in the mosquito vector and validate polyamine biosynthesis pathway enzymes as drug targeting candidates for malaria parasite transmission blocking.

The structure of lipoyl synthase, a remarkable enzyme that performs the last step of an extraordinary biosynthetic pathway.

Lipoic acid is assembled on its cognate proteins (e.g. the E2 subunit of pyruvate dehydrogenase). An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthetase to a specific lysine residue of the cognate protein followed by sulfur insertion at C6 and C8 of the octanoyl chain. The challenging chemistry of this last step is performed by the radical S-adenosylmethionine (SAM) enzyme lipoyl synthase (LipA). In this issue of the Biochemical Journal, Harmer et al. report the first crystal structure of a lipoyl synthase and demonstrate that it contains two [4Fe-4S] clusters, the canonical radical SAM cluster plus a second auxiliary cluster having an unprecedented serine ligand. The structure provides strong support for the model in which the auxiliary cluster donates the lipoate sulfur atoms.

Changes in SAM2 expression affect lactic acid tolerance and lactic acid production in Saccharomyces cerevisiae.

BackgroundThe great interest in the production of highly pure lactic acid enantiomers comes from the application of polylactic acid (PLA) for the production of biodegradable plastics. Yeasts can be considered as alternative cell factories to lactic acid bacteria for lactic acid production, despite not being natural producers, since they can better tolerate acidic environments. We have previously described metabolically engineered Saccharomyces cerevisiae strains producing high amounts of L-lactic acid (>60 g/L) at low pH. The high product concentration represents the major limiting step of the process, mainly because of its toxic effects. Therefore, our goal was the identification of novel targets for strain improvement possibly involved in the yeast response to lactic acid stress.ResultsThe enzyme S-adenosylmethionine (SAM) synthetase catalyses the only known reaction leading to the biosynthesis of SAM, an important cellular cofactor. SAM is involved in phospholipid biosynthesis and hence in membrane remodelling during acid stress. Since only the enzyme isoform 2 seems to be responsive to membrane related signals (e.g. myo-inositol), Sam2p was tagged with GFP to analyse its abundance and cellular localization under different stress conditions. Western blot analyses showed that lactic acid exposure correlates with an increase in protein levels. The SAM2 gene was then overexpressed and deleted in laboratory strains. Remarkably, in the BY4741 strain its deletion conferred higher resistance to lactic acid, while its overexpression was detrimental. Therefore, SAM2 was deleted in a strain previously engineered and evolved for industrial lactic acid production and tolerance, resulting in higher production.ConclusionsHere we demonstrated that the modulation of SAM2 can have different outcomes, from clear effects to no significant phenotypic responses, upon lactic acid stress in different genetic backgrounds, and that at least in one genetic background SAM2 deletion led to an industrially relevant increase in lactic acid production. Further work is needed to elucidate the molecular basis of these observations, which underline once more that strain robustness relies on complex cellular mechanisms, involving regulatory genes and proteins. Our data confirm cofactor engineering as an important tool for cell factory improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-014-0147-7) contains supplementary material, which is available to authorized users.

Metabolite-dependent regulation of gene expression inTrypanosoma brucei

Mechanisms regulating gene expression in trypanosomatid protozoa differ significantly from those in other eukaryotes. Transcription of the genome appears to be more or less constitutive with the polyadenylation and trans-splicing of large polycistronic RNAs producing monocistronic RNAs whose translation may then depend upon information within their 3' untranslated regions (3'UTRs). Various 3'UTR sequences involved in life-cycle stage-dependent differential gene expression have been described. Moreover, several RNA-binding proteins have been implicated in regulating expression of these transcripts through altering either their stability or their ability to interact with ribosomes. In this issue of Molecular Microbiology Xiao et al. report on a regulatory element within the 3'UTR of the transcript that encodes the polyamine pathway regulatory protein called prozyme. It appears that the RNA element controls translation of the prozyme RNA causing expression to be upregulated when levels of decarboxylated S-adenosylmethionine (dcAdoMet) are depleted. Since prozyme activates the enzyme S-adenosylmethionine decarboxylase (AdoMetDC), which is responsible for the production of dcAdoMet, losing this metabolite leads to upregulation of prozyme, activation of AdoMetDC and restoration of optimal levels of dcAdomet. The system thus represents a novel metabolite-sensing regulatory circuit that maintains polyamine homeostasis in these cells.

Quantum chemistry studies of adenosine 2503 methylation by S-adenosylmethionine-dependent enzymes

Ribosome methylation is important for life processes and is mainly catalyzed by radical S-Adenosylmethionine (SAM) enzymes. Two SAM molecules serve as the cofactor by providing the 5 ′-deoxyadenosyl radical for substrate activation and the methyl. Recently, Booker and coworkers (Science 2011, 332, 604) proposed an alternative mechanism for a pair of radical SAM enzymes, RlmN and Cfr, which respectively methylate the C2 and C8 of adenosine 2503. Their deuterium labeling experiments reveal that methyl group does not transfer directly from SAM to adenosine, instead it passes to Cys355 first, then onto adenosine. In this article, this new reaction mechanism is studied using density functional theory with B3LYP hybrid functional. The reaction system is simulated using small model compounds in the gas phase, and the protein environment is approximated using polarizable continuum model. The structures of the transition states and the intermediates are identified, and their free energies are calculated. The activation barriers indicate that the proposed reaction mechanism is plausible. The formation of a disulfide bond is found to be the rate-limiting step. © 2012 Wiley Periodicals, Inc.

ChemInform Abstract: Cyanide and Carbon Monoxide Ligand Formation in Hydrogenase Biosynthesis

AbstractReview: 127 refs.

Cytochemical and cytological properties of perineuronal oligodendrocytes in the mouse cortex

Neuronal cell bodies are associated with glial cells collectively referred to as perineuronal satellite cells. One such satellite cell is the perineuronal oligodendrocyte, which is unmyelinating oligodendrocytes attaching to large neurons in various neural regions. However, little is known about their cellular characteristics and function. In this study, we identified perineuronal oligodendrocytes as 2',3'-cyclic nucleotide 3'-phosphodiesterase-positive cells attaching to neuronal perikarya immunostained for microtubule-associated protein 2, and examined their cytochemical and cytological properties in the mouse cerebral cortex. 2',3'-Cyclic nucleotide 3'-phosphodiesterase-positive perineuronal oligodendrocytes were immunonegative to representative glial markers for astrocytes (brain-type lipid binding protein and glial fibrillary acidic protein), microglia (Iba-1) and NG2(+) glia. However, almost all perineuronal oligodendrocytes expressed glia-specific or glia-enriched metabolic enzymes, i.e. the creatine synthetic enzyme S-adenosylmethionine:guanidinoacetate N-methyltransferase and L-serine biosynthetic enzyme 3-phosphoglycerate dehydrogenase. As to molecules participating in the glutamate-glutamine cycle, none of the perineuronal oligodendrocytes expressed the plasmalemmal glutamate transporters GLAST and GLT-1, although nearly half of the perineuronal oligodendrocytes were immunopositive for glutamine synthetase. Cytologically, perineuronal oligodendrocytes were mainly distributed in deep cortical layers (layers IV-VI), and attached directly and tightly to neuronal cell bodies, making a long concave impression to the contacting neurons. Interestingly, they attached more to glutamatergic principal neurons than to GABAergic interneurons, and this became evident at postnatal day 14, when the cerebral cortex develops and maturates. These cytochemical and cytological properties suggest that perineuronal oligodendrocytes are so differentiated as to fulfill metabolic support to the associating principal cortical neurons, rather than to regulate their synaptic transmission.

Sam, Sahh and Map gene expression during cell division and paralytic shellfish toxin production of Alexandrium catenella (Dinophyceae)

L.D. Harlow, A. Negri, G.M. Hallegraeff and A. Koutoulis. 2007. Sam, Sahh and Map gene expression during cell division and paralytic shellfish toxin production of Alexandrium catenella (Dinophyceae). Phycologia 46: 666–674. DOI: 10.2216/07-25.1The expression of genes potentially involved in paralytic shellfish toxin (PST) biosynthesis was quantified during cell division of the dinoflagellate Alexandrium catenella. Basic precursors of the neurotoxic PST molecule(s), such as S-adenosylmethionine (SAM), have been hypothesised, but no genes coding for PST production have been definitively identified in dinoflagellates. Sam encodes the enzyme SAM synthetase and two other candidate PST genes S-adenosylhomocysteine hydrolase (Sahh) and methionine aminopeptidase (Map) have been previously identified in the closely related PST producing dinoflagellate Alexandrium fundyense. PST production and expression of Sam, Sahh and Map were examined concurrently during cell division in A. catenella. The PST profile of A. catenella was dominated by C2 (30–37 mol%), GTX5 (12–19 mol%) and GTX6 (27–33 mol%) and was constant over the cell cycle. However, the net cellular PST production rate varied over the cell cycle and was highest (127 fmol cell−1 h−1) during the G2+M phase of the cell cycle (56% cells in G2+M), slowing considerably (−14 fmol cell−1 h−1) as cells entered the G1 phase (66% cells in G1). Quantitative real time PCR revealed that Sam, Sahh and Map were up-regulated (doubling in each case) during PST production and the G2+M phase of the cell division cycle before irradiance. Alexandrium catenella actively produced PSTs during this dark period, suggesting that photon irradiance was not a direct trigger for PST production. Interactions between cell division and PST production appear complex and the present study has demonstrated correlations between PST production and expression of Sam, Sahh and Map, which warrants further investigation.

S-adenosylmethionine synthetase genes from eleven marine dinoflagellates

L.D. Harlow, A. Koutoulis and G.M. Hallegraeff. 2007. S-adenosylmethionine synthetase genes from eleven marine dinoflagellates. Phycologia 46: 46–53. DOI: 10.2216/06-28.1Paralytic shellfish poisoning toxins (PSTs) such as saxitoxin are believed to be synthesised from precursor molecules including arginine, S-adenosylmethionine (SAM) and acetate. The enzyme SAM synthetase is a good candidate as an early acting enzyme in the PST biosynthetic pathway. We have used degenerate PCR to identify the gene encoding SAM synthetase, Sam, in dinoflagellates. Several different PCR products were cloned and sequenced from PST-producing strains of the dinoflagellates Alexandrium minutum, A. catenella and Gymnodinium catenatum and primers specific to dinoflagellate Sam used for further sequence analysis in 11 species of toxic and nontoxic dinoflagellate genera, including: Alexandrium, Gymnodinium, Karenia, Karlodinium, Noctiluca, Prorocentrum and Takayama. At the nucleotide level, Sam clones were unique to dinoflagellates and the most commonly identified Sam was highly conserved between dinoflagellate species. Dinoflagellate Sam G + C content was both typical (60.8%) or lower (40.7%) compared to A. tamarense. The derived protein sequences showed a low and equal level of similarity to Sam from other species representing a range of Kingdoms. DNA sequence information for dinoflagellate Sam provides important insights for dinoflagellate codon usage, which will facilitate primer design to target novel dinoflagellate genes.

Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase

The enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) is involved in the biosynthesis of the hypermodified tRNA nucleoside queuosine. It is unprecedented in nature as it uses the cofactor S-adenosylmethionine as the donor of a ribosyl group. We have determined the crystal structure of Bacillus subtilis QueA at a resolution of 2.9 Å. The structure reveals two domains representing a 6-stranded β-barrel and an αβα-sandwich, respectively. All amino acid residues invariant in the QueA enzymes of known sequence cluster at the interface of the two domains indicating the localization of the substrate binding region and active center. Comparison of the B. subtilis QueA structure with the structure of QueA from Thermotoga maritima suggests a high domain flexibility of this enzyme.

A Dual Upstream Open Reading Frame-based Autoregulatory Circuit Controlling Polyamine-responsive Translation

A novel form of translational regulation is described for the key polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC). Plant AdoMetDC mRNA 5' leaders contain two highly conserved overlapping upstream open reading frames (uORFs): the 5' tiny and 3' small uORFs. We demonstrate that the small uORF-encoded peptide is responsible for constitutively repressing downstream translation of the AdoMetDC proenzyme ORF in the absence of increased polyamine levels. This first example of a sequence-dependent uORF to be described in plants is also functional in Saccharomyces cerevisiae. The tiny uORF is required for normal polyamine-responsive AdoMetDC mRNA translation, and we propose that this is achieved by control of ribosomal recognition of the occluded small uORF, either by ribosomal leaky scanning or by programmed -1 frameshifting. In vitro expression demonstrated that both the tiny and the small uORFs are translated. This tiny/small uORF configuration is highly conserved from moss to Arabidopsis thaliana, and a more diverged tiny/small uORF arrangement is found in the AdoMetDC mRNA 5' leader of the single-celled green alga Chlamydomonas reinhardtii, indicating an ancient origin for the uORFs.

Eugenol reduces growth and increases activity of S-adenosylmethionine decarboxylase in the phytopathogenic fungusBotrytis fabae

This study was undertaken to examine the possibility that eugenol-induced reductions in growth ofBotrytis fabae are associated with alterations in polyamine metabolism.B. fabae was grown in liquid medium amended with different concentrations of eugenol. Changes in fungal biomass, and activities of enzymes of polyamine biosynthesis and catabolism were studied. An examination was also made of the incorporation of radioactivity from ornithine into polyamines. Activity of the polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC) and flux of label from ornithine into the polyamine spermine were greatly increased inB. fabae grown in the presence of eugenol. However, no significant changes were observed in polyamine catabolism or in the concentrations of free polyamines in treated fungal tissue.

Altered growth and polyamine catabolism following exposure of the chocolate spot pathogen Botrytis fabae to the essential oil of Ocimum basilicum

Biomass of the fungal pathogen Botrytis fabae in liquid culture amended with two chemotypes of the essential oil of basil, Ocimum basilicum, was reduced significantly at concentrations of 50 ppm or less. The methyl chavicol chemotype oil increased the activity of the polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC), but polyamine concentrations were not significantly altered. In contrast, the linalol chemotype oil decreased AdoMetDC activity in B. fabae, although again polyamine concentrations were not altered significantly. However activities of the polyamine catabolic enzymes diamine oxidase (DAO) and polyamine oxidase (PAO) were increased significantly in B. fabae grown in the presence of the essential oil of the two chemotypes. It is suggested that the elevated activities of DAO and PAO may be responsible, in part, for the antifungal effects of the basil oil, possibly via the generation of hydrogen peroxide and the subsequent triggering of programmed cell death.

Altered growth and polyamine catabolism following exposure of the chocolate spot pathogen Botrytis fabae to the essential oil of Ocimum basilicum

Biomass of the fungal pathogen Botrytis fabae in liquid culture amended with two chemotypes of the essential oil of basil, Ocimum basilicum, was reduced significantly at concentrations of 50 ppm or less. The methyl chavicol chemotype oil increased the activity of the polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC), but polyamine concentrations were not significantly altered. In contrast, the linalol chemotype oil decreased AdoMetDC activity in B. fabae, although again polyamine concentrations were not altered significantly. However activities of the polyamine catabolic enzymes diamine oxidase (DAO) and polyamine oxidase (PAO) were increased significantly in B. fabae grown in the presence of the essential oil of the two chemotypes. It is suggested that the elevated activities of DAO and PAO may be responsible, in part, for the antifungal effects of the basil oil, possibly via the generation of hydrogen peroxide and the subsequent triggering of programmed cell death.