A DNA polymerase with a single mutation and a divalent calcium cofactor catalyzes the synthesis of unnatural N3'→P5' phosphoramidate (NP) bonds to form NP-DNA. However, this template-directed ...phosphoryl transfer activity remains orders of magnitude slower than native phosphodiester synthesis. Here, we used time-resolved x-ray crystallography to show that NP-DNA synthesis proceeds with a single detectable calcium ion in the active site. Using insights from isotopic and elemental effects, we propose that one-metal-ion electrophilic substrate activation is inferior to the native two-metal-ion mechanism. We found that this deficiency in divalent activation could be ameliorated by trivalent rare earth and post-transition metal cations, substantially enhancing NP-DNA synthesis. Scandium(III), in particular, confers highly specific NP activity with kinetics enhanced by more than 100-fold over calcium(II), yielding NP-DNA strands up to 100 nucleotides in length.
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme with diverse biological functions in DNA synthesis. Nicotinamide phosphoribosyltransferase (NAMPT) is a key rate‐limiting enzyme ...involved in NAD+ biosynthesis in mammals. We developed the first chemical tool for optical control of NAMPT and NAD+ in biological systems using photoswitchable proteolysis‐targeting chimeras (PS‐PROTACs). An NAMPT activator and dimethylpyrazolazobenzene photoswitch were used to design highly efficient PS‐PROTACs, enabling up‐ and down‐reversible regulation of NAMPT and NAD+ in a light‐dependent manner and reducing the toxicity associated with inhibitor‐based PS‐PROTACs. PS‐PROTAC was activated under 620 nm irradiation, realizing in vivo optical manipulation of antitumor activity, NAMPT, and NAD+.
The first activator‐based photoswitchable proteolysis‐targeting chimera (PS‐PROTAC) was developed for the optical control of NAMPT and NAD+ in biological systems. The novel PS‐PROTAC enabled the reversible regulation of NAMPT and NAD+, resulting in a significant reduction in target‐related toxicity compared to conventional NAMPT degraders or inhibitors. Furthermore, PS‐PROTAC allowed for the in vivo optical manipulation of antitumor activity, NAMPT, and NAD+.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Auxotrophs are unable to synthesize all the metabolites essential for their metabolism and rely on others to provide them. They have been intensively studied in laboratory-generated and -evolved ...mutants, but emergent adaptation mechanisms to auxotrophy have not been systematically addressed. Here, we investigated auxotrophies in bacteria isolated from Arabidopsis thaliana leaves and found that up to half of the strains have auxotrophic requirements for biotin, niacin, pantothenate and/or thiamine. We then explored the genetic basis of auxotrophy as well as traits that co-occurred with vitamin auxotrophy. We found that auxotrophic strains generally stored coenzymes with the capacity to grow exponentially for 1-3 doublings without vitamin supplementation; however, the highest observed storage was for biotin, which allowed for 9 doublings in one strain. In co-culture experiments, we demonstrated vitamin supply to auxotrophs, and found that auxotrophic strains maintained higher species richness than prototrophs upon external supplementation with vitamins. Extension of a consumer-resource model predicted that auxotrophs can utilize carbon compounds provided by other organisms, suggesting that auxotrophic strains benefit from metabolic by-products beyond vitamins.
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NUK, SBMB, SBNM, UL, UM, UPUK
Our present study evaluated the underlying molecular-mechanism(s) associated with the observed enhanced transcript levels and concomitant functional activity of 3-hydroxy-3-methylglutaryl coenzyme A ...reductase 1 (NtHMGR1), a rate-limiting enzyme of cytosolic mevalonate (MVA) pathway of terpenoids biosynthesis, by gibberellin A3 (GA3) treatment in model cultivated tobacco, Nicotiana tabacum L. Based on the transcription run-on and cordycepin chase assays, our results demonstrated that tobacco seeds-priming with GA3 causes a relative and significantly enhanced transcriptional rate and mRNA stability of NtHMGR1. Taken together, our study established that GA3 mediated transcriptional and post-transcriptional regulatory control as one of the mechanisms for the observed enhanced transcript-levels and consequently enhanced functional activity of NtHMGR1.
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IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, UL, UM, UPUK
Fluorescent silver nanoclusters (Ag NCs) displaying dual-excitation and dual-emission properties have been developed for the specific detection of NAD+ (nicotinamide adenine dinucleotide, oxidized ...form). With the increase of NAD+ concentrations, the longer wavelength emission (with the peak at 550 nm) was gradually quenched due to the strong interactions between the NAD+ and Ag NCs, whereas the shorter wavelength emission (peaking at 395 nm) was linearly enhanced. More important, the dual-emission intensity ratio (I395/I550), fitting by a single-exponential decay function, can efficiently detect various NAD+ levels from 100 to 4000 μM, as well as label NAD+/NADH (reduced form of NAD) ratios in the range of 1–50.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a 4Fe–4S cluster ligated by three cysteine residues. The remaining, unligated, iron ion of ...the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5′-deoxyadenosyl radical. The 5′-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron–sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron–sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
•Diverging roles for the auxiliary clusters in RS sulfur-donating enzymes are proposed.•Structures of auxiliary cluster-containing SPASM and twitch domains revealed.•Intermediates are isolated in the biosynthesis of the MoCo and H-cluster cofactors.•Auxiliary clusters in RS enzymes are involved in complex heterocycle biosynthesis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of ...methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max L. Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.
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BFBNIB, EMUNI, FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NMLJ, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Translational GTPases are universally conserved GTP hydrolyzing enzymes, critical for fidelity and speed of ribosomal protein biosynthesis. Despite their central roles, the mechanisms of ...GTP‐dependent conformational switching and GTP hydrolysis that govern the function of trGTPases remain poorly understood. Here, we provide biochemical and high‐resolution structural evidence that eIF5B and aEF1A/EF‐Tu bound to GTP or GTPγS coordinate a monovalent cation (M+) in their active site. Our data reveal that M+ ions form constitutive components of the catalytic machinery in trGTPases acting as structural cofactor to stabilize the GTP‐bound “on” state. Additionally, the M+ ion provides a positive charge into the active site analogous to the arginine‐finger in the Ras‐RasGAP system indicating a similar role as catalytic element that stabilizes the transition state of the hydrolysis reaction. In sequence and structure, the coordination shell for the M+ ion is, with exception of eIF2γ, highly conserved among trGTPases from bacteria to human. We therefore propose a universal mechanism of M+‐dependent conformational switching and GTP hydrolysis among trGTPases with important consequences for the interpretation of available biochemical and structural data.
Synopsis
X‐ray structures of eIF5B and aEF1A reveal the presence of a monovalent cation in the active site, thus offering insight on the mechanism of GTP hydrolysis and prompting the re‐interpretation of earlier studies on translational GTPases.
Biochemical and structural data reveal that translational GTPases eIF5B, aEF1A and EF‐Tu bind monovalent cations (M+) in their catalytic center.
The M+ ion is bound in the same position as in other M+‐dependent GTPases and analogous to the arginine‐finger in the Ras‐RasGAP system.
The M+ ion acts as a structural and catalytic cofactor in translational GTPases.
The coordination shell for the monovalent cation is universally conserved among translational GTPases, suggesting a universal mechanism of M+‐dependent conformational switching and GTP hydrolysis.
X‐ray structures of eIF5B and aEF1A reveal the presence of a monovalent cation in the active site, thus offering insight on the mechanism of GTP hydrolysis and prompting the re‐interpretation of earlier studies on translational GTPases.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The relationship between genetic molecules and metabolism is one of the longest-standing problems for the origin of life. A central molecule within early metabolism is the coenzyme nicotinamide ...adenine dinucleotide (NAD(H)), a modified ribonucleotide and reducing agent. Yet, without enzymes, NADH does not reduce carbonyl compounds, its primary metabolic substrates, leading to an apparent paradox regarding its role in the evolution of metabolism. We now report that abundant metal ions turn on a nonenzymatic, stereoselective, and potentially primordial reduction reaction of keto acids by NADH. Kinetic, mechanistic, and computational studies elucidate the reaction mechanism and the way stereochemistry is transferred. Complexes of metals with RNA-derived coenzymes could have mediated the transition from inorganic to organic reducing agents and the propagation of chirality in early metabolism.
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•The synergy of metal ions and the coenzyme NADH links genetic molecules to early metabolism•Demonstration of chirality transfer in a nonenzymatic metabolic reaction•Metal ions enable the activation and preorganization of substrates instead of enzymes•Computational insights into the mechanism and selectivity of chirality transfer
Coenzymes are thought to have played a central role in the emergence of metabolism. However, studies in the context of prebiotic chemistry face the problem that outside of enzymes, many such coenzymes do not react with their biological substrates. Previous work suggests nicotinamide adenine dinucleotide (NAD) to be one of the most ancient coenzymes and to be central to early metabolism. Yet, these models suffer from the logical gap that without enzymes, the reduced coenzyme NADH does not react with keto acids, some of its primary biological substrates.
We now report that aluminum or iron ions are catalysts for the reduction of keto acids by NADH. The ions mimic some of the roles of enzymes, such as the activation of substrates and the preorganization of keto acids with NADH. Moreover, the reaction proceeds with moderate stereoselectivity. Our work gives insight into how an important coenzyme could have participated in a primitive metabolism that predated enzymes.
We show that metal ions catalyze the reduction of keto acids by the coenzyme NADH in water, a reaction that otherwise requires complex enzymes to proceed. The reaction is partially stereoselective, as NADH is a chiral hydride donor, yielding hydroxy acids with small to moderate enantiomeric excess. Analysis of the reaction mechanism by experiments and computations illustrates that the metal ions mimic multiple roles of enzymes by activating the substrates and pre-organizing them for an intramolecular reaction.
Protein kinases form one of the largest protein families and are found in all species, from viruses to humans. They catalyze the reversible phosphorylation of proteins, often modifying their activity ...and localization. They are implicated in virtually all cellular processes and are one of the most intensively studied protein families. In recent years, they have become key therapeutic targets in drug development as natural mutations affecting kinase genes are the cause of many diseases. The vast amount of data contained in the primary literature and across a variety of biological data collections highlights the need for a repository where this information is stored in a concise and easily accessible manner. The UniProt Knowledgebase meets this need by providing the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Here, we describe the expert curation process for kinases, focusing on the Caenorhabditis elegans kinome. The C. elegans kinome is composed of 438 kinases and almost half of them have been functionally characterized, highlighting that C. elegans is a valuable and versatile model organism to understand the role of kinases in biological processes.
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