QueE: A Radical SAM Enzyme Involved in the Biosynthesis of 7-Deazapurine Containing Natural Products

Not all 5'-deoxyadenosines are created equal: Tracing the provenance of 5'-deoxyadenosine formed by the radical S-adenosyl-L-methionine enzyme 7-carboxy-7-deazaguanine synthase

Members of the radical S-adenosyl-L-methionine (rSAM) enzyme superfamily cleave SAM to generate the highly reactive 5'-deoxyadenosyl radical (dAdo·), where dAdo· initiates the reaction by an H-atom transfer from the substrate to form 5'-deoxyadenosine (dAdo) in nearly every member of the superfamily. However, in all rSAM enzymes, SAM also undergoes reductive cleavage to form dAdo in a reaction uncoupled from the product's formation. Herein, we examine the dAdo that is formed under catalytic conditions with the rSAM enzyme 7-carboxy-7-deazaguanine synthase (QueE), which catalyzes the radical-mediated transformation of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG). We propose that the dAdo that is observed under catalytic conditions can be traced to multiple shunt pathways, which are not all truly uncoupled from catalysis. Indeed, in one case, we demonstrate that the dAdo can form due to the reductive quenching of the initially generated substrate radical by the very same reducing system used to reductively cleave SAM to initiate catalysis. The insights from this work are generally applicable to all members of the rSAM family, as they influence the choice of reducing system to avoid the non-productive shunt pathways that interfere with catalysis.

COG database update 2024

The Clusters of Orthologous Genes (COG) database, originally created in 1997, has been updated to reflect the constantly growing collection of completely sequenced prokaryotic genomes. This update increased the genome coverage from 1309 to 2296 species, including 2103 bacteria and 193 archaea, in most cases, with a single representative genome per genus. This set covers all genera of bacteria and archaea that included organisms with 'complete genomes' as per NCBI databases in November 2023. The number of COGs has been expanded from 4877 to 4981, primarily by including protein families involved in bacterial protein secretion. Accordingly, COG pathways and functional groups now include secretion systems of types II through X, as well as Flp/Tad and type IV pili. These groupings allow straightforward identification and examination of the prokaryotic lineages that encompass-or lack-a particular secretion system. Other developments include improved annotations for the rRNA and tRNA modification proteins, multi-domain signal transduction proteins, and some previously uncharacterized protein families. The new version of COGs is available at https://www.ncbi.nlm.nih.gov/research/COG, as well as on the NCBI FTP site https://ftp.ncbi.nlm.nih.gov/pub/COG/, which also provides archived data from previous COG releases.

Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator

In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.

Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator

In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.

Intermolecular electron transfer in radical SAM enzymes as a new paradigm for reductive activation

Radical S-adenosyl-L-methionine (rSAM) enzymes bind one or more Fe-S clusters and catalyze transformations that produce complex and structurally diverse natural products. One of the clusters, a 4Fe-4S cluster, binds and reductively cleaves SAM to generate the 5'-deoxyadenosyl radical, which initiates the catalytic cycle by H-atom transfer from the substrate. The role(s) of the additional auxiliary Fe-S clusters (ACs) remains largely enigmatic. The rSAM enzyme PapB catalyzes the formation of thioether cross-links between the β-carbon of an Asp and a Cys thiolate found in the PapA peptide. One of the two ACs in the protein binds to the substrate thiol where, upon formation of a thioether bond, one reducing equivalent is returned to the protein. However, for the next catalytic cycle to occur, the protein must undergo an electronic state isomerization, returning the electron to the SAM-binding cluster. Using a series of iron-sulfur cluster deletion mutants, our data support a model whereby the isomerization is an obligatorily intermolecular electron transfer event that can be mediated by redox active proteins or small molecules, likely via the second AC in PapB. Surprisingly, a mixture of FMN and NADPH is sufficient to support both the reductive and the isomerization steps. These findings lead to a new paradigm involving intermolecular electron transfer steps in the activation of rSAM enzymes that require multiple iron-sulfur clusters for turnover. The implications of these results for the biological activation of rSAM enzymes are discussed.

Characterization of the cobalamin-dependent radical S-adenosyl-l-methionine enzyme C-methyltransferase Fom3 in fosfomycin biosynthesis

Fosfomycin is a clinically used broad-spectrum antibiotic that has the structure of an oxirane ring with a phosphonic acid substituent and a methyl substituent. In nature, fosfomycin is produced by Streptomyces spp. and Pseudomonas sp., but biosynthesis of fosfomycin significantly differs between the two bacteria, especially in the incorporation mechanism of the methyl group. It has been proposed that the cobalamin-dependent radical S-adenosyl-l-methionine (SAM) enzyme Fom3 is responsible for the methyl-transfer reaction in Streptomyces fosfomycin biosynthesis. In this chapter, we describe the experimental methods to characterize Fom3. We performed the methylation reaction with the purified recombinant Fom3, revealing that Fom3 recognizes a cytidylylated 2-hydroxyethylphosphonate as a substrate and catalyzes stereoselective methylation of the sp³ carbon at the C2 position to afford cytidylylated (S)-2-hydroxypropylphosphonate. Reaction analysis using deuterium-labeled substrates showed that the 5'-deoxyadenosyl radical generated by reductive cleavage of SAM stereoselectively abstracts the pro-R hydrogen atom of the CH bond at the C2 position of cytidylylated 2-hydroxyethylphosphonate. Therefore, the C-methylation reaction catalyzed by Fom3 proceeds with inversion of the configuration at the C2 position. Experimental methods to elucidate the chemical structures of the substrate and products and the stereochemical course in the Fom3-catalyzed reaction could give information to progress investigation of cobalamin-dependent radical SAM C-methyltransferases.

Hypermodified DNA in Viruses of E. coli and Salmonella

The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.

Eukaryotic TYW1 Is a Radical SAM Flavoenzyme

TYW1 is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine-containing tRNA^Phe, forming 4-demethylwyosine-containing tRNA^Phe. Homologues of TYW1 are found in both archaea and eukarya; archaeal homologues consist of a single domain, while eukaryal homologues contain a flavin binding domain in addition to the radical SAM domain shared with archaeal homologues. In this study, TYW1 from Saccharomyces cerevisiae (ScTYW1) was heterologously expressed in Escherichia coli and purified to homogeneity. ScTYW1 is purified with 0.54 ± 0.07 and 4.2 ± 1.9 equiv of flavin mononucleotide (FMN) and iron, respectively, per mole of protein, suggesting the protein is ∼50% replete with Fe–S clusters and FMN. While both NADPH and NADH are sufficient for activity, significantly more product is observed when used in combination with flavin nucleotides. ScTYW1 is the first example of a radical SAM flavoenzyme that is active with NAD(P)H alone.