Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Abstract

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous cofactor participating in numerous redox reactions. It is also a substrate for regulatory modifications of proteins and nucleic acids via the addition of ADP-ribose moieties or removal of acyl groups by transfer to ADP-ribose. In this study, we use in-depth sequence, structure and genomic context analysis to uncover new enzymes and substrate-binding proteins in NAD-utilizing metabolic and macromolecular modification systems. We predict that Escherichia coli YbiA and related families of domains from diverse bacteria, eukaryotes, large DNA viruses and single strand RNA viruses are previously unrecognized components of NAD-utilizing pathways that probably operate on ADP-ribose derivatives. Using contextual analysis we show that some of these proteins potentially act in RNA repair, where NAD is used to remove 2 0 -3 0 cyclic phosphodiester linkages. Likewise, we predict that another family of YbiA-related enzymes is likely to comprise a novel NAD-dependent ADP-ribosylation system for proteins, in conjunction with a previously unrecognized ADP-ribosyltransferase. A similar ADP-ribosyltransferase is also coupled with MACRO or ADP-ribosylglycohydrolase domain proteins in other related systems, suggesting that all these novel systems are likely to comprise pairs of ADP-ribosylation and ribosylglycohydrolase enzymes analogous to the DraG-DraT system, and a novel group of bacterial polymorphic toxins. We present evidence that some of these coupled ADP-ribosyltransferases/ribosylglycohydrolases are likely to regulate certain restriction modification enzymes in bacteria. The ADP-ribosyltransferases found in these, the bacterial polymorphic toxin and host-directed toxin systems of bacteria such as Waddlia also throw light on the evolution of this fold and the origin of eukaryotic polyADP-ribosyltransferases and NEURL4-like ARTs, which might be involved in centrosomal assembly. We also infer a novel biosynthetic pathway that might be involved in the synthesis of a nicotinate-derived compound in conjunction with an asparagine synthetase and AMPylating peptide ligase. We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations.

Identification and Characterization of the Missing Pyrimidine Reductase in the Plant Riboflavin Biosynthesis Pathway

“…Thus, besides being fused to PyrR in plants, COG3236 is also fused in certain g-proteobacteria (e.g. Vibrio spp., Photobacterium profundum) to a homolog of RibA, the first enzyme of riboflavin synthesis (de Souza and Aravind, 2012), and the phs1 mutant is flavin deficient (Ouyang et al, 2010). These strands of evidence both reinforce a connection with the riboflavin pathway.…”

NAD homeostasis in the bacterial response to DNA/RNA damage

“…with 2 ,3 -cyclic phosphate ends [56]. Ligation of damaged RNA, likely resulting in 2 -phosphate containing products, might then require the 2 -dephosphorylation step catalyzed by KptA [55].…”

“…However, since tRNA splicing that occurs in bacteria is self-catalyzed [53,54], the role of KptA in bacterial biology remains obscure. It has been hypothesized that KptA might be an RNA processing enzyme able to repair the RNA damaged by toxic endoribonucleases [55]. Indeed, metal-independent endoribonucleases tend to generate RNA fragments similar to RNA intermediates formed during tRNA splicing, i.e.…”

Protein and DNA Modifications: Evolutionary Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics

“…Prokaryotic members of both superfamilies from which the eukaryotic representatives were derived appear to have played predominantly metabolic roles. Representatives of the RPD3/ HDAC superfamily appear to have a role in acetoin/polyamine metabolism (Ramirez and Tolmasky 2010), whereas those of the sirtuin superfamily regulate acyl CoA biosynthesis and nicotinamide dinucleotide (NAD) metabolism (Avalos et al 2004;de Souza and Aravind 2012). In addition to a representative from the archaeal precursor, eukaryotes appear to have acquired several sirtuins from bacteria in the course of their evolution.…”

“…Although members of the sirtuin superfamily can catalyze mono-ADP ribosylation, the best-understood modifications of histones are catalyzed by the poly-ADP-ribose polymerase (PARP) family (Fig. 4E) that belongs to the ADP-ribosyltransferase (ART) superfamily (Laing et al 2011;de Souza and Aravind 2012). At least two PARPs, including the histone-modifying PARP1 are reconstructed as being present in the LECA (Citarelli et al 2010).…”