Comparative Genomics of NAD Biosynthesis in Cyanobacteria

Abstract

Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. Cyanobacteria are among the oldest life forms on earth (64). Their unique role in biogeochemical cycles such as photosynthesis, nitrogen fixation (6, 20) and generation, and homeostasis of oxygenic atmosphere (14) makes this diverse group of bacteria essential for all terrestrial life. Not surprisingly, cyanobacteria attract growing attention in various areas of basic and applied research (11). Recent breakthroughs in genome sequencing opened new opportunities for a fundamental understanding of cyanobacterial physiology and evolution. For example, a comparative genome analysis provided new insights into the photosynthetic machinery of cyanobacteria and related species (12,54,59).Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. In addition to its role in innumerable redox reactions, NAD participates as a cosubstrate in a number of metabolic and regulatory processes. Some of these processes, such as NAD-dependent protein deacetylation catalyzed by the CobB/ SIR2 enzyme family (68), are leading to the depletion of the NAD pool. Among other enzymes consuming NAD are a NAD-dependent DNA ligase characteristic of bacteria (73) Although most of the biochemical transformations involved in NAD biosynthesis, salvage, and recycling were analyzed in great detail (for reviews, see references 3, 33, 35, and 48), those studies were historically focused on a few model species. NADmediated links between metabolic and signaling networks recently revealed in eukaryotic cells (16,69,78) triggered a new wave of research in yeast and mammals (for recent reviews, see references 31 and 60). At the same time, relatively little is known about NAD biosynthesis in cyanobacteria. Although many NAD biosynthetic genes are annotated in public archives (e.g., Cyanobase [http://www.kazusa.or.jp/cyanobase/] and KEGG [http://www.genome.ad.jp/kegg/]), some of these annotations are imprecise and have not been consistently projected across all the sequenced cyanobacteria. Moreover, we are not aware of any attempt at metabolic reconstruction of respective pathways in any of the divergent cyanobacterial species. When we began this study, only one of the NAD biosynthetic enzymes, archaea-like nicotinamide mononucleotide (NMN) adenylyltransferase from Synechocystis sp. strain PCC 6803 (encoded by

Genomics-driven Reconstruction of Acinetobacter NAD Metabolism

“…1). Previously described members of NadV family share a fold and a general catalytic mechanism of phosphoribosyl transfer with the PncB family (41) but display a distinct substrate specificity for Nm (21,42). The same strict substrate preference for Nm over Na (ϳ5,000-fold) was observed by us for the recombinant purified abNadV enzyme (Table 3), confirming its role in the nondeamidating route.…”

“…They are scarcely distributed in bacteria, typically as fusion proteins with ADP-ribose pyrophosphatase. In most cases they are present in addition to (rather than instead of) NadD in the context of a dispensable nicotinamide salvage/recycling pathway, which is initiated by the conversion of nicotinamide to NMN by nicotinamide phosphoribosyltransferase (NMPRT) of the NadV family (21). The recently established essential role of NadM in F. tularensis first highlighted this family as an alternative drug target in NAD biogenesis of bacterial pathogens.…”

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

“…12,13,[50][51][52][53][54][55] While there is diversity in the NAD-centered pyridine nucleotide cycle across bacteria, especially in terms of the different routes of salvage and overlap with de novo synthesis, the following key enzymes have been recognized as key players in the pathway ( Fig. 1): 12,13,[50][51][52][53][54][55] (1) a multi-domain carboxylating nicotinate/ quinolinate phosphoribosyltransferase (nadC in Fig. 1) capable of synthesizing nicotinate monophosphate ribonucleotide (NaMN) from quinolinic acid during de novo synthesis of NAD; (2) the PncA nicotinamidase that initiates the classical salvage arm of the pathway by catalyzing the hydrolysis of free nicotinamide (NM) to nicotinate (NaM); (3) the nicotinate phosphoribosyltransferase pncB, a TIM barrel enzyme of the NAPRTase family, that transfers a phosphoribosyl moiety to nicotinate thus generating nicotinate D-ribonucleotide (NaMN); (4) a HIGH nucleotidyltransferase (NadD) that adenylates the nucleotide formed in the prior steps using ATP to form the dinucleotide; (5) a PP-loop fold NAD synthase (NadE) that adenylates the carboxyl group of nicotinate using ATP and subsequently ligates it to ammonia to form a nicotinamide moiety.…”

“…12,13,[50][51][52][53][54][55] While there is diversity in the NAD-centered pyridine nucleotide cycle across bacteria, especially in terms of the different routes of salvage and overlap with de novo synthesis, the following key enzymes have been recognized as key players in the pathway ( Fig. 1): 12,13,[50][51][52][53][54][55] (1) a multi-domain carboxylating nicotinate/ quinolinate phosphoribosyltransferase (nadC in Fig.…”

Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis

“…The general approach was originally described by Overbeek et al (17), and its application was recently illustrated for the analysis of NAD metabolism in cyanobacteria (27). Briefly, a subsystem is initiated by defining a list of functional roles (enzymes, transporters, and regulators) immediately associated with a biological process under study.…”