REVIEW ARTICLES Nucleotide metabolism pathway: the achilles’ heel for bacterial pathogens Sujata Kumari1,2,* and Prajna Tripathi1,3 1National Institute of Immunology, New Delhi 110 067, India 2Present address: Department of Zoology, Magadh Mahila College, Patna University, Patna 800 001, India 3Present address: Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062, India de novo pathway, the nucleotides are synthesized from Pathogens exploit their host to extract nutrients for their survival. They occupy a diverse range of host simple precursor molecules. In the salvage pathway, the niches during infection which offer variable nutrients preformed nucleobases or nucleosides which are present accessibility. To cause a successful infection a patho- in the cell or transported from external environmental gen must be able to acquire these nutrients from the milieu to the cell are utilized to form nucleotides. host as well as be able to synthesize the nutrients on its own, if required. Nucleotides are the essential me- tabolite for a pathogen and also affect the pathophysi- Purine biosynthesis pathway ology of infection. This article focuses on the role of nucleotide metabolism of pathogens during infection The purine biosynthesis pathway is universally conserved in a host. Nucleotide metabolism and disease pathoge- in living organisms (Figure 1). As an example, we here nesis are closely related in various pathogens. Nucleo- present the pathway derived from well-studied Gram- tides, purines and pyrimidines, are biosynthesized by positive bacteria Lactococcus lactis. In the de novo the de novo and salvage pathways. Whether the patho- pathway the purine nucleotides are synthesized from sim- gen will employ the de novo or salvage pathway dur- ple molecules such as phosphoribosyl pyrophosphate ing infection is dependent on various factors, like (PRPP), amino acids, CO2 and NH3 by a series of enzy- availability of nucleotides, energy condition and pres- matic reactions. The first ten reactions lead to the synthe- ence of enzymes of the particular pathway. Under- sis of inosine monophosphate (IMP). Further, adenosine standing the nucleotide metabolism of a pathogen within its host will provide a key insight into the host– monophosphate is synthesized from IMP by the action of pathogen interaction and will also aid in the develop- adenylosuccinate synthase (purA) and adenylosuccinate ment of novel therapeutic strategies. lyase (purB), while guanosine monophosphate is pro- duced from IMP by the help of enzyme IMP dehydroge- nase (guaB) and guanosine monophosphate synthase Keywords: Drug target, host niches, nucleotide biosyn- (guaA). The enzymes of this pathway are highly regu- thesis, pathogens, virulence. lated. The first step of the pathway is a rate-limiting step catalysed by the enzyme encoded by phosphoribosyl NUCLEOTIDES are essential metabolites for all living pyrophosphate amidotransferase (purF). organisms. They play a vital role in all biological aspects Purines are synthesized in the salvage pathway from of the cell. Most importantly, they are the building blocks nucleobases and nucleosides which are either present inside for synthesis of DNA and RNA, and hence are involved the cell or transported into the cell by various nucleobase in replication and transcription processes. Nucleotides are and nucleoside transporters. Purine nucleoside phospho- also the constituents of essential coenzymes like NAD and rylases catalyse the conversion of purine nucleosides into FAD1. They are also known to activate the precursors invol- their corresponding nucleobase and ribose-1-phosphate. ved in lipid and carbohydrate synthesis2,3 and are the sole Purine nucleobases are converted into nucleoside mono- energy currency of the cell. Further, cyclic derivatives of phosphate by the activity of nucleobase phosphoribosyl purine nucleotides, cAMP and cGMP, serve as intracellu- transferases. Nucleoside kinases catalyse the conversion lar second messengers in numerous signalling pathways4. of nucleoside monophosphate into nucleoside di- or tri- phosphate. Nucleotide biosynthesis pathway Pyrimidine biosynthesis pathway Nucleotides, purines and pyrimidines, are biosynthesized in the cell by the de novo or salvage pathway. In the Like the purine biosynthesis pathway, the pyrimidine bio- synthesis pathway is also conserved across all organisms *For correspondence. (e-mail: [email protected]) (Figure 2). The pathway described here is again derived 1458 CURRENT SCIENCE, VOL. 120, NO. 9, 10 MAY 2021 REVIEW ARTICLES Figure 1. Purine biosynthesis by de novo and salvage pathways. The de novo pathway is denoted by solid arrows, while the salvage pathway is denoted by dashed arrows. Reactions common to them are denoted by solid and dashed arrows. The genes encoding the enzymes involved are indicated. PRPP, Phosphoribosyl pyrophosphate; PRA, Phosphoribosyl amine; GAR, Glycinamide ribonucleotide; FGAR, Formylglycinamide ribonucleotide; FGAM, Formylglycinamidine ribonucleotide; AIR, Aminoimidazole ribonucleotide; CAIR, Phosphoribosyl car- boxyaminoimidazole; SAICAR, Succinocarboxyamide carboxyaminoimidazole ribonucleotide; AICAR, Aminoi- midazole carboxamide ribonucleotide; FAICAR, Formaminoimidazole carboxamide ribonucleotide; IMP, Inosine monophosphate; XMP, Xanthosine monophosphate; GMP, Guanosine monophosphate; GDP, Guanosine diphos- phate; GTP, Guanosine triphosphate; dGDP, Deoxyguanosine diphosphate; dGTP, Deoxyguanosine triphosphate; sAMP, Adenylsuccinate; AMP, Adenosine monophosphate; ADP, Adenosine diphosphate; ATP, Adenosine tri- phosphate; dADP, Deoxyadenosine diphosphate; dATP, Eoxyadenosine triphosphate. purF, PRPP amidotransfe- rase; purD, GAR synthase; purN, GAR transformylase; purQLS, FGAM synthase; purM, AIR synthase; purEK, CAIR synthase; purC, SAICAR synthase; purB, Adenylosuccinate lyase; purH, IMP cyclohydolase; guaB, IMP dehydrogenase; guaA, GMP synthase; gmk, Guanylate kinase; pyk, Pyruvate kinase; nrdEF, Aerobic ribonucleotide diphosphate reductase; nrdDG, Anaerobic riobonucleotide triphosphate reductase; purA, Adenylosuccinate syn- thase; purB, Adenylosuccinate lyase; adk, Adenylate kinase; pnp, Purine nucleoside phosphorylase; add, Adeno- sine deaminase; apt, Adenine phosphoribosyltransferse; hpt, Hypoxanthine/guanine phosphoribosyltransferase and xpt, Xanthine phosphoribosyltransferse. from L. lactis. The de novo synthesis of the pyrimidine form, i.e. uracil, cytosine and thymine respectively, by nucleoside triphosphates, uridine monophosphate (UTP) pyrimidine nucleoside phosphorylases. Uracil is con- and cytidine triphosphate (CTP), occurs in a linear path- verted to UMP by the enzyme uracil phosphoribosytrans- way initiated by the formation of carbamoyl phosphate ferase. Cytosine is deaminated to uracil by the enzyme from bicarbonate, glutamine and ATP. The pyrimidine cytosine deaminase. The uracil thus produced is also con- base orotate is produced from carbamoyl phosphate in verted to UMP. The UMP produced by uracil and cyto- three steps and a phosphoribosyl group is subsequently sine is converted to UDP, UTP and CTP, as discussed attached to orotate resulting in the formation of pyrimi- earlier for de novo nucleotide biosynthesis. dine nucleotide orotidine 5′-monophosphate (OMP). Uridine monophosphate (UMP) is formed by decarbox- De novo or salvage: which one to rely on during ylation of OMP and converted to UTP by kinase reac- infection tions. Lastly, CTP is produced from UTP by replacing the 4′-OH group with an amino group. The enzymes involved It is still an intriguing question about the utilization of de in this pathway are tightly regulated. CTP synthase, novo or salvage pathway during the infection process. catalysing the formation of CTP from UTP, is regulated The de novo pathway synthesizes nucleotides on its own allosterically by guanosine triphosphate (GTP)5. and hence it may be required to sustain in the niches that The salvage pathway uses pyrimidine bases and nuc- have very low nucleotide availability. On the other hand, leosides to synthesize pyrimidine nucleotides. The pyri- the salvage pathway is energy-efficient, unlike the de novo midine bases or nucleosides are produced either by pathway and hence may be favourable in conditions of low nucleotide degradation inside the cell or imported from energy availability or rapid multiplication for maintaining external environment into the cell by permeases. Uridine, the nucleotide pool. Some pathogens, like unicellular cytidine and thymidine are converted to their nucleobase parasites, lack the de novo pathway and rely completely CURRENT SCIENCE, VOL. 120, NO. 9, 10 MAY 2021 1459 REVIEW ARTICLES Figure 2. Pyrimidine biosynthesis pathway – de novo and salvage pathway. The solid arrows represent the de novo pathway and dashed arrows represent salvage pathway. The enzymes catalysing the reactions are denoted by their gene names. CP, Carbamoyl phosphate; CAA, Carbamoylaspartate; DHO, Dihydroorotate; OMP, Orotate monophosphate; UMP, Uridine monophosphate; UDP, Uridine monophosphate; UTP, Uridine monophosphate; dUMP, Deoxyuridine monophosphate; dUDP, Deoxyuridine monophopsphate; dUTP, Deoxyuridine triphosphate; CMP, Cytidine monophosphate; CDP, Cytidine diphosphate; CTP, Cytidine triphosphate; dCMP, Deoxycytidine monophosphate; dCDP, Deoxycytidine diphosphate; dCTP, Deoxycytidine triphosphate; dTMP, Thymidine mono- phosphate; dTDP, Thymidine diphosphate; dTTP, Thymidine triphosphate. carAB, Carbamoylphosphate; pyrB, Aspartate transcarbamoylase; pyrC, Dihydroorotase;