Awakening sleeper cells: a narrative review on bacterial magic spot synthetases as potential drug targets to overcome persistence

Abstract

Magic spot synthetases are emerging targets to overcome persistence caused by stringent response. The 'stringent response' is a bacterial stress survival mechanism, which results in the accumulation of alarmones (also called Magic spots) leading to the formation of dormant persister cells. These 'sleeper cells' evade antibiotic treatment and could result in relapse of infection. This review broadly investigates the phenomenon of stringent response and persistence, and specifically discusses the distribution, classification, and nomenclature of proteins such as Rel/SpoT homologs (RSH), responsible for alarmone synthesis. The authors further explain the relevance of RSH as potential drug targets to break the dormancy of persister cells commonly seen in biofilms. One of the significant factors that initiate alarmone synthesis is nutrient deficiency. In a starved condition, ribosome-associated RSH detects deacylated tRNA and initiates alarmone synthesis. Accumulation of alarmones has a considerable effect on bacterial physiology, virulence, biofilm formation, and persister cell formation. Preventing alarmone synthesis by inhibiting RSH responsible for alarmone synthesis will prevent or reduce persister cells' formation. Magic spot synthetases are thus potential targets that could be explored to overcome persistence seen in biofilms.

Keywords: Alarmone synthesis; Bacterial magic spots; Bacterial stress survival mechanism; Rel/SpoT homologs; Stringent response; Wake persister cells.

Fig. 1

Synthesis of pppGpp from ATP and GTP. Synthesis occurs by the transfer of diphosphate from ATP to 3′-OH oxygen of GTP. Color indicates the transfer

Fig. 2

Domain organization of Rel/SpoT homologs. The hydrolase domain is not functional in monofunctional RSH. Solid shapes represent active domains. The dotted rectangle represents non-functional HD domain. Small alarmone synthetases and small alarmone hydrolases have synthetase and hydrolase domains, respectively. HD hydrolysis domain, Synth synthetase domain, TGS threonyl tRNA synthetase, GTPase, and SpoT, AH alpha helical, ZFD zinc finger domain, ACT aspartate kinase–chorismate mutase–TyrA domain.

Fig. 3

Result of multiple sequence alignment of HD domains of RelA of Escherichia coli (P0AG20), Rel of Enterococcus faecium (A0A132P4Q3), and, SpoT of Pseudomonas aeruginosa (A0A069Q2V6). It can be found that HDXXED motif (highlighted using a circle) is present in bifunctional Rel and SpoT. The absence of this motif in RelA is the reason behind lack of hydrolytic activity. (Asterisk) Multiple sequence alignment was done using Clustal Omega platform

Fig. 4

A The 3D representation of the ligand GDP within the binding pocket of Rel of Streptococcus equisimilis. B The different amino acid residues surrounding the ligand GDP in the synthetase region of Rel of Streptococcus equisimilis. (Asterisk) Structures were taken from Protein data bank and processed using Schrodinger™ software