The nucleotide pGpp acts as a third alarmone in Bacillus, with functions distinct from those of (p)ppGpp

Abstract

The alarmone nucleotides guanosine tetraphosphate and pentaphosphate, commonly referred to as (p)ppGpp, regulate bacterial responses to nutritional and other stresses. There is evidence for potential existence of a third alarmone, guanosine-5′-monophosphate-3′-diphosphate (pGpp), with less-clear functions. Here, we demonstrate the presence of pGpp in bacterial cells, and perform a comprehensive screening to identify proteins that interact respectively with pGpp, ppGpp and pppGpp in Bacillus species. Both ppGpp and pppGpp interact with proteins involved in inhibition of purine nucleotide biosynthesis and with GTPases that control ribosome assembly or activity. By contrast, pGpp interacts with purine biosynthesis proteins but not with the GTPases. In addition, we show that hydrolase NahA (also known as YvcI) efficiently produces pGpp by hydrolyzing (p)ppGpp, thus modulating alarmone composition and function. Deletion of nahA leads to reduction of pGpp levels, increased (p)ppGpp levels, slower growth recovery from nutrient downshift, and loss of competitive fitness. Our results support the existence and physiological relevance of pGpp as a third alarmone, with functions that can be distinct from those of (p)ppGpp.

Inducible expression of (pp)pGpp synthetases in Staphylococcus aureus is associated with activation of stress response genes

“…One may speculate that pGpp detected in vivo might be enzymatically derived from NuDiX hydrolase, NahA, an enzyme that in B . subtilis efficiently produces pGpp by hydrolyzing (p)ppGpp [ 73 ]. In this organism, pGpp potently regulates the purine biosynthesis pathway but in contrast to (p)ppGpp does not interact with the GTPases.…”

Unique features of magic spot metabolism in Clostridioides difficile

“…35 To date, every organism that synthesizes pGpp directly or indirectly also synthesizes ppGpp and pppGpp. 31,40,47,[62][63] Utilization of GDP and GTP to exclusively synthesize pGpp by both a RSH and a SAS enzyme has not previously been reported. While it is still possible that RelC synthesizes the longer forms of magic spot despite its non-conserved guanosine binding motif, the dependence of CdRSH and CdRelQ on guanosine βphosphate bond hydrolysis indicates that pGpp is a very important, and possibly the only, clostridial alarmone.…”

“…While some SAS enzymes can directly synthesize pGpp using GMP as a substrate, there is little precedent for a synthetase to produce the triphosphate signal using GDP or GTP as substrates. 31,40,[47][48][49]62 There are no known examples of an organism that produces pGpp exclusively. Direct synthesis of pGpp via hydrolysis of GDP or GTP 5' beta phosphate bonds has only been reported as a minor in vitro activity of E. coli RSH, dependent on the presence of an EKDD motif in the synthetase active site.…”

Stringent Response in Mycobacteria: From Biology to Therapeutic Potential

“…However, subsequent research has shown that several bacterial phyla, including actinobacteria, produce alarmones, (p)ppGpp, upon amino acid starvation [13,16,[24][25][26][27][28]. Additionally, in recent years, a third alarmone, pGpp, has been discovered in several bacteria, which has further expanded the repertoire of stringent response [29][30][31][32][33][34]. Thus, the three alarmones-pGpp, ppGpp, and pppGpp-are now collectively referred to as (pp)pGpp and are mediators of stringent response in bacteria.…”