The remarkable ability of bacteria to colonize diverse habitats relies on their efficient response to environmental changes. To achieve this, bacteria have evolved a repertoire of stress-sensing and response systems to regulate their cellular processes. A widely conserved mechanism is through utilization of nucleotide second messengers as stress- responsive regulators. Notable examples include the classic cAMP [1], the stringent response alarmone (p)ppGpp (guanosine tetra- or pentaphosphates) [2] and putative oxidative stress alarmone AppppA [3], as well as cyclic dinucleotides c-di-AMP [4] and c-di-GMP [5]. These nucleotide second messengers are widely present in the bacterial domain of life and their turnover is controlled by specific synthetases and hydrolases. For example, (p)ppGpp is synthesized and hydrolyzed by multidomain and single-domain RelA–SpoT Homolog (RSH) enzymes 6, 7, 8. On the other hand, c-di-GMP is produced by diguanylate cyclase enzymes [9] and degraded by phosphodiesterases (PDE-A) [10]. Similar to c-di-GMP, c-di-AMP synthesis and hydrolysis are mediated through deadenylate cyclases and dedicated PDE-A 11, 12. In addition to the established (p)ppGpp and cyclic dinucleotides, nucleotides such as cGAMP 13, 14, 15, 16, pGpp [17], and (p)ppApp 18•, 19, 20, 21 have also emerged as new members of the nucleotide second messenger family. Recent explosion of antiphage research has also uncovered many new cyclic nucleotides [22] such as cyclic mononucleotide cNMP produced by pyrimidine cyclases [23], as well as cyclic dinucleotides produced by cyclic dinucleotide-based antiphage signaling systems 13, 24, 25, 26 that are induced upon phage infection.

In general, regulation by nucleotide second messengers is mediated through direct interaction with target proteins that are often enzymes or transcription factors or riboswitches 27, 28, 29. Despite the common regulatory principles, different nucleotide second messengers appear to have evolved specific regulatory roles [30]. For example, (p)ppGpp accumulates in response to stresses such as amino acid starvation 7, 31, and reprograms transcription 32, 33, downregulates purine nucleotide biosynthesis [34], and curtails macromolecular biosynthesis 35, 36; c-di-AMP is inducible by high potassium and is strongly involved in cell wall homeostasis and osmoregulation 27, 37; while c-di-GMP responds to a variety of environmental cues 38, 39 as well as surface sensing [40], and is bestknown for controlling biofilm formation and lifestyle transitions 28, 41. The diverse regulatory roles by various nucleotide messengers facilitate integrated regulation of cellular processes in biofilms [42] as well as throughout bacterial growth cycle [43]. Apart from ‘division of labor’ by different nucleotide messengers, new studies have begun to reveal crosstalk between these signaling systems, with many notable examples involving (p)ppGpp. In terms of bacterial physiology, the central role of (p)ppGpp in stress response and cellular metabolism makes it an ideal candidate for crosstalk with other nucleotide messengers. In this brief review, we summarize the mechanisms underlying (p)ppGpp crosstalk with other nucleotide second messengers and discuss their biological importance.