Identification of Four Kinds of 2',3'-cNMPs in Escherichia coli and a Method for Their Preparation

Insights into the metabolism, signaling, and physiological effects of 2',3'-cyclic nucleotide monophosphates in bacteria

2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have been discovered within both prokaryotes and eukaryotes in the past decade and a half, raising questions about their conserved existence in cells. In plants and mammals, wounding has been found to cause increased levels of 2',3'-cNMPs. Roles for 2',3'-cNMPs in plant immunity suggest that their regulation may be valuable for both plant hosts and microbial pathogens. In support of this hypothesis, a plethora of microbial enzymes have been found with activities related to these molecules. Studies in bacteria suggest that 2',3'-cNMPs are also produced in response to cellular stress and modulate expression of numerous genes. 2',3'-cNMP levels affect bacterial phenotypes, including biofilm formation, motility, and growth. Within E. coli and Salmonella enterica, 2',3'-cNMPs are produced by RNA degradation by RNase I, highlighting potential roles for Type 2 RNases producing 2',3'-cNMPs in a range of organisms. Development of cellular tools to modulate 2',3'-cNMP levels in bacteria has allowed for interrogation of the effects of 2',3'-cNMP concentration on bacterial transcriptomes and physiology. Pull-downs of cellular 2',3'-cNMP binding proteins have identified the ribosome and in vitro studies demonstrated that 2',3'-cNMPs decrease translation, suggesting a direct mechanism for 2',3-cNMP-dependent control of bacterial phenotypes. Future studies dissecting the cellular roles of 2',3'-cNMPs will highlight novel signaling pathways within prokaryotes and which can potentially be engineered to control bacterial physiology.

Binding of 2',3'-Cyclic Nucleotide Monophosphates to Bacterial Ribosomes Inhibits Translation

The intracellular small molecules 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have recently been rediscovered within both prokaryotes and eukaryotes. Studies in bacteria have demonstrated that 2',3'-cNMP levels affect bacterial phenotypes, such as biofilm formation, motility, and growth, and modulate expression of numerous genes, suggesting that 2',3'-cNMP levels are monitored by cells. In this study, 2',3'-cNMP-linked affinity chromatography resins were used to identify Escherichia coli proteins that bind 2',3'-cNMPs, with the top hits including all of the ribosomal proteins, and to confirm direct binding of purified ribosomes. Using in vitro translation assays, we have demonstrated that 2',3'-cNMPs inhibit translation at concentrations found in amino acid-starved cells. In addition, a genetically encoded tool to increase cellular 2',3'-cNMP levels was developed and was demonstrated to decrease E. coli growth rates. Taken together, this work suggests a mechanism for 2',3-cNMP levels to modulate bacterial phenotypes by rapidly affecting translation.

Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria

Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.

Kanamycin-induced production of 2',3'-cyclic AMP in Escherichia coli

In contrast to the well-characterized second messenger adenosine 3',5'-cyclic monophosphate (3',5'-cAMP), the biological roles of its isomer 2',3'-cAMP remain largely unknown, especially in bacteria. Recent work reported that RNase I-dependent elevation of 2',3'-cNMP levels in Escherichia coli correlated with reduced biofilm production, and separate studies demonstrated E. coli ribonuclease activation in response to aminoglycoside antibiotics. Here we report that E. coli produced 2',3'-cAMP in response to kanamycin at sub-inhibitory levels. Surprisingly, other aminoglycosides like streptomycin or gentamicin did not generate levels of 2',3'-cAMP detectable by ³¹P NMR. Interestingly, because 2',3'-cAMP is also produced in E. coli strains expressing a plasmid-encoded kanamycin resistance gene but not by other ribosome-targeting antibiotics, this kanamycin-specific production may not reflect disrupted protein synthesis. Overall, this finding provides a link between aminoglycoside-induced ribonuclease activity and 2',3'-cAMP production in E. coli.

Nucleoside 2',3'-Cyclic Monophosphates in Aphanizomenon flos-aquae Detected through Nuclear Magnetic Resonance and Mass Spectrometry

Aphanizomenon flos-aquae (AFA) cyanobacteria from Klamath Lake (Oregon) are considered a "superfood" due to their broad nutritional profile that has proved to have health-enhancing properties. The AFA metabolome is quite complex. Here, we present a study that, combining multinuclear ¹H, ³¹P, and ¹³C Nuclear Magnetic Resonance (NMR) spectroscopy and high-resolution mass spectrometry, led to the detection of uncommon phosphorylated metabolites in AFA. We focused our attention on ³¹P NMR signals at 20 ppm, a chemical shift that usually points to the presence of phosphonates. The molecules contributing to 20 ppm ³¹P NMR signals revealed, instead, to be nucleoside 2',3'-cyclic monophosphates. These metabolites were fully characterized by multinuclear ¹H, ³¹P, and ¹³C NMR spectroscopy and high-resolution mass spectrometry.

2',3'-cGMP exists in vivo and comprises a 2',3'-cGMP-guanosine pathway

The discovery in 2009 that 2',3'-cAMP exists in biological systems was rapidly followed by identification of 2',3'-cGMP in cell and tissue extracts. To determine whether 2',3'-cGMP exists in mammals under physiological conditions, we used ultraperformance LC-MS/MS to measure 2',3'-cAMP and 2',3'-cGMP in timed urine collections (via direct bladder cannulation) from 25 anesthetized mice. Urinary excretion rates (means ± SE) of 2',3'-cAMP (15.5 ± 1.8 ng/30 min) and 2',3'-cGMP (17.9 ± 1.9 ng/30 min) were similar. Mice also excreted 2'-AMP (3.6 ± 1.1 ng/20 min) and 3'-AMP (9.5 ± 1.2 ng/min), hydrolysis products of 2',3'-cAMP, and 2'-GMP (4.7 ± 1.7 ng/30 min) and 3'-GMP (12.5 ± 1.8 ng/30 min), hydrolysis products of 2',3'-cGMP. To validate that the chromatographic signals were from these endogenous noncanonical nucleotides, we repeated these experiments in mice (n = 18) lacking 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), an enzyme known to convert 2',3'-cyclic nucleotides to their corresponding 2'-nucleotides. In CNPase-knockout mice, urinary excretions of 2',3'-cAMP, 3'-AMP, 2',3'-cGMP, and 3'-GMP were increased, while urinary excretions of 2'-AMP and 2'-GMP were decreased. Infusions of exogenous 2',3'-cAMP increased urinary excretion of 2',3'-cAMP, 2'-AMP, 3'-AMP, and adenosine, whereas infusions of exogenous 2',3'-cGMP increased excretion of 2',3'-cGMP, 2'-GMP, 3'-GMP, and guanosine. Together, these data suggest the endogenous existence of not only a 2',3'-cAMP-adenosine pathway (2',3'-cAMP → 2'-AMP/3'-AMP → adenosine), which was previously identified, but also a 2',3'-cGMP-guanosine pathway (2',3'-cGMP → 2'-GMP/3'-GMP → guanosine), observed here for the first time. Because it is well known that adenosine and guanosine protect tissues from injury, our data support the concept that both pathways may work together to protect tissues from injury.