Putative Nucleotide-Based Second Messengers in the Archaeal Model Organisms Haloferax volcanii and Sulfolobus acidocaldarius

Abstract

Research on nucleotide-based second messengers began in 1956 with the discovery of cyclic adenosine monophosphate (3′,5′-cAMP) by Earl Wilbur Sutherland and his co-workers. Since then, a broad variety of different signaling molecules composed of nucleotides has been discovered. These molecules fulfill crucial tasks in the context of intracellular signal transduction. The vast majority of the currently available knowledge about nucleotide-based second messengers originates from model organisms belonging either to the domain of eukaryotes or to the domain of bacteria, while the archaeal domain is significantly underrepresented in the field of nucleotide-based second messenger research. For several well-stablished eukaryotic and/or bacterial nucleotide-based second messengers, it is currently not clear whether these signaling molecules are present in archaea. In order to shed some light on this issue, this study analyzed cell extracts of two major archaeal model organisms, the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius, using a modern mass spectrometry method to detect a broad variety of currently known nucleotide-based second messengers. The nucleotides 3′,5′-cAMP, cyclic guanosine monophosphate (3′,5′-cGMP), 5′-phosphoadenylyl-3′,5′-adenosine (5′-pApA), diadenosine tetraphosphate (Ap4A) as well as the 2′,3′-cyclic isomers of all four RNA building blocks (2′,3′-cNMPs) were present in both species. In addition, H. volcanii cell extracts also contain cyclic cytosine monophosphate (3′,5′-cCMP), cyclic uridine monophosphate (3′,5′-cUMP) and cyclic diadenosine monophosphate (3′,5′-c-di-AMP). The widely distributed bacterial second messengers cyclic diguanosine monophosphate (3′,5′-c-di-GMP) and guanosine (penta-)/tetraphosphate [(p)ppGpp] could not be detected. In summary, this study gives a comprehensive overview on the presence of a large set of currently established or putative nucleotide-based second messengers in an eury- and a crenarchaeal model organism.

To be or not to be an anti-CRISPR: AcrIII-1 and the importance of working with native biological systems

“…Contrastingly, little is known about nucleotide secondary messengers in archaea. A recent study identified the presence of several cyclic and linear nucleotide molecules in S. acidocaldarius and H. volcanii , although their biological role remains to be determined (Braun et al 2021). Up to date, the only described role for cA 4 is related to type III CRISPR-Cas immunity and future work shall elucidate alternative functions of cA 4 and other secondary nucleotides in archaea, a very likely scenario given that the role of nucleotide messengers in defense is a conserved feature in the other domains of life.…”

Biofilm formation is intrinsic to the origin of life

“…Furthermore, one might ask the question why in particular cyclic di-AMP and cyclic di-GMP had been selected to ubiquitously direct biofilm related physiology and metabolism. As an argument from a chemical perspective, in comparison to the monocyclic cyclic AMP and cyclic GMP, the covalent bonds in the di-cyclic molecules experience less tension and thus lead to more stable molecules [113] On the other hand, a wide spectrum of diverse cyclic di-nucleotides including cyclic AMP-GMP, cyclic oligo-nucleotides and even pyrimidine-based cyclic nucleotides have been recently unravelled to occur [114][115][116]. To what extent these and other nucleotide-based signaling molecules play a role in physiology and metabolism of the majority of under-investigated environmental microbes beyond phage defense systems remains to be determined.…”

Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

“…Indeed, OG0001177 and OG0001178 proteins are associated with pilus assembly proteins and/or surface proteins, while OG0001176 and OG0000094 can be associated with cell shape or gene regulation (the latter is not identified in our pipeline but its gene is always located downstream of the OG0001176 gene). Cluster D is related to nucleic acid metabolism or cellular signal transduction (Braun et al 2021), whereas cluster E code for the four proteins that compose the methyl-coenzyme M reductase, which is implied in methane formation (Chen et al 2020). Very recently, two potential clusters for PM biosynthesis were identified using bacterial proteins from PG biosynthesis as BLAST queries (Subedi et al 2021) was not considered for phylogenetic analysis because, compared to the aforementioned proteins, no homologous protein was identified in the representative bacterial database (nor for OG0001215 and OG0000138).…”