Cyclic di-nucleotide signaling enters the eukaryote domain

Abstract

Cyclic (c-di-GMP) is the prevalent intracellular signaling intermediate in bacteria. It triggers a spectrum of responses that cause bacteria to shift from a swarming motile phase to sessile biofilm formation. However, additional functions for c-di-GMP and roles for related molecules, such as c-di-AMP and c-AMP-GMP continue to be uncovered. The first usage of cyclic-di-nucleotide (c-di-NMP) signaling in the eukaryote domain emerged only recently. In dictyostelid social amoebas, c-di-GMP is a secreted signal that induces motile amoebas to differentiate into sessile stalk cells. In humans, c-di-NMPs, which are either produced endogenously in response to foreign DNA or by invading bacterial pathogens, trigger the innate immune system by activating the expression of interferon genes. STING, the human c-di-NMP receptor, is conserved throughout metazoa and their closest unicellular relatives, suggesting protist origins for human c-di-NMP signaling. Compared to the limited number of conserved protein domains that detect the second messengers cAMP and cGMP, the domains that detect the c-di-NMPs are surprisingly varied.

Keywords: 2′3′-cGAMP; Dictyostelium; STING; biofilm; cGAS; cyclic di-AMP; cyclic di-GMP; diadenylate cyclase; diguanylate cyclase; stalk cell differentiation.

Figure 1. Phylogenetic analysis of STING and cGAS proteins

The major vertebrate and invertebrate phyla were individually screened for homologs of human STING and cGAS proteins using BlastP. A few representative best hits for each phylum were selected, which were then used for a reverse screen of mammalian genomes. For STING, the reverse search yielded mouse and bat STING proteins. However, invertebrate cGAS homologs yielded mammalian Mab21 proteins as bidirectional hits. Protein sequences were aligned using M-coffee (53). After deletion of segments with poor consensus alignment, sequences were subjected to Bayesian inference for establishment of phylogenetic relationships between proteins (54). Analysis were run for 1 million generations under a mixed amino-acid model with rate variation between sites estimated by a gamma distribution. Bayesian inference posterior probabilities (BIPPs) of tree nodes are indicated by colored dots. Gene identifiers of the proteins are annotated with functional domain architectures and color-coded to represent the phyla from which they are derived. Corresponding species names are listed in the legends to supplemental figures 1 and 2.