A NewN-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei

Abstract

i Sponges harbor a remarkable diversity of microbial symbionts in which signal molecules can accumulate and enable cell-cell communication, such as quorum sensing (QS). Bacteria capable of QS were isolated from marine sponges; however, an extremely small fraction of the sponge microbiome is amenable to cultivation. We took advantage of community genome assembly and binning to investigate the uncultured majority of sponge symbionts. We identified a complete N-acyl-homoserine lactone (AHL)-QS system (designated TswIR) and seven partial luxI homologues in the microbiome of Theonella swinhoei. The TswIR system was novel and shown to be associated with an alphaproteobacterium of the order Rhodobacterales, here termed Rhodobacterales bacterium TS309. The tswI gene, when expressed in Escherichia coli, produced three AHLs, two of which were also identified in a T. swinhoei sponge extract. The taxonomic affiliation of the 16S rRNA of Rhodobacterales bacterium TS309 to a sponge-coral specific clade, its enrichment in sponge versus seawater and marine sediment samples, and the presence of spongespecific features, such as ankyrin-like domains and tetratricopeptide repeats, indicate a likely symbiotic nature of this bacterium. Symbiosis between metazoans and microbes exists in virtually every environment, including in marine sponges (phylum Porifera) (1). Marine sponges are important members of shallow and deep reef communities and are a rich source of secondary metabolites with pharmaceutical potential, and these metabolites are often produced by the sponges' microbial symbionts (2, 3). These host-associated bacteria are sponge specific and can comprise up to 35% of the sponge volume (4), spanning at least 47 bacterial phyla (5).In recent years, symbioses between microorganisms and eukaryotic hosts have received growing attention. The host, together with all its symbionts, is now seen as a single entity designated the holobiont, defined as the sum of the genetic information of the host and its microbiota (6). Sponge holobionts provide an enclosed niche in which extensive interactions among dense and diverse microbial populations are accomplished (7). The mechanisms underlying cell-cell interactions among bacteria within the sponge and the genetic regulation systems controlling gene expression in sponge symbionts are largely unknown. One of the best understood microbial quorum-sensing (QS) systems is the one that uses N-acyl-homoserine lactones (AHLs) as signals (e.g., 8-10). QS enables bacteria to regulate their gene expression in a population density-dependent manner. At a low cell density, low levels of AHLs, which diffuse in and out of the bacterial cell, are present. As the bacterial density increases, especially for bacteria enclosed in niches, AHLs accumulate, and once they reach a critical level (quorum), they interact with LuxR cognate receptor proteins, which then affect target gene expression (11). A canonical AHL-QS system produces AHLs via the LuxI family AHL synthase protein and responds to them via the LuxR co...

Isolation of Marine Paracoccus sp. Ss63 from the Sponge Sarcotragus sp. and Characterization of its Quorum‐Sensing Chemical‐Signaling Molecules by LC‐MS/MS Analysis

“…A recent culture‐independent study revealed a novel QS system associated with an uncultured Rhodobacteraceae bacterium, which was shown to represent approximately 3 % of the sponge microbiome. The LuxI homolog ( tswI ) was expressed heterologously, and was shown to produce some of the same signal molecules detected in the sponge tissue 20. Thus, AHL‐QS systems are present in sponges, and appear to be a common feature in Alphaproteobacteria of the Rhodobacterales order.…”

Ontogenetic Changes in the Bacterial Symbiont Community of the Tropical Demosponge Amphimedon queenslandica: Metamorphosis Is a New Beginning

“…symbiont has been postulated to aid in attachment to the eukaryotic host and in avoidance of the host's immune response (Alex and Antunes, 2015). ANK-repeat proteins (ARPs) have been identified in abundance in the genomes of multiple sponge-associated bacteria (Liu et al, 2010;Thomas et al, 2010;Siegl et al, 2011;Fan et al, 2012;Hentschel et al, 2012;Tian et al, 2014;Alex and Antunes, 2015;Burgsdorf et al, 2015b;Britstein et al, 2016), including in the most dominant core symbiont of A. queenslandica, OTU 1, although not in OTU 4 (Gauthier et al, 2016). ARPs from bacterial symbionts have been experimentally shown to influence sponge-bacterial interactions, specifically via interfering with phagocytosis as a possible mechanism to escape digestion in a sponge host (Nguyen et al, 2014).…”

Draft Genomes Shed Light on the Dual Bacterial Symbiosis that Dominates the Microbiome of the Coral Reef Sponge Amphimedon queenslandica

“…Single-cell genomic and metagenomics studies have contributed to correlating particular traits with specific symbiont lineages Siegl et al, 2011;Kamke et al, 2013;Gao et al, 2014;Tian et al, 2014;Wilson et al, 2014;Burgsdorf et al, 2015;Britstein et al, 2016), revealing functional gene convergence in phylogenetically-distinct microbial communities with core features that likely reflect adaptation of microorganisms to the sponge host environment Hentschel et al, 2012). Traits that have repeatedly been reported in prokaryote symbionts of poriferans include versatile nutrient utilization, protection from environmental and host-specific stress, and eukaryotic-like proteins Hentschel et al, 2012).…”