Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses.

Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermotolerant from thermosensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.

Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress.

BACKGROUND: Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity events, which occur during summer seasons and can involve salinity dropping ~ 10 PSU correlate with declines in coral cover, and these events are predicted to increase in frequency and severity under future climate change scenarios. In other marine invertebrates, exposure to low salinity causes increased expression of genes involved in proteolysis, responses to oxidative stress, and membrane transport, but the effects that changes in salinity have on corals have so far received only limited attention. To better understand the coral response to hypo-osmotic stress, here we investigated the transcriptomic response of the coral Acropora millepora in both adult and juvenile life stages to acute (1 h) and more prolonged (24 h) exposure to low salinity. RESULTS: Differential gene expression analysis revealed the involvement of both common and specific response mechanisms in Acropora. The general response to environmental stressors included up-regulation of genes involved in the mitigation of macromolecular and oxidative damage, while up-regulation of genes involved in amino acid metabolism and transport represent specific responses to salinity stress. CONCLUSIONS: This study is the first comprehensive transcriptomic analysis of the coral response to low salinity stress and provides important insights into the likely consequences of heavy rainfall and runoff events on coral reefs.

Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals.

BACKGROUND: Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific bacteria can also produce this compound. Corals are major sources of DMSP, but the molecular basis for its biosynthesis is unknown in these organisms. RESULTS: Here we used salinity stress, which is known to trigger DMSP production in other organisms, in conjunction with transcriptomics to identify coral genes likely to be involved in DMSP biosynthesis. We focused specifically on both adults and juveniles of the coral Acropora millepora: after 24 h of exposure to hyposaline conditions, DMSP concentrations increased significantly by 2.6 fold in adult corals and 1.2 fold in juveniles. Concomitantly, candidate genes enabling each of the necessary steps leading to DMSP production were up-regulated. CONCLUSIONS: The data presented strongly suggest that corals use an algal-like pathway to generate DMSP from methionine, and are able to rapidly change expression of the corresponding genes in response to environmental stress. However, our data also indicate that DMSP is unlikely to function primarily as an osmolyte in corals, instead potentially serving as a scavenger of ROS and as a molecular sink for excess methionine produced as a consequence of proteolysis and osmolyte catabolism in corals under hypo-osmotic conditions.

Trm112p is a 15-kDa zinc finger protein essential for the activity of two tRNA and one protein methyltransferases in yeast.

The degenerate base at position 34 of the tRNA anticodon is the target of numerous modification enzymes. In Saccharomyces cerevisiae, five tRNAs exhibit a complex modification of uridine 34 (mcm(5)U(34) and mcm(5)s(2)U(34)), the formation of which requires at least 25 different proteins. The addition of the last methyl group is catalyzed by the methyltransferase Trm9p. Trm9p interacts with Trm112p, a 15-kDa protein with a zinc finger domain. Trm112p is essential for the activity of Trm11p, another tRNA methyltransferase, and for Mtq2p, an enzyme that methylates the translation termination factor eRF1/Sup45. Here, we report that Trm112p is required in vivo for the formation of mcm(5)U(34) and mcm(5)s(2)U(34). When produced in Escherichia coli, Trm112p forms a complex with Trm9p, which renders the latter soluble. This recombinant complex catalyzes the formation of mcm(5)U(34) on tRNA in vitro but not mcm(5)s(2)U(34). An mtq2-0 trm9-0 strain exhibits a synthetic growth defect, thus revealing the existence of an unexpected link between tRNA anticodon modification and termination of translation. Trm112p is associated with other partners involved in ribosome biogenesis and chromatin remodeling, suggesting that it has additional roles in the cell.

The NRAMP6 metal transporter contributes to cadmium toxicity.

NRAMP (natural resistance-associated macrophage protein) homologues are evolutionarily conserved bivalent metal transporters. In Arabidopsis, AtNRAMP3 and AtNRAMP4 play a key role in iron nutrition of the germinating plantlet by remobilizing vacuolar iron stores. In the present paper we describe the molecular and physiological characterization of AtNRAMP6. AtNRAMP6 is predominantly expressed in the dry seed embryo and to a lesser extent in aerial parts. Its promoter activity is found diffusely distributed in cotyledons and hypocotyl, as well as in the vascular tissue region of leaf and flower. We show that the AtNRAMP6 transcript coexists with a partially spliced isoform in all shoot cell types tested. When expressed in yeast, AtNRAMP6, but not its misspliced derivative, increased sensitivity to cadmium without affecting cadmium content in the cell. Likewise, Arabidopsis transgenic plants overexpressing AtNRAMP6 were hypersensitive to cadmium, although plant cadmium content remained unchanged. Consistently, a null allele of AtNRAMP6, named nramp6-1, was more tolerant to cadmium toxicity, a phenotype that was reverted by expressing AtNRAMP6 in the mutant background. We used an AtNRAMP6::HA (where HA is haemagglutinin) fusion, shown to be functional in yeast, to demonstrate through immunoblot analysis of membrane fractions and immunofluorescence localization that, in yeast cells, AtNRAMP6 is targeted to a vesicular-shaped endomembrane compartment distinct from the vacuole or mitochondria. We therefore propose that AtNRAMP6 functions as an intracellular metal transporter, whose presence, when modified, is likely to affect distribution/availability of cadmium within the cell.

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

N(2)-Monomethylguanosine-10 (m(2)G10) and N(2),N(2)-dimethylguanosine-26 (m(2)(2)G26) are the only two guanosine modifications that have been detected in tRNA from nearly all archaea and eukaryotes but not in bacteria. In Saccharomyces cerevisiae, formation of m(2)(2)G26 is catalyzed by Trm1p, and we report here the identification of the enzymatic activity that catalyzes the formation of m(2)G10 in yeast tRNA. It is composed of at least two subunits that are associated in vivo: Trm11p (Yol124c), which is the catalytic subunit, and Trm112p (Ynr046w), a putative zinc-binding protein. While deletion of TRM11 has no detectable phenotype under laboratory conditions, deletion of TRM112 leads to a severe growth defect, suggesting that it has additional functions in the cell. Indeed, Trm112p is associated with at least four proteins: two tRNA methyltransferases (Trm9p and Trm11p), one putative protein methyltransferase (Mtc6p/Ydr140w), and one protein with a Rossmann fold dehydrogenase domain (Lys9p/Ynr050c). In addition, TRM11 interacts genetically with TRM1, thus suggesting that the absence of m(2)G10 and m(2)(2)G26 affects tRNA metabolism or functioning.

Erratum: Publisher Correction: Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis.

[This corrects the article DOI: 10.1038/s42003-018-0098-3.].

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis.

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage.

rRNA molecules undergo extensive posttranscriptional modification, predominantly 2'-O-ribose methylation and pseudouridine formation, both of which are guided by the numerous small nucleolar RNAs in eukaryotes. Here, we describe an exception to this rule. The essential yeast nucleolar protein Spb1p is a site-specific rRNA methyltransferase modifying the universally conserved G2922 that is located within the A loop of the catalytic center of the ribosome. The equivalent position in bacteria is the docking site for aminoacyl-tRNA, and it is critical for translation. In sharp contrast to other 2'-O-methylriboses that are formed on the primary transcript, Gm2922 appears at a late processing stage, during the maturation of the 27S pre-rRNA. Thus, eukaryotes have maintained a site-specific enzyme to catalyze the methylation of a nucleotide that plays a crucial role in ribosome biogenesis and translation.

mRNA decay is rapidly induced after spore germination of Saccharomyces cerevisiae.

Spores from the yeast Saccharomyces cerevisiae can germinate and resume their vegetative growth when placed in favorable conditions. Biochemical studies on germination have been limited by the difficulty of obtaining a pure population of spores germinating synchronously. Here, we report that spores can be purified and sorted according to their size by centrifugal elutriation and that these spores are able to germinate synchronously. Synchronizing their development has allowed reevaluating certain parameters of germination, and we demonstrate that both transcription and translation are induced very rapidly after germination induction. Spores contain mRNAs that are stable for several months in spores kept at 4 degrees C. Germination induction leads to very rapid degradation of these mRNAs, thus providing a simple model to study induction of mRNA decay in eukaryotes. mRNAs from the spore are polyadenylated, capped, and cosediment on sucrose gradients with ribosomes and polysomes and with components of the mRNA degradation machinery. The presence of polysomes in the spores led us to evaluate the activity of the translation apparatus in these cells. We present evidence that there is ongoing transcription and translation in nongerminating yeast spores incubated in water at 30 degrees C, suggesting that these activities could play a role in spore long term survival.

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase.

Mitochondria of the yeast Saccharomyces cerevisiae assemble their ribosomes from ribosomal proteins, encoded by the nuclear genome (with one exception), and rRNAs of 15S and 21S, encoded by the mitochondrial genome. Unlike cytoplasmic rRNA, which is highly modified, mitochondrial rRNA contains only three modified nucleotides: a pseudouridine (Psi(2918)) and two 2'-O-methylated riboses (Gm(2270) and Um(2791)) located at the peptidyl transferase centre of 21S rRNA. We demonstrate here that the yeast nuclear genome encodes a mitochondrial protein, named Mrm2, which is required for methylating U(2791) of 21S rRNA, both in vivo and in vitro. Deletion of the MRM2 gene causes thermosensitive respiration and leads to rapid loss of mitochondrial DNA. We propose that Mrm2p belongs to a new class of three eukaryotic RNA-modifying enzymes and is the orthologue of FtsJ/RrmJ, which methylates a nucleotide of the peptidyl transferase centre of Escherichia coli 23S rRNA that is homologous to U(2791) of 21S rRNA. Our data suggest that this universally conserved modified nucleotide plays an important function in vivo, possibly by inducing conformational rearrangement of the peptidyl transferase centre.

Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop.

The genome of Saccharomyces cerevisiae encodes three close homologues of the Escherichia coli 2'-O-rRNA methyltransferase FtsJ/RrmJ, designated Trm7p, Spb1p and Mrm2p. We present evidence that Trm7p methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop, both in vivo and in vitro. In a trm7Delta strain, which is viable but grows slowly, translation is impaired, thus indicating that these tRNA modifications could be important for translation efficiency. We discuss the emergence of a family of three 2'-O-RNA methyltransferases in Eukaryota and one in Prokaryota from a common ancestor. We propose that each eukaryotic enzyme is located in a different cell compartment, in which it would methylate a different RNA that can adopt a very similar secondary structure.