- Research article
- Open Access
Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species
BMC Evolutionary Biologyvolume 19, Article number: 126 (2019)
L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C.
By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans.
Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.
L-ascorbate is an essential vitamin in humans. This vitamin has anti-oxidant properties, and in humans its consumption correlates with an increased protection against degenerative diseases and cancer , although it may exhibit a pro-oxidative effect at high doses [2, 3]. It is also a well-studied co-factor of enzymes involved in collagen synthesis, facilitates the differentiation of dopaminergic neurons in vitro, and is known to be indispensable for proper fetal brain development and cognitive function [4,5,6,7]. More recently, it has been shown that L-ascorbate is also a co-factor of enzymes involved in DNA or histones demethylation (e.g. TET1 and JMJD3), thus acting as a modulator of epigenetic modifications .
Despite the biological importance of Vitamin C, several mammal species such as primates, guinea pig, and some bat species, have lost the ability to synthesize this vitamin due to the loss of a functional GULO gene. This gene encodes a L-gulonolactone oxidase that is involved in the last step of the Vitamin C synthesis pathway [8, 9]. This is the reason why, in humans, a diet that is deficient in Vitamin C, leads to the lethal deficiency disease scurvy. Animal species where the GULO gene has been lost usually retain the remaining genes of the pathway, including the Regucalcin/SMP30 (Senescence Marker Protein 30) gene, which encodes a gluconolactonase that produces GULO’s substrate [8, 10]. This observation suggests that the other genes of the pathway play critical functions. For example, in mammals, Regucalcin is a regulator of cellular Ca2+ levels, several nuclear processes, and also acts as a transcription factor [11, 12].
Mammals are not the only animal group where GULO gene loss has been identified. Indeed, some Passeriformes birds and Teleostei fish species also lack a GULO gene. Although Vitamin C could be detected in many species [10, 13,14,15,16], most Protostomes were thought not to have a GULO gene. Nevertheless, recently, the GULO gene has been identified in the annotated genomes of five Araneae, Priapulida, Brachiopoda and Gastropoda species . Therefore, the GULO gene has not been completely lost in Protostomian species. There are, however, three Protostomian lineages where a GULO gene has not been detected, although a large number of genomes has been analysed, namely the Insects (116 genomes), Nematoda (35 genomes) and Platyhelminthes (nine genomes) . In non-Bilateria, the GULO gene has been found in Anthozoan and Placozoan species [10, 17], showing that, in animals, having a GULO gene is the ancestral state. In this work we present evidence that GULO is also present in the Myxozoa (non-Bilaterian), Acari and Annelida groups (Protostomian), and thus that GULO is present in most non-Bilaterian and Protostomian lineages.
Despite the observation that there is no GULO gene in insects, there is little doubt that Vitamin C is important in this group of species. For instance, in D. melanogaster, L-ascorbate levels increase during aging, and Vitamin C supplemented food contributes to the extension of the average and the maximum life-span of flies [3, 16]. The higher levels of L-ascorbate found in the midgut lumen of the Orgyia leucostigma moth are believed to be responsible for the superior tolerance of this species against tannin, a ROS-inducing agent . In beetles (Callosobrochus maulatus), L-ascorbate levels decrease in a dose-dependent manner in response to the presence of different ROS-inducing insecticides, possibly by aiding enzymatic antioxidant systems such as catalase, superoxide dismutase (SOD) and peroxidase (POX) . In ladybirds (Cryptolaemus montrouzieri Mulsant), the genes related to L-ascorbate metabolism were found to be specifically altered in response to cold-stress, but not in response to heat-stress .
Although there is no GULO gene in the nematode C. elegans, this species was recently shown to be able to synthesize L-ascorbate from its food source, Escherichia coli . Therefore, it has been proposed that C. elegans uses an alternative enzyme, or pathway, to synthetize L-ascorbate, although the gene responsible for it has not been identified . This observation raises the possibility that in insects, such as D. melanogaster, an alternative pathway for the synthesis of Vitamin C is also present. Indeed, it has been reported that flies raised in the absence of L-ascorbate, have increased levels of Vitamin C in response to a brief cold shock (10 min, 4 °C) . It could, however, be argued that the source of Vitamin C is the microbiome. This is a possibility because, although it is usually considered that prokaryotes do not depend on, or synthetize, Vitamin C, several L-ascorbate-producing bacteria that live in symbiosis with metazoan hosts have been identified, such as Mycobacterium tuberculosis, Pantoea citrea and a particular strain of Pseudomonas aeruginosa that colonizes the human host [22,23,24,25]. Moreover, it has been shown that in D. melanogaster, the microbiome is able to provide vitamins (such as Vitamin B1) in amounts that can support the viability of its offspring . Therefore, in this work we also address whether Vitamin C is synthesized in Drosophila by the microbiome or by the fly. We also looked at whether, as suggested by the brief cold exposition experiments performed by Massie et al. , Vitamin C levels increase under the cold-acclimation conditions usually used in the literature (one day at 15 °C). This experiment could provide further evidence for Vitamin C synthesis, since cold acclimation induces oxidative stress , and Vitamin C is a well-known anti-oxidant . Therefore, its production could be regulated by the fly when exposed at low temperatures. We show that in non-Bilateria as well as in Protostomia, not being able to synthesize Vitamin C is likely the exception rather than the rule.
Non-Bilateria and Protostomia species have putative functional GULO orthologs
The implementation of a fast an efficient protocol for the identification of GULO gene in annotated genomes led to the identification of this gene in 118 species, in groups such as the Anthozoa (non-Bilaterian), Araneae, Priapulida, Brachiopoda and Gastropoda (Protostomians) . This result motivated us to use non-annotated genomes of further non-Bilateria and Protostomia species that belong to phylogenetic groups that were not well represented in . Furthermore, since many taxonomic groups are represented by a reduced number of annotated species genomes only, we decided to perform our own annotations using these genomes to avoid loss of information that could arise from poor annotations that were eventually removed in . The details of the gene annotation procedures here used can be found in supplementary Additional file 1 Table S1.
It should be noted that our de novo GULO-like gene annotations lack an ATG start codon. Nevertheless, given the alignments between our gene annotations and the mouse GULO gene, it seems that the first GULO coding exon codes for the ATG codon only. Therefore, although no start codon was annotated, we are confident that these annotations represent functional genes.
For the phylogenetic analysis only sequences harbouring the HWXK motif were considered, since this motif is conserved amongst members of the vanillyl-alcohol oxidase (VAO) flavoproteins family that includes besides GULO the genes that encode plant L-galactono-1,4-lactone dehydrogenases (GLDH) and fungi D-arabinono-1,4-lactone oxidases (ALO) that synthetize L-ascorbate and D-erythorbate, respectively . Ten CDSs from non-Bilateria and Protostomia species here annotated, that appear as an external group to the fungi sequences in the consensus phylogeny (Additional file 2 Figure S1), likely represent other genes that also contain a FAD-domain . Interestingly, all GULO CDS identified in  as well as those that here cluster with the reference CDSs from animals were found to encode proteins with the HWAK motif, while the CDSs outside the fungi outgroup, with the exception of those from R. microplus and K. iwatai, encode proteins with the HWGK motif (Additional file 2 Figure S1). The sequence from R. microplus seems to be a contamination, since it has high homology to a CDS from a bacterial species (data not shown). The CDS from K. iwatai was maintained in our dataset since it clustered with the other sequences encoding proteins with a HWGK motif with low posterior credibility support value (Additional file 2 Figure S1). These observations strongly suggest that, in animals, true GULO orthologs always encode proteins with the HWAK motif. Currently, there is no protein structure available for GULO that we can use to address the impact of the Alanine methyl group (−CH3) that is absent in Glycine at the HWXK motif. Therefore, we relied on the in silico predictions obtained with the I-TASSER server. The predicted structure of the M. musculus GULO (NP_848862.1) is shown in Fig. 1A, where it can be seen that the HWAK conserved motif is exposed at the surface, and that it is adjacent to the Glu-Arg (Glutamic acid and Arginine) pair, known to be involved in optimal catalysis by aldonolactone oxidoreductases . Furthermore, the GULO FAD-binding domain is also exposed at various sites, one of which in the proximity of the HWAK motif region (Fig. 1B). The M. musculus GULO G111 amino acid, implicated in the ability to use molecular oxygen as an electron acceptor in aldonolactone oxidation reactions [29, 30] is located in an internal region of the protein. When we change the alanine of the HWAK motif to a glycine, and repeat the analysis, the HWGK motif is now in an internal region of the protein (Fig. 1C). The Glu-Arg pair is now barely at the surface as well. The FAD-binding region is still well exposed at the protein surface, in two separate regions, while the G111 amino acid remains unexposed (Fig. 1D). Therefore, a single amino acid change is predicted to cause a drastic conformational change, further suggesting that the HWAK motif is under strong purifying selection. In the future, the identification of GULO genes can thus be easily made in annotated genomes by performing a simple Blast PHI (pattern-hit initiated) search using this motif.
Since the sequences coding for proteins without the HWAK motif are distantly related to the GULO gene sequences, and thus could have an impact on the phylogenetic reconstruction, we repeated the phylogenetic analysis using only the sequences encoding proteins with this motif (Fig. 2). This phylogenetic analysis clearly shows that, in addition to the groups where a GULO gene was previously identified in , there is an apparently functional GULO gene in Placozoa and Myxozoa (non-Bilaterians) and in Acari and Annelida (Protostomians). Although the results regarding Myxozoa should be regarded with some caution, as the Myxozoan HWAK containing sequence is identified as a GULO sequence only in the phylogenetic tree obtained after excluding HWGK sequences, the presence of the highly specific HWAK GULO motif supports the interpretation that in Myxozoa there is indeed a GULO gene. Animals synthesize ascorbic acid starting from D-glucose, and D-glucuronic acid is one of the intermediate products of the vitamin C synthesis pathway. The latter product is used by the pentose phosphate pathway, and thus it is not surprising that the genes that encode the enzymes that catalyse the intermediary steps of the conversion of D-glucose into D-glucuronic acid are essential genes. D-glucuronic acid is also used by Regucalcin to produce L-gulono-gamma-lactone. Then GULO uses L-gulono-gamma-lactone to produce 2-keto-gulono-gamma-lactone that is spontaneously converted into ascorbic acid . Since regucalcin is also an essential gene that is involved in calcium homeostasis, not surprisingly the loss of the ability to synthesize vitamin C is always associated with loss of the GULO gene.
The Acari species analyzed are representative of two Acari superorders, namely Acariformes, and Parasitiformes. Within the Parasitiformes, we were able to annotate a putative GULO gene in two species belonging to the Ixodidae family included in the Ixodida order (I. scapularis and R. microplus), although with further phylogenetic analysis we uncovered that the R. microplus annotation obtained may be the result of genome contamination. Curiously, the I. scapularis annotation also shows irregular placement in the obtained phylogenies for this dataset, when observing the taxonomic context. This is probably due to the complexity of our dataset regarding the greatly divergent species analyzed rather than a problem with our annotation, and as such, we consider GULO to be present in this species. This consideration is supported by the results of Wheeler et al., where I. scapularis was presented as a species with an identifiable GULO gene, although no details are given by these authors . Additionally, the I. ricinus species (also included in the Ixodida order) genome had features of a possible GULO gene presence, however the tblastn alignment was scattered across many genomic scaffolds. Therefore, we cannot confidently infer the presence or absence of GULO in I. ricinus, but given the results obtained for I. scapularis, it is possible to extrapolate that a GULO gene may be present in the Ixodida order, specifically in the Ixodinae subfamily in which these two species are included. We could not annotate a putative GULO gene in the four remaining Parasitiformes species (G. occidentalis, V. destructor, V. jacobsoni and T. mercedesae) belonging to the Mesostigmata order (Gamasina infraorder), due to the lack of sequence homology in the performed tblastn search. This result presents strong evidence regarding the possible loss of GULO in the Mesostigmata lineage. The remaining nine Acari species analyzed belong to the Acariformes, where a GULO gene seems to be present in most species (Fig. 3).
Although we show the presence of the GULO gene in the Gastropoda, within the Mollusca phylum, this gene is lost in the Bivalvia lineage and may or not be present in the Cephalopoda group. The results for the Molusca group are summarized in Fig. 4. It is likely that GULO was lost in the Bivalvia class but was present in the common ancestral of both Bivalvia and Gastropoda taxonomic groups, given that this gene is maintained in the majority of the gastropods analyzed. Inside the Gastropoda group, GULO may have been recently lost in B. glabrata, a member of the Planorboidea superfamily included in one of the Gastropoda subclasses, Heterobranchia, since it appears present in two closely related species, L. stagnalis and R. auricularia. Regarding the Cephalopoda group, we cannot infer the presence or absence of GULO since only one representative genome was available for inquiry, belonging to O. bimaculoides. Nevertheless, GULO seems to not be present at least in this species.
Similarly to I. scapularis, it should be noted that the B. belcheri, N. vectensis, I. scapularis, T. adhaerens and P. caudatus species are misplaced within the animal branch of the Bayesian consensus tree (Fig. 2), but given that we are analysing species that have been diverging for more than 650 million years , such misplacements are not that uncommon. For instance, they could be due to the lack of synapomorphy due to multiple nucleotide substitutions or stochastic errors that lead to erratic phylogenies, or random nucleotide substitutions that create sequence similarities that result in the clustering of distantly related lineages, or even due to different species-specific evolutionary rates [39, 40]. Figure 5 shows a summary of our findings regarding GULO presence/absence in the different non-Bilateria and Protostomia animal lineages. It should be noted that in order to state that a GULO gene is missing in a given lineage we require that no GULO ortholog, with all expected features, is detected in at least three species from that lineage. In conclusion, a GULO gene is found in the non-Bilateria Placozoa, Myxozoa and Anthozoa classes, and in the Protostomian Araneae family, the Gastropoda class, the Acari subclass, and the Priapulida, Annelida and Brachiopoda phyla lineages (Fig. 5). Nevertheless, it is not present in the Pancrustacea (Hexapoda and Crustacea), Nematoda, Platyhelminthes, and Bivalvia. Therefore, the GULO gene has been lost multiple times independently within Protostomia.
D. melanogaster synthesizes vitamin C
Although L-ascorbate is biologically important in insects (see “Background”), there is a general consensus that invertebrates obtain L-ascorbate from their diet rather than synthetizing it, which agrees with the lack of a GULO ortholog in this taxonomic group [16,17,18]. Nevertheless, recently, it has been shown that the invertebrate C. elegans is able to synthesize L-ascorbate, likely by a yet to be identified pathway . Therefore, we started exploring the hypothesis that insects may also synthesize L-ascorbate. The Oregon-R flies here used have been maintained in the lab for many generations and the food we use to rear them does not contain any source of Vitamin C. This was confirmed by attempting to detect Vitamin C in both fresh and male-inhabited 7-days old food using the same HPLC methodology used and sample amount (20 mg) as for the fly samples (see below; Additional file 3 Figure S2). Given this observation, we reasoned that, if D. melanogaster gets all Vitamin C from the diet, we should not be able to detect L-ascorbate in our Oregon-R flies. Nevertheless, this is not the case (Fig. 6A and B). Significant Vitamin C levels are observed both in males and females, although there is a striking difference between them (males: 16.0 ± 1.8 μM; females: 48.6 ± 4.4 μM). The body weight (wet weight) of female flies is approximately 50% higher than male bodies and thus, cannot alone explain the 3-fold higher L-ascorbate levels measured in female bodies. It should be noted that, in order to ensure the identity of the peak corresponding to L-ascorbate, we have treated a sample with 10 units of ascorbate oxidase, which led to the extinction of the L-ascorbate peak (Fig. 6A). Moreover, the levels of L-ascorbate we have determined in 7 days old Oregon R male flies (0.0902 +/− 0.015 μg/fly) are within the same range of those determined in  in flies with a similar age raised under similar conditions and which ranged approximately from 0.04 to 0.10 μg/fly. It is difficult to compare Vitamin C levels in small animals such as Drosophila flies and large invertebrate and vertebrates because our measurements are for whole flies, while measurements for larger animals are usually given for specific tissues, but is similar to that reported for the mullet brain, the rat liver, or the guinea pig lung and brain, for instance (see ).
Given the above results, we have raised the hypothesis that the fly’s microbiome may be responsible, or at least contributing to, the synthesis of L-ascorbate and we repeated the analysis using axenic flies. Since these flies must be kept under sterile conditions until collection, male and female flies could not be separated after hatch. Therefore, to ensure that the mating state was not affecting the L-ascorbate levels observed, we have also measured this vitamin in control conditions using 7-days-old male and female flies that were kept together during that time-frame. Although there are differences between the genders, no significant differences are observed between the L-ascorbate levels measured in mated, virgin or axenic individuals from the same gender (Fig. 6B), suggesting that the microbiome does not influence or contributes for the synthesis of this vitamin.
We also expanded the D. melanogaster microbiome ex-vivo, by inoculating MRS liquid medium with a homogenate obtained from 25 whole individuals, previously washed with sodium hypochlorite solution (2.7% v/v) to remove any environmental microbial contaminants (see “Methods”). The MRS media was chosen given that it allows the propagation of several bacteria genera that have been implicated in L-ascorbate synthesis, including Gluconobacter, Gluconacetobacter and Acetobacter [41,42,43]. No L-ascorbate was found in the supernatant or in the pellet of bacterial cells. Therefore, the microbiome is not the source of the observed L-ascorbate.
Given that a previous study by Massie et al. has shown that a brief cold exposition (10 min at 4 °C) results in an increase of the L-ascorbate levels in Oregon-R male flies , we tested whether cold acclimation could also trigger a similar response using our strain, which would reinforce the idea that L-ascorbate is synthetized by the fly. We have assessed L-ascorbate levels in flies raised in standard conditions, in flies subjected to cold acclimation (one day at 15 °C), and in flies that were allowed to recover at 25 °C for one day (Labelled as “Control”, “Cold acclimation”, and “Recovery”, respectively, in Fig. 7). The flies used in these experiments were 7-days-old male flies. We observed a 23% decrease in the L-ascorbate levels after one day of cold acclimation, which was recovered back to the levels measured in control flies, after recovery (Fig. 7). Therefore, in contrast to the results reported in , obtained after a very short cold exposure, flies exposed to the usual cold-acclimation protocol have lowered levels of Vitamin C, possibly because it is being used as an anti-oxidant to protect the cell from oxidative damage.
In conclusion, the above experiments strongly suggest that, as reported for C. elegans, D. melanogaster synthetizes Vitamin C using a yet to be identified pathway. Therefore, in Protostomians the lack of a GULO gene cannot be equated with inability to synthesize L-ascorbate.
The phylogenetic analyses here performed clearly show that the GULO gene is present in the non-Bilateria Placozoa, Myxozoa and Anthozoa groups, and in the Protostomian Araneae family, the Gastropoda class, the Acari subclass, and the Priapulida, Annelida and Brachiopoda phyla lineages. In animals, GULO always encodes a protein with a HWAK motif, that is also present in the fungi sequences here used as references. GULO seems to be thus, a very ancient gene. How far back in time GULO orthologs can be found remains to be determined. This gene was lost independently multiple times, both within the Protostomia (in the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia), as here shown, as well as within the Deuterostomia.
In Protostomia, the absence of a GULO gene does not, however, imply that a given species is unable to synthesize Vitamin C. Although no GULO gene was identified in 35 Nematode genomes , C. elegans has been shown to be able to synthesize L-ascorbate . Here we show that: i) D. melanogaster flies raised for many generations in Vitamin C free food still show high L-ascorbate levels; ii) Vitamin C levels are gender-specific; iii) axenic flies have similar Vitamin C levels to mated and virgin control flies; iv) when expanded ex vivo no L-ascorbate is detected in the fly microbiome; and v) when exposed to cold acclimation conditions, L-ascorbate levels drop but then return to normal levels when flies are brought back to standard conditions. These results can only be explained if D. melanogaster flies synthesize Vitamin C, likely via an alternative pathway, or using another enzyme that is able to catalyse the same reaction as GULO. The aforementioned results, also illustrate the importance of the synthesis and maintenance of L-ascorbate levels for the D. melanogaster capacity to respond to cold stresses, and likely to other abiotic stresses, and emphasises the importance of elucidating the pathway by which this model organism produces this vitamin. Such knowledge could then be extended to other, less genetically-accessible, insect species where L-ascorbate is also playing, or adding, important functions in the cell [16, 18,19,20].
The GULO gene always encodes a protein with a HWAK motif, and this property can be used to quickly and easily identify the GULO gene using Blast PHI searches. It has been shown that individual mutations in the histidine, tryptophan and lysine residues of HWXK motif lead to complete enzymatic activity loss, largely related with the ineptitude of the affected proteins to bind to their cofactor . The impact of changing the alanine at the HWAK motif was not yet addressed in vivo, but our protein structure predictions suggest that changing the alanine at the HWAK motif by a glycine has a profound impact on protein structure. Moreover, mammal GULO and fungi ALO proteins, which contain a HWAK motif, establish a covalent bond with their FAD cofactor, while bacterial L-gulonolactone dehydrogenase (GULDH) and the protozoans Trypanosoma cruzi and Trypanosoma brucei ALO, which contain a HWGK motif, are thought to bind non-covalently to a flavin cofactor and FMN, respectively [22, 44,45,46,47]. Here we find that the HWAK motif region and the GULO FAD-binding domain are located close to each other in the predicted structure of the M. musculus GULO protein, and this may be important for establishing a covalent bond with the FAD cofactor. Given these observations, it is possible that the presence of an alanine at the HWAK motif confers a stronger and permanent covalent bond between GULO and the correspondent cofactor due to distinct protein configuration relative to the HWGK alternative, in which the protein/cofactor interaction may be much weaker. This, in turn can be related to distinct catalytic properties between the two proteins.
Non-Bilaterian and Protostomians synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.
Identification of GULO orthologs in non-Bilaterian and Protostomian species with non-annotated genomes
Using the non-Bilaterian and Protostomian taxonomic group names as queries, we downloaded 35 non-annotated species genomes from NCBI (https://www.ncbi.nlm.nih.gov/assembly/; four non-Bilaterian genomes and 31 Protostomian genomes excluding Insects, Nematoda and Platyhelminthes; see Results). In addition, we re-analysed 29 non-Bilateria and Protostomian species genomes analysed in , and were able to obtain putative GULO annotations for some species where such gene has not been annotated, or where the gene shows an unexpected length. Only genomes from the GenBank database were downloaded, since many of the species of interest did not have a representative genome in the RefSeq database. The SEDA software (http://www.sing-group.org/seda/) was used to identify and annotate putative GULO orthologs. Since, when performing a tblastn (BLAST algorithm version: 2.7.1+) with SEDA, it is possible to retrieve the high-scoring segment pairs (HSPs) as well as the flanking regions, in our case, 5000 nucleotides on both sides of the HSPs, we first performed this operation using the GULO protein sequence from Mus musculus as a query (NP_848862.1), an expect value of 0.05, and the genomes of interest as subject, to obtain the genome regions of interest. Nucleotide sequences were further processed using the “Grow sequences” operation included in the SEDA software, with a selected minimum overlap of 2500 nucleotides. This step allows the growing of overlapping sequences, simplifying the annotation process. The sequences were then annotated by hand (under the assumption that intron splice sites follow the canonical GT-AG rule), using the results of tblastn searches as a guide (the M. musculus (NP_848862.1) GULO protein was used as query and the word size was set to two). Moreover, if none of the putative exons encoded a protein with the typical HWXK amino acid pattern , no annotation was attempted. Several non-Bilateria and Protostomian GULO representative sequences identified in  were added to this dataset, as well as a set of GULO sequences to be used as references, namely M. musculus (NP_848862.1), Xenopus laevis (OCT81467.1), Priapulus caudatus (XP_014666894.1), Gallus gallus (XP_015140704.1), Alligator mississippiensis (KYO43973.1), Lepisosteus oculatus (XP_015207781.1), Branchiostoma belcheri (XP_019645195.1), Nematostella vectensis (EDO44935.1), Saccharomyces cerevisiae S288C (NP_013624.1) and Metarhizium majus ARSEF 297 (XP_014580409.1). The ADOPS pipeline was used to perform the alignment and the phylogenetic analyses . The MUSCLE alignment algorithm was used as implemented in T-Coffee . Sequences were first aligned at the amino acid level and the corresponding nucleotide alignment obtained. Only codons with a support value above two were used for the Bayesian (MrBayes ) phylogenetic analyses. The General Time-Reversible (GTR) model of sequence evolution was used, allowing for among-site rate variation and a proportion of invariable sites. Third codon positions were allowed to have a gamma distribution shape parameter different from that of first and second codon positions. Two independent runs of 5000,000 generations with four chains each (one cold and three heated chains) were performed. Convergence was achieved, since the potential scale reduction factor for all parameters was around 1.00. Trees were sampled at every 100th generation with a defined burn-in of 25% for the complete analysis (the first 12,500 samples were discarded). The resulting Bayesian trees, in Nexus format, were converted to Newick format using the Format Conversion Website (http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi), and imported to MEGA X (https://www.megasoftware.net/) to root the consensus tree .
Inferred GULO protein structures
Protein structure predictions were obtained using the I-TASSER server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/). The model with the highest C-score was always chosen as being the most likely protein structure. The C-score is usually between − 5 and 2, and values close to 2 indicate a model with higher confidence. For the M. musculus GULO (NP_848862.1), we obtained two models with C-score values of 0.22 and 0.68. The change of an alanine by a Glycine at the HWXK motif in this sequence results in three alternative prediction models with C-scores of − 0.65, − 0.41 and 0.00.
D. melanogaster husbandry
Oregon-R flies, obtained from the Drosophila Stock Centre (http://blogs.cornell.edu/Drosophila/), were reared at 25 °C, with a relative humidity of 70%, under a 12 h light-dark cycle. Flies were fed with yeast-based medium (YBM) containing 40 g.l− 1 wheat flour, 80 g.l− 1 sugar, 10 g.l− 1 agar, 100 g.l− 1 yeast extract, 4 g.l− 1 NaCl, 5 ml.l− 1 propionic acid and 45 g.l− 1 Methyl 4-hydroxybenzoate. Unless stated otherwise, flies were always collected under brief CO2 anaesthesia, and all experimental groups were matched for age.
Generation of axenic D. melanogaster
To generate axenic flies, Oregon-R flies were placed in a cage, where a plate containing a wet paste of yeast extract was introduced, and where the flies were allowed to lay eggs during 2 h. The yeast and eggs mixture was then resuspended in water and the eggs collected using a sieve and transferred to an Eppendorf tube. The eggs were pelleted by centrifugation at 350 g and washed twice with a sodium hypochlorite solution (2.7% v/v) for 2.5 min, to remove the chorion and thus all microbial cargo (as described in ). From this moment on all steps were performed under sterile conditions. The dechorinated eggs were washed three times using a sterile saline triton solution (300 μl.l− 1 Triton X-100, 4 g.l− 1 NaCl) and then placed in UV-sterilized food containers. To test whether the microbiome was effectively removed in axenic flies, three axenic flies and three individuals raised under routine conditions (controls), were collected, washed with sodium hypochlorite solution (2.7% v/v), and homogenized in 200 μl of a sterile 0.9% (w/v) NaCl solution. One hundred microliters of the homogenate were spread in Luria-Bertoli (LB) solid medium and the plates incubated at 25 °C for 2 days. Bacterial growth was observed in the control plates, but not in the plates inoculated with homogenates from axenic flies.
Preparation of crude homogenates from D. melanogaster
For each tested condition, crude extracts were prepared using an extraction buffer containing 0.1 mM diethylenetriaminepentaacetic acid and 0.01 M HEPES buffer, pH 7.2 (both from Sigma-Aldrich) based on the method described by . Briefly, 25 individuals were homogenized using 500 μl of extraction buffer in a Dounce homogenizer, which was rinsed with another 500 μl of extraction buffer. The resulting 1 ml of crude extract was then centrifuged at 9000 g for 5 min, and 850 μl of the supernatant were collected and centrifuged again at 20,000 g for 20 min. The resulting supernatant was divided into three individual technical replicates (250 μl each), which were centrifuged for another 15 min at 20,000 g and the clear supernatants were immediately used to measure L-ascorbate concentration using High Pressure Liquid Chromatography (HPLC). All centrifugations were performed at 4 °C, and all steps performed in ice.
Assessment of L-ascorbate concentration using HPLC
L-ascorbate was detected using HPLC, based on the method described by . Briefly, 90 μl of clear extracts were injected into a LiChrospher® 100 RP-18 (5 μm) LiChroCART® 250–4 reversed-phase column (Merck) and separated at a flow rate of 1 ml.min− 1 (25 °C). Two buffers were used on the chromatographic analysis, buffer A consisting of 20 mM triethylammonium acetate (Sigma-Aldrich), pH 6.0, and buffer B containing 20 mM triethylammonium acetate in 40% acetonitrile (Merck), pH 6.0. The gradients used to elute the samples were exactly those described in  and the L-ascorbate signal was detected at 265 nm. To estimate L-ascorbate concentration in the crude homogenates, L-ascorbate (Sigma-Aldrich) standards of 25, 50 and 100 μM where prepared using extraction buffer as solvent, to obtain a calibration curve. To guaranty the identity of the L-ascorbate peak, 10 Units of ascorbate oxidase (Sigma-Aldrich) were added to 200 μl of crude extract and the mixture incubated for 20 min at 25 °C prior to injection into the HPLC apparatus.
Determination of L-ascorbate in microbiome cultures expanded ex vivo
To test if the microbiome of flies contributes to the production of L-ascorbate we have measured the amount of L-ascorbate produced by microbiome cultures that were expanded ex vivo in De Man, Rogosa and Sharpe (MRS) media. For that, 25 flies were anesthetized with CO2 and washed with sodium hypochlorite solution (2.7% v/v) followed by three washes with sterile water. Then, the flies were homogenized in a total volume of 1 ml of 0.9% (w/v) NaCl solution and this suspension was used to inoculate 100 ml of MRS medium supplemented, or not, with 2% w/v glucose. The inoculated flasks were incubated at 25 and 30 °C, and the microbial growth was followed by measuring the absorbance at 600 nm. Samples were collected 1, 2 and 3 days after inoculation, and L-ascorbate levels were determined in the supernatant and in the pellet of bacterial cells. To determine L-ascorbate in the supernatant, 900 μl of the clear medium were combined with 100 μl of 10x extraction buffer prior to injection in the HPLC. To determine L-ascorbate in the pellet, cells were resuspended in 1 ml of 1% SDS (Sodium dodecyl sulfate), 0.2 M NaCl solution and vortexed for 1 min. The homogenate was centrifuged at 18,000 g for 5 min (4 °C) and 800 μl of the supernatant were combined with 200 μl of 10x extraction buffer prior to injection into the HPLC.
Cold acclimation experiments
Seven-days-old male flies that were separated from females 8 h after hatching and kept for 7 days under control conditions were used. Cold acclimation stress was induced by transferring the flies (in vials with food) to a 15 °C chamber and kept at this temperature for one day (condition labeled as “cold acclimation, 1d, 15 °C”; see Results). Then, for recovery, the containers were transferred to 25 °C and kept at this temperature for another day. Each condition was tested in triplicate, and 25 flies were collected per condition for HPLC analysis. All samples were snap-frozen in liquid nitrogen and kept at − 80 °C.
Automatic Detection Of Positively Selected Sites
Flavin adenine dinucleotide
General time-reversible model
Hydroxyethyl piperazineethanesulfonic acid
High-Performance Liquid Chromatography
High-scoring segment pairs
Jumonji Domain-Containing Protein 3
De Man, Rogosa and Sharpe
National Center for Biotechnology Information database
Reactive Oxigen species
Sodium dodecyl sulfate
SEquence DAtaset builder
Senescence Marker Protein 30
Ten-eleven translocation methylcytosine dioxygenase 1
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SING group thanks the CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure.
This work is financed by the project Norte-01-0145-FEDER-000008 - Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). S. F. Henriques is supported by a post-doctoral fellowship also funded by the above mentioned project. SING group is supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) by the ED431C2018/55-GRC grant. H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068–0). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
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Table S1. Summary of the annotation process on the downloaded non-Bilaterian and Protostomian genomes. The rows display information on the analysed species taxonomic groups and names, while the columns present information on the annotations steps performed on the species genomes and the obtained final results. The annotation steps were performed in succession from left to right, and show respectively if any sequences were retrieved from the initial tblastn, if the obtained sequences had a conserved HWXK motif, if the obtained alignment was residual or considerable, if the sequences had exons spread across several scaffolds, if the final obtained coding sequence had stop codons, and the final CDS alignment coverage. (XLSX 11 kb)
Figure S1. Phylogenetic relationship amongst the putative GULO orthologs identified amongst all Protostomian and non-Bilaterian species with annotated and non-annotated genomes. Two Fungi GULO CDS were used to assist the rooting the consensus tree (red pane). GULO CDS of six deuterostomian species, representing the Actinopteri, Amphibia, Euarchontoglires, Aves, Reptilia and Cephalochordata groups, were used to facilitate the identification of functional GULO orthologs amongst Animal species (green pane). GULO CDS grouped outside the fungi group and that do not have the HWAK motif were removed to obtain Fig. 2. Higher taxonomic classifications for common species are shown on the right. (TIF 120810 kb)
Figure S2. Chromatograms obtained from the analyses of three replicates of fresh (A1-A3) and male-inhabited 7-days old (B1-B3) food. L-ascorbate levels were assessed in homogenates containing 20 mg of food per millilitre of extraction buffer using reverse-phase HPLC, as described in “Material and Methods”. For each condition, individual food samples are represented with a suffix number (1–3). The chromatograms depict three lines representative of the processed technical replicas for each sample (blue, orange and green, respectively), and one indicative of a 25 μM L-ascorbate standard (black). All samples analysed show an absence of L-ascorbate. (TIF 53095 kb)
Nucleotide alignment used in the phylogenetic analyses presented in Additional file 2 Figure S1. (PDF 244 kb)