Figures
Abstract
In Drosophila melanogaster the doublesex (dsx) and fruitless (fru) regulatory genes act at the bottom of the somatic sex determination pathway. Both are regulated via alternative splicing by an upstream female-specific TRA/TRA-2 complex, recognizing a common cis element. dsx controls somatic sexual differentiation of non-neural as well as of neural tissues. fru, on the other hand, expresses male-specific functions only in neural system where it is required to built the neural circuits underlying proper courtship behaviour. In the mosquito Aedes aegypti sex determination is different from Drosophila. The key male determiner M, which is located on one of a pair of homomorphic sex chromosomes, controls sex-specific splicing of the mosquito dsx orthologue. In this study we report the genomic organization and expression of the fru homologue in Ae. aegypti (Aeafru). We found that it is sex-specifically spliced suggesting that it is also under the control of the sex determination pathway. Comparative analyses between the Aeafru and Anopheles gambiae fru (Angfru) genomic loci revealed partial conservation of exon organization and extensive divergence of intron lengths. We find that Aeadsx and Aeafru share novel cis splicing regulatory elements conserved in the alternatively spliced regions. We propose that in Aedes aegypti sex-specific splicing of dsx and fru is most likely under the control of splicing regulatory factors which are different from TRA and TRA-2 found in other dipteran insects and discuss the potential use of fru and dsx for developing new genetic strategies in vector control.
Citation: Salvemini M, D'Amato R, Petrella V, Aceto S, Nimmo D, Neira M, et al. (2013) The Orthologue of the Fruitfly Sex Behaviour Gene Fruitless in the Mosquito Aedes aegypti: Evolution of Genomic Organisation and Alternative Splicing. PLoS ONE 8(2): e48554. https://doi.org/10.1371/journal.pone.0048554
Editor: Immo A. Hansen, New Mexico State University, United States of America
Received: July 21, 2012; Accepted: September 26, 2012; Published: February 13, 2013
Copyright: © 2013 Salvemini et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by WHO Grant A30289 (2004–2006) to Giuseppe Saccone. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors Derric Nimmo, Marco Neira and Luke Alphey are employees of Oxitec Ltd. and have employment and equity interest in Oxitec. Oxitec and the University of Naples “Federico II” hold intellectual property related to the subject matter of this paper. All other authors declare no interest. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.
Introduction
The fruitless gene of D. melanogaster (Dmfru) encodes transcription factors, of which one has a key role in the determination of male sexual behaviour, and the others are required for multiple non sex-specific developmental functions [1], [2], [3], [4], [5], [6], [7]. Male courtship in Drosophila is an elaborate ritual that involves multiple sensory inputs and complex motor outputs showing largely a fixed-action pattern (male versus female orientation, tapping the female, singing by vibrating the wing, licking female genitalia and curling his abdomen for copulation) [8]. Certain fru loss-of-function alleles disrupt both male courtship behaviour and sexual orientation: performance of the male courtship ritual is reduced, and it is directed indiscriminately at either sex [9], [10], [11], [12], [13]. Strong fru alleles completely abolish male courtship behaviour, while weaker fru alleles can disrupt individual steps of this courtship [9], [11]. These observations suggest that fru is required during development to let the adult male brain execute each step of the courtship ritual, not just a single critical step. Hence sexual behaviour is apparently “hard wired” in the Drosophila CNS, leaving little plasticity, if any. However no easily detectable neuronal anatomical differences that might account for the dramatically different sexual behaviours of males and females have been found in the overall 100.000 neurons fly brain, until recently. Indeed in contrast to the preliminary conclusion that in Drosophila the fruitless circuit (2000 fru+ neurons forming an interconnected circuit) is anatomically largely isomorphic in the two sexes [14], [15], substantial differences in wiring and gross anatomy between male and female fly brains have been recently discovered [16]. Even more interesting is the very recent finding that the Drosophila males can learn to distinguish (by a male pheromone lingered on mated females cuticles) and then court virgin females rather then mated ones, revealing plasticity in an innate behaviour [17]. Those olfactory neurons and mushroom bodies neurons, involved in this courtship learning, express FRU in males and use dopamine as an instructive-learning signal. This suggests that differences in neuronal anatomy of specific brain regions, might underlie the profound differences in behaviour between males and females in Drosophila [18], and presumably in many other species as well.
fru is one of the most complex genes of Drosophila and also one of the largest, spanning about 130 kb. All FRU isoforms contain a BTB (Broad-complex, Tramtrack and Bric-a-brac) domain, which serves as dimerization interface and a C-terminal C2H2 zinc-finger domain for the DNA binding function [19]. The FRU proteins are encoded by eighteen different transcripts which arise from four alternative non-sex-specific promoters (P1–P4) and alternative splicing at both the 5′ and 3′ ends [10], [12], [20], [21]. The fru functions dedicated to promote male sexual behaviour are mediated by transcripts, derived from the most distal fru promoter (P1), which undergo male-specific alternative splicing; female-specific fru transcripts appear not to encode a functional protein. The sex-specific fru mRNAs are detectable from 3rd instar larval stage till adulthood [22]. Transcripts derived from the other known Dmfru promoters (P2, P3 and P4 – located between P1 and the first BTB encoding exon) are present in both sexes from embryonic stage (P3 and P4), mediating the correct development of neuronal tissues [9], [23], or from pupal stage (P2), involved in the differentiation of imaginal-disc derivatives [9], [22].
In parallel to fru, the doublesex gene controls nearly all somatic sexual differences outside the nervous system, as well as many aspects of the nervous system sexual dimorphism. Both genes act as the bottom regulators of the somatic sex determination cascade of D. melanogaster and they are regulated through common cis elements via alternative splicing by a complex containing the serine-arginine-rich splicing regulators transformer (TRA) and transformer-2 (TRA-2) [24], [25]. Of these, TRA-2 protein is present in both males and females, but functional TRA is expressed only in females. The female-specific splicing of fru and dsx pre-mRNAs requires the binding of these proteins to TRA/TRA-2 binding sites: 13 nt cis-acting elements present in multiple clustered copies only in female-specific exons of both genes [26], [27]. Putative conserved TRA/TRA-2 binding sites have been identified in all female-specific exons of the known dsx dipteran homologs [28]. In particular, in the Dmfru locus, three TRA/TRA-2 binding sites are present in the fru female-specific exon [27], located immediately upstream (50–230 nt away) of a female-specific 5′ splice donor site, and 1.3 kb downstream the 5′ donor site of the preceding exon. Both Dmfru male- and female-specific 5′ donor splicing sites are canonical splicing sites [27]; however, binding of the TRA/TRA2 enhancer complex activates the female-specific 5′ splice site, while its activity is not required for the processing of the fru pre-mRNA in males [29], [30].
Recent insights from non-drosophilid dipteran and non-dipteran insects suggest an evolutionarily conserved role for FRU in innate sexual behaviour (for a review see [17]). In the dipteran An. gambiae [31] and in the hymenopteran Nasonia vitripennis [32] fru orthologues show conservation of sex-specific alternative splicing and male-specific protein expression in neural tissues. The female-specific exons of both Angdsx and Angfru genes each contain short sequences resembling the TRA/TRA-2 binding sites but showing degeneration and a lack of a consensus. The authors proposed that this observation indicates that the TRA/TRA-2 dependent mechanism of sex-specific splicing could be conserved in mosquitoes [31], [33]. In contrast a tra orthologue seems to be absent from both Anopheles and Aedes genomes [31], [34]. In the hymenopteran Nasonia vitripennis the fru architecture is essentially identical to Drosophila and the P1-transcripts undergo a conserved sex-specific splicing regulation. These findings suggest that conserved fru sex-specific splicing evolved prior to the split between Hymenoptera and Diptera (250–300 Myr) rather than acquired independently in both lineages [32]. In orthopteran insects, as various grasshoppers of Chorthippus spp. [35], the desert locust Schistocerca gregaria [36] and the cockroach Blatella germanica [37], fru orthologues were isolated but no sex-specific transcripts were detected by RT-PCR analysis. In spite of this, fru nymphal RNAi knockdown experiments revealed that in S. gregaria and B. germanica fru orthologues play important roles respectively in the regulation of successful copulation in the adult male [36] and in male sexual behaviour [37]. This suggests that the function of the fru gene as master regulator of male sexual behaviour has been conserved during insect evolution [36].
Due to the complex genomic organization of the Drosophila fru locus and the low expression level of the fru sex-specific transcripts, restricted in many cases to small cluster of neurons [22], [38], [39], automatic annotation usually fails to identify a complete fru orthologue in sequenced genomes, despite an increasing number of corresponding ESTs. This suggests that a manually curated in silico search followed by a molecular data validation may currently be required to unambiguously identify a complete fru locus.
In this work we present a detailed structural analysis of the fru gene in the mosquito Aedes aegypti (Aeafru), focusing on the evolution of its genomic organization and splicing regulation. Ae. aegypti is a major arboviral disease vector and has been studied for decades both for basic science and to develop new control methods. Despite this, very little is known about the genetic control of some significant aspects of its biology, including sex determination and reproductive behaviour, that could be important targets for the future control strategies [40], [41]. Current knowledge about sex determination in Ae. aegypti is restricted to the primary signal which, as observed for other mosquitoes, comprises an autosomal locus, M, which has a dominant male determiner, not yet molecularly identified [34], and to the evolutionarily conserved double switch gene doublesex (Aeadsx). The Aeadsx gene is thought to be involved in the developmental control of sex-specific somatic tissues, based on its conservation of sex-specific alternative splicing and of encoded sex-specific proteins [42]. When compared to dsx orthologues in other dipteran species, [28], [43], Aeadsx sex-specific splicing regulation seems to be more complex, suggesting the possibility of somewhat divergent regulation.
The courtship behaviour of Ae. aegypti has been much less studied and understood, as for many mosquito species with a swarming reproductive behaviour [44]. In this species both sexes interact acoustically by shifting their flight tones to match, resulting in a courtship duet [45]. Which are the key genetic regulators of Aedes promoting this complex sex-specific sexual behaviour? An Aedes orthologue of Drosophila fru would be a plausible candidate, if functionally conserved. Such conservation is likely considering that the Anopheles gambiae fru (Angfru) has a conserved sex-specific splicing regulation and that both mosquito species show a similar sexual behaviour [31]. With the aim to address this question we isolated the Aeafru gene and we reported the first developmental expression analysis of the fru gene outside drosophilids. Furthermore a sequence comparison of the female-specifically regulated exons of Aeafru and Aeadsx led us to identify new putative cis-acting elements, shared by both dsx and fru, potentially involved in their sex-specific alternative splicing, suggesting that a novel sex-specific upstream splicing regulator(s) has been recruited in Ae. aegypti during evolution.
Results and Discussion
Molecular characterization of the Aeafru gene
As observed for Drosophila and An. gambiae, fru seems to be a single copy gene in Ae. aegypti.
A putative fru orthologue was predicted in the supercontig 1.199 of the AaegL1.2 annotation of the Ae. aegypti genome sequence as the AAEL006301 gene, which however seems to be incomplete.
Using the AAEL006301 gene prediction as our start point, we searched for additional Aeafru exons encoding the apparently missing portions. By combining a classical PCR-based approach with available bioinformatic and genomic tools (see Methods) we identified: 1) a sex-specifically regulated exon, named exon P1, located 420 kb upstream of the E055109 exon, encoding a putative FRUM N-terminal amino acid portion; 2) a non-sex-specifically regulated exon, named exon P2, located 230 kb upstream the E055109 exon, encoding a short additional FRU N-terminal and 3) two putative alternative zinc-finger encoding exons, corresponding to zinc-finger type A and B, located between E055113 and E055114 exons, in the 3′ region of the AAEL06301 gene, in a conserved position respect to the Dmfru and Angfru genes (Figure 1A).
(A) Schematic drawing of the fru genomic in Ae. aegypti (not to scale). We renamed the five common Aeafru exons as C1, C2, C3, C4 and C5 and the zinc finger type C encoding exon as zC. Ensembl exon names (Ensembl id: AAEL006301) are shown in parentheses above exons. Translational start (ATG) and stop (TGA, TAA) sites are marked. The exons C1 and C2 encode the BTB domain; the exons C3, C4 and C5 encode the connecting region; the terminal exon zC encodes the type C zinc-finger domain. Exon P1 (named exon S in Demir et al., 2005) is divided in two sub-regions, a male- (P1-m in blue) and a female-specific (P1-f in pink) portion, which are alternatively spliced in a sex-specific mode. This regulation results in different 5′ encoding regions with a male-specific ATG signal in exon P1-m and multiple stop signals in exon P1-f that lead in female to the use of a non-sex-specific ATG signal in exon C1. Exon P2 is present in both sexes and encodes a short non-sex-specific N-terminal box 8 aa long. (B) RT-PCR amplifications of Aeafru sex-specific and common cDNA fragments on sexed adult Ae. aegypti mosquitoes. Primers used in the PCR amplifications are indicated as short red arrows in Fig. 1A.
Using primer pairs specific for P1 and P2 exons and for the exons E055110 and E055111 of the Aeafru gene, RT-PCR experiments were performed on RNA samples extracted from adult sexed Ae. aegypti mosquitoes and both sex-specific and non-sex-specific Aeafru cDNA fragments were successfully amplified, confirming these predicted exons (Figure 1B). RT-PCR analysis with a forward primer located in P1 exon and a reverse primer located in P2 exon failed to produce any cDNA amplification product, suggesting that the two exons are mutually exclusive in the mRNAs (data not shown). As the corresponding homologous Drosophila fru P2 exon is transcribed from a different promoter from the one responsible of P1 exon transcription, we speculate that Aedes has a similar mechanism leading to alternative transcripts.
Three cDNA products were cloned and sequenced: a male-specific cDNA (700 bp), a female-specific cDNA (2000 bp) and a common cDNA (800 bp). Conceptual translation of these cDNA sequences and subsequent aminoacid sequence comparison with An. gambiae FRU isoforms confirmed their orthology. 5 and 3′ RACE RT-PCR analyses led to obtain additional fru-specific sequences which then were assembled with the previous ones leading to obtain three longer cDNAs named AeafruP1-m-C (1870 bp; male-specific), AeafruP1-f-C (3169 bp; female-specific) and AeafruP2-C (1907 bp; common to both sexes), encoding the Ae. aegypti FRUMC (601 aa), FRUC (552 aa) and FRUP2-C (560 aa) isoforms respectively. Interestingly, as in Drosophila and in Anopheles, in Aedes the P1-f female-specific exon introduces a stop codon interrupting the ORF which starts in the P1-m exon, and suggesting that, as in Drosophila, no full length FRU is expressed in females from this promoter. The alignment of the three Aeafru cDNA sequences and of the in silico identified alternative zinc finger encoding exons (zA and zB) with the AAEL006301 genomic sequence led us to define an updated Aeafru genomic organization represented in Figure 1A.
The comparison of the putative AeaFRU isoforms with the FRU isoforms of D. melanogaster and An. gambiae is presented in Figure 2. The alignments revealed, as expected, high conservation of the BTB and ZnF-C domains between the three species, but very low similarity between the connector and male-specific N-terminal domains. Higher conservation of the male-specific N-terminal extension domain (65% identity) and of the connector region (43% identity) is observed comparing the sequences of the two mosquitoes only.
Protein sequence alignment of the fru isoforms of D. melanogaster, An. gambiae and Ae. aegypti. The conserved BTB domain and zinc finger domains are boxed in grey. Bold letters indicate amino acid identity among Drosophila, Anopheles and Aedes or between two of them. Intron positions are indicated by solid triangles and position of 3′ alternative splicing site is indicated by AS triangles. Gaps were introduced in the alignments to maximize similarity. The sequences are divided into: (A) a male-specific N-terminal portion encoded by AeaP1 transcripts; (B) an alternative common N-terminal portion encoded by AeaP2 transcripts (the N-terminal extension of the Aedes FRUP2-C isoform is similar to the Drosophila FRU isoforms encoded by transcripts derived from the P3 promoter; in these Dmfru transcripts an ATG signal, located upstream the ATG present in the exon C1, leads to the in frame insertion of a short conserved amino acid box in both species); (C) a portion, common to males and females, including the BTB domain, the connector region and the zinc finger type C domain; (D) putative in silico identified zinc-finger type A and B domains of Ae. aegypti aligned with the homologous domains of D. melanogaster and An. gambiae.
Evolution of the Aeafru genomic organization
The Aeafru gene is contained within a large genomic region of 533 kb, significantly larger then the Drosophila 130 kb-long fru. To analyse the evolution of the fru genomic organization we compared the gene structure in Drosophila, Anopheles and Aedes (Figure 3).
Due to its complex structure, with multiple promoters and 5′ and 3′ alternative splicing, we compare the homologous portion of fru genes, starting with the sex-specific regulated region and ending with the ZnF-C domain encoding exon. fru-P1 common (but encoding the male-specific N-terminus) and female-specific exons are represented as blue boxes and pink boxes, respectively. Green boxes represent the non-sex-specific exons encoding BTB domain and connector region of FRU proteins while terminal grey boxes represent the ZnF-C domain encoding exons. White rectangles represent TRA/TRA-2 binding sites. The Drosophila fru corresponding region spans 98 Kb and is organized in 7 exons and 6 introns, with 6 common exons, preceded by the sex-specific regulated region with a male-specific and a female-specific exons. DmfruMC translation initiates at the ATG within exon P1-m and terminates within the ZnF-C encoding exon C, while in the case of DmfruC translation initiates at the ATG within the BTB encoding exon C1 and terminates within at the same stop signal in exon ZnF-C.
Aeafru consists of eight exons and seven introns that vary markedly in length; to date, Aeafru intron 4 (424374 bp) is the largest intron reported in Ae. aegypti [34] and its sequence analysis reveals a high frequency of repetitive elements of various nature (constituting about 40% of whole intron sequence). The five non-sex-specific Aeafru exons (C1-C2-C3-C4-C5) have a corresponding similarity to the 5 non-sex-specific exons of Drosophila and Anopheles fru genes. The highest conservation is observed for exon C1 and C2, whose encoded amino acid domains are essentially the same in all three species; exon C3, C4 and C5 exhibit a more variable size and amino acid content of the encoded domain. Exon zC (zinc-finger encoding exon) is highly conserved respect both Drosophila and Anopheles species. Finally, exon P1 exhibits a conserved male-specific encoded N-terminal domain and a sex-specific alternative splicing regulation, as observed in the Drosophila and Anopheles orthologues. An extensive divergence in intron length of the Aeafru gene was observed respect to Drosophila and Anopheles (Figure 3). The fru gene of An. gambiae is contained within a 90 kb genomic region; the Ae. aegypti genomic sequence is ∼5.8-fold larger. This difference is due to the presence of very large introns in the Ae. aegypti homologue, with an average intron size of 88 kb, in contrast to the observed average intron size for Angfru (16 kb). This is consistent with the overall difference in the genome size of the two species; ∼243 Mbp for An. gambiae and ∼1.31 Gbp for Ae. aegypti. This difference is mostly due to the high frequency of repetitive sequences which constitute about 50% of the Ae. aegypti genome [3]. We searched for repetitive elements within Aeafru introns using the CENSOR software [46] and we observed the presence of multiple copies of a wide range of elements in all introns, except for the short intron 3 (75 bp long) (Figure S1, Table S1 and Table S2).
To assess the degree of genomic microsynteny between the fru containing region of Ae. aegypti (supercontig 1.199–1,9 Mb long) and An. gambiae (X chromosome – from 1,23 Mb to 1,48 Mb) and to analyse its nature, we compared the virtual amino acid sequences encoded by all the putative genes present in both regions, identifying and locating on genomic positions the respective putative orthologues in the two species. This analysis reveals a complex situation with substantial absence of synteny between the two fru-containing regions (Figure S2).
Phylogenetic relationship and molecular evolution of the Aeafru gene
To determine the phylogenetic position of the Aeafru gene we aligned its nucleotide sequence encoding the BTB domain to the corresponding region of the fru orthologues of 22 insect species (Figure 4). We included in this analysis the fru sequence of the arboreal mosquito species Sabethes cyaneus (Sacfru), that we have recently isolated. Males of the Sa. cyaneus exhibit a complex stereotyped courtship behaviour [47]; this feature makes Sa. cyaneus a very interesting species for future studies of courtship behaviour evolution and functional RNAi mediated knockdown assays in mosquitoes.
(A) NJ and MP consensus trees based on nucleotide alignment of the BTB encoding region of the fru gene of different insect species. (B) Diagram showing the BTB and the connector domain of the fru gene in four mosquito species. The dN, dS and dN/dS (ω) values for each domain are reported below the scheme.
The mean evolutionary divergence estimated over the aligned sites (excluding gaps, 342 nucleotide positions on 348 total sites) is 0.38±0.055. The Neighbour-Joining (NJ) and Maximum Parsimony (MP) bootstrap consensus trees are shown in Figure 4A. The topology of both trees reveals a general agreement between the gene genealogy of the BTB domain encoding region and the insect phylogeny.
In particular, Aeafru and Sacfru BTB constitute a highly statistically significant cluster (100% bootstrap percentage) together with the other mosquito sequences (Culex quinquefasciatus and An. gambiae.
Subsequently, nucleotide sequences encoding the BTB and the connector domain of Ae. aegypti and Sa. cyaneus were compared to the corresponding region of the two fru genes of mosquitoes available in GenBank: An. gambiae and Cu. quinquefasciatus. The mean evolutionary divergence estimated over the aligned sites encoding the mosquito BTB and connector domains (excluding gaps, 345 nucleotide positions on 348 total sites for the BTB domain and 462 nucleotide positions on 765 total sites for the connector domain) are 0.283±0.03 and 0.402±0.03, respectively. Mean non-synonymous (dN) and synonymous (dS) substitution rates and their ratios (ω) were calculated among the nucleotide sequences of the mosquito fru orthologues available, partitioned into BTB and connector domain (Figure 4B). Both regions are subjected to strong purifying selection, with a relaxation of selective constraints in the connector region revealed by the ω value of the connector domain (0.232) significantly higher than that observed in the BTB domain (0.089).
Developmental expression analysis of the Aeafru gene
fru does not influence a behaviour as it happens, but rather acts during development to create the potential for a behaviour [9]. To analyze the developmental expression pattern of the Aeafru gene, we performed an RT-PCR analysis on total RNA extracted from different stages, from embryonic till adulthood, using primer pairs spanning the P1 sex-specifically regulated exon or the P2 exon and the common region of the gene (Figure 5). We used the rp49 gene, constitutively expressed in Ae. aegypti [42], as endogenous positive control (Figure 5B). This analysis confirmed the existence in Ae. aegypti of two classes of transcripts with two different developmental expression patterns.
(A) Aeafru gene, transcripts and protein isoforms. Transcripts derived from a putative AeaP1 promoter consist of seven exons with six introns and are alternatively spliced. The transcripts derived from promoter AaeP2 consist of seven exons and six introns and share with AaeP1 ones the common exons C1-C2-C3-C4-C5 and the zinc-finger exon zC but have the upstream exon P2 with and an alternative ATG signal which use led to the translation of AeaFRUP2-C isoform. The translation of all isolated Aeafru-C isoforms terminates in both sexes at the stop codon (TAA) in the zinc-finger exon zC. Primers used in the following amplifications are indicated as short red arrows. (B) Aedes aegypti ribosomal gene rp49 positive control. (C) Aeafru P1 and P2 developmental expression patterns. (D) Aeafru expression pattern on single sexed larval samples. Sexing of samples was performed using Aeadsx primer pair described in [42], which produces a unique amplification signal of 0.5 Kb in the male sample and two amplification signals, of 1.5 and 1.0 Kb, in the female sample. These signals correspond to Aeadsx gene sex-specifically spliced transcripts. E = 0–36 h old embryos; L12 = early larvae; L34 = late larvae; P = pupae; M = adult males; F = adult female. All samples are composed of mixed sexes except for larvae and pupae samples of panel C, which are constitute of single sexed late larvae or pupae.
The first class of transcripts (presumably derived from an Ae. aegypti promoter which could correspond to the fru-P1 promoter of D. melanogaster) amplified with fru1/fru3 primers, are detected from 3rd instar larval stage till adulthood, as reported for Drosophila fru-P1 transcripts. These transcripts are alternatively spliced in a sex-specific manner, leading to the production of the AeafruP1-m-C and AeafruP1-f-C mRNAs (Fig. 5C.1). RT-PCR analyses on single 3rd–4th instar larvae and pupae, sexed using dsx sex-specific splicing (Figures 5D.1), detected the male-specifically spliced AeaP1 fru transcript (using fru1/fru3 primers; Fig. 5D.2) as well as the female-specifically spliced one (using fru2f/fru3 primers; Fig. 5D.3). These sex-specific fru transcripts share a common 5′ exonic region, as shown by the RT-PCR with fru1/fru1rev primers, indicating that the P1 promoter is active in both sexes (Fig. 5D.4).
At adult stage female-specific amplification product was observed at lower level respect to male-specific ones in our non quantitative conditions; however, this result is consistent with a recent microarray study in which a probe located in the common region (exon C4) of the Aeafru gene detected a 3-fold expression in adult males respect to females [48]. These data suggest that fru female-specific transcripts may be turned over more rapidly in Ae. aegypti at larval, pupal and adult stages.
In Drosophila, even if male- and female-specific fru-P1 transcripts are present at a similar level in both the male and female central nervous system (CNS), FRU protein is not detected in the female. This suggested that the female-specific transcripts are not translated, and also indicates that the presence/absence of the FRU protein, rather than sex-specific structural differences, is responsible for the sexually dimorphic actions of the fru gene in the CNS of D. melanogaster flies [21], [49].
The second class of Aeafru transcripts (amplified with fru1c/fru3 primers and corresponding to the AeafruP2-C mRNA) is non-sex-specific and, as observed in Drosophila, possiblyderived from a different promoter respect to P1 promoter) that seems to be active from embryonic stage till adulthood (Fig. 5C.2). The non-sex-specific transcript was also detected in sexed larvae and pupae samples (data not shown). The P3 and P4 promoters of D. melanogaster fru gene, also exhibit a similar constitutive transcriptional activity [9], [23].
In silico analysis of the Aeafru splicing sites
Aeafru P1 transcripts undergo sex-specific alternative splicing from late larval stage till adulthood. An in silico analysis of the 5′ donor/3′ acceptor splicing sites (5′ss/3′ss) at Aeafru exon/intron junctions was performed to find suboptimal sites, using the 5′ss consensus (MAG/GTRAGT) and 3′ss consensus (YnNYAG/G; n = 8,02+/−2,15) as in [42]. The results are reported in Figure S3–A.
This analysis revealed that the Aeafru gene, as the Drosophila orthologue, exhibits two canonical 5′ss, although used in vivo as alternative sex-specific [27]. In contrast, in Anopheles the female-specific 5′ ss of the sex-specifically regulated fru exon is a suboptimal splicing site (Figure S3–B).
To score the intrinsic strength (independently from additional flanking signals) of the two sex-specific alternative 5′ donor splice sites, the male-specific P1-m and the female-specific P1-f, as well as of the corresponding common 3′ ss acceptor of exon C1, in the Aaefru gene, the MaxEntScan algorithm was applied [50]. This program is based on an approach for modelling the sequences of short motifs such as those involved in RNA splicing which accounts for non-adjacent as well as adjacent dependencies between positions. Although MaxEntScan scores are derived from human splice sites, this approach was recently used successfully to predict the D. melanogaster splice site strength according with the observation that Drosophila splice-site motifs are highly similar to human, and many spliceosomal components involved in splice-site recognition are highly conserved [51], [52], [53]. Results are reported in Figure S3–B.
This analysis confirmed the previously described results and revealed that Aeafru P1 female-specific splicing site (MaxEntScan score = 10.65), as well as the Drosophila female-specific 5′ss (MaxEntScan score = 11.37), are significantly stronger than the respective alternative male-specific 5′ss (Dm MaxEntScan score = 8.89; Aea MaxEntScan score = 9.79). Surprisingly also in Drosophila the fru female-specific 5′ss, which requires TRA/TRA-2 activation, is predicted to be stronger (MaxEntScan score = 11.37), then the male-specific one, which is used by default (Dm MaxEntScan score = 8.89). Most likely also the genomic contest including the flanking intronic sequences contribute to define the relative strength of these splice sites. Hence it is unclear from these data in which of the two sexes the splicing regulation requires additional sex-specific upstream factors.
In order to further investigate how alternative splicing used for fru is controlled in Aedes males and females, we searched for known cis splicing elements as well as for novel ones.
Known splicing regulatory cis-elements of the Aeafru and Aeadsx genes
In other dipteran species the fru and dsx genes share common upstream regulators. In Drosophila the TRA/TRA-2 binding sites (13 nt long) [54], the RBP1 binding sites (7 nt long) [55] and the TRA-2 ISS (5 nt long) [56] are involved in both splicing activation or repression of dsx and fru pre-mRNA. Hypothesizing that in Ae. aegypti a similar situation exists we searched for conservation in both genes of previously characterized cis-elements involved in alternative splicing regulation of insects sex-specifically regulated genes.
We analyzed the Aeafru P1 exon and its flanking regions (500 bp-long upstream and downstream intronic sequence), using the regular expression tool of MACAW alignment software and we found: 1) nine putative type-B RBP1 binding sites (7 out of 7 nt conserved) and 2) three putative TRA-2 ISS (5 out of 5 nt conserved). Considering such high sequence conservation it is likely that these elements are involved in controlling alternative splicing of this fru region. In Figure S4 we provide a graphical representation of the identified putative cis-elements and in Table S3 their sequence and position respect to the male-specific and female-specific 5′ss. The three putative TRA-2 ISS in Drosophila are clustered while in Aedes are dispersed along the Aeafru P1 exon and flanking regions. Interestingly, 4 out of 9 putative RBP1 type-B binding sites form a cluster located close to the female-specific 5′ss. The RBP1 type-B binding site is present only in one copy and in a non conserved position with the respect of Dmfru and Angfru homologs. In contrast, we have found 3 sequences showing only some similarity to the 13 nt long Drosophila TRA/TRA-2 binding site consensus (see Table S3). Although showing some divergence, the relative positions of these 3 putative cis elements appear to be conserved with the respect of Drosophila. These putative Aeafru TRA/TRA-2 binding elements exhibit a higher sequence variability respect to the Drosophila TRA/TRA-2 binding sites, with major variations occurring within the first four and last other four bases of the 13 nt long sequence. Even though each putative Aeafru TRA/TRA-2 has some similarity when compared with the TRA/TRA-2 consensus of Drosophila (9 or 10 nucleotides identical out of 13) comparing the various Aedes fru TRA/TRA-2 binding sites no consensus can be defined even if slightly different from the Drosophila one (Figure S5). In the Aeadsx female-specific exons, the putative TRA/TRA-2 binding elements are similarly divergent [42].
In contrast to the situation in mosquitoes, the TRA/TRA-2 binding sites identified in other dipteran species are highly conserved in their consensus sequence and relative position in genes such as dsx, fru and transformer (tra) [43], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66].
Novel putative splicing regulatory cis-elements of the Aeafru and Aeadsx genes
We then conceived a different approach to the identification of putative regulatory cis-elements involved in the sex-specific alternative splicing. In Drosophila, as we have described before, dsx and fru share a common and highly conserved 13 nt long cis regulatory element, recognised by TRA and TRA-2, which is repeated various times in both genes. In Aedes aegypti, which apparently lacks a TRA homologue, if another analogous splicing factor plays a similar regulatory role in one sex (either the female or the male one), a parallel evolutionary constraint acting on a novel corresponding cis element shared by both dsx and fru, could have been maintained its recognition sequence during evolution. If this is the case, we might expect to observe a conserved multicopy distribution of a motif, forming a cluster in proximity of the regulated alternative splicing sites. Indeed the position of splicing regulatory elements within a gene has often been shown to influence their impact on splicing of its pre-mRNA and to let them work as either enhancers or silencers. This has been best studied for the SR proteins, which usually enhance splicing when bound in an exon but are inhibitory as intron-binding factors [67].
Performing a comparative analysis of the nucleotide sequences corresponding to the female-specific exons (fru P1-f and dsx 5a) of both the Ae. aegypti genes, flanked by 500 bp-long upstream and downstream sequences using MEME tool [68], 38 conserved motifs were identified (Figure S6, we arbitrarily selected as conserved a motif including 8–12 bp long sequence with 0 substitution and 13–15 bp long sequence with 0–2 substitutions). Most of them (28/38) are present in single copies in both dsx and fru, but 10 are present in multiple copies. Seven motifs have more then 2 copies in one or both genes (Figure S6). The 4 longer single copy motifs (11–15) are all localised either in the 2 flanking introns of Aeadsx or within the exon of Aeafru. This peculiar opposite localisation may indicate a functional significance. Previous studies have suggested that motifs of larger size seem to play important role in splicing regulation [69]. To verify if some of these identified motifs correspond to or contain described metazoan regulatory elements involved in splicing regulation, we searched in RegRNA, an integrated web server of a variety of regulatory RNA motif databases [70]. We found 9 known regulatory elements that intersect with our predicted elements (Table S4). These previously described cis elements are shorter (4–7 nt long) but contained within 14 out of 38 identified motifs. Some of these elements constitute binding sites for known RNA binding proteins, as SRp20, SRp40 or hnRNP-G, and for neuronal-specific RNA binding protein as Nova-1 protein. Their sequence conservation in both fru and dsx support their involvement in the splicing either to define exon-intron boundaries and/or to assist other cis regulatory elements, for example the remaining novel ones, in the specification of the sex-specific regulatory events. These results indicate a possible involvement of these conserved motifs in the regulation of the sex-specific alternative splicing of dsx and fru in Ae. aegypti and represent a starting point for future functional analyses.
Usually, cis splicing regulatory elements are present in multiple copies and can be easily expanded during evolution [71]. For example the TRA/TRA-2 binding sites involved in the autoregulation of transformer gene have a different copy number in other dipteran species ranging from 6 (Ceratitis) to 46 (Musca domestica) [63].
We then investigated which of the conserved motifs found in Aeafru and Aeadsx are present in multiple copies and form clusters (a localized group of repeated copies of one single cis element) or even patterns (multiple copies of a localized group of different cis elements, showing ordered succession).
We performed a sliding window analysis by sampling 100 nucleotide long sequences every 50 nucleotides in both fru and dsx. We scored these windows in log10 (see Methods) and we graphed the results coupled with the scheme of the two analyzed regions (Figure 6). Interestingly three high-score regions, have been identified, all very close to either the female-specific Aeadsx 3′ss or Aeafru 5′ss.
Schematic diagram of the sliding window analysis performed on (A) Aeadsx and (B) Aeafru sex-specifically regulated regions. Both regions are represented in scale and aligned with the corresponding sliding window graph. Each sliding window is 100 bp long and overlaps for 50 bp with the following and preceding sliding windows; each x axis position represent the nucleotide position of the centre of the sequence window. Scores (y axis) are calculated as described in Methods Section and are expressed in log10 of the total sliding window score multiplied for 2. Motif legend is reporter below graphs.
Comparing the elements contained in the two regions we observed the presence of: 1) a cluster of motif 22, with two copies in Aeadsx and three copies in Aeafru; 2) a pattern, located downstream of Aeadsx 3′ss (in the exon) and Aeafru 5′ss (in the intron), composed by motifs 23-22-13 (orange-purple triangles, blue rectangle). Out of 38 motifs, the 8 nt long motif 22 (indicated in Figure 6 by a purple triangle) has the highest number of copies, with 5 in dsx and 6 in fru. The motif 23 has 2 copies in dsx (in the exon) and 3 in fru (in the intron). Motif 13 has one copy in the Aeadsx (exon) and 4 copies in Aeafru (3 flanking the exon/intron border). Hence the splicing control of dsx and fru is most likely based on more then one shared and repeated element and on more then one upstream splicing regulator recognising these elements.
Upstream regulators of Aeafru in mosquitoes
As previously reported, the tra homologue seems to be absent in the genome of Ae. aegypti as well as in that of An. gambiae [31], [72], even though conserved in the hymenopteran Nasonia vitripennis genome [73].
We further searched for the presence of tra sequences within both genomes, using BLAST with the TRA-CAM domain of TRA [59], but no significant putative orthologues were isolated. These data suggest that the tra function is most likely substituted by a different splicing factor, controlling fru and dsx. However this novel splicing factor could still interact with TRA-2, as the corresponding gene is functionally conserved as essential auxiliary player in female sex determination in another dipteran species such as Drosophila, Ceratitis and Musca [63]. Furthermore, it is known that in the complex TRA/TRA-2 the TRA-2 protein has the stronger and more specific binding activity to TRA/TRA-2 binding sites cis elements [54].
TRA-2 belongs to the SR-related protein family and is directly required for female-specific splicing of dsx and fru pre-mRNA in Drosophila [27], [74] as well as in other distantly related dipteran species such as Tephritidae and Muscidae [75], [76]. Its secondary structure is organized in a arginine-serine rich domain, an RNA recognition motif (RRM – 81 aa long) followed by a 19 aa-long stretch named Linker region which is a unique feature of the tra-2 homologs, and a second C-terminal RS domain. The RRM and the Linker region represent the most conserved domains of the TRA-2 proteins among dipteran and non-dipteran homologs.
The BLAST search for tra-2, using as virtual probe the conserved RRM and linker domains (RRM+Linker) of D. melanogaster, found four putative homologs within the genome of Ae. aegypti (AAEL009224, AAEL006416, AAEL009222 and AAEL004293) as well as two putative homologs within the genome of An. gambiae (AGAP006798 and a second unannotated putative tra-2 homolog, identified starting from the EST gb|BM620287.1) The presence of multiple copies of the tra-2 gene in these two dipteran genomes is a new feature, since tra-2 is a single copy gene in Drosophilidae and apparently also in Tephritidae [75], [77], [78].
We investigated if this evolutionary feature had impact on the evolution of the TRA-2 sequence in mosquitoes. We compared the amino acid sequence of the RRM+Linker of the six TRA-2 homologs of mosquitoes to the corresponding domains present in tra-2 orthologues of dipteran species (D. melanogaster, C. capitata, Anastrepha obliqua, Lucilia cuprina, M. domestica and Glossina morsitans), of the hymenopteran Apis mellifera and of the brachiopod crustacean Daphnia pulex. In addition, we included the corresponding domains of the Homo sapiens hTRA-2α homolog, which, although not involved in sex determination, is surprisingly able to functionally replace the endogenous tra-2 gene in XX (chromosomally female) transgenic Drosophila individuals homozygous for the loss-of-function tra-2B mutation [79].
Interestingly, we found that the mosquitoes' TRA-2 RRM+Linker has the lowest amino acid conservation when compared to Drosophila or even H. sapiens TRA-2. The NJ tree of the examined amino acid sequences showed a statistically supported group including all the non-mosquito species (bootstrap percentage 78%), whereas the six mosquito TRA-2 paralogs belong to a separate group (Figure 7). This may correlate with the high degeneration of the putative TRA/TRA-2-like binding sites discernable in Aeadsx and Aeafru. Hence other upstream sex-specific splicing regulators have been most likely recruited in the mosquito lineage. Indeed preliminary results of embryonic RNAi experiments against three out of four Ae. aegypti tra-2 paralogs failed to alter the dsx splicing at larval stages, or to produce intersexual phenotypes at adult stages (data not shown). Alternatively one or more of the Aedes TRA-2 proteins could have co-evolved a new specificity for one or more of the new identified motifs shared between Aeadsx and Aeafru genes.
(A) NJ consensus tree based on nucleotide alignment of the RRM+Linker encoding regions of the tra-2 gene of different insect and non insect species. (B) Table with the percentage of identity of the same nucleotide sequences analysed in the NJ tree. (C) WebLogo consensus sequences of TRA/TRA-2 binding sites of the indicated species. Only for mosquito species is it not possible to define a clear consensus sequence.
Conclusions
Sexual differentiation of Ae. aegypti seems to be, as in other dipteran species, under the control not only of dsx but also of the fru gene. The Aeafru gene is conserved in its genomic organisation even though, compared with other orthologues, the introns of Aeafru are much longer. Furthermore, Aeafru produces sex-specific transcripts from late larval, through pupal stages until adulthood, similarly to Drosophila. The sex-specificity of fru expression is achieved by an apparently conserved splicing regulation based on two 5′ alternative splice sites. This conservation of structure and sex-specific splicing suggests functional conservation, which would imply involvement of Aeafru in brain sexual differentiation and the control of sex behaviour.
The fru sex-specific regulation has been extensively studied in D. melanogaster, demonstrating the key role of TRA and TRA-2 splicing regulators in promoting female-specific fru and dsx splicing. In the Aedes genome, no TRA orthologues have been found. In contrast, four TRA-2 paralogues are present, which however group apart in a NJ phylogenetic tree with the respect of the other known dipteran and even non dipteran orthologues. Hence, most probably these TRA-2 paralogues evolved different sequence binding specificity and novel functions, after gene duplication and selective pressure relaxation. Furthermore, no well conserved TRA/TRA-2 binding sites have been found in both fru and dsx of Aedes, while they are highly conserved in many other dipteran species [42], [63]. Hence changes in the putative upstream splicing regulators (absence of tra and evolution by gene duplication and sequence divergence of tra-2) and in the splicing mechanisms of dsx gene (3′ splice site versus exon skipping) seem to be paralleled by changes in the putative cis acting elements. Interestingly, fru, unlike dsx, maintained a very similar 5′ alternative splicing pattern in Aedes, in spite of changes in the upstream splicing regulators.
We investigated whether Aedes dsx and fru might share a common sex-specific splicing regulator, even if this is not TRA and/or TRA-2. We found multiple novel motifs around the alternative sex-specific splice sites of Aedes dsx and fru, three of them forming a pattern present in both genes. Furthermore, a cluster of 3 motifs has been found to overlap the 3′ splice site region of the Aedes dsx female-specific first exon as well as to localise close to the Aedes fru female-specific 5′ splice site (200 nt away), similar to the localisation of the TRA/TRA-2 binding sites in Drosophila fru. It is interesting to note that motif of this cluster contains also an RBP1 binding site type B sequence. Hence, one may speculate that a sex-specific splicing factor or splicing regulatory complex might bind to these two regions. We propose that these findings may indicate a common splicing control exerted in parallel on both genes by novel sex-specific splicing factors.
We tried to approach the problem of how fru is sex-specifically regulated in Ae. aegypti. As the two alternative 5′ splice sites are apparently optimal we would expect a splicing competition mechanism.
As both the dsx 5a exon 3′female-specific ss and the fru exon P1-f 5′ female-specific ss appear to be optimal, the action of the sex-specific splicing factor would be to repress their use in males, rather than promoting it in females. This in turn implies some sex specificity of the splicing system. Furthermore, this splicing repression could be achieved by a direct action of the male-determining gene of Aedes, which would encode a splicing factor in this case, as proposed also for Aeadsx [42]. The future cloning of the Aedes M gene will help to understand if it directly regulates dsx and fru, promoting male-pattern splicing [80].
Further knowledge of the molecular mechanisms involved in regulation of gene expression related to sex determination and sexual differentiation in vector species, such as Aedes aegypti, would contribute to the development of novel control strategies whereby the vector is modified genetically for example to eliminate females, and to release sterilized males [41]. Transcriptional female-specific cis-acting regulatory DNA fragments have been used in combination with sex-specific alternative splicing to develop a first transgenic sexing strain in Ae. aegypti, [81], [82], [83]. This study will help to choose new genomic regions of either dsx or fru to build up sex-specifically expressible transgenes useful for sexing males and vector control.
Materials and Methods
Cloning strategy of the Aeafru gene
To identify the male-specific region of the Aeafru gene, we searched for the putative 5′ upstream portion within the genomic supercontig containing the putative Aeafru gene (AAEL006301 – supercontig 1.199). Using the 49 aa male-specific region of the FRUMC protein of An. gambiae as virtual probe in a TBLASTN search, a distantly linked but highly significant hit (70% of identity; 34/49 aa identical) was obtained. Subsequently, we performed a BLASTN search on ESTs database at NCBI site (http://www.ncbi.nlm.nih.gov/) using as virtual probe a 126 bp sequence encoding the N-terminal domain starting with the common ATG codon, to isolate the upstream transcribed sequences of the Aeafru gene. We identified five partially overlapping ESTs (DV373639.1; DV334145.1; DV332858.1; DV324359.1; DV270086.1), containing 5′ upstream sequences located 260 kb upstream the non-sex-specific ATG codon of the Aeafru exon C1. Finally, we utilized the An. gambiae coding sequences of exons zA and zB (zA: [GenBank: AY785361]; from position +1437. zB: [GenBank: XM_311072]; from position +1314) for the in silico identification of putative homologous exons in Aeafru locus. We used these sequences as virtual probes in a BLASTX analysis on the Ae. aegypti genomic database and we successfully identified two regions in the supercontig 1.199 encoding the putative zing finger type A (92% of identity respect to Anopheles homolog) and B (72% of identity respect to Anopheles homolog) of the Aeafru gene.
Cloning of the fru cDNA of Sabethes cyaneus
Total RNA was extracted from males (M) and females (F) of Sa. cyaneus adult mosquitoes using the TRIZOL Reagent (Invitrogen). Aliquots of 1 μg of each RNA were treated with RNase free-DNase I (Ambion), and first strand cDNAs were synthesized by Megascript system (Ambion) according to manufacturer's instruction. 1/40 of cDNA template was used in 50 µl PCRs containing primer pairs designed on the most conserved positions of the nucleotide alignment of BTB and zinc-finger C encoding sequences of the Aeafru and Angfru genes. The reaction mixture contained 50 mM KCl, 10 mM Tris·HCl (pH 8.3), 1.5 mM MgCl2, 1 µM each primer, 200 µM dNTPs (Roche), and 2.5 units Taq DNA polymerase (Roche). Appropriate annealing temperatures and cycle numbers were adjusted empirically for each primer pairs (Methods S1).
Rapid amplification of cDNA ends (RACE) and sequence analyses
The 5′- and 3′- ends of the Aeafru cDNAs were determined with the Smart Race amplification kit (Clontech Laboratories). Reverse transcription was performed as recommended by the supplier. cDNAs containing open reading frames (ORFs) were cloned into the pGEMT-Easy Vector (Promega) and sequenced with the Applied Biosystem BigDye 1.1 sequencing kit. Sequence alignments were performed with the ClustalW software. Sequence alignments were accomplished with the ClustalW software or MAFFT online alignment tool. The following Ae. aegypti cDNA sequences AeafruP1-m-C [GenBank: JX186753], AeafruP1-f-C [GenBank: JX186754], AeafruP2-C [GenBank: JX186755] and Sa. cyaneus cDNA sequence Sacfru-C [GenBank: JX186756] were deposited in GenBank.
Nucleic acids extractions and RT-PCR analyses
Genomic DNA and total RNA were extracted from males (M) and females (F) of Ae. aegypti adult mosquitoes and from the different developmental stages embryos (E), larvae of 1st and 2nd instar (L12), larvae of 3rd and 4th instar (L34), single sexed L34 larvae and single sexed pupae using the TRIZOL Reagent (Invitrogen). Aliquots of 1 μg of each RNA were treated with RNase free-DNase I Amplification Grade (Invitrogen) and first strand cDNAs were synthesized by Superscript First-Strand Synthesis System (Invitrogen) according to manufacturer's instruction. 1/20 of cDNA template was used in 50 µl PCRs containing primer pairs specific for the various cDNAs, 50 mM KCl, 10 mM Tris·HCl (pH 8.3), 1.5 mM MgCl2, 1 µM each primer, 200 µM dNTPs (Roche), and 2.5 units Taq DNA polymerase (Roche). Appropriate annealing temperatures and cycle numbers were adjusted to individual primer pairs (see Methods S1). Positive controls and standardization was performed as described in [42].
Phylogenetic and evolutionary analysis
Nucleotide sequence encoding the BTB domain of the fru cDNAs of Ae. aegypti (AeafruBTB) and Sa. cyaneus (SacfruBTB) were aligned to the corresponding region of the fru gene of 21 insect species downloaded from GenBank (Methods S1) and the nucleotide sequence encoding the RRM+Linker region of the tra-2 cDNAs of Ae. aegypti and An. gambiae were aligned to the corresponding region of the tra-2 gene of 9 insect species downloaded from GenBank (see Methods S1) using the MAFFT software. The resulting alignment files (348 and 273 sites, respectively) was used to perform Maximum Parsimony (MP) and Neighbor-Joining analyses using the MEGA 5 software [84], with 1000 bootstrap replicates.
Nucleotide sequences encoding the BTB and the connector domain of the fru cDNAs of Ae. aegypti and Sa. cyaneus were separately aligned to the corresponding region of the fru gene of two different mosquito species, Cu. quinquefasciatus and An. gambiae using the MAFFT software. The resulting alignment files (348 sites for the BTB domain and 765 sites for the connector domain) were used to estimate the pairwise synonymous (dS) and nonsynonymous (dN) nucleotide substitution rates within the partitioned domains (BTB and connector) using the Jukes-Cantor distance model with the modified Nei-Gojobori method, implemented in MEGA 5 software. The mean pairwise ratios of dN/dS (ω) were calculated and used to examine whether the BTB and the connector domains of the available fru genes of mosquitoes evolve under purifying constraint for amino acid sequences (ω<1), positive selection for amino acid changes (ω>1), or neutrally (ω = 1) and to compare the selective pressures that act on the two domains.
Measurements of splice-site strength with MaxEntScan
MaxEntScan models short sequence motifs and accounts for relationships between adjacent and non adjacent nucleotide positions to assess how well a sequence conforms to the well-established 5′ss or 3′ss consensus motif. We used these scores as an indication of splice-site strength. The 5′ss sequence is defined as position (−3, +6) and the 3′ss sequence at position (−20, +3), relative to the exon–intron junction.
In silico MEME analyses
Nucleotide sequences of female-specific exon 5a of the dsx gene and exon P1-f of the fru gene of Ae. aegypti, flanked by 500 bp-long upstream and downstream sequences, were analyzed by MEME online tool (see Methods S1). This web server allows for the identification of short motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs.
The search was conducted for eight times with motif lengths ranging from 8 to 15 and with 0–2 mutations per motif. Default values were used for all other parameters except for the occurrence of the motifs (set to any number of repetition) and the maximum number to search (set to 50).
With these settings we identified 105 sequences clustered in 38 conserved motifs, with p-value higher than 1.0e-4. As negative control we repeated the MEME analysis with the same parameter on shuffled sequences obtained with uShuffle java applet (k-let: 2). With these randomized sequences we cannot identified the same type and number of motifs obtained with normal sequences.
Sliding window analysis on MEME motifs
To verify if there was an enrichment of putative regulatory elements, identified by MEME analysis, near the splice sites of Aeadsx and Aeafru sex-specifically regulated regions we performed a sliding window analysis and defined a scoring scheme, inspired to the papers of Ule et al., 2006 and Brooks et al., 2011 [53], [85]. We sampled, using a modified version of REcount perl script (available at http://splicing.rockefeller.edu/map/REcount.zip) 100 nucleotide long sequences every 50 nucleotides from the female-specific Aeafru P1-f and Aeadsx 5a exons, flanked by 500 bp-long upstream and downstream sequences. We counted for each 100 nt-long window the number of MEME identified motifs and we defined a window-score calculated in the following way:
- 1 point for each MEME motif.
- 1 additional point for each MEME motif with at least three copies in the Aeafru or Aeadsx analyzed sequences.
- 1 additional point for each MEME motif with an identical MEME motif in +/−100 bp (cluster forming motifs) in the Aeafru or Aeadsx analyzed sequences.
- 1 additional point for each MEME motif with at least two different MEME motifs in +/−200 bp with the same relative order (pattern forming motifs) in the Aeafru or Aeadsx analyzed sequences. This is and additive point i.e. if a MEME motif forms two different patterns it gains +2 points, if it forms 3 different patterns it gains +3 points etc.
The total score for each window was expressed as the log10 (2× Score).
Supporting Information
Figure S1.
Censor analysis of Aeafru introns. Graphical output of Censor analysis on Aeafru intron sequences. For a legend see: http://www.girinst.org/censor/help.html#GRAPH. For the intron 1 (424 kb-long) the output is reported for the whole sequence and for 42,4 kb-long sub regions of the same intron. For each Aeafru intron the number of repetitive elements per kb (NoRE/kb) and the percentage of repetitive element nucleotides respect to intron nucleotides (REbp) are reported.
https://doi.org/10.1371/journal.pone.0048554.s001
(PDF)
Figure S2.
Microsyntheny of mosquitoes fru containing regions. Ensembl genome browser view of the fru containing regions of Ae. aegypti and An. gambiae genomes. The homologues are connected by braked lines. The green arrow indicates a putative chromosomal breakpoint site involved in genomic rearrangement after the split of the two species. Only 3 genes (Aeafru, AAEL006293 and AAEL006290) out of 22 present in the Aedes supercontig 1.199 exhibit conserved synthenic relationship with their Anopheles putative orthologues (Angfru, AGAP00079 and AGAP00078, respectively); of the remaining 19, 3 genes (AAEL006304, AAEL006285 and AAEL006288) have not a homolog in Anopheles and 16 correspond to Anopheles putative homologs located in different genomic positions. Interestingly, microsynteny was found between the second half of the Aedes supercontig 1.199, downstream the fru gene, and a genomic region located on the chromosome 3R of Anopheles (position 5, 7–5, 8 Mb). We identified two duplication events occurred in this region of Ae. aegypti, with the AAEE006296 and the AAEL006292 genes corresponding to the Anopheles AGAP008103 gene and the AAEL006302 and AAEL006289 corresponding to the Anopheles AGAP008101 gene. The Anopheles fru-containing region contains 15 genes. 3 out of 15 genes exhibit synthenic relationship with the Aedes putative homologs, including Angfru (AGAP00080 – fru, AGAP00078 and AGAP00079). Of the remaining 12, one gene has no homolog in Aedes (AGAP00084) and 11 correspond to Aedes putative homologs located in different genomic positions. For these genes we observed a peculiar situation, with 4 couples of Anopheles genes corresponding to couples of Aedes putative orthologues located in 4 different Aedes supercontigs (AGAP013356 and AGAP00075 – Aedes supercontig 1.127; AGAP013406 and AGAP00076 – Aedes supercontig 1.487; AGAP00081 and AGAP00082 – Aedes supercontig 1.166; CPR129 and AGAP00085 – Aedes supercontig 1.894). This finding suggests that the fru-containing region in Anopheles has been involved in multiple genome shuffling events after the split of the two species, according with previous. Finally, we identified two intronic genes (AGAP00088 and AGAP013490) located within the gene AGAP00086, corresponding to the Aedes orthologue AAEL013684, and hence, most probably, due to a duplication event in An. gambiae.
https://doi.org/10.1371/journal.pone.0048554.s002
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Figure S3.
Exon/Intron junctions and MaxEntScan scores of fru genes. A) Coding sequences are shown in upper case letters and non-coding regions in lower case letters. The 5′ss consensus sequence is MAG/GTRAGT and the 3′ss consensus is YnNYAG. The number of pyrimidines (N° of Y) in the 12 bp preceding the 3′ ss (NYAG) is indicated for each 3′ss. The consensus number of pyrimidines for Ae. aegypti (8,02±2,15) is derived from the tabulation of 4688 Ae. aegypti splice-acceptor sites [36]. M = A or C. R = A or G nucleotide. Y = T or C or nucleotide. N = any nucleotide. B) Schematic representation of fru-P1 gene. Shaded in grey negative MaxEntScan scores. The scores are in bits and a higher MaxEntScan score correspond to a stronger splice-site sequence. A ss with a MaxEntScan score of 12–13 is a strong ss while negative scores are usually associated with decoy splicing sites (Yeo G. pers. comm.).
https://doi.org/10.1371/journal.pone.0048554.s003
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Figure S4.
Schematic representation of the position of the identified putative cis-elements involved in splicing regulation of Aeadsx and Aeafru. We identified in Aeafru P1 exon an additional putative TRA/TRA-2 binding site located close to the male-specific 5′ss, which appears to be highly conserved in the very same region of Drosophila fru, although previously not reported, and in the Anopheles orthologue Angfru genes (data not shown).
https://doi.org/10.1371/journal.pone.0048554.s004
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Figure S5.
Consensus sequences of TRA/TRA-2 binding sites. Consensus sequences of TRA/TRA-2 binding sites of D. melanogaster, An. gambiae and Ae. aegypti dsx, fru and dsx+fru genes obtained with WebLogo web tool. The absence of a consensus is clear for mosquitoes genes.
https://doi.org/10.1371/journal.pone.0048554.s005
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Figure S6.
Graphical representation and list of motifs identified by MEME analysis. Schematic graphical representation and tabular list of the motifs identified by MEME analysis in Aeafru and Aeadsx genes.
https://doi.org/10.1371/journal.pone.0048554.s006
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Methods S1.
Lists of primers, GenBank accession numbers and web tools utilized in this paper.
https://doi.org/10.1371/journal.pone.0048554.s007
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Table S1.
Modified Censor output of repetitive elements identified in Aeafru intronic regions. The identified repetitive elements greatly vary in length and among them the most abundant are the NON-LTR/Jockey LINE-1_AA element [86], detected in 38 copies, and the NON-LTR/SINE Feilai elements [87], detected in 36 copies.
https://doi.org/10.1371/journal.pone.0048554.s008
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Table S2.
Ae. aegypti intron analysis. Tabular output of Aedes aegypti intron analysis. The average number of repetitive elements per kb (indicated as NoRE/kb) in Aeafru introns is 2,03±0,28 while the average percentage of nucleotides of the identified repetitive elements with the respect to the nucleotides of the Aeafru introns (indicated as REbp) is 34,56%±19,54 (Figure S1). To compare these values with the average values of the Ae. aegypti introns, we analysed 1000 randomly chosen Ae. aegypti introns (size range from 1 to 130 kb) with the CENSOR software, defining an average NoRE/kb (2,19±0,68) and REbp (47,22±17,75%) intron values for this species. This analysis indicates that within the introns of Ae. aegypti the number of repetitive elements per kb is almost constant, with a value of about 2, while the size of these elements is variable, ranging from 30% to 60% of the whole intron sequences. The NoRE/kb and REbp values of the Aeafru introns do not deviate significantly this observation.
https://doi.org/10.1371/journal.pone.0048554.s009
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Table S3.
Regulatory elements in the sex-specifically regulated region of fru homologs. Sequence of the putative Aeafru cis identified in the female-specific exon P1-f. The upper case indicate conserved nucleotides respect to the consensus sequences of Drosophila. The distance of these elements from the male- and female-specific 5′ splicing donor sites are indicated.
https://doi.org/10.1371/journal.pone.0048554.s010
(PDF)
Table S4.
Correspondence between MEME identified motifs and motif from RegRNA database. The nucleotides of MEME motifs corresponding to RegRNA motifs areshaded in light grey.
https://doi.org/10.1371/journal.pone.0048554.s011
(PDF)
Acknowledgments
We are grateful to Remo Sanges (Zoological Station “Anthon Dohrn” – Naples, Italy) for helpful suggestions on bioinformatic sequence data analysis. We deeply thank Paola Santoro (National Institute of Statistic – ISTAT, Rome, Italy) for the helpful suggestions on statistical data analysis. We thank Bruno Arcà (Department of Functional and Structural Biology – University of Naples “Federico II” – Naples, Italy) and Fabrizio Lombardo (Department of Public Health, Parasitology Section – University of Rome “La Sapienza” – Rome, Italy) for providing the Aedes aegypti developmental samples. We thank Sandra H. South and Göran Arnqvist (Evolutionary Biology Centre – Uppsala University, Sweden) and Woodbridge A. Foster (Ohio State University) for Sa. cyaneus adult samples. We thank Maria Sica (Department of Biological Sciences, University of Naples “Federico II” – Naples, Italy) for her qualified technical assistance. GS greatly thanks Kitsos Louis (IMBB – Crete, Greece), who suggested and encouraged him to start a sex determination Aedes aegypti project.
Author Contributions
Designed research: MS GS. Performed the molecular cloning experiments, the developmental expression analyses and in silico analyses: MS. Performed Sa. cyaneus cloning experiments and helped with molecular biology experiments: RD. Performed Ae. aegypti intron analysis and helped with molecular biology experiments: VP. Performed phylogenetic and molecular evolutionary analyses: SA. Helped with molecular biology experiments: DN MN. Analyzed and discussed data: MS RD VP SA DN MN LA LCP GS. Read and approved the final manuscript: MS RD VP SA DN MN LA LCP GS. Wrote the paper: MS SA LA GS.
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