SHORT COMMUNICATION Cloning and Sequence Analysis of the Circadian Clock Genes period and timeless in Aedes albopictus (Diptera: Culicidae) KEITH SUMMA, JENNIFER M. URBANSKI, XIUMEI ZHAO, MONICA POELCHAU, 1 AND PETER ARMBRUSTER Department of Biology, Reiss 406, Georgetown University, 37th and O Streets NW, Washington, DC 20057-1229 J. Med. Entomol. 49(3): 777Ð782 (2012); DOI: http://dx.doi.org/10.1603/ME11171 ABSTRACT The genes period (per) and timeless (tim) are core components of the circadian clock that regulates a wide range of rhythmic biochemical, physiological, and behavioral processes in prokaryotes and eukaryotes. We used degenerate polymerase chain reaction (PCR) and Rapid AmpliÞcation of cDNA Ends (RACE) to clone and sequence the entire cDNAs of both the per and tim genes in Aedes albopictus (Skuse). We also used the 5⬘ end of the Ae. albopictus per cDNA to identify previously unannotated sequence coding for the N-terminal region of the PERIOD protein in Aedes aegypti L. We sequenced genomic DNA of one mosquito from each of three geographically distinct populations (New Jersey, Florida, and Brazil), and identiÞed three introns in the per gene and eight introns in the tim gene. Phylogenetic analyses and comparison of functional domains support the orthology of the newly identiÞed per and tim genes. Analysis of nonsynonymous to synonymous substitution rates indicates that both the per and tim genes have evolved under strong selective constraint subsequent to the divergence of Ae. albopictus and Ae. aegypti. Taken together, these results provide resources that can be used to investigate the molecular genetics of circadian phenotypes in Ae. albopictus and other culicids, to perform comparative analyses of insect circadian clock function, and also to conduct phylogeographic analyses using single-copy nuclear introns. KEY WORDS period, timeless, circadian clock, Aedes albopictus Circadian rhythms are endogenous, self-sustaining biological rhythms with a period of ⬇24 h that are nearly ubiquitous in nature (Dunlap et al. 2004). Circadian rhythms provide an adaptive mechanism coordinating biochemical, physiological, and behavioral activities with the rhythmic patterns of light, temperature, and other factors that ßuctuate periodically according to the daily rotation of the Earth. These rhythms are programmed by an internal biochemical oscillator (i.e., “clock”) that consists of core molecular machinery that is well conserved among Metazoans (Harmer et al. 2001). The molecular underpinnings of the circadian clock have been particularly well characterized in Drosophila melanogaster (Meigen) where the core clock consists of a set of proteins that form an autoregulatory negative feedback loop with a period of ⬇24 h (Dunlap 1999, Young 2000, Panda et al. 2002, Allada and Chung 2010). Brießy, the circadian proteins CLOCK (CLK) and CYCLE (CYC) dimerize in the nucleus, where they bind E-box elements in target gene promoters and activate transcription of a number of downstream genes, including period (per) and timeless (tim). The PER and TIM proteins then form a dimer in the cytoplasm that translocates to the nucleus, 1 Corresponding author, e-mail: [email protected]. where it physically interacts with and inhibits CLKCYC, thereby repressing transcription. Temporal delays between these activation and repression steps, as well as posttranslational modiÞcation of core clock components, give rise to stable 24 h oscillations in gene expression that characterize circadian rhythms and underlie the generation of overt 24 h behavioral rhythms, such as locomotor activity (Allada and Chung 2010). Additionally, light-induced negative regulation of TIMELESS by the photoreceptor CRYPTOCHROME (CRY) (Ceriani et al. 1999) provides a mechanism for entrainment, coordinating the internal circadian clock with the exogenous light:dark cycle. Although many basic elements of the circadian clock appear to be relatively well conserved among Metazoans, it is becoming increasingly clear that signiÞcant evolutionary modiÞcations of the circadian clock have taken place during the divergence of insects (Rubin et al. 2006, Yuan et al. 2007, Sandrelli et al. 2008). Recently, there has been increased interest regarding the molecular basis of circadian rhythms in vector mosquitoes (Gentile et al. 2006, 2009; Das and Dimopoulos 2008; Rund et al. 2011; Ptitsyn et al. 2011). Indeed, a variety of crucial behavioral traits related to disease transmission such as ßight activity, host seeking, and blood feeding have been shown to have a circadian basis (Clements 1999, Das and Dimopoulos 0022-2585/12/0777Ð0782$04.00/0 䉷 2012 Entomological Society of America 778 JOURNAL OF MEDICAL ENTOMOLOGY Vol. 49, no. 3 Table 1. Percent identity of amino acid sequences in conserved functional domains of the inferred PERIOD and TIMELESS proteins between Ae. albopictus and those of Ae. aegypti and D. melanogaster PERIOD NLS (%) PAS-A (%) PAS-B (%) PAC (%) CLD (%) Ae. aegypti D. melanogaster 93 84 97 69 97 58 95 64 98 69 TIMELESS NLS (%) 32aa (%) PER-1 (%) PER-2 (%) CLD (%) AD (%) Ae. aegypti D. melanogaster 100 100 100 85 97 65 99 64 53 18 87 0 2008). For example, Das and Dimopolous (2008) demonstrated a circadian basis to blood feeding behavior in Anopheles gambiae (Giles) and showed that RNAimediated knockdown of three clock genes signiÞcantly affected blood feeding activity. Gentile et al. (2006, 2009) have examined the circadian expression of eight clock genes in Aedes aegypti L. and Culex quinquefasciatus (Say). Their results (Gentile et al. 2009) show that despite distinct locomotor activity patterns, the circadian expression of these genes is well-conserved, except for the clock gene Cry2, which may play a role in mediating species-speciÞc differences in rhythmic behaviors. Ptitsyn et al. (2011) and Rund et al. (2011) have identiÞed multiple molecular pathways exhibiting circadian expression patterns, as well as rhythmic expression of per and tim, in Ae. aegypti and A. gambiae respectively. Further genetic studies of circadian-controlled processes have the potential to yield important insights into the molecular bases of key traits affecting both Þtness and disease transmission of vector mosquito species. Herein, we report on the sequence and comparative analysis of the two core clock genes per and tim in the Asian tiger mosquito, Ae. albopictus (Skuse). First, we used degenerate polymerase chain reaction (PCR) and Rapid AmpliÞcation of cDNA Ends (RACE) to clone and sequence both genes. Next, these sequences were used in BLAST searches to identify a previously unannotated region of the per gene encoding the Nterminal region of the PER protein in Ae. aegypti. Finally, we sequenced genomic DNA of a single mosquito from each of three geographically distinct populations (New Jersey, Florida, and Brazil) to identify introns within the Ae. albopictus per and tim genes. These results provide resources that can be used to investigate the molecular genetics of circadian phenotypes in Ae. albopictus and other Culicids, to conduct comparative analyses of circadian clock function in insects, and to perform phylogeographic analyses using single-copy nuclear introns. Materials and Methods A lab F7 colony of Ae. albopictus from Vero Beach, FL. was maintained in the laboratory under a 16:8 h (light:dark) photoperiod at 21⬚C and near-optimal conditions as described previously (Armbruster and Hutchinson 2002, Armbruster and Conn 2006). Seven to 14 d old adult males and females were collected at 16 h after light onset (Zeitgeiber time (ZT) 16) because studies in other Diptera indicated that clock gene expression peaks around the time of light to dark transition (Gvakharia et al. 2000; Warman et al. 2000; Goto and Denlinger 2002; Gentile et al. 2006, 2009). Adults were CO2 anesthetized, frozen at ⫺80⬚C and ⬇200 heads were removed from the adult bodies on dry ice and returned to ⫺80⬚C before RNA extraction. RNA was extracted from adult heads using TRI Reagent (Sigma-Aldrich, St. Louis, MO) followed by isopropanol precipitation (Sambrook and Russell 2001). The RNA was then resuspended in nuclease free water at a concentration of 50 ng/l and stored at ⫺80⬚C. cDNA synthesis was performed with the SMART PCR cDNA Synthesis Kit (Clontech, Mountain View, CA) and oligo-dT priming according to the supplierÕs instructions. Reverse transcription was conducted with the following thermal proÞle: 42⬚C for 2 min, after which 1 l of reverse transcriptase was added, 42⬚C for 50 min, 70⬚C for 15 min, after which 1 l of RNase H was added, and 37⬚C for 20 min. The degenerate primers PERC2FOR and PERD2REV and TIMAFOR and TIMC2REV (Supp. Appendix A [online only]) were designed based on the published sequences of insect per and tim available from NCBI. PCR ampliÞcation was performed using the BD Advantage 2 PCR Enzyme System Kit (Clontech) with 1 l of cDNA at ⬇1 g/l, 0.5 l BD Advantage 2 Polymerase Mix, 0.5 l 50X dNTP mix, 2.5 l BD Advantage 2 PCR Buffer, and 1 l of both the forward and reverse primer, each at a concentration of 10 M. The temperature proÞle for both the per and tim ampliÞcations consisted of 5 min at 94⬚C, followed by 30 cycles of 1 min at 94⬚C, 1 min at 48⬚C, 1 min at 72⬚C, followed by 5 min at 72⬚C. Per and tim ampliÞcation products of the expected size were excised from a 1% agarose gel and puriÞed using a NucleoTrap Gel Extraction Kit (Clontech) according to the manufacturerÕs instructions. The products were then cloned into a pCR 2.1-TOPO vector used to transform TOP10 One Shot cells (Invitrogen, Carlsbad, CA). Plasmids were puriÞed using the WizardPlus Miniprep DNA puriÞcation system (Promega, Madison, WI) and inserts were sequenced using modiÞed M13 primers (Supp. Appendix A [online only]) and Big Dye terminator chemistry. Contig assembly was performed with Sequencher v. 4.5 (Gene Codes Corporation, Ann Arbor, MI). To determine the complete cDNA sequence of the putative Ae. albopictus per and tim genes we performed Rapid AmpliÞcation of cDNA Ends (RACE) using the BD SMART RACE cDNA AmpliÞcation kit May 2012 SUMMA ET AL.: period AND timeless GENES IN Aedes albopictus (Clontech). Gene-speciÞc primers (Supp. Appendix A [online only]) were used to PCR-amplify 5⬘ and 3⬘ RACE products that were gel puriÞed, cloned, and sequenced as described above. Contig assembly was performed as described above and the inferred amino acid sequences were deduced by using ORF Finder (http://www.ncbi.nlm.nih.gov/projects/gorf/) followed by BlastP searches to verify sequence identity. To identify introns and assess sequence variation across partial regions of both genes we sequenced an ⬇3.3 Kb fragment of the per gene and two fragments of the tim gene, one ca. 2.2 Kb and the other ca. 1.9 Kb. Each of these three regions was sequenced from genomic DNA of individual mosquitoes collected from each of three populations: 1) Burlington, NJ; 2) Fort Lauderdale, FL; and c) Salvador, Bahia State, Brazil. Genomic DNA was isolated using methods described by Severson (1997). PCR reactions consisted of 21 l sterile H2O, 1 l of template genomic DNA, 1 l each of forward and reverse primers (10 M concentration) and a single “ready-to-go” PCR bead (Amersham Pharmacia, Buckinghamshire, United Kingdom). The thermal proÞle consisted of 5 min at 98⬚C followed by 35 cycles of 30 s at 94⬚C, 1 min at 58 Ð 60⬚C, 1 min at 72⬚C and then a Þnal 10 min extension period at 72⬚C. PCR products were puriÞed using Centri-Spin columns (Princeton Separations, Adelphia, NJ) before sequencing and contig assembly as described above. Genomic sequences were aligned against corresponding cDNA sequences in ClustalW and introns were identiÞed by visual inspection as well as comparison to the predicted translation sequence. To conduct phylogenetic analyses of inferred dipteran PER and TIM proteins we obtained cDNA or amino acid sequences of the following taxa from NCBI or VectorBase (accession numbers for PER and TIM, respectively, are indicted in parentheses): 1) Ae. aegypti (XP_001658976, AAY40757.1); 2) Cx. quinquefasciatus (XP_001849299.1, XP_001848611.1); 3) A. gambiae (AGAP001856, AGAP008288); 4) Sarcophaga bullata (BAB85488, BAB85487); 5) Chymomyza costata (BAA28711, BAB91179); 6) D. melanogaster (NP_525056.2, P49021.2); and 7) D. virilis (P12349, AAB94930). We used Antheraea pernyi (Q17062, AAF66996) as an outgroup in these analyses. The current Ae. aegypti per annotation on VectorBase (AaegL1.2) is incomplete because the predicted protein sequence begins with a glycine residue rather than methionine and is missing 98 N-terminal amino acids relative to the predicted Ae. albopictus PER protein. The DNA sequence encoding this missing N-terminal section in Ae. aegypti is located ⬇30 Kb upstream of the incomplete annotated sequence between bases 494063Ð 494358 on supercontig 1.303. The resulting sequence matches the corresponding Ae. albopictus per sequence with 79% identity at the amino acid level and 81% identity at the nucleotide level. This missing inferred amino acid sequence was joined to the annotated inferred Ae. aegypti protein sequence for phylogenetic analysis described below. Inferred amino acid sequences of both PER and TIM were aligned in ClustalW with a gap opening 779 Table 2. Intron characteristics for Ae. albopictus period and timeless genes based on genomic DNA sequence of one mosquito from each of a New Jersey, Florida, and Brazil period Intron 1 Intron 2 Intron 3 timeless Intron 1 Intron 2 Intron 3 Intron 4 Intron 5 Intron 6 Intron 7 Intron 8 Positiona Lengthb (bp) ⌸c Indel sites 2,964 3,250 3,663 96 106 86 0.14 0.07 0.26 0 0 34 872 1,122 1,568 1,711 1,999 2,222 2,420 2,847 61 51 69 98 96 156 67 61 0.13 0.00 0.02 0.08 0.08 0.10 0.12 0.04 2 9 0 1 0 2 1 5 a Position no. relative to sequence as presented in Appendices B (period) and C (timeless). b Based on sequence from Burlington, NJ. c Nucleotide diversity (Nei and Li 1979). penalty of 15 and a gap extension penalty of 0.3. (Supp. Appendices D and E [online only]). Neighbor joining trees were constructed in MEGA4 (Tamura et al. 2007) with Poisson corrected amino acid distances and 1,000 bootstrap replicates. Conserved functional domains of both proteins were identiÞed based on visual inspection of the protein alignments and comparison with previous annotations in D. melanogaster (Myers et al. 1995, Saez and Young 1996, Ousley et al. 1998), Lucilla cuprina (Warman et al. 2000), and Ae. aegypti (Gentile et al. 2006). Percent amino acid identity was computed between functional domains of the Ae. albopictus, Ae. Aegypti, and D. melanogaster inferred protein sequences using BlastP. We also computed the ratio of nonsynonymous (dN) to synonymous (dS) substitutions between orthologues of per and tim in Ae. albopictus and Ae. aegypti to test for evidence of positive selection acting on each gene. Codon-based alignments were constructed using PAL2NAL (Suyama et al. 2006) and dN/dS ratios were computed using a sliding window analysis in DNAsp v.5 (Librado and Rozas 2009). We also searched for short areas of conserved sequence in the 5⬘ and 3⬘ UTRs of per and tim in Ae. albopictus, An. gambiae, and D. melanogaster (UTRs for these genes are not annotated in Ae. aegypti). We used the web-based program MEME (Multiple EM for Motif Elicitation; http://meme.sdsc.edu/ meme/cgi-bin/meme.cgi; Bailey and Elkan 1994) with the following modiÞcation to the default settings: we searched for 5Ð50 bp motifs, where each motif could occur two to three times per UTR. For the per 3⬘ UTR, we were only able to use sequence from Ae. albopictus and D. melanogaster, as this UTR is not annotated in An. gambiae. We report only motifs that have Þve or more perfectly conserved consecutive bases across all three species. Finally, we calculated the average nucleotide diversity, ⌸ (Nei and Li 1979), among genomic DNA samples from three populations (New Jersey, Florida, and Brazil) for three per and eight tim intron sequences (Table 2). 780 JOURNAL OF MEDICAL ENTOMOLOGY Vol. 49, no. 3 Fig. 1. Neighbor-joining tree of Dipteran (A) PERIOD and (B) TIMELESS inferred amino acid sequences based on Poisson corrected distances with the Lepidopteran A. pernyi as the outgroup. Percent bootstrap support based on 1,000 replicates with only values ⬎50% shown on tree. Results Degenerate PCR using primers PERC2FOR and PERD2REV (Supp. Appendix A [online only]) produced a single fragment of the expected size (ca. 500 bp). Subsequent sequencing of 3⬘ and 5⬘ RACE PCR products yielded a cDNA sequence of 4,900 bp with 546 bp in the 5⬘ UTR, an open reading frame of 3,897 bp and 457 bp in the 3⬘ UTR (GenBank JN559769; Supp. Appendix B [online only]). The presence of a stop codon as well as polyadenylation signal (AATAAA) and poly-A tail indicates that the entire 3⬘ end of the transcript was sequenced. The deduced protein sequence contains 1298 amino acids, and a BlastP search against the NCBI nonredundant protein database indicated 39% amino acid identity (Evalue ⫽ 0.0) to the PER protein in D. melanogaster. The deduced amino acid sequence of PER in Ae. albopictus has particularly high similarity to PER in Ae. aegypti in several putative functional domains, with percent amino acid identities ranging from 93Ð98% for the nuclear localization signal (NLS; Vosshall et al. 1994), PER-ANRT-SIM (PAS-A, PAS-B; Zhulin et al. 1997), PAS-associated C-terminal (PAC; Zhulin et al. 1997), and cytoplasmic localization (CLD; Saez and Young 1996) domains (Table 1A). Percent amino acid identity between the Ae. albopictus and D. melanogaster PER sequences is also high in these functional domains, ranging from 58 to 84% (Table 1A). The D. melanogaster PER contains a threonineglycine (TG) repeat region that is thought to contribute to temperature compensation of the circadian clock (Sawyer et al. 1997), but there is only one TG pair in Ae. albopictus (Supp. Appendix B [online only]) and all other Culicids considered here. Degenerate PCR using primers TIMAFOR and TIMC2REV (Supp. Appendix A [online only]) also produced a single fragment of the expected size (ca. 1,000 bp). Sequencing of 5⬘ and 3⬘ RACE products yielded a cDNA of 6,269 bp with 1,243 bp in the 5⬘ UTR, an open reading frame of 3,756 bp, and 1,270 bp in the 3⬘ UTR (GenBank JN559770; Supp. Appendix C [online only]). The tim cDNA contains a stop codon and poly-A tail but it does not have a canonical polyadenylation signal in the 3⬘ UTR. The deduced amino acid sequence contains 1,251 amino acids and has a high level of similarity (47% amino acid identity, Evalue 0.0) to the TIM protein in D. melanogaster. Similarity between putative functional domains of the inferred TIM proteins is also high between Ae. albopictus and Ae. aegypti, ranging from 97Ð100% identity for the NLS (Saez and Young 1996), the 32 amino acid region (32aa; Ousley et al. 1998), the PER interaction domains (PER-1 and PER-2; Saez and Young 1996), 87% for the acidic domain region (AD; Myers et al. 1995), and 54% for the CLD (Saez and Young 1996) region (Table 1B). Percent identity for the NLS, 32aa, PER-1 and PER-2 regions between Ae. albopictus and D. melanogaster is also high, ranging from 64 Ð100% (Table 1B). However, the CLD region is far less conserved (18% identity) between Ae. albopictus and D. melanogaster, and the AD region appears to have completely lost amino acid sequence similarity (% similarity ⫽ 0; Table 1B). Phylogenetic analysis of putative orthologues of PER (Fig. 1A) and TIM (Fig. 1B) inferred amino acid May 2012 SUMMA ET AL.: period AND timeless GENES IN Aedes albopictus sequences from a diverse group of Diptera indicates a well supported topology that is consistent with the established taxonomic relationships among these species. A sliding-window analysis of dN/dS between the per nucleotide sequences of Ae. albopictus and Ae. aegypti indicates that dN/dS ranges from 0 to 0.55 across the length of the coding sequence with an overall average of 0.09. These results imply that the per locus has been under strong purifying selection during the divergence of Ae. albopictus and Ae. aegypti. The dN/dS for tim nucleotide sequences of Ae. albopictus and Ae. aegypti shows one narrow peak with values of ca. 1.5 around nucleotide position 1,000 of the open reading frame. However, similar to per, dN/dS values range from 0 to 0.5 throughout all other areas of the sequence and the overall dN/dS ratio is 0.17. These results imply that while there may be narrow regions of the tim gene that are evolving in a neutral fashion between Ae. albopictus and Ae. aegypti, the majority of the gene sequence is evolving under strong selective constraint, similar to the per gene. We identiÞed two short areas of conserved sequence in the 5⬘ UTR of per, four in the 3⬘ UTR of per, two in the 5⬘ UTR of tim, and zero in the 3⬘ UTR of tim (Supp. Appendices B and C [online only]). These sequences may be of interest for future functional investigation. Analysis of genomic DNA sequence fragments of both per and tim from individual mosquitoes from each of New Jersey, Florida, and Brazil revealed three introns in the per gene ranging from 86 to 106 bp, and eight introns in the tim gene ranging from 51 to 156 bp. Overall nucleotide diversity (⌸) ranged from 0.00 to 0.26 between intron sequences from the three geographically disparate samples (Table 2), suggesting that these noncoding regions might provide useful markers for phylogeographic analyses. Discussion The circadian clock is an endogenous oscillator comprised of an autoregulatory feedback loop that regulates a wide range of rhythmic biochemical, physiological, and behavioral processes in prokaryotes and eukaryotes (Dunlap et al. 2004). Phylogenetic analyses based on per and tim inferred amino acid sequences from Ae. albopictus and a diverse group of Diptera indicate a strongly supported topology that is consistent with taxonomic classiÞcation of these species and is highly congruent between both the per and tim trees (Fig. 1). Overall percent amino acid identity between Ae. albopictus and Ae. aegypti was high for both per (83%) and tim (84%) and in several functional domains identities ranged between 87Ð100% (Table 1). These results strongly support the orthology of the newly identiÞed per and tim sequences in Ae. albopictus to previously identiÞed per and tim genes in Ae. aegypti and other Diptera. D. melanogaster has a paralogue of the timeless gene called timeless2/ timeout (Benna et al. 2000, Dunlap et al. 2004), but when this paralogue is included in the phylogenetic analysis of inferred TIMELESS sequences from Fig. 1B it is positioned externally to all other sequences, in- 781 dicating that none of the sequences we included in our analysis were paralogous rather than orthologous gene copies of tim. In addition to the relevance to circadian biology, the sequence data we present from introns of the per and tim genes may provide useful molecular markers for phylogeographic analysis of Ae. albopictus populations. Such markers would be particularly valuable for Ae. albopictus, which is infected with two strains of the endosymbiotic bacterial parasite Wolbachia (Armbruster et al. 2003). Wolbachia-induced cytoplasmic incompatibility is well known to reduce mitochondrial DNA variation (Turelli and Hoffmann 1991, 1995), consistent with the low observed mitochondrial DNA diversity within and among geographic populations of Ae. albopictus (Birungi and Munstermann 2002, Usmani-Brown et al. 2009). Single copy microsatellite markers have also proven difÞcult to isolate from Ae. albopictus, further limiting variable molecular markers available for phylogeographic analysis in this mosquito. Therefore, single-copy nuclear introns may be valuable resources for population-level analyses of genetic diversity. We found a wide range of nucleotide diversity among introns from both the per and tim genes as well varying levels of insertion/deletion (indel) diversity (Table 2). 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