Evolutionary analysis of the kinesin light chain genes in the yellow fever mosquito Aedes aegypti: gene duplication as a source for novel early zygotic genes
© Biedler and Tu; licensee BioMed Central Ltd. 2010
Received: 22 February 2010
Accepted: 8 July 2010
Published: 8 July 2010
The maternal zygotic transition marks the time at which transcription from the zygotic genome is initiated and a subset of maternal RNAs are progressively degraded in the developing embryo. A number of early zygotic genes have been identified in Drosophila melanogaster and comparisons to sequenced mosquito genomes suggest that some of these early zygotic genes such as bottleneck are fast-evolving or subject to turnover in dipteran insects. One objective of this study is to identify early zygotic genes from the yellow fever mosquito Aedes aegypti to study their evolution. We are also interested in obtaining early zygotic promoters that will direct transgene expression in the early embryo as part of a Medea gene drive system.
Two novel early zygotic kinesin light chain genes we call AaKLC2.1 and AaKLC2.2 were identified by transcriptome sequencing of Aedes aegypti embryos at various time points. These two genes have 98% nucleotide and amino acid identity in their coding regions and show transcription confined to the early zygotic stage according to gene-specific RT-PCR analysis. These AaKLC2 genes have a paralogous gene (AaKLC1) in Ae. aegypti. Phylogenetic inference shows that an ortholog to the AaKLC2 genes is only found in the sequenced genome of Culex quinquefasciatus. In contrast, AaKLC1 gene orthologs are found in all three sequenced mosquito species including Anopheles gambiae. There is only one KLC gene in D. melanogaster and other sequenced holometabolous insects that appears to be similar to AaKLC1. Unlike AaKLC2, AaKLC1 is expressed in all life stages and tissues tested, which is consistent with the expression pattern of the An. gambiae and D. melanogaster KLC genes. Phylogenetic inference also suggests that AaKLC2 genes and their likely C. quinquefasciatus ortholog are fast-evolving genes relative to the highly conserved AaKLC1-like paralogs. Embryonic injection of a luciferase reporter under the control of a 1 kb fragment upstream of the AaKLC2.1 start codon shows promoter activity at least as early as 3 hours in the developing Ae. aegypti embryo. The AaKLC2.1 promoter activity reached ~1600 fold over the negative control at 5 hr after egg deposition.
Transcriptome profiling by use of high throughput sequencing technologies has proven to be a valuable method for the identification and discovery of early and transient zygotic genes. The evolutionary investigation of the KLC gene family reveals that duplication is a source for the evolution of new genes that play a role in the dynamic process of early embryonic development. AaKLC2.1 may provide a promoter for early zygotic-specific transgene expression, which is a key component of the Medea gene drive system.
The early embryo is transcriptionally inactive and all RNAs present that are needed for embryonic development have been maternally deposited during oogenesis. The onset of zygotic transcription marks the beginning of the maternal-zygotic transition (MZT) whereby maternal RNAs are progressively degraded and zygotic transcription takes over, providing the necessary gene products for development [1–4]. Recent large-scale studies have tried to determine what genes or groups of genes are expressed during Drosophila development [1, 2]. At least some of the early zygotic genes such as bottleneck  are fast-evolving or subject to turnover in dipteran insects because a homolog of the Drosophila bottleneck is not found in any of the sequenced mosquito genomes. To study the evolution of early zygotic genes through comparative analysis, we set out to identify early zygotic genes in the yellow fever mosquito Aedes aegypti by transcriptome profiling, taking advantage of large-scale Illumina sequencing. We have determined the MZT starting in Ae. aegypti within 2-3 hr after egg deposition, based on Illumina transcriptome profiling and RT-PCR. This time is just before or at the beginning of pole cell formation at 3 hr . Early zygotic transcription at this time is developmentally consistent with reports from Drosophila that indicate transcription starting as early as cycle 8 , also just before the onset of pole cell formation. We focused on the purely zygotic genes that do not have a maternal contribution. Thus, we were searching for transcripts that were not present in the embryos 0-2 hr after egg deposition but started to appear 2-4 hr after egg deposition.
One of the early and pure zygotic genes identified was a kinesin light chain (KLC) gene that is the focus of this study. The three classes of cytoskeleton molecular motors include kinesin, dynein, and myosin, with kinesin and dynein using microtubules as a track for transport and myosin depending on actin filaments . Kinesins are a diverse family of proteins as demonstrated by phylogenies based on the heavy chain [9, 10] and are involved in a variety of cellular transport roles . The conventional kinesin (kinesin-I) is a heterotetramer having two kinesin heavy chains characterized by ATPase-dependent motor activity and two kinesin light chains (KLCs). KLCs are accessory proteins that have a C-terminal tetratricopeptide repeat (TPR) domain comprising approximately 34 residues that binds cargo for transport . Here we report the discovery of two novel embryonic-specific KLC genes we call AaKLC2 in Aedes aegypti (Ae. aegypti) and their likely ortholog in C. quinquefasciatus. We analyze these genes in comparison to other KLC genes in diverse organisms and suggest gene duplication as a source for the purely zygotic AaKLC2 genes, which are fast-evolving.
Another goal of this research was related to efforts to develop a gene drive system for mosquitoes, which may be used to spread pathogen-resistant genes into mosquito populations to control mosquito-borne infectious disease. A natural gene drive system comprised of maternal effect dominant embryonic arrest (Medea) factors was first discovered in the flour beetle T. castaneum . In this system, Medea is comprised of a maternally expressed toxin that is passed on to all embryos of a Medea-bearing female, and a tightly linked zygotically expressed antidote that is only made in Medea-bearing embryos. As a result, only Medea-bearing offspring of a Medea-bearing female will survive, which leads to the fixation of the Medea allele in the population. Chen et al. 2007 successfully engineered and demonstrated a Medea system in D. melanogaster that employs the use of maternal-specific and zygotic-specific promoters to drive expression of toxin and antidote genes, respectively . Developing a Medea system in mosquitoes requires the identification of early zygotic genes in the mosquito species of interest due to the difficulty of finding orthologs to D. melanogaster zygotic genes as mentioned above. We identified the zygotic-specific AaKLC2.1 and demonstrated strong promoter activity of its upstream sequence in Ae. aegypti early embryos.
Identification of two early zygotic kinesin light chain genes AaKLC2.1 and AaKLC2.2
Kinesin Light Chain Gene Transcription Profile By Illumina Sequencing
Structural and genomic analysis of AaKLC2 and other KLC genes
Unlike the AaKLC2-like genes, AaKLC1-like genes have longer ORFs and at least one intron (Figure 1, right column). Interestingly, these AaKLC1-like genes have conservation of intron position in some cases. For example, 4 introns have conserved positions between Ae. aegypti and An. gambiae, and one intron position is conserved in Ae. aegypti, An. gambiae, and D. melanogaster. In addition, one intron position and length is conserved between Ae. aegypti and D. melanogaster.
Phylogenetic inference of KLC genes demonstrates a diverse evolutionary history
Published kinesin phylogenies have focused on the kinesin heavy chain. Here we present a KLC phylogeny including representatives from mosquito, fly, wasp, honeybee, worm, fish, frog, sea urchin, squid, monkey, cow, chicken, mouse, rat, human, and bacteria (Figure 2). Like kinesin heavy chain phylogeny, KLC phylogeny is also rather diverse having many paralogous groups, with most of the diversity existing in mammals. For example, humans have 4 paralogous KLC genes. In contrast, the holometabolous insects surveyed have 1 KLC gene in common that includes AaKLC1 in Ae. aegypti. The AaKLC2 genes that are zygotic-specific (see below) and their likely ortholog in C. quinquefasciatus appear to be restricted to species of Culicinae because similar sequences could not be detected in the genome sequences of the mosquito An. gambiae or other insects. Interestingly, the AaKLC2 genes and the C. quinquefasciatus AaKLC2-like gene are fast-evolving genes relative to the highly conserved AaKLC1-like genes. Shown are the only KLC genes detected in insects resulting from BLAST searches using divergent KLC genes from the phylogeny as queries.
The phylogeny indicates that the AaKLC2-like genes arose prior to the divergence of Ae. aegypti and An. gambiae lineages, suggesting an event that predates the divergence of Culicinae and Anophelinae. This is perplexing because AaKLC2-like genes are not detected in Anopheline mosquitoes An. gambiae and An. stephensi, which suggests that AaKLC2-like genes arose within Culicinae after Culicinae/Anophelinae divergence and prior to the divergence of Aedes and Culex genera. Also curious is that Ae. aegypti AAEL11410 and C. quinquefasciatus CPIJ002971 KLC aa sequences do not obtain each other as reciprocal best hits by blastp. However, the structural and phylogenetic inference supports their grouping (the clade credibility value is 0.99 for the node at the divergence of KLC1-like and KLC2-like clades). Genomic survey of more species will be needed to elucidate this matter.
Expression analysis indicates that AaKLC2 genes are transiently expressed in the early zygotic stage while AaKLC1 is ubiquitously expressed
Evidence for Expression of Kinesin Light Chain Genes
all life stages1
various developmental stages2
various developmental stages3
Early zygotic promoter activity of AaKLC2.1 upstream sequence in Ae. aegypti embryos
A novel set of purely zygotic genes: duplications, fast evolution, and possible function
AaKLC2-like genes are only found in Culicinae mosquitoes Ae. aegypti and C. quinquefasciatus. However the AaKLC1-like genes are found in all surveyed holometabolous insects and are quite conserved in their structure and expression profiles. Thus it is likely that AaKLC2 genes are the paralogs that took on a new expression profile and possibly a new function in Culicinae. It is also interesting that in addition to the duplication that gave rise to the AaKLC2 gene lineage, there has been another duplication resulting in AaKLC2.1 and AaKLC2.2.
The AaKLC2-like genes appear to be fast-evolving genes according to their branch length (Figure 2). For example, AaKLC2.1 and the C. quinquefasciatus AaKLC2-like gene (CPIJ002971) have 44% aa identity, while AaKLC1 and the C. quinquefasciatus AaKLC1-like gene (CPIJ015771) have 94% aa identity. A curious question is whether AaKLC2-like genes have been under positive selection. However, we were unable to perform nonsynonymous/synonymous (dN/dS) analysis due to the divergence of the AaKLC2 and the C. quinquefasciatus CPIJ002971.
The presence of at least one highly conserved KLC gene (e.g. AaKLC1-like) in all of insects is not surprising given its indispensable role in intracellular transport, but it is interesting why a novel zygotic-specific KLC arose in Culicinae. The genome sizes of Ae. aegypti and C. quinquefasciatus are approximately three and two times larger than An. gambiae  possibly providing more evolutionary freedom for gene expansion early in Culicinae. A large proportion of Drosophila early and transient zygotic genes were found to be involved in neurogenesis and dorso-ventral patterning . Also noteworthy is that a KLC gene has been implicated in translocation of dorsal determinants in Xenopus . Although we do not have experimental evidence of AaKLC2 function in the embryo, it seems plausible that these genes may play a similar role in early embryonic development, given their early and transient zygotic-specific expression profile. Specialization of KLC genes is a recurrent event in evolution. In rat and mouse it was found that KLC3 is restricted to spermatid tails while KLC1 and KLC2 are only found in testis before meiosis . A rat KLC isoform was found to associate with mitochondria in cultured cells . In mouse it was also found that two KLCs were present in the central and peripheral nervous system, but one is enriched in sciatic nerve exons and the other is enriched in the olfactory bulb glomeruli . These examples of KLC specialization are from mammals and are consistent with the KLC diversity in mammals demonstrated in Figure 2. Therefore, the fact that we can only find one conserved KLC gene in holometabolous insects (AaKLC1) underscores the generation of AaKLC2 genes as an interesting evolutionary event, demonstrating the potential for KLC specialization in this taxonomic group.
Potential applications of an early zygotic promoter in the context of the Medea gene drive system
We demonstrated that the promoter region of the two AaKLC2 genes can direct early zygotic transcription in the Ae. aegypti embryo. Thus this promoter may be useful to direct the expression of the antidote gene as part of the Medea gene drive system [12, 13]. The AaKLC2 genes are expressed specifically, transiently, and early in the embryonic stage, which makes them good candidates to drive the antidote expression. The antidote needs to be delivered at the appropriate time for embryonic rescue, providing the replacement of mRNA that was targeted by the maternal toxin. In addition, lack of antidote expression in the ovary will eliminate antagonist effects to the toxin. Lastly, purely zygotic expression will eliminate concerns of ectopic expression that could reduce fitness and thus reduce gene drive efficiency.
We have discovered a novel set of KLC genes in Ae. aegypti that we call AaKLC2.1 and AaKLC2.2, and have demonstrated that they are purely zygotic. These are the first reported in any mosquito species and they have a newly evolved expression pattern relative to the AaKLC1 genes. We have also identified a likely AaKlC2 gene ortholog in C. quinquefasciatus. Its similar structure and lack of representation in ESTs suggests that it is also a zygotic gene. AaKLC2-like genes appear to be restricted to Culicinae, as they are not detected in An. gambiae or An. stephensi, or other genome sequences. Genomic survey of more species and additional expression analyses will be needed to test these hypotheses. Data from ESTs and hybridization experiments in addition to our transcriptome and expression analysis by RT-PCR support the existence of two distinct KLC gene groups, the zygotic AaKLC2-like genes, and the highly conserved AaKLC1-like genes that are found in all mosquitoes and insects surveyed. We also demonstrated strong promoter activity of the AaKLC2 gene upstream sequence in Ae. aegypti early embryos. Large-scale transcriptome profiling has proven to be a valuable method for the identification of early and transient zygotic-specific genes. These technologies have allowed us to rapidly achieve results for a specific objective. Moreover, as we are currently acquiring and analyzing more transcriptome data, we will be able to investigate the complex and dynamic expression of genes in the early embryo and conduct comparative evolutionary studies with other mosquito species and Drosophila.
Total RNA was isolated using TRIZOL RNA isolation reagent (Molecular Research Center) from Ae. aegypti Liverpool strain embryos at time points 0-2, 2-4, 4-8, and 8-12 hr. RNA was sent to Illumina (illumina.com) for poly-A RNA transcriptome sequencing. Approximately 4.4-6.1 million mappable reads of 33 nt in length were obtained per sample (Additional File 1). Annotated transcripts were used as queries for blastn searches against the Illumina transcriptome sequence reads in different samples, to count the number of sequence reads per annotated transcript per sample. E-value of 1e-7 was used as cutoff for the BLAST analysis. Normalization method is described in the footnotes of Table 1. See Additional File 1 for a tabulated summary of the Illumina RNA sequence data and Additional File 2 for a FASTA file of the Illumina reads that matched the three KLC transcripts AAEL011410, AAEL014967, and AAEL012472.
Mosquito rearing and embryo collection
Ae. aegypti Liverpool strain mosquitoes were reared in incubators at 28°C and 60% relative humidity on a 16 hr light/8 hr dark photoperiod. Larvae and pupae were fed Sera Micron Fry Food with brewer's yeast, and Purina Game Fish Chow. Mosquitoes were blood-fed on female Hsd:ICR (CD-1®) mice (Harlan Laboratories http://www.harlan.com). Embryos were collected anywhere from 72 to 96 hr post blood meal.
Phylogenetic Inference was performed using MrBayes v3.1.2 . A total of forty-one conceptually translated amino acid (aa) sequences were obtained from NCBI. Sequences were aligned using ClustalX v2.0  (pairwise alignment parameters: gap opening = 10.0, gap extend = 0.1; multiple alignment parameters: gap opening = 10.0, gap extend = 0.2). The final alignment of approximately 400 aa used for phylogenetic inference was cropped to include obvious regions of conservation and contained the predicted TPR and Rab5-binding domains (see Additional File 3 for aa sequences and Additional File 4 for alignment in FASTA format). MrBayes was used to test 10 fixed-rate aa models, choosing the Jones model exclusively (posterior probability = 1.0) after running 700,000 generations. The tree is rooted using KLC sequences from two prokaryotic species.
RNA isolation and RT-PCR
Total RNA was isolated for different life stages and ovaries from Ae. aegypti Liverpool strain mosquitoes using the TRIZOL RNA isolation reagent (Molecular Research Center). RNA was treated with Turbo DNA-free (Ambion) to remove any residual genomic DNA. 1 ug total RNA was used for cDNA synthesis with the First Strand cDNA Synthesis Kit and Oligo dT20 (Invitrogen). The final 21 microliter (ul) reaction volume was diluted by adding 21 ul of nuclease-free H20. One ul of this was used for 30 cycles of PCR with Taq Polymerase, dNTPs, and 10× buffer (Takara). Genomic and transcript sequences from the Ae. aegypti genome  were retrieved from http://aaegypti.vectorbase.org/index.php and http://www.ensembl.org/index.html. A 467 base region of AaKLC2.1 (transcript ID: AAEL011410-RA) cDNA was amplified using forward primer 5'-CTACCAGAAGCCATCAAACAT-3' Tm = 60.5°C, and reverse primer 5'- GATTCACTGTCACCATTCTGTGT-3' Tm = 62.8°C. A 464 base region of AaKLC2.2 (transcript ID: AAEL011410-RA) cDNA was amplified using forward primer 5'- CCCGAAGCCATTAAACAC-3' Tm = 60.5°C and reverse primer 5'- TGATTCACTGTCACCATTCTGTAC-3' Tm = 62.7°C. Both of these PCR products were cloned and sequenced to verify the primer's specificity for each transcript. A 550 base region of AaKLC1 (transcript ID: AAEL012472-RA) cDNA spanning 3 introns was amplified using forward primer 5'- ACTATGTTGAACATCCTGGCTTTAG-3' Tm = 63.1°C, and reverse primer 5'- TCGATTTGTTCTCTTCTCTTTCTTC-3' Tm = 62.8°C. The expected genomic product size is 28.8 kb. As a control for cDNA synthesis and for gel loading, a 562 base region of the ribosomal protein S7 (RPS7) cDNA was amplified using forward primer 5'-ATGGTTTTCGGATCAAAGG-3' Tm = 61.3°C, and reverse primer 5'-GGAATTCGAACGTAACGTCAC-3' Tm = 63.2°C. The expected genomic size is 5.5 kb. Negative control reactions without the use of reverse transcriptase were performed to test for genomic DNA contamination.
Embryonic injection and luciferase assay
Ae. aegypti Liverpool strain embryos were injected with pGL3-basic firefly luciferase reporter plasmid (Promega) containing 1042 bp of the 5' UTR and upstream genomic sequence of the AaKLC2.1 early transient zygotic gene (gene ID: AAEL011410). For each injection group, an average of 45 embryos were injected at approximately 1 hr after deposition with 0.30 ug/ul of plasmid either with or without (negative control) insert. A Renilla luciferase reporter pRL-null (Promega) with the D. melanogaster actin promoter was used as an injection control at 0.15 ug/ul. 1× Injection Buffer used was 5 mM KCl 0.1 mM NaH2PO4 pH 7.2, sterile filtered. Embryos were homogenized in Cell Culture Lysis Buffer at 3 hr and 5 hr after deposition and assayed for luciferase activity using the Luciferase Assay System (Promega) and a Glomax 20/20 luminometer (Promega). Samples were read for 10 seconds. Injection needles were pulled from World Precision Instruments Kwik-Fil Borosilicate Glass Capillaries (item # 1B100F-4) on a Sutter Instrument P-2000 Micropipette Puller at the following settings: Heat = 270, Fil = 3, Vel = 37, Del = 250, Pul = 134. Injections were performed using an Eppendorf FemtoJet allowing injection solution to free-flow through the needle with the compensation pressure (Pc) set at ~3750 hPa. Injection Pressure setting (Pi) not used. The needle is held in a World Precision Instruments Micromanipulator (model M3301L) http://www.wpiinc.com. Microscope used was a Leica CM E.
JB is a Research Scientist at Virginia Polytechnic Institute and State University
ZT is a Professor at Virginia Polytechnic Institute and State University
We thank Randy Saunders for help with embryo injections for the luciferase assay and Dr. Chunhong Mao for bioinformatics help. This work was supported by FNIH grant GC7 #316, and the Virginia Experimental Station.
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