MosquI, a novel family of mosquito retrotransposons distantly related to the Drosophila I factors, may consist of elements of more than one origin

RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.

The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

BACKGROUND

The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito.

RESULTS

Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism.

CONCLUSIONS

Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster.

Molecular cloning and temporal-spatial expression of I element in gregarious and solitary locusts

It has been reported that many genes and small RNAs are associated with density-dependent polyphenism in locusts. However, the regulatory mechanism underlying gene transcription is still unknown. Here, by analysis of transcriptome database of the migratory locust, we identified abundant transcripts of transposable elements, which are mediators of genetic variation and gene transcriptional regulation, mainly including CR1, I, L2 and RTE-BovB. We cloned one I element, which represents the most abundant transcripts in all transposable elements, and investigated its developmental and tissue-specific expression in gregarious and solitary locusts. Although there are no significant differences of I element expression in whole bodies between gregarious and solitary locusts at various developmental stages, this I element exhibits high expression level and differential expression pattern between gregarious and solitary locusts in central and peripheral nervous tissues, such as brain, antenna and labial palps. These results suggest that I element is potentially involved in the response of neural systems to social environmental changes in locusts.

Embryonic desiccation resistance in Aedes aegypti: presumptive role of the chitinized serosal cuticle

Background

One of the major problems concerning dengue transmission is that embryos of its main vector, the mosquito Aedes aegypti, resist desiccation, surviving several months under dry conditions. The serosal cuticle (SC) contributes to mosquito egg desiccation resistance, but the kinetics of SC secretion during embryogenesis is unknown. It has been argued that mosquito SC contains chitin as one of its components, however conclusive evidence is still missing.

Results

We observed an abrupt acquisition of desiccation resistance during Ae. aegypti embryogenesis associated with serosal cuticle secretion, occurring at complete germ band extension, between 11 and 13 hours after egglaying. After SC formation embryos are viable on dry for at least several days. The presence of chitin as one of the SC constituents was confirmed through Calcofluor and WGA labeling and chitin quantitation. The Ae. aegypti Chitin Synthase A gene (AaCHS1) possesses two alternatively spliced variants, AaCHS1a and AaCHS1b, differentially expressed during Ae. aegypti embryonic development. It was verified that at the moment of serosal cuticle formation, AaCHS1a is the sole variant specifically expressed.

Conclusion

In addition to the peritrophic matrix and exoskeleton, these findings confirm chitin is also present in the mosquito serosal cuticle. They also point to the role of the chitinized SC in the desiccation resistance of Ae. aegypti eggs. AaCHS1a expression would be responsible for SC chitin synthesis. With this embryological approach we expect to shed new light regarding this important physiological process related to the Ae. aegypti life cycle.

Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors

The health of aquatic species is dependent on interactions between the environment, pathogens and the host. Under intensive shrimp aquaculture, environmental conditions can degrade, causing significant stress to the cultured organisms. To investigate the effect of environmental stress on shrimp hemocyte gene expression profiles, we applied suppression subtractive hybridization (SSH) in juvenile Penaeus monodon exposed to hyperthermal, hypoxic or hyposmotic conditions. Random sequencing of 258 clones from the SSH revealed 176 distinct sequences of which 58 shared high similarity to sequences in the public databases. The three most common groups of identifiable unique sequences in the SSH libraries were the POL region of non-LTR retrotransposons (31%), genes with immune or potential immune functions (30%), and genes involved in protein synthesis and processing (18%). Stress-regulated differential expression was further verified by quantitative qRT-PCR, with seven out of eight randomly selected genes showing qRT-PCR profiles that conformed to the patterns predicted by SSH. Hence this work provides a list of genes which appear to be up- or down-regulated in response to stress, providing a basis for studying the genetic response of shrimp to environmental stress.

Nimbus (BgI): an active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata

The freshwater snail Biomphalaria glabrata is closely associated with the transmission of human schistosomiasis. An ecologically sound method has been proposed to control schistosomiasis using genetically modified snails to displace endemic, susceptible ones. To assess the viability of this form of biological control, studies towards understanding the molecular makeup of the snail relative to the presence of endogenous mobile genetic elements are being undertaken since they can be exploited for genetic transformation studies. We previously cloned a 1.95kb BamHI fragment in B. glabrata (BGR2) with sequence similarity to the human long interspersed nuclear element (LINE or L1). A contiguous, full-length sequence corresponding to BGR2, hereafter-named nimbus (BgI), has been identified from a B. glabrata bacterial artificial chromosome (BAC) library. Sequence analysis of the 65,764bp BAC insert contained one full-length, complete nimbus (BgI) element (element I), two full-length elements (elements II and III) containing deletions and flanked by target site duplications and 10 truncated copies. The intact nimbus (BgI) contained two open-reading frames (ORFs 1 and 2) encoding the characteristic hallmark domains found in non-long terminal repeat retrotransposons belonging to the I-clade; a nucleic acid binding protein in ORF1 and an apurinic/apyrimidinic endonuclease, reverse transcriptase and RNase H in ORF2. Phylogenetic analysis revealed that nimbus (BgI) is closely related to Drosophila (I factor), mosquito Aedes aegypti (MosquI) and chordate ascidian Ciona intestinalis (CiI) retrotransposons. Nimbus (BgI) represents the first complete mobile element characterised from a mollusk that appears to be transcriptionally active and is widely distributed in snails of the neotropics and the Old World.

hAT element population genetics in Anopheles gambiae s.l. in Mozambique

Herves is a functional Class II transposable element in Anopheles gambiae belonging to the hAT superfamily of elements. Class II transposable elements are used as gene vectors in this species and are also being considered as genetic drive agents for spreading desirable genes through natural populations as part of an effort to control malaria transmission. In this study, Herves was investigated in populations of Anopheles gambiae s.s., Anopheles arabiensis and Anopheles merus in Mozambique over a period of 2 years. The copy number of Herves within these three species was approximately 5 copies per diploid genome and did not differ among species or between years. Based on the insertion-site occupancy-frequency distribution and existing models of transposable element dynamics, Herves appears to be transpositionally active currently or, at least recently, in all species tested. Ninety-five percent of the individuals within the populations of the three species tested contained intact elements with complete Herves transposase genes and this is consistent with the idea that these elements are currently active.

APE-type non-LTR retrotransposons: determinants involved in target site recognition

Non-long terminal repeat (Non-LTR) retrotransposons represent a diverse and widely distributed group of transposable elements and an almost ubiquitous component of eukaryotic genomes that has a major impact on evolution. Their copy number can range from a few to several million and they often make up a significant fraction of the genomes. The members of the dominating subtype of non-LTR retrotransposons code for an endonuclease with homology to apurinic/apyrimidinic endonucleases (APE), and are thus termed APE-type non-LTR retrotransposons. In the last decade both the number of identified non-LTR retrotransposons and our knowledge of biology and evolution of APE-type non-LTR retrotransposons has increased tremendously.

Transposable elements in mosquitoes

We describe the current state of knowledge about transposable elements (TEs) in different mosquito species. DNA-based elements (class II elements), non-LTR retrotransposons (class I elements), and MITEs (Miniature Inverted Repeat Transposable Elements) are found in the three genera, Anopheles, Aedes and Culex, whereas LTR retrotransposons (class I elements) are found only in Anopheles and Aedes. Mosquitoes were the first insects in which MITEs were reported; they have several LTR retrotransposons belonging to the Pao family, which is distinct from the Gypsy-Ty3 and Copia-Ty1 families. The number of TE copies shows huge variations between classes of TEs within a given species (from 1 to 1000), in sharp contrast to Drosophila, which shows only relatively minor differences in copy number between elements (from 1 to 100). The genomes of these insects therefore display major differences in the amount of TEs and therefore in their structure and global composition. We emphasize the need for more population genetic data about the activity of TEs, their distribution over chromosomes and their frequencies in natural populations of mosquitoes, to further the current attempts to develop a transgenic mosquito unable to transmit malaria that is intended to replace the natural populations.

Retroelements: tools for sex chromosome evolution

Many eukaryotic taxa inherit a heteromorphic sex chromosome pair. It is a generally accepted hypothesis that the sex chromosome pair is derived from a pair of homologous autosomes that has developed after the occurrence of a sex differentiator in an evolutionary process into two structurally and functionally different partners. In most of the analyzed systems the occurrence of the dominant sex differentiator is paralleled by the suppression of recombination within and close by that region. The recombinational isolation can spread in an evolutionary selection process from neighboring regions finally over the whole chromosome. Suppression of recombination strongly biases the distribution of retrotransposons in the genome. Our results and that from others indicate that the major force driving the evolution of Y chromosomes are retrotransposons, remodeling euchromatic chromosome structures into heterochromatic ones. In our model, intact or already eroded retrotransposons become trapped due to their inherent transposition mechanisms in non-recombining regions. The massive accumulation of retrotransposons interferes strongly with the activity of genes. We hypothesize that Y chromosome degeneration is a stepwise evolutionary process: (1) Massive accumulation of retrotransposons occurs in the non-recombining regions. (2) Heterochromatic nucleation centers are formed as a consequence of genomic defense against invasive parasitic elements; the established nucleation centers become epigenetically inherited. (3) Spreading of heterochromatin from the nucleation centers into flanking regions induces in an adaptive process gene silencing of neighbored genes that could either be still intact or in an already eroded condition, e.g., showing point mutations, deletions, insertions; the retroelements should be subjects to the same forces of deterioration as the genes themselves. (4) Constitutive silenced genes are not committed to the same genetic selection pressure as active genes and therefore more exposed to the decay process. (5) Gene dosage balance is reestablished by the parallel evolution of dosage compensation mechanisms. The evolving secondary sex chromosomes, neo-X and neo-Y, of Drosophila miranda are revealed to be a unique and potent model system to catch the evolutionary Y deterioration process in progress.

The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3' tandem repeats and the poly(dA) tail

A novel family of tRNA-related SINEs named gecko was discovered in the yellow fever mosquito, Aedes aegypti. Approximately 7200 copies of gecko were distributed in the A. aegypti genome with a significant bias toward A + T-rich regions. The 3' end of gecko is similar in sequence and identical in secondary structure to the 3' end of MosquI, a non-LTR retrotransposon in A. aegypti. Nine conserved substitutions and a deletion separate gecko into two groups. Group I includes all gecko that end with poly(dA) and a copy that ends with AGAT repeats. Group II comprises gecko elements that end with CCAA or CAAT repeats. Members within each group cannot be differentiated when the 3' repeats are excluded in phylogenetic and sequence analyses, suggesting that the alterations of 3' tails are recent. Imperfect poly(dA) tail was recorded in group I and partial replication of the 3' tandem repeats was frequently observed in group II. Genomic evidence underscores the importance of slippage retrotransposition in the alteration and expansion of the tandem repeat during the evolution of gecko sequences, although we do not rule out postinsertion mechanisms that were previously invoked to explain the evolution of Alu-associated microsatellites. We propose that the 3' tandem repeats and the poly(dA) tail may be generated by similar mechanisms during retrotransposition of both SINEs and non-LTR retrotransposons and thus the distinction between poly(dA) retrotransposons such as L1 and non-poly(dA) retrotransposons such as I factor may not be informative.

Mosquito transposable elements

The completion of the genome assembly for the African malaria mosquito, Anopheles gambiae, and continuing genomic efforts for the yellow fever mosquito, Aedes aegypti, have allowed the use of bioinformatics tools to identify and characterize a diverse array of transposable elements (TEs) in these and other mosquito genomes. An overview of the types and number of both RNA-mediated and DNA-mediated TEs that are found in mosquito genomes is presented. A number of novel and interesting TEs from these species are discussed in more detail. These findings have significant implications for our understanding of mosquito genome evolution and for future modifications of natural mosquito populations through the use of TE-mediated genetic transformation.

Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect

The adzuki bean beetle, Callosobruchus chinensis, is triple-infected with distinct lineages of Wolbachia endosymbiont, wBruCon, wBruOri, and wBruAus, which were identified by their wsp (Wolbachia surface protein) gene sequences. Whereas wBruCon and wBruOri caused cytoplasmic incompatibility of the host insect, wBruAus did not. Although wBruCon and wBruOri were easily eliminated by antibiotic treatments, wBruAus persisted over five treated generations and could not be eliminated. The inheritance pattern of wBruAus was, surprisingly, explained by sex-linked inheritance in male-heterozygotic organisms, which agreed with the karyotype of C. chinensis (2n = 20, XY). Quantitative PCR analysis demonstrated that females contain around twice as much wsp titer as males, which is concordant with an X chromosome linkage. Specific PCR and Southern blot analyses indicated that the wBruAus-bearing strain of C. chinensis contains only a fraction of the Wolbachia gene repertoire. Several genome fragments of wBruAus were isolated using an inverse PCR technique. The fragments exhibited a bacterial genome structure containing a number of ORFs typical of the alpha-proteobacteria, although some of the ORFs contained disruptive mutations. In the flanking region of ftsZ gene, a non-long terminal repeat (non-LTR) retrotransposon sequence, which is typical of insects but not found from bacteria, was present. These results strongly suggest that wBruAus has no microbial entity but is a genome fragment of Wolbachia endosymbiont transferred to the X chromosome of the host insect.

Intra- and inter-specific diversity of Tc3-like transposons in nematodes and insects and implications for their evolution and transposition

Tc3 of Caenorhabditis elegans is one of the founding members of the Tc1 family which includes DNA transposons in vertebrates, insects, nematodes and fungi. It is one of the best characterized eukaryotic transposons in terms of structure and transposition mechanism. A Tc3-like transposon MsqTc3 has been recently described in a mosquito. Here we present the characterization of a number of Tc3-like transposons in C. elegans, Caenorhabditis briggsae, and Drosophila melanogaster, which has revealed high levels of inter- and intra-specific diversity and further suggests a broad distribution of the Tc3-like transposons. These newly defined transposons and the previously described Tc3 and MsqTc3 form a highly divergent yet distinct clade in the Tc1 family. The above phylogenetic analysis of the Tc3-like transposons and their high levels of intra-specific diversity underscore interesting questions of their evolutionary dynamics in their respective hosts. The majority of the Tc3-like transposons contain two putative binding sites for their transposases. The first is near the terminus and the second is approximately 164-184 bp from the first site. Comparative analysis suggests that the second binding site may have been maintained for an important function in vivo. There is a large amount of variation in the length (27-566 bp) and structure of the terminal inverted repeats (TIRs) of Tc3-like transposons. Long (318-566 bp) TIRs that extend significantly beyond the second binding site are only found in the first described Tc3 and its close relatives, whose transposases form a recently derived clade among the Tc3-like transposons. Thus, these unique TIRs may have evolved recently together with their corresponding transposases.

Expanding the diversity of the IS630-Tc1-mariner superfamily: discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons

A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

Maque, a family of extremely short interspersed repetitive elements: characterization, possible mechanism of transposition, and evolutionary implications

Database analysis revealed a novel family of very short interspersed repetitive elements named Maque in the African malaria mosquito, Anopheles gambiae. Past mobility of Maque was demonstrated by evidence of its insertion that resulted in a target duplication. Approximately 220 copies of Maque were present in the A. gambiae genome. Although only approximately 60 bp long, Maque has the appearance of a distinct transposition unit. Eleven of the 12 Maque elements found in the database were flanked by 9-14 bp direct repeats, indicating that their transposition was relatively recent. Sequence comparison and phylogenetic analyses suggest that there are at least two subgroups within the Maque family, suggesting that they may have been originated from more than one source. Five of the 12 Maque elements had at least one other repetitive element nearby. Three of the Maque elements were found near genes. However, Maque was not found in the coding regions of genes or in any of the expressed sequence tags (ESTs), which is consistent with its significantly biased distribution toward A + T rich regions. Several characteristics of Maque indicate that it is likely a non-autonomous retro-element. The evolutionary origin of Maque and the differences between Maque and other known retro-elements including short interspersed repetitive elements (SINEs) are discussed. A hypothesis is proposed in which short sequences containing just the reverse transcriptase recognition signal (RTRS) could potentially contribute to exon shuffling and the genesis of some primordial SINEs.

Genetic and physical mapping in mosquitoes: molecular approaches

The genetic background of individual mosquito species and populations within those species influences the transmission of mosquito-borne pathogens to humans. Technical advances in contemporary genomics are contributing significantly to the detailed genetic analysis of this mosquito-pathogen interaction as well as all other aspects of mosquito biology, ecology, and evolution. A variety of DNA-based marker types are being used to develop genetic maps for a number of mosquito species. Complex phenotypic traits such as vector competence are being dissected into their discrete genetic components, with the intention of eventually using this information to develop new methods to prevent disease transmission. Both genetic- and physical-mapping techniques are being used to define and compare genome architecture among and within mosquito species. The integration of genetic- and physical-map information is providing a sound framework for map-based positional cloning of target genes of interest. This review focuses on advances in genome-based analysis and their specific applications to mosquitoes.

Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti

A novel family of miniature inverted repeat transposable elements (MITEs) named Pony was discovered in the yellow fever mosquito, Aedes aegypti. It has all the characteristics of MITEs, including terminal inverted repeats, no coding potential, A+T richness, small size, and the potential to form stable secondary structures. Past mobility of PONY: was indicated by the identification of two Pony insertions which resulted in the duplication of the TA dinucleotide targets. Two highly divergent subfamilies, A and B, were identified in A. aegypti based on sequence comparison and phylogenetic analysis of 38 elements. These subfamilies showed less than 62% sequence similarity. However, within each subfamily, most elements were highly conserved, and multiple subgroups could be identified, indicating recent amplifications from different source genes. Different scenarios are presented to explain the evolutionary history of these subfamilies. Both subfamilies share conserved terminal inverted repeats similar to those of the Tc2 DNA transposons in Caenorhabditis elegans, indicating that Pony may have been borrowing the transposition machinery from a Tc2-like transposon in mosquitoes. In addition to the terminal inverted repeats, full-length and partial subterminal repeats of a sequence motif TTGATTCAWATTCCGRACA represent the majority of the conservation between the two subfamilies, indicating that they may be important structural and/or functional components of the Pony elements. In contrast to known autonomous DNA transposons, both subfamilies of PONY: are highly reiterated in the A. aegypti genome (8,400 and 9, 900 copies, respectively). Together, they constitute approximately 1. 1% of the entire genome. Pony elements were frequently found near other transposable elements or in the noncoding regions of genes. The relative abundance of MITEs varies in eukaryotic genomes, which may have in part contributed to the different organizations of the genomes and reflect different types of interactions between the hosts and these widespread transposable elements.

Structure and location of a ferritin gene of the yellow fever mosquito Aedes aegypti

We have isolated and sequenced a genomic clone encoding the 24- and 26-kDa ferritin subunits in the mosquito Aedes aegypti (Rockefeller strain). The A. aegypti gene differs from other known ferritin genes in that it possesses an additional intron and an unusually large second intron. The additional intron is located within the 5' untranslated region, between the CAP site and the start codon. The second intron contains numerous putative transposable elements. In addition, unlike the human and rat ferritin genes, the A. aegypti ferritin gene is a single copy gene, located at 88.3% FLpter on the q-arm of chromosome 1. Primer extension analysis indicates that the A. aegypti ferritin gene has multiple transcriptional start sites. A differential usage of these sites is observed with varied cellular iron concentrations.