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This paper analyzes the nucleotide sequences of three viruses: Kunjin, west Nile, and yellow fever. Each virus has one long open reading frame of greater than 10,200 nucleotides that codes for four structural and seven nonstructural genes. The Kunjin and west Nile viruses are the most closely related pair, when assessed on the basis of matches between their nucleotide sequences. As would be expected, the matching is least for bases at third-position codon sites and is greatest for second-position sites. Statistics are presented for the numbers of mismatches that are transitions or transversions. Nucleotide base usage is also reported. To each of the 33 virus-gene segments, nonhomogeneous Markov chain models have been fitted to describe the sequences of nucleotide bases. The models allow for different transition probabilities ("transition" is used in the mathematical sense here) and for different degrees of dependency, at the three sites in the codons. Reasonably satisfactory fits can be obtained for many of the genes by using models that are first order for both first- and second-position sites in the codon but that are second order for third-position sites. One consequence of such a model is that the correlation between one amino acid and the next is limited to the correlation of the last base of the former with the first base of the latter. Other consequences are that the model can (and does) prohibit the occurrence of stop codons within a gene and that subsequences of only first-position bases, or only third-position bases, are also first-order Markov chains. In theory, second-position subsequences may not be Markov chains at all. In practice, the data suggest that each of these subsequences is effectively a zero-order Markov chain, i.e., bases spaced three apart are statistically independent. Stationarity of nucleotide base distributions can be interpreted in either of two ways: (1) spatially along the sites or (2) temporally at each site. These interpretations must often be inconsistent, when the former allows for Markov dependence between adjacent sites whereas the latter assumes independence between sites. The inconsistency can be overcome, for these viruses, if subsequences at different codon positions are analyzed separately.
Mol Biol Evol 1992 Jul
PMID:A stochastic analysis of three viral sequences. 132 21

The amount of glutathione S-transferase-2 (GST-2) protein and enzyme activity in a mutant strain (strain GG) of the yellow fever mosquito (Aedes aegypti) is approximately 25-fold higher than in the wild-type (++) strain. The mode of inheritance of the GG phenotype was studied in F1 and backcross progeny using GST enzyme assays, isozyme-specific antisera, and Northern blot analysis. Enzyme assay of parental and F1 progeny showed that the ++ phenotype was dominant to the GG phenotype. This was true for larvae as well as for all tissues examined in adults in both sexes. Immunoblotting experiments showed that, like the ++ strain, F1 larvae and adults express very low levels of GST-2 protein compared with the GG strain. Northern blotting experiments showed that the steady-state levels of GST-2 mRNA in parental and F1 hybrid larvae closely matched the enzyme activity and immunological data. These results suggest the existence of a trans-acting regulatory locus that acts to repress GST-2 mRNA transcription and/or decrease GST-2 mRNA stability in ++ and F1 hybrids. GST enzyme activity in backcross progeny, however, did not segregate into the two distinct phenotypes (low and high) predicted for a single locus, dominant allele model. Backcross progeny expressed a wide range of GST activity and GST-2 protein amount with no apparent fit to simple Mendelian ratios. These backcross data suggest that additional loci are also involved in regulating GST-2 isozyme expression.(ABSTRACT TRUNCATED AT 250 WORDS)
Mol Gen Genet 1992 Aug
PMID:Genetic and molecular evidence for a trans-acting regulatory locus controlling glutathione S-transferase-2 expression in Aedes aegypti. 150 45

We have isolated a cDNA clone after reverse transcription of the genomic RNA of Asibi yellow fever virus whose structure suggests it was formed by self-priming from a 3'-terminal hairpin of 87 nucleotides in the genomic RNA. We have also isolated a clone from cDNA made to Murray Valley encephalitis virus RNA that also appears to have arisen by self-priming from a 3'-terminal structure very similar or identical to that of yellow fever. In addition, 3'-terminal sequencing of the S1 strain of dengue 2 RNA shows that this RNA is also capable of forming a 3'-terminal hairpin of 79 nucleotides. Furthermore, we have identified two 20-nucleotide sequence elements which are present in the 3' untranslated region of all three viruses; one of these sequence elements is repeated in Murray Valley encephalitis and dengue 2 RNA but not in yellow fever RNA. In all three viruses, which represent the three major serological subgroups of the mosquito-borne flaviviruses, the 3'-proximal conserved sequence element, which is found immediately adjacent to the potential 3'-terminal hairpin, is complementary to another conserved domain near the 5' end of the viral RNAs, suggesting that flavivirus RNAs can cyclize (calculated delta G less than -11 kcal; 1 kcal = 4.184 kJ).
J Mol Biol 1987 Nov 05
PMID:Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences. 282 33

An in situ hybridization technique was developed for the strand-specific detection of yellow fever virus (YFV) RNA. An 35S-labeled, transcribed RNA probe was used to detect positive-sense polarity YFV genomic RNA in infected C6/36 (Aedes albopictus) cells, dissected mosquito tissues, and sections of plastic-embedded, YFV-infected Aedes aegypti mosquitoes. Mosquito tissues fixed in buffered Formalin retained morphological integrity. The low concentrations of probe used yielded high specific signal on infected specimens and low background signal on uninfected specimens.
Mol Cell Probes 1988 Dec
PMID:Detection of yellow fever virus nucleic acid in infected mosquitoes by RNA:RNA in situ hybridization. 290 76

The sequence of 5400 bases corresponding to the 5'-terminal half of the Murray Valley encephalitis virus genome has been determined. The genome contains a 5' non-coding region of about 97 nucleotides, followed by a single continuous open reading frame that encodes the structural proteins followed by the non-structural proteins. Amino acid sequence homology between the Murray Valley encephalitis and yellow fever (Rice et al., 1985) polyproteins is 42% over the region sequenced. The start points of the various Murray Valley encephalitis virus-coded proteins have been assigned on the basis of this homology and a consistent set of potential proteolytic cleavage sites identified, the sequences of which are similar in Murray Valley encephalitis and yellow fever. The deduced Murray Valley encephalitis gene order is 5'-C-prM (M)-E-NS1-ns2a-ns2b-NS3-3'. The genome organization of Murray Valley encephalitis and yellow fever appears to be identical and the sizes of the predicted virus-coded proteins similar between the two viruses. Both viruses encode a basic capsid protein followed by three glycoproteins; the glycoproteins appear to have the conventional topology of N terminus outside with a C-terminal membrane-spanning domain. There are conserved glycosylation sites in prM, the precursor to the M protein of the virion, and in NS1, a non-structural protein of uncertain function. The glycosylation sites in E, the major envelope protein of the virion, are not conserved as to position. We predict the existence, in flavivirus-infected cells, of two small, hydrophobic peptides, ns2a and ns2b, which show only limited amino acid sequence homology. Finally, about half of the amino acid sequence of NS3 has been obtained; NS3 is a hydrophilic non-structural protein that shows 55% amino acid sequence similarity between Murray Valley encephalitis and yellow fever over the region sequenced and is probably involved in RNA replication.
J Mol Biol 1986 Feb 05
PMID:Partial nucleotide sequence of the Murray Valley encephalitis virus genome. Comparison of the encoded polypeptides with yellow fever virus structural and non-structural proteins. 300 29

We are interested in cloning insecticide resistance genes from vector mosquitos for use as selectable markers in their genetic transformation. As a first step towards this goal, we here report the functional homomultimeric expression of a gamma-aminobutyric acid (GABA) receptor subunit gene, Resistance to dieldrin (Rdl), from the yellow fever mosquito Aedes aegypti in baculovirus-infected insect cell lines. Replacement of alanine296 with a serine leads to approximately 100-fold insensitivity to picrotoxin as previously observed in Drosophila. This shows not only that the mosquito GABA receptor cDNA is functional but also that it can be simply mutated to resistance. Strategies for incorporation of this cDNA into a minigene for the genetic transformation of mosquitoes are discussed.
Insect Mol Biol 1994 Nov
PMID:Functional expression of insecticide-resistant GABA receptors from the mosquito Aedes aegypti. 770 14

Codon usage was compiled for fourteen chromosomal genes and four retrotransposons from the mosquito Anopheles gambiae. Variation exists among chromosomal genes in the degree of bias. The genes showing the highest bias are probably most highly expressed. In these genes, the base composition at the third codon position is much richer in G + C than is the overall coding sequence. Thus, codon usage is biased toward G- or C-ending codons. Codon usage in each retrotransposon is quite different, not only from chromosomal genes but also from the other retrotransposons. Codon usage comparisons among homologous genes from An. gambiae and two other Dipterans, the yellow fever mosquito Aedes aegypti and the fruitfly Drosophila melanogaster, show that while there are similarities, particularly between An. gambiae and D. melanogaster in the preference for G- and C-ending codons, each species has evolved a distinct pattern of codon usage.
Insect Mol Biol 1993
PMID:Codon usage patterns in chromosomal and retrotransposon genes of the mosquito Anopheles gambiae. 826 95

Pyruvate carboxylase (PC, pyruvate: carbon dioxide ligase [ADP-forming], EC 6.4.1.1) was purified from the yellow fever mosquito, Aedes aegypti. The purified PC showed two polypeptides of similar M(r) (133 and 128 k). The N-terminal sequences of both polypeptides were shown to be very similar, if not identical. A polyclonal antiserum against the 133 kDa polypeptide cross-reacted strongly with the 128 kDa polypeptide. PC was found in all tissues examined. Using a semi-quantitative Western blot assay, PC was shown to be concentrated in the indirect flight muscles and fat body preparations. The ratios of the 133 to 128 kDa polypeptides were shown to differ in various tissues and an Aedes albopictus cell line. The indirect flight muscle was the only tissue in which the 128 kDa polypeptide was more abundant, while both the midgut and the cell line showed almost exclusively the 133 kDa polypeptide. Both peptides were present in varying amounts in brain, malpighian tubule, ovary and fat body preparation. The two isoforms of PC could play different roles in the flight muscle and other tissues. Clones covering a complete cDNA of PC of A. aegypti were obtained using a directional approach. The 3952 bp nucleotide sequence, including a 3585 bp coding region, was determined from these cDNA clones. The deduced 1195 amino acid sequence has a calculated M(r) of 132,200. A putative mitochondrial targeting sequence was determined by comparing the deduced amino acid sequence to the N-terminal sequences of the mature protein. The presence of a mitochondrial targeting sequence indicates that the mosquito PC encoded by the cloned cDNA may be localized in the mitochondria. After the targeting sequence, three functional domains were identified in the following order; biotin carboxylase (BC), carboxyltransferase (CT) and biotin carboxyl carrier protein (BCCP). The mosquito PC showed very high similarity to PCs from other sources (55.1-75.2% identity). Genomic Southern analysis indicated that there could be two similar PC genes or a single PC gene with allelic polymorphism in the A. aegypti genome. The evolutionary relationship of PCs among different organisms was consistent with the accepted evolutionary relationship of their host organisms. The evolution of the domain structures of the biotin-dependent carboxylases including PC was also investigated. This analysis indicates that biotin-dependent carboxylases evolved from a common origin. The analysis also provides evidence for early gene duplication events that shaped the family of biotin-dependent carboxylases. Clear evidence for the coevolution of BC and BCCP domains is presented, although they are associated with very different CT domains and the relative position of the three functional domains varies between members of the biotin-dependent carboxylases.
Insect Biochem Mol Biol 1997 Feb
PMID:Biochemical, molecular, and phylogenetic analysis of pyruvate carboxylase in the yellow fever mosquito, Aedes aegypti. 906 23

We report the cloning and primary characterization of both cDNA and genomic fragments from the white gene of the yellow fever mosquito, Aedes aegypti. Comparisons of the conceptual translation product with white genes from four other species within the order Diptera show that the Ae. aegypti gene is most similar to the white gene of the mosquito vector of human malaria, Anopheles gambiae (86% identity and 92% similarity). The analysis of the primary sequence of genomic DNA at the 5'-end of the coding region revealed the presence of an intron that is also present in An. gambiae, but not in the vinegar fly, Drosophila melanogaster. The isolated clones of the Ae. aegypti white gene will enable the construction of a marker gene for use in the development of a germline transformation system for this species.
Insect Mol Biol 1997 Aug
PMID:The white gene from the yellow fever mosquito, Aedes aegypti. 927 47

Genomic DNA fragments encoding a salivary gland-specific alpha-amylase gene, Amylase I (Amy I), and an additional amylase, Amylase II (AmyII) of the yellow fever mosquito, Aedes aegypti, were isolated and characterized. Two independently isolated DNA fragments, G34-F and G34-14A, encode polymorphic alleles of Amy I. A 3.2 kilobase (kb) EcoR I fragment of G34-F, F2, has been sequenced in its entirety and contains 832 base pairs (bp) of the 5'-end, non-coding and putative promoter regions that are adjacent to 2.4 kb of the Amy I coding region. One intron, 59 bp in length, is found towards the 3'-end of the clone. A third genomic clone, 3A, corresponding to Amy II, was sequenced and shown not to contain the primary DNA sequence that encodes the 260 amino acid region that uniquely characterizes the amino terminal end of the Amy I product. Amy I was assigned by restriction fragment length polymorphism (RFLP) mapping to chromosome 2 (23.0 cM) and Amy II to chromosome 1 (44.0 cM). Amy I and Amy II are highly polymorphic and there may be multiple linked copies at each locus. Comparisons between Amy I and Amy II are presented for the putative promoter and conceptual translation products. The identification of two distinct amylase genes and their separate linkage assignments provides evidence for a multigene family of alpha-amylases in Ae. aegypti.
Insect Biochem Mol Biol
PMID:Evidence for two distinct members of the amylase gene family in the yellow fever mosquito, Aedes aegypti. 944 77


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