Structural organization of the mitochondrial DNA control region in Aedes aegypti

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 931-937 ◽  
Author(s):  
Juan C. Rondan Dueñas ◽  
Cristina N Gardenal ◽  
Guillermo Albrieu Llinás ◽  
Graciela M Panzetta-Dutari
Keyword(s):  
Mitochondrial Dna ◽  
Aedes Aegypti ◽  
Control Region ◽  
Sequence Similarity ◽  
Mosquito Species ◽  
Repeat Unit ◽  
12S Rrna ◽  
Rrna Gene ◽  
Rich Region ◽  
Stem Loop

The complete A+T - rich region of Aedes aegypti mitochondrial DNA has been cloned and sequenced. In Argentinean populations of the species, a polymorphism in the length of the amplified fragment was observed. Nucleotide sequence comparison of the shortest and longest A+T - rich amplified fragments detected revealed the presence of 2 types of tandemly repeated blocks. The size variation observed in natural populations is mainly due to the presence of a variable number of a 181 bp tandem repeat unit, located toward the 12S rRNA gene end. The size of the longest A+T - rich region was of 2070 bp, representing the largest control sequence reported for any mosquito species. Few relevant short blocks of primary-sequence similarity conserved in the control region of mosquitoes and other insects were detected scattered throughout the whole region. Five putative stem-loop secondary structures were found, one of them flanked by conserved sequences described in other insects. Our results suggest that there are no universal models of structure–function relations in the control region of insect mtDNA. In addition, we identified a short A+T - rich variable segment in the Ae. aegyti control region that would be suitable for population genetic studies.Key words: mitochondrial DNA, A+T - rich region, repeated elements, conserved blocks, Aedes aegypti.

scholarly journals Drug targeting of aminoacyl-tRNA synthetases in Anopheles species and Aedes aegypti that cause malaria and dengue

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Soumyananda Chakraborti ◽  
Jyoti Chhibber-Goel ◽  
Amit Sharma
Keyword(s):  
Aedes Aegypti ◽  
Drug Targets ◽  
Viral Infections ◽  
Sequence Similarity ◽  
Mosquito Species ◽  
Physicochemical Characteristics ◽  
Computational Techniques ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Relationship Of

Abstract Background Mosquito-borne diseases have a devastating impact on human civilization. A few species of Anopheles mosquitoes are responsible for malaria transmission, and while there has been a reduction in malaria-related deaths worldwide, growing insecticide resistance is a cause for concern. Aedes mosquitoes are known vectors of viral infections, including dengue, yellow fever, chikungunya, and Zika. Aminoacyl-tRNA synthetases (aaRSs) are key players in protein synthesis and are potent anti-infective drug targets. The structure–function activity relationship of aaRSs in mosquitoes (in particular, Anopheles and Aedes spp.) remains unexplored. Methods We employed computational techniques to identify aaRSs from five different mosquito species (Anopheles culicifacies, Anopheles stephensi, Anopheles gambiae, Anopheles minimus, and Aedes aegypti). The VectorBase database (https://vectorbase.org/vectorbase/app) and web-based tools were utilized to predict the subcellular localizations (TargetP-2.0, UniProt, DeepLoc-1.0), physicochemical characteristics (ProtParam), and domain arrangements (PfAM, InterPro) of the aaRSs. Structural models for prolyl (PRS)-, and phenylalanyl (FRS)-tRNA synthetases—were generated using the I-TASSER and Phyre protein modeling servers. Results Among the vector species, a total of 37 (An. gambiae), 37 (An. culicifacies), 37 (An. stephensi), 37 (An. minimus), and 35 (Ae. aegypti) different aaRSs were characterized within their respective mosquito genomes. Sequence identity amongst the aaRSs from the four Anopheles spp. was > 80% and in Ae. aegypti was > 50%. Conclusions Structural analysis of two important aminoacyl-tRNA synthetases [prolyl (PRS) and phenylanalyl (FRS)] of Anopheles spp. suggests structural and sequence similarity with potential antimalarial inhibitor [halofuginone (HF) and bicyclic azetidine (BRD1369)] binding sites. This suggests the potential for repurposing of these inhibitors against the studied Anopheles spp. and Ae. aegypti.

Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 188-202 ◽  
Author(s):  
Stephen L. Cameron ◽  
Michael F. Whiting
Keyword(s):  
Control Region ◽  
Repeat Unit ◽  
General Characteristic ◽  
Nucleotide Composition ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stem Loop ◽  
Protein Coding ◽  
Repeat Units ◽  
Mt Genome

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.

Identification of the 12S rRNA Gene Promoter in Leptomonas seymouri Mitochondrial DNA

2004 ◽  
Vol 38 (6) ◽  
pp. 839-843 ◽  
Author(s):  
M. A. Vasil'eva ◽  
E. A. Bessolitsina ◽  
E. M. Merzlyak ◽  
A. A. Kolesnikov
Keyword(s):  
Mitochondrial Dna ◽  
Gene Promoter ◽  
12S Rrna ◽  
Rrna Gene ◽  
12S Rrna Gene

Divergence in mitochondrial DNA of Near Eastern water frogs with special reference to the systematic status of Cypriote and Anatolian populations (Anura, Ranidae)

2001 ◽  
Vol 22 (4) ◽  
pp. 397-412 ◽  
Author(s):  
Torsten Ohst ◽  
Wolfgang Böhme ◽  
Robert Schreiber ◽  
Jörg Plötner
Keyword(s):  
Mitochondrial Dna ◽  
Sister Group ◽  
12S Rrna ◽  
Rrna Gene ◽  
Near Eastern ◽  
Water Frogs ◽  
Central Asian ◽  
12S Rrna Gene ◽  
Southern Turkey ◽  
Asian Water

AbstractWater frogs from Anatolia, Syria, Jordan, and central Asia (Turkmenistan, Uzbekistan, Kazakhstan) were compared on the basis of the complete mitochondrial (mt) ND3 gene (340 bp), two flanking mt t-RNA gene fragments (26 bp), and a 374 bp fragment of the mt 12S rRNA gene. A total of 27 haplotypes were found among the investigated individuals. Anatolian water frogs differed from Syrian and Jordanian Rana bedriagae by 2.2-3.4% of the analysed sites. The observed divergence (2.8-4.1%) between the Cypriote water frogs and frogs from the surrounding mainland (southern Turkey, west Syria) was in the same range as between R. bedriagae and European R. ridibunda (3.1-3.9%). These results suggest that neither the Cypriote nor the Anatolian water frogs represent R. bedriagae. Furthermore, maximum parsimony and neighbour-joining trees showed a clear subdivision of Asian water frogs into three Anatolian lineages, two central Asian lineages, a Cypriote lineage and the bedriagae lineage. In all trees the Cypriote lineage branches off first and a clade formed by two Anatolian lineages is placed as the sister group of water frogs from Turkmenistan and Uzbekistan, whereas the phylogenetic positions of R. bedriagae, the Ceyhan lineage, the Kazakhstan lineage and R. ridibunda remain unclear.

Structure and evolution of the mitochondrial control region of the pollen beetle Meligethes thalassophilus (Coleoptera: Nitidulidae)

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 196-207 ◽  
Author(s):  
Emiliano Mancini ◽  
Alessio De Biase ◽  
Paolo Mariottini ◽  
Alessandro Bellini ◽  
Paolo Audisio
Keyword(s):  
Control Region ◽  
Tandem Repeats ◽  
Population Level ◽  
Mitochondrial Control Region ◽  
Variable Number ◽  
12S Rrna ◽  
Rrna Gene ◽  
Length Variation ◽  
Pollen Beetle ◽  
Repeat Elements

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the pollen beetle Meligethes thalassophilus is described. This mtDNA CR represents the longest sequenced for beetles so far, since the entire nucleotide sequence ranges from ~5000 to ~5500 bp. The CR of M. thalassophilus is organized in three distinct domains: a conserved domain near the tRNAIle gene, a variable domain flanking the 12S rRNA gene, and a relatively large central tandem array made up of a variable number of ~170 bp repeats that is responsible for the intraspecific length variation observed. Like other CRs found in insects, the M. thalassophilus CR contains two long homopolymeric runs that may be involved in mtDNA replication. Furthermore, conserved stem-and-loop structures in the repetitive domain were identified and their possible role in generating length variation is examined. Intraspecific comparison of the tandem repeat elements of M. thalassophilus suggests mechanisms of concerted evolution leading to homogenization of the repetitive region. The utility of such an array of tandem repeats as a genetic marker for assessing population-level variability and evolutionary relationships among populations is discussed. Finally, the technical difficulties found in isolating the mtDNA CR in beetles are remarked upon.

scholarly journals Distinct families of site-specific retrotransposons occupy identical positions in the rRNA genes of Anopheles gambiae.

1992 ◽  
Vol 12 (11) ◽  
pp. 5102-5110 ◽  
Author(s):  
N J Besansky ◽  
S M Paskewitz ◽  
D M Hamm ◽  
F H Collins
Keyword(s):  
Anopheles Gambiae ◽  
Sequence Similarity ◽  
Mosquito Species ◽  
Target Site ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Wild Female ◽  
Site Specific ◽  
Gambiae Complex

Two distinct site-specific retrotransposon families, named RT1 and RT2, from the sibling mosquito species Anopheles gambiae and A. arabiensis, respectively, were previously identified. Both were shown to occupy identical nucleotide positions in the 28S rRNA gene and to be flanked by identical 17-bp target site duplications. Full-length representatives of each have been isolated from a single species, A. gambiae, and the nucleotide sequences have been analyzed. Beyond insertion specificity, RT1 and RT2 share several structural and sequence features which show them to be members of the LINE-like, or non-long-terminal-repeat retrotransposon, class of reverse transcriptase-encoding mobile elements. These features include two long overlapping open reading frames (ORFs), poly(A) tails, the absence of long terminal repeats, and heterogeneous 5' truncation of most copies. The first ORF of both elements, particularly ORF1 of RT1, is glutamine rich and contains long tracts of polyglutamine reminiscent of the opa repeat. Near the carboxy ends, three cysteine-histidine motifs occur in ORF1 and one occurs in ORF2. In addition, each ORF2 contains a region of sequence similarity to reverse transcriptases and integrases. Alignments of the protein sequences from RT1 and RT2 reveal 36% identity over the length of ORF1 and 60% identity over the length of ORF2, but the elements cannot be aligned in the 5' and 3' noncoding regions. Unlike that of RT2, the 5' noncoding region of RT1 contains 3.5 copies of a 500-bp subrepeat, followed by a poly(T) tract and two imperfect 55-bp subrepeats, the second spanning the beginning of ORF1. The pattern of distribution of these elements among five siblings species in the A. gambiae complex is nonuniform. RT1 is present in laboratory and wild A. gambiae, A. arabiensis, and A. melas but has not been detected in A. quadriannulatus or A. merus. RT2 has been detected in all available members of the A. gambiae complex except A. merus. Copy number fluctuates, even among the offspring of individual wild female A. gambiae mosquitoes. These findings reflect a complex evolutionary history balancing gain and loss of copies against the coexistence of two elements competing for a conserved target site in the same species for perhaps millions of years.

scholarly journals Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration

2016 ◽  
Author(s):  
Fenfang Chen ◽  
Hongyu Ma ◽  
Chunyan Ma ◽  
Heng Zhang ◽  
Mengdi Zhao ◽  
...  
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Start Codon ◽  
12S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
Rna Genes

In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.

Mitochondrial DNA reveals high genetic divergence between populations of Chalcides mertensi Klausewitz, 1954 (Reptilia: Scincidae) from Tunisia

2013 ◽  
Vol 34 (3) ◽  
pp. 389-399
Author(s):  
Massimo Giovannotti ◽  
Paola Nisi Cerioni ◽  
Andrea Splendiani ◽  
Mohsen Kalboussi ◽  
Paolo Ruggeri ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nadh Dehydrogenase ◽  
Mitochondrial Gene ◽  
Rflp Analysis ◽  
12S Rrna ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Sidi Bouzid ◽  
Exhaustive Study

Genetic diversity of four populations of Chalcides mertensi (Klausewitz, 1954) from Tunisia was analyzed by means of the Restriction Fragment Length Polymorphism (RFLP) analysis of two fragments of mitochondrial DNA (mtDNA) encompassing NADH dehydrogenase subunits 1 and 2 (ND-1/2) and NADH dehydrogenase subunits 3, 4 and 4L (ND-3/4). Phylogenetic relationships between haplotypes were inferred by analysing the sequence of 396 base pairs at the 5′ end of the mitochondrial gene encoding cytochrome b and a segment of 12S rRNA gene (386 bp). The results of this study highlighted a pronounced genetic divergence between the populations from northern (Ain Soltane and Tabarka) and southern (Kasserine and Sidi Bouzid) Tunisia, that the phylogenetic analysis recovered as two distinct taxonomic entities. These two groups of populations can therefore be ascribed to two distinct taxa, with southern populations probably representing the typical C. mertensi, whereas northern individuals are likely to represent a new species of grass swimming Chalcides. The divergence between these two taxonomic entities can be referred to palaeogeographic and palaeoclimatic events that have affected northwestern Africa during the last 10 Million years. The analysed populations show a low genetic variability that can be related to the past climatic and geologic events and the colonization processes that took place with environmental amelioration, and to the peripheral position of these populations in the distributional range of the species. However, a more exhaustive study, including Algerian and Moroccan skink populations will be necessary in order to clarify these issues.

Distinct families of site-specific retrotransposons occupy identical positions in the rRNA genes of Anopheles gambiae

1992 ◽  
Vol 12 (11) ◽  
pp. 5102-5110
Author(s):  
N J Besansky ◽  
S M Paskewitz ◽  
D M Hamm ◽  
F H Collins
Keyword(s):  
Anopheles Gambiae ◽  
Sequence Similarity ◽  
Mosquito Species ◽  
Target Site ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Wild Female ◽  
Site Specific ◽  
Gambiae Complex

Two distinct site-specific retrotransposon families, named RT1 and RT2, from the sibling mosquito species Anopheles gambiae and A. arabiensis, respectively, were previously identified. Both were shown to occupy identical nucleotide positions in the 28S rRNA gene and to be flanked by identical 17-bp target site duplications. Full-length representatives of each have been isolated from a single species, A. gambiae, and the nucleotide sequences have been analyzed. Beyond insertion specificity, RT1 and RT2 share several structural and sequence features which show them to be members of the LINE-like, or non-long-terminal-repeat retrotransposon, class of reverse transcriptase-encoding mobile elements. These features include two long overlapping open reading frames (ORFs), poly(A) tails, the absence of long terminal repeats, and heterogeneous 5' truncation of most copies. The first ORF of both elements, particularly ORF1 of RT1, is glutamine rich and contains long tracts of polyglutamine reminiscent of the opa repeat. Near the carboxy ends, three cysteine-histidine motifs occur in ORF1 and one occurs in ORF2. In addition, each ORF2 contains a region of sequence similarity to reverse transcriptases and integrases. Alignments of the protein sequences from RT1 and RT2 reveal 36% identity over the length of ORF1 and 60% identity over the length of ORF2, but the elements cannot be aligned in the 5' and 3' noncoding regions. Unlike that of RT2, the 5' noncoding region of RT1 contains 3.5 copies of a 500-bp subrepeat, followed by a poly(T) tract and two imperfect 55-bp subrepeats, the second spanning the beginning of ORF1. The pattern of distribution of these elements among five siblings species in the A. gambiae complex is nonuniform. RT1 is present in laboratory and wild A. gambiae, A. arabiensis, and A. melas but has not been detected in A. quadriannulatus or A. merus. RT2 has been detected in all available members of the A. gambiae complex except A. merus. Copy number fluctuates, even among the offspring of individual wild female A. gambiae mosquitoes. These findings reflect a complex evolutionary history balancing gain and loss of copies against the coexistence of two elements competing for a conserved target site in the same species for perhaps millions of years.

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