Identification of camelid specific residues in mitochondrial ATP synthase subunits (original) (raw)
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Molecular Study of Energy Related Mitochondrial Genes in Arabian and Bactrian Camels
American Journal of Biochemistry and Biotechnology, 2013
The single-humped camel, Camelus dromedaries inhabiting Afro-Arabia and the double-humped camel, Camelus bactrianus inhabiting central Asia are the only species in their genus. The present study aimed to amplify and partially sequence the mitochondrial DNA genes encoding for NADH dehydrogenase subunit 1, cytochrome c oxidase subunit 1, ATP synthase subunit 6 (ATP6), cytochrome b and displacement region (d-loop) in the single-humped camel and compare it to their counterparts already sequenced for the doublehumped camel. These energy-related genes showed amino acid substitutions gradually increased according to their locations among macromolecular energy transducers. Both ATP synthase 6 in the central core and cytochrome b in the inner mitochondrial membrane acquired the greatest substitutions of 5 and 7 amino acids, respectively. Cytochrome c oxidase is the terminal complex of the electron transport chain of the inner mitochondrial membrane and it showed no substitutions. These substitutions seemed to be correlated with the energy metabolism in both camel phenotypes. The d-loop showed tandem repeats of six nucleotides at its 3` end with polymorphism between both species without any evidence relates such variation to energy production.
BMC Evolutionary Biology, 2017
Background: Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. Results: We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia. We found significantly higher differentiation at the ATP6 locus across Tunisia, with sub-humid Mediterranean, semi-arid, and arid Sahara climate than for fourteen unlinked supposedly neutrally evolving nuclear microsatellites and mt control region sequences. This suggested positive selection on ATP6 sequences, which was confirmed by several codon-based tests for one sequence site that together with a second site translated into four different amino acids. Positive selection on ND2 sequences was also confirmed by several codon-based tests. The corresponding frequencies of the two most prevalent variants at each locus varied significantly across climate regions, and our logistic general linear models of occurrence of those proteins indicated significant effects of mean annual temperature for ATP6 and mean minimum temperature of the coldest month of the year for ND2, independent of geographical location, annual precipitation, and the respective co-occurring protein at the second locus. Moreover, presence of the ancestral ATP6 protein, as inferred from phylogenetic networks, was positively affected by the simultaneous presence of the derived ND2 protein and vice versa, independent of temperature, precipitation, or geographic location. Finally, we obtained a significant coevolution signal for the ancestral ATP6 and derived ND2 sequences and vice versa. Conclusions: positive selection was strongly suggested by the population genetic approach and the codon-based tests in both mtDNA genes. Moreover, the two most prevalent proteins at the ATP6 locus were distributed at significantly varying frequencies across the study area with a significant effect of mean annual temperature on the occurrence of the ATP6 proteins independent of geographical coordinates and the co-occuring ND2 protein variant. For ND2, occurrence of the two most frequent protein variants was significantly influenced by the mean minimum temperature of the coldest month, independent of the co-occurring ATP6 protein variant and geographical coordinates. This strongly suggests direct involvement of ambient temperature in the adaptation of the studied mtOXPHOS genes.
Rapid evolution of cytochrome c oxidase subunit II in camelids (Tylopoda, Camelidae)
Journal of Bioenergetics and Biomembranes, 2006
Within Cetartiodactyl species, both New and Old World camelids are uniquely adapted to the extremely hot and dry climates of African-Asian territories and to the high altitude cold and hypoxic environment of the whole Andean area. In order to investigate the potential association between these particular adaptations and mitochondrial aerobic energy production, we examined the camelid genes of cytochrome c oxidase subunits I, II, and III and the replacement of amino acids inferred. We found that all subunits had undergone a number of replacements in sites otherwise conserved in other cetartiodactyls. Changes of COXI and COXIII were mainly located in the transmembrane helices of proteins. For COXII, although most of the changes did not occur in sites directly involved in electron transfer, a shift of D by T at 115 position of Old World camelid might modify electrostatic interactions with cytochrome c. COXII also showed an increased relative evolutionary rate respect to other cetartiodactyls compared.
Mitochondrial DNA structure and organization of the control region of South American camelids
Molecular Ecology Notes, 2004
This work presents the mitochondrial DNA molecular organization of the control region (CR) of South American camelids. Sequencing of five individuals each of guanaco, llama, alpaca and vicuna species showed that this region spans 1060 bp including three conserved sequence blocks (CSB I-III) adjacent to the tRNAPhe gene, a conserved central domain and one extended termination-associated sequence in the 3′ ′ ′ ′ domain of the CR close to the tRN-APro gene. A repeated array formed by three units of 26 bp was detected between CSB I and II. Alignment of the CR sequences from the four species shows a 337-bp segment that includes most of the nucleotide variability with 10 polymorphic sites. We suggest the use of this segment as a molecular marker to infer data on camelid genetic relationships and population diversity studies.
IUBMB Life, 2020
In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 and ATP8 genes among three groups, namely, fishes, aves, and mammals which thrive in three different habitats as no work was reported yet. The coding sequences of these genes were retrieved from the National Center for Biotechnology Information to explore the similarities and dissimilarities of codon usage of each gene among these groups. Low values of synonymous codon usage order in fishes, aves, and mammals for ATP6 and ATP8 genes suggested that the CUB of ATP6 and ATP8 genes was low. In ATP6 gene, overall GC contents in fishes, aves and mammals were (mean ± SD) 44.09 ± 3.10, 46.65 ± 1.90, and 39.41 ± 2.89%, respectively, whereas in ATP8 gene, the overall GC contents were 42.76 ± 4.38, 44.16 ± 2.43, and 34.19 ± 3.82% in fishes, aves, and mammals, that is, both genes were found to be AT rich. In ATP6 gene, the codon AGC was overrepresented in fishes but under-represented in aves and mammals, whereas in ATP8 gene, the codon GCC was overrepresented in fishes but underrepresented in aves and mammals. The pattern of codon usage was different in these genes and varied among groups as evident from correspondence analysis. The slope of the regression line in neutrality plot was lower than 0.5, which revealed that the role of natural selection was higher than mutation pressure in shaping the CUB in ATP6 and ATP8 genes.
COMPARATIVE ANALYSIS OF ATP6 MITOCHONDRIAL GENE DIVERSITY IN ARABIAN AND NON-ARABIAN HORSE BREEDS
Arabian horse breeds are famous for their strength, disease resistance and endurance. Originating from Arabian Peninsula, their progeny is considered among the best horse breeds of the world. Maternally inherited mitochondrial genome represents high genetic diversity in modern horse population. ATP6 gene of mt DNA from 46 horse samples of Middle Eastern Arabian, Western Arabian, mixed (hybrid) Arabians and non-Arabians were sequenced and analyzed to assess the genetic diversity and phylogenetic relationships among them. We have found nine haplotypes in our study. Totally, 99-nucleotide base substitutions were observed with seven variables, which accounted for six transitions and one transversion. Four single nucleotide polymorphismswereobserved in our study. Arabian horse breeds showed high diversity and shared many haplotypes among the population.The observed haplotype diversity and the average evolutionary divergence over all the sequence pairs were 0.8141 and 0.007 respectively.In addition, these datasets may also be useful for strain genotyping, data conservation, effective breeding and individual breed selection for desirable traits.
Scientific Reports
The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and highaltitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineagespecific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS < 1 in the concatenated protein-coding genes suggested purifying selection as driving force for shaping mitogenome diversity in camels. Additional analyses of the functional divergence in amino acid changes between species-specific lineages indicated fixed substitutions in various genes, with radical effects on the physicochemical properties of the protein products. The evolutionary time estimates revealed a divergence between domestic and wild Bactrian camels around 1.1 [0.58-1.8] million years ago (mya). This has major implications for the conservation and management of the critically endangered wild species, Camelus ferus.
Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History
Molecular Biology and Evolution, 2015
Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicu~nas). These results contradict previous morphologybased phylogenetic models for Camelops, which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.
ANALYSIS OF CODON USAGE PATTERN IN MITOCHONDRIAL ATPASE 6 IN SOME MAMMALIAN SPECIES
Background: Codon bias is the unequal use of synonymous codons, some codons are more preferred than others. Synonymous codons encoding amino acids range from two to six, usually differing in the third position. However, the patterns of synonymous codon usage differ among the genes of an organism and among different organisms. Some codons that encode an amino acid are more frequently used then others by the genome. This bias is very common in highly expressed gene. Mammals are the most advanced group of organisms in animal kingdom. Several species are used for research in genetics and in drug discovery for testing of the newly isolated/synthesized drugs. In taxonomy and species testing, only those DNA regions which have interspecies variation are used to distinguish closely related species. Each mitochondrion has its own DNA in multiple copies. It has a strong protein coat which protects mitochondrial DNA from bacterial enzyme degradation. Mitochondria have a high rate of evolution and responsible for maternal inheritance. For this reason mitochondrial DNA regions are widely used for species testing. The study of codon usage bias pattern is useful for better understanding the process of evolution in terms of molecular biology, mRNA translation and design of transgenes, new gene discovery, detecting lateral gene transfer and for analyzing the functional conservation of gene expression. Methods and Result: In this study we analyzed codon usage pattern of genes encoding mitochondrial atpase6 in different species of mammals. From our study it is evident that leucine is the most frequent amino acid in atpase6 encoded by the most preferred codon CTA in the mammalian species analyzed. Most frequent codons usually favor A or C at the 3rd codon position. The average GC3% is 43.51±3.42 whereas AT3% is 56.48±3.42. To further analyze we performed the linear regression analysis between the observed ENC (effective number of codons) value and the base composition at third codon position (Wobble codon position). These results showed that the ENC is negatively affected by A3 and T3 and positively affected by G3 and C3. A significant positive correlation was observed between overall A and A3% (r =0.9065, p <0.001), C and C3% (r = 0.9238, p < 0.001), GC and GC3% (r = 0.9244, p < 0.001). But significant negative correlation was observed between overall A and GC3% ( r = -0.7350 , p<0.05), T and G3%( r =-0.7639, p<0.05 ), T and C3%( r =- 0.7946, p<0.01). ENC showed a highly significant positive correlation with overall GC content (r =0.9479, p<0.001) and GC3 (r = 0.9387, p<0.001). Conclusion: In our findings, we observed the codon usage bias in atpase6 in mammalian species is not remarkable. However in mitochondrial atpase6, frequent codons favour A or C at the 3rd codon position. All the results supported that mutation pressure plays a major role in the codon usage pattern in atpase 6 in mammalian species.