Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

Tripoli, Gaetano; D’Elia, Domenica; Barsanti, Paolo; Caggese, Corrado

doi:10.1186/gb-2005-6-2-r11

Cited by 47 publications

(33 citation statements)

References 53 publications

(49 reference statements)

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“…Among these microsynteny some were remarkably inverted, duplicated such as PpWOX3 / PmWOX3 , PbWOX1 / PpWOX1 , and FvWOX13C/PpWOX13B ( Figure 3 ). Usually, genome segments in the same group may evolve from a single sequence, which led to species differentiation (Tripoli et al, 2005; Jing et al, 2016). However, sequence fragments from the same group are considered to be homologous genes, and their genetic evolution resulted in species segregation (Tripoli et al, 2005; Jing et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

“…Usually, genome segments in the same group may evolve from a single sequence, which led to species differentiation (Tripoli et al, 2005; Jing et al, 2016). However, sequence fragments from the same group are considered to be homologous genes, and their genetic evolution resulted in species segregation (Tripoli et al, 2005; Jing et al, 2016). Remarkably, with the construction of the phylogenetic tree, the conservation of microsynteny in different families gradually emerged.…”

Section: Resultsmentioning

confidence: 99%

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Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca

et al. 2017

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WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca

et al. 2017

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“…Individuals often carry heteroplasmic mtDNA sequences (a non-clonal population of mitochondrial genomes, typically consisting of wild-type and mutant mtDNA molecules) [44,45]. Furthermore, many nuclearencoded mitochondrial genes are also present in duplicates, and these duplicates often exhibit tissue-specific expression [46][47][48]. Thus, allelic variation within particular mtDNA-and nuclear-encoded genes can co-segregate, and thus potentially interact, even within an individual, and this might have hitherto unrealized medical and evolutionary implications.…”

Section: Mitonuclear Interactions and Coevolutionary Processesmentioning

confidence: 99%

“…Considering that heteroplasmy [11,40,44,45,107] and gene duplication of mitochondrial genes [46][47][48] are pervasive across taxa, the intraindividual level provides a new frontier for exploration of the evolutionary and medical significance of the mitonuclear interaction. A very striking example of the potential for intraindividual mitonuclear interaction was found in mice with artificially induced heteroplasmy between two wild-type mtDNAs, that of the Balb/cByJ mouse and that of the NZB/ BINJ mouse [108].…”

Section: Intraindividual Interactions and Biomedical Implicationsmentioning

confidence: 99%

Mitonuclear interactions: evolutionary consequences over multiple biological scales

Wolff

Ladoukakis

Enrı́quez

et al. 2014

Phil. Trans. R. Soc. B

204

218

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Fundamental biological processes hinge on coordinated interactions between genes spanning two obligate genomes—mitochondrial and nuclear. These interactions are key to complex life, and allelic variation that accumulates and persists at the loci embroiled in such intergenomic interactions should therefore be subjected to intense selection to maintain integrity of the mitochondrial electron transport system. Here, we compile evidence that suggests that mitochondrial–nuclear (mitonuclear) allelic interactions are evolutionarily significant modulators of the expression of key health-related and life-history phenotypes, across several biological scales—within species (intra- and interpopulational) and between species. We then introduce a new frontier for the study of mitonuclear interactions—those that occur within individuals, and are fuelled by the mtDNA heteroplasmy and the existence of nuclear-encoded mitochondrial gene duplicates and isoforms. Empirical evidence supports the idea of high-resolution tissue- and environment-specific modulation of intraindividual mitonuclear interactions. Predicting the penetrance, severity and expression patterns of mtDNA-induced mitochondrial diseases remains a conundrum. We contend that a deeper understanding of the dynamics and ramifications of mitonuclear interactions, across all biological levels, will provide key insights that tangibly advance our understanding, not only of core evolutionary processes, but also of the complex genetics underlying human mitochondrial disease.

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“…Thus, there are both ubiquitous (L, for liver) and heart and muscle-specific (H) isoforms of subunits VIa and VIIa 5 in all mammals, and some species also have L and H variants of COX VIII (2, 8,12). Multiple COX VIa and VIIa isoforms and cognate genes are also present in lower metazoan species including Drosophila (13). Biochemical studies have suggested that COX H may confer sensitivity of muscle COX activity and respiration to cellular energy demands (14).…”

mentioning

confidence: 99%

Nuclear Respiratory Factor 1 Controls Myocyte Enhancer Factor 2A Transcription to Provide a Mechanism for Coordinate Expression of Respiratory Chain Subunits

Ramachandran

Gulick

2008

Journal of Biological Chemistry

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Nuclear respiratory factors NRF1 and NRF2 regulate the expression of nuclear genes encoding heme biosynthetic enzymes, proteins required for mitochondrial genome transcription and protein import, and numerous respiratory chain subunits. NRFs thereby coordinate the expression of nuclear and mitochondrial genes relevant to mitochondrial biogenesis and respiration. Only two of the nuclear-encoded respiratory chain subunits have evolutionarily conserved tissue-specific forms: the cytochrome c oxidase (COX) subunits VIa and VIIa heart/muscle (H) and ubiquitous (L) isoforms. We used genome comparisons to conclude that the promoter regions of COX6A H and COX7A H lack NRF sites but have conserved myocyte enhancer factor 2 (MEF2) elements. We show that MEF2A mRNA is induced with forced expression of NRF1 and that the MEF2A 5-regulatory region contains an evolutionarily conserved canonical element that binds endogenous NRF1 in chromatin immunoprecipitation (ChIP) assays. NRF1 regulates MEF2A promoter-reporters according to overexpression, RNA interference underexpression, and promoter element mutation studies. As there are four mammalian MEF2 isotypes, we used an isoform-specific antibody in ChIP to confirm MEF2A binding to the COX6A H promoter. These findings support a role for MEF2A as an intermediary in coordinating respiratory chain subunit expression in heart and muscle through a NRF1 3 MEF2A 3 COX H transcriptional cascade. MEF2A also bound the MEF2A and PPARGC1A promoters in ChIP, placing it within a feedback loop with PGC1␣ in controlling NRF1 activity. Interruption of this cascade and loop may account for striated muscle mitochondrial defects in mef2a null mice. Our findings also account for the previously described indirect regulation by NRF1 of other MEF2 targets in muscle such as GLUT4. The electron transport chain (ETC)4 consists of four multisubunit enzyme complexes within the inner mitochondrial (mito) membrane. These act in concert to transfer electrons from succinate or NADH to molecular oxygen while pumping protons from the matrix to the intermembranous space, establishing the electrochemical gradient required for oxidative phosphorylation (OXPHOS) (1). Nuclear genes encode all of the components of complex II, but the other complexes have subunits encoded by both mito (ETC mito ) and nuclear (ETC nucl ) genes (1, 2). Appropriate ETC subunit stoichiometry requires the coordinate expression of genes on the two genomes and an accounting for a variable number of mito genomes per cell (2, 3). This is orchestrated by the nuclear respiratory (transcription) factors, NRF1 and NRF2 (2-5). These structurally unrelated factors, encoded by nuclear genes, regulate the transcription of TFAM, TFB1M, and TFB2M, nuclear genes of the mito transcription factor Tfam (mtTFA) (6) and Tfbm specificity factors (7). Tfam and Tfbm proteins are imported into mito where they direct transcription from both heavy and light strands of mito DNA (mtDNA). These transcripts are processed to yield the various ETC mito mRNAs, as well as rRN...

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Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

Cited by 47 publications

References 53 publications

Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca

Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca

Mitonuclear interactions: evolutionary consequences over multiple biological scales

Nuclear Respiratory Factor 1 Controls Myocyte Enhancer Factor 2A Transcription to Provide a Mechanism for Coordinate Expression of Respiratory Chain Subunits

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