Subunit change in cytochrome c oxidase: identification of the oxygen switch in Dictyostelium

Bisson, Roberto

doi:10.1093/emboj/16.4.739

Cited by 12 publications

(7 citation statements)

References 47 publications

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“…Another way to adapt efficiently to a change in the growth conditions is by modifying the association of complexes as suggested recently for iron respiration in A. ferrooxidans [ 15 ]. In the case of the cytochrome c oxidase complex of Dictyostelium discoideum , the oxygen concentration induces a switch between two interchangeable subunit isoforms of the cytochrome c oxidase [ 84 - 86 ]. This switch has been shown to be due to transcriptional regulation and also to different stabilities of the two subunits toward oxygen [ 86 ].…”

Section: Resultsmentioning

confidence: 99%

“…In the case of the cytochrome c oxidase complex of Dictyostelium discoideum , the oxygen concentration induces a switch between two interchangeable subunit isoforms of the cytochrome c oxidase [ 84 - 86 ]. This switch has been shown to be due to transcriptional regulation and also to different stabilities of the two subunits toward oxygen [ 86 ].…”

Section: Resultsmentioning

confidence: 99%

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Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

et al. 2009

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BackgroundAcidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus.ResultsBioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa3 oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool.ConclusionBioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

et al. 2009

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“…This suggests that the organism may be retooling some of its capacity for redox chemistry at the end of exponential growth. It is known that other organisms will exchange cytochrome C oxidase subunits to remain more metabolically versatile in response to changing redox state [ 33 ]. The other 12 genes include 6 putative genes which lack annotation ( vng0602C, vng1182H, vng1486H, vng2197H, vng2199H and vng2412H ), a putative putative haloacid dehalogenase-like hydrolase ( vng0719G ), a putative iron-sulfur cluster containing protein ( vng1184Gm ), a putative universal stress protein ( vng1898C ), a putative phosphoribosyl transferase ( vng1912G ), a heavy-metal transporting CPx-type ATPase ( vng2201G ) and an putative aminopeptidase ( vng2546G ).…”

Section: Resultsmentioning

confidence: 99%

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

Facciotti

Pang

et al. 2010

BMC Syst Biol

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BackgroundRapidly characterizing the operational interrelationships among all genes in a given organism is a critical bottleneck to significantly advancing our understanding of thousands of newly sequenced microbial and eukaryotic species. While evolving technologies for global profiling of transcripts, proteins, and metabolites are making it possible to comprehensively survey cellular physiology in newly sequenced organisms, these experimental techniques have not kept pace with sequencing efforts. Compounding these technological challenges is the fact that individual experiments typically only stimulate relatively small-scale cellular responses, thus requiring numerous expensive experiments to survey the operational relationships among nearly all genetic elements. Therefore, a relatively quick and inexpensive strategy for observing changes in large fractions of the genetic elements is highly desirable.ResultsWe have discovered in the model organism Halobacterium salinarum NRC-1 that batch culturing in complex medium stimulates meaningful changes in the expression of approximately two thirds of all genes. While the majority of these changes occur during transition from rapid exponential growth to the stationary phase, several transient physiological states were detected beyond what has been previously observed. In sum, integrated analysis of transcript and metabolite changes has helped uncover growth phase-associated physiologies, operational interrelationships among two thirds of all genes, specialized functions for gene family members, waves of transcription factor activities, and growth phase associated cell morphology control.ConclusionsSimple laboratory culturing in complex medium can be enormously informative regarding the activities of and interrelationships among a large fraction of all genes in an organism. This also yields important baseline physiological context for designing specific perturbation experiments at different phases of growth. The integration of such growth and perturbation studies with measurements of associated environmental factor changes is a practical and economical route for the elucidation of comprehensive systems-level models of biological systems.

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“…In the slime mold Dictyostelium discoideum , there is an isoform pair of CcO subunit 7. Here, CcO7e, which is expressed under normoxic conditions, is replaced by CcO7s under hypoxia, and this switching is mediated by an oxygen‐dependent transcriptional element located in the short intergenic region between the two adjacent genes [26]. Analysis of the yeast and Dictyostelium CcO hypoxia‐regulated promoters revealed that the mammalian ORE sequence is absent in both organisms, which agrees with our functional model that the expression of CcO4‐2 represents a unique protective adaptation found in the highly oxygenated respiratory system in higher organisms, rather than being an adaptation to very low oxygen levels, under which yeast CcO5b and Dictyostelium CcO7s are expressed.…”

Section: Discussionmentioning

confidence: 99%

Transcription of mammalian cytochrome c oxidase subunit IV‐2 is controlled by a novel conserved oxygen responsive element

et al. 2007

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Oxygen sensing and the adaptation to varying oxygen concentrations are fundamental for the survival of species from bacteria to humans. Oxygen regulation can occur at both the intake stage and the usage stage. In higher organisms, which depend largely on aerobic energy metabolism, usage takes place largely at the last step of the mitochondrial respiratory chain, the transfer of electrons from cytochrome c to oxygen, catalyzed by cytochrome c oxidase (CcO; EC 1.9.3.1).In vertebrates, oxygen supply is also regulated via a unique mechanism in the lungs for hypoxic response. Other tissues (and, indeed, the bronchial circulatory system of the lung) react to a hypoxic trigger by vasodilation, thereby increasing blood flow to under-oxygenated regions. In the pulmonary circulation of the lungs, however, the converse effect, hypoxic vasoconstriction, is critical for shunting blood to more highly ventilated regions to help optimize the ventilation of deoxygenated blood. Subunit 4 of cytochrome c oxidase (CcO) is a nuclear-encoded regulatory subunit of the terminal complex of the mitochondrial electron transport chain. We have recently discovered an isoform of CcO 4 (CcO4-2) which is specific to lung and trachea, and is induced after birth. The role of CcO as the major cellular oxygen consumer, and the lung-specific expression of CcO4-2, led us to investigate CcO4-2 gene regulation. We cloned the CcO4-2 promoter regions of cow, rat and mouse and compared them with the human promoter. Promoter activity is localized within a 118-bp proximal region of the human promoter and is stimulated by hypoxia, reaching a maximum (threefold) under 4% oxygen compared with normoxia. CcO4-2 oxygen responsiveness was assigned by mutagenesis to a novel promoter element (5¢-GGACGTTCCCACG-3¢) that lies within a 24-bp region that is 79% conserved in all four species. This element is able to bind protein, and competition experiments revealed that, within the element, the four core bases 5¢-TCNCA-3¢ are obligatory for transcription factor binding. CcO isolated from lung showed a 2.5-fold increased maximal turnover compared with liver CcO. We propose that CcO4-2 expression in highly oxygenated lung and trachea protects these tissues from oxidative damage by accelerating the last step in the electron transport chain, leading to a decrease in available electrons for free radical formation.Abbreviations CcO, cytochrome c oxidase; CcO4-2, CcO subunit 4-2 gene; Egr1, early growth response factor 1; EMSA, electrophoretic mobility shift assay; HIF-1a, hypoxia-inducible factor 1a; ORE, oxygen responsive element; OREF, ORE binding factor; RACE, rapid amplification of cDNA ends; ROS, reactive oxygen species.

show abstract

Subunit change in cytochrome c oxidase: identification of the oxygen switch in Dictyostelium

Cited by 12 publications

References 47 publications

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

Transcription of mammalian cytochrome c oxidase subunit IV‐2 is controlled by a novel conserved oxygen responsive element

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