MitoProt, a Macintosh application for studying mitochondrial proteins

Claros, M. Gonzalo

doi:10.1093/bioinformatics/11.4.441

Cited by 143 publications

(146 citation statements)

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“…Local hydrophobicity (͗H͘) was calculated by using a scanning window of 17 and 19 residues, respectively. The average regional hydrophobicity (͗H͘ 60 -80 ), termed mesohydrophobicity, was calculated by scanning for the average maximum hydrophobicity using scanning windows from 60-80 residues and averaging the values, as described by Claros et al (8) using the MITOPROT V1.0 program (21).…”

Section: Methodsmentioning

confidence: 99%

Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochromecoxidase

Daley

Clifton

Whelan

2002

Proc. Natl. Acad. Sci. U.S.A.

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Subunit 2 of cytochrome c oxidase (Cox2) in legumes offers a rare opportunity to investigate factors necessary for successful gene transfer of a hydrophobic protein that is usually mitochondrialencoded. We found that changes in local hydrophobicity were necessary to allow import of this nuclear-encoded protein into mitochondria. All legume species containing both a mitochondrial and nuclear encoded Cox2 displayed a similar pattern, with a large decrease in hydrophobicity evident in the first transmembrane region of the nuclear encoded protein compared with the organelle-encoded protein. Mitochondrial-encoded Cox2 could not be imported into mitochondria under the direction of the mitochondrial targeting sequence that readily supports the import of nuclear encoded Cox2. Removal of the first transmembrane region promotes import ability of the mitochondrial-encoded Cox2. Changing just two amino acids in the first transmembrane region of mitochondrial-encoded Cox2 to the corresponding amino acids in the nuclear encoded Cox2 also promotes import ability, whereas changing the same two amino acids in the nuclear encoded Cox2 to what they are in the mitochondrial-encoded copy prevents import. Therefore, changes in amino acids in the mature protein were necessary and sufficient for gene transfer to allow import under the direction of an appropriate signal to achieve the functional topology of Cox2.

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Section: Methodsmentioning

confidence: 99%

Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochromecoxidase

Daley

Clifton

Whelan

2002

Proc. Natl. Acad. Sci. U.S.A.

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“…Protein Sequence Analysis-Mitochondrial targeting sequences were analyzed using MitoProt II (23,24). The same program was used to calculate the segments with high local hydrophobicity (ϽHϾ) in a distance comprising 13 to 17 residues.…”

Section: Methodsmentioning

confidence: 99%

Subunit II of Cytochrome c Oxidase in Chlamydomonad Algae Is a Heterodimer Encoded by Two Independent Nuclear Genes

Pérez-Martı́nez

Antaramián

Vázquez-Acevedo

et al. 2001

Journal of Biological Chemistry

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The mitochondrial genomes of Chlamydomonad algae lack the cox2 gene that encodes the essential subunit COX II of cytochrome c oxidase. COX II is normally a single polypeptide encoded by a single mitochondrial gene. In this work we cloned two nuclear genes encoding COX II from both Chlamydomonas reinhardtii and Polytomella sp. The cox2a gene encodes a protein, COX IIA, corresponding to the N-terminal portion of subunit II of cytochrome c oxidase, and the cox2b gene encodes COX IIB, corresponding to the C-terminal region. The cox2a and cox2b genes are located in the nucleus and are independently transcribed into mRNAs that are translated into separate polypeptides. These two proteins assemble with other cytochrome c oxidase subunits in the inner mitochondrial membrane to form the mature multi-subunit complex. We propose that during the evolution of the Chlorophyte algae, the cox2 gene was divided into two mitochondrial genes that were subsequently transferred to the nucleus. This event was evolutionarily distinct from the transfer of an intact cox2 gene to the nucleus in some members the Leguminosae plant family.

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“…To determine possible compartmentalization of TAG synthesis in this organism, SignalP (Petersen et al, 2011), ChloroP (Emanuelsson et al, 1999), Mitoprot (Claros, 1995), and HECTAR (Gschloessl et al, 2008) were used to predict subcellular localization of the 13 DGAT genes. A Type II signal anchor was detected in DGAT-2A, 2H, and 2K (Supplemental Data Set 6).…”

Section: Tag Synthesis Via the Kennedy Pathwaymentioning

confidence: 99%

Choreography of Transcriptomes and Lipidomes ofNannochloropsisReveals the Mechanisms of Oil Synthesis in Microalgae

et al. 2014

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To reveal the molecular mechanisms of oleaginousness in microalgae, transcriptomic and lipidomic dynamics of the oleaginous microalga Nannochloropsis oceanica IMET1 under nitrogen-replete (N+) and N-depleted (N-) conditions were simultaneously tracked. At the transcript level, enhanced triacylglycerol (TAG) synthesis under N-conditions primarily involved upregulation of seven putative diacylglycerol acyltransferase (DGAT) genes and downregulation of six other DGAT genes, with a simultaneous elevation of the other Kennedy pathway genes. Under N-conditions, despite downregulation of most de novo fatty acid synthesis genes, the pathways that shunt carbon precursors from protein and carbohydrate metabolic pathways into glycerolipid synthesis were stimulated at the transcript level. In particular, the genes involved in supplying carbon precursors and energy for de novo fatty acid synthesis, including those encoding components of the pyruvate dehydrogenase complex (PDHC), glycolysis, and PDHC bypass, and suites of specific transporters, were substantially upregulated under N-conditions, resulting in increased overall TAG production. Moreover, genes involved in the citric acid cycle and b-oxidation in mitochondria were greatly enhanced to utilize the carbon skeletons derived from membrane lipids and proteins to produce additional TAG or its precursors. This temporal and spatial regulation model of oil accumulation in microalgae provides a basis for improving our understanding of TAG synthesis in microalgae and will also enable more rational genetic engineering of TAG production.

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MitoProt, a Macintosh application for studying mitochondrial proteins

Cited by 143 publications

References 0 publications

Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochromecoxidase

Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochromecoxidase

Subunit II of Cytochrome c Oxidase in Chlamydomonad Algae Is a Heterodimer Encoded by Two Independent Nuclear Genes

Choreography of Transcriptomes and Lipidomes ofNannochloropsisReveals the Mechanisms of Oil Synthesis in Microalgae

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