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Michel Fevre - One of the best experts on this subject based on the ideXlab platform.

  • the glucose repressor cre1 from sclerotinia sclerotiorum is functionally related to crea from aspergillus nidulans but not to the mig Proteins from saccharomyces cerevisiae
    FEBS Letters, 1999
    Co-Authors: Geraldine Vautard, Pascale Cotton, Michel Fevre
    Abstract:

    We isolated the putative glucose repressor gene cre1 from the phytopathogenic fungus Sclerotinia sclerotiorum. cre1 encodes a 429 amino Acid Protein 59% similar to the carbon catabolite repressor CREA from Aspergillus nidulans. In addition to the overall amino Acid sequence relatedness between CRE1 and CREA Proteins, cre1 can functionally complement the A. nidulans creAd30 mutation as assessed by repression of the alcohol dehydrogenase I gene expression. The CRE1 region carrying the two zinc fingers is also very similar to the DNA binding domains of the Saccharomyces cerevisiae glucose repressors Mig1p and Mig2p. Despite the presence in the CRE1 Protein of several motifs involved in the regulation of Mig1p activity, cre1 cannot complement mig deficiencies in S. cerevisiae. These data suggest that glucose repression pathways may have evolved differently in yeasts and filamentous fungi.

Jeffrey S Simske - One of the best experts on this subject based on the ideXlab platform.

Ajit Kumar - One of the best experts on this subject based on the ideXlab platform.

  • Information theory and signal processing methodology to identify nucleic Acid-Protein binding sequences in RNA-Protein interactions
    2019 53rd Annual Conference on Information Sciences and Systems (CISS), 2019
    Co-Authors: Harry Shaw, Nagarajan Pattabiraman, Deborah Preston, Tatiana Ammosova, Yuri Obukhov, Sergei Nekhai, Ajit Kumar
    Abstract:

    RNA binding Proteins are known to modulate an impressive array of cellular processes. Recent studies have focused on a variety of techniques to analyze RNA-Protein (RBP) complex formation including NMR, X-ray crystallography, and mass spectrometry. To explore the factors that regulate RBP formation, we developed a computational method as a step prior to biochemical validation of RBP by mass spectrometry. Here we describe a methodology to predict the sequences involved in RNA-Protein complex formation including transient interactions. The approach is based on an information entropy-based algorithm calibrated against known ΔG and binding probabilities for RNA nucleotides-amino Acid residues. The method is then used to predict binding sites of specific RNA associated Proteins identified by mass spectroscopy of RNA associated Proteins. The estimates of specific nucleotide peptide interactions was based on the Gibbs free energy of nucleotide-peptide fragments in a given RBP complex, and a dynamic model that uses multiple binding sites within a nucleotide-peptide fragment to quantify the binding affinity of weak and transient RNA-Protein interactions. A concept originally described by Claude Shannon is now being used to foster a new paradigm for assisting in the search for specific RNA-Protein binding sites. In this paper we will detail the following information, in order: 1. An information-theoretic based approach to modelling RNA-Protein interactions down to specific RNA-Protein complex motifs based upon information entropy; 2. The theory applied to a calibration dataset of known RNA-Protein interactions to predict the RNA-Protein binding motifs; 3. A prediction of RNA-Protein binding motifs on a set of co-immunoprecipitation assays.

  • information theory and signal processing methodology to identify nucleic Acid Protein binding sequences in rna Protein interactions
    Conference on Information Sciences and Systems, 2019
    Co-Authors: Harry Shaw, Nagarajan Pattabiraman, Deborah Preston, Tatiana Ammosova, Yuri Obukhov, Sergei Nekhai, Ajit Kumar
    Abstract:

    RNA binding Proteins are known to modulate an impressive array of cellular processes. Recent studies have focused on a variety of techniques to analyze RNA-Protein (RBP) complex formation including NMR, X-ray crystallography, and mass spectrometry. To explore the factors that regulate RBP formation, we developed a computational method as a step prior to biochemical validation of RBP by mass spectrometry. Here we describe a methodology to predict the sequences involved in RNA-Protein complex formation including transient interactions. The approach is based on an information entropy-based algorithm calibrated against known $\Delta \mathrm {G}$ and binding probabilities for RNA nucleotides-amino Acid residues. The method is then used to predict binding sites of specific RNA associated Proteins identified by mass spectroscopy of RNA associated Proteins. The estimates of specific nucleotide peptide interactions was based on the Gibbs free energy of nucleotide-peptide fragments in a given RBP complex, and a dynamic model that uses multiple binding sites within a nucleotide-peptide fragment to quantify the binding affinity of weak and transient RNA-Protein interactions. A concept originally described by Claude Shannon is now being used to foster a new paradigm for assisting in the search for specific RNA-Protein binding sites. In this paper we will detail the following information, in order: 1. An information-theoretic based approach to modelling RNA-Protein interactions down to specific RNA-Protein complex motifs based upon information entropy; 2. The theory applied to a calibration dataset of known RNA-Protein interactions to predict the RNA-Protein binding motifs; 3. A prediction of RNA-Protein binding motifs on a set of co-immunoprecipitation assays.

Geraldine Vautard - One of the best experts on this subject based on the ideXlab platform.

  • the glucose repressor cre1 from sclerotinia sclerotiorum is functionally related to crea from aspergillus nidulans but not to the mig Proteins from saccharomyces cerevisiae
    FEBS Letters, 1999
    Co-Authors: Geraldine Vautard, Pascale Cotton, Michel Fevre
    Abstract:

    We isolated the putative glucose repressor gene cre1 from the phytopathogenic fungus Sclerotinia sclerotiorum. cre1 encodes a 429 amino Acid Protein 59% similar to the carbon catabolite repressor CREA from Aspergillus nidulans. In addition to the overall amino Acid sequence relatedness between CRE1 and CREA Proteins, cre1 can functionally complement the A. nidulans creAd30 mutation as assessed by repression of the alcohol dehydrogenase I gene expression. The CRE1 region carrying the two zinc fingers is also very similar to the DNA binding domains of the Saccharomyces cerevisiae glucose repressors Mig1p and Mig2p. Despite the presence in the CRE1 Protein of several motifs involved in the regulation of Mig1p activity, cre1 cannot complement mig deficiencies in S. cerevisiae. These data suggest that glucose repression pathways may have evolved differently in yeasts and filamentous fungi.

Vladimír Pevala - One of the best experts on this subject based on the ideXlab platform.

  • The role of Lon-mediated proteolysis in the dynamics of mitochondrial nucleic Acid-Protein complexes
    Scientific Reports, 2017
    Co-Authors: Nina Kunová, Gabriela Ondrovičová, Jana Bellová, Ľuboš Ambro, Lucia Martináková, Veronika Kotrasová, Eva Kutejová, Jacob A. Bauer, Vladimír Pevala
    Abstract:

    Mitochondrial nucleoids consist of several different groups of Proteins, many of which are involved in essential cellular processes such as the replication, repair and transcription of the mitochondrial genome. The eukaryotic, ATP-dependent protease Lon is found within the central nucleoid region, though little is presently known about its role there. Aside from its association with mitochondrial nucleoids, human Lon also specifically interacts with RNA. Recently, Lon was shown to regulate TFAM, the most abundant mtDNA structural factor in human mitochondria. To determine whether Lon also regulates other mitochondrial nucleoid- or ribosome-associated Proteins, we examined the in vitro digestion profiles of the Saccharomyces cerevisiae TFAM functional homologue Abf2, the yeast mtDNA maintenance Protein Mgm101, and two human mitochondrial Proteins, Twinkle helicase and the large ribosomal subunit Protein MrpL32. Degradation of Mgm101 was also verified in vivo in yeast mitochondria. These experiments revealed that all four Proteins are actively degraded by Lon, but that three of them are protected from it when bound to a nucleic Acid; the Twinkle helicase is not. Such a regulatory mechanism might facilitate dynamic changes to the mitochondrial nucleoid, which are crucial for conducting mitochondrial functions and maintaining mitochondrial homeostasis.