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Grazia Isaya - One of the best experts on this subject based on the ideXlab platform.

  • 90 – Mitochondrial Intermediate Peptidase
    Handbook of Proteolytic Enzymes, 2004
    Co-Authors: Grazia Isaya
    Abstract:

    Publisher Summary This chapter examines the structural chemistry and the preparation of Mitochondrial Intermediate Peptidase (MIP). MIP denotes cleavage of Intermediate-sized Mitochondrial proteins to the mature form. MIP activity can be measured by incubation of in vitro translated octapeptide-containing precursors with isolated mitochondria. Under such conditions, the cleavage catalyzed by MIP is at the end of a Mitochondrial protein import reaction which also involves outer membrane receptors, outer and inner membrane translocation complexes, molecular chaperones and MPP. If the precursor is incubated directly with Mitochondrial matrix or purified enzyme, initial cleavage by MPP is required to observe processing of the Intermediate by MIP. This requirement is circumvented when MIP activity is determined using an Intermediate protein as the substrate. Intermediates that are translated in vitro from a methionine artificially placed at the octapeptide N-terminus can be processed to the mature form by MIP independent of the presence of MPP. Native RMIP has been purified 2250-fold from rat liver Mitochondrial matrix with a final yield of about 2%. Expression of recombinant enzyme has been achieved in S. cerevisiae.

  • 90 Mitochondrial Intermediate Peptidase
    Handbook of Proteolytic Enzymes (Second Edition)#R##N#Aspartic and Metallo Peptidases, 2004
    Co-Authors: Grazia Isaya
    Abstract:

    Publisher Summary This chapter examines the structural chemistry and the preparation of Mitochondrial Intermediate Peptidase (MIP). MIP denotes cleavage of Intermediate-sized Mitochondrial proteins to the mature form. MIP activity can be measured by incubation of in vitro translated octapeptide-containing precursors with isolated mitochondria. Under such conditions, the cleavage catalyzed by MIP is at the end of a Mitochondrial protein import reaction which also involves outer membrane receptors, outer and inner membrane translocation complexes, molecular chaperones and MPP. If the precursor is incubated directly with Mitochondrial matrix or purified enzyme, initial cleavage by MPP is required to observe processing of the Intermediate by MIP. This requirement is circumvented when MIP activity is determined using an Intermediate protein as the substrate. Intermediates that are translated in vitro from a methionine artificially placed at the octapeptide N-terminus can be processed to the mature form by MIP independent of the presence of MPP. Native RMIP has been purified 2250-fold from rat liver Mitochondrial matrix with a final yield of about 2%. Expression of recombinant enzyme has been achieved in S. cerevisiae.

  • Mitochondrial processing Peptidases.
    Biochimica et Biophysica Acta, 2002
    Co-Authors: Oleksandr Gakh, Patrizia Cavadini, Grazia Isaya
    Abstract:

    Three Peptidases are responsible for the proteolytic processing of both nuclearly and Mitochondrially encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. Mitochondrial processing Peptidase (MPP) cleaves the vast majority of Mitochondrial proteins, while inner membrane Peptidase (IMP) and Mitochondrial Intermediate Peptidase (MIP) process specific subsets of precursor polypeptides. All three enzymes are structurally and functionally conserved across species, and their human homologues begin to be recognized as potential players in Mitochondrial disease.

  • Functional and genomic analysis of the human Mitochondrial Intermediate Peptidase, a putative protein partner of frataxin.
    Genomics, 2000
    Co-Authors: Anne Chew, Giorgio Sirugo, John P. Alsobrook, Grazia Isaya
    Abstract:

    Abstract We showed recently that the yeast Mitochondrial Intermediate Peptidase (YMIP polypeptide; gene symbol, OCT1 ) promotes Mitochondrial iron uptake by catalyzing the maturation of iron-utilizing proteins and exacerbates the Mitochondrial iron accumulation that results from loss of yeast frataxin, a Mitochondrial protein required for Mitochondrial iron efflux. This suggests that the human MIP (HMIP polypeptide; gene symbol MIPEP ) may be one of the loci predicted to influence the clinical manifestations of Friedreich's ataxia (FRDA), an autosomal recessive neurodegenerative disease caused by lack of human frataxin. To begin to test this hypothesis, we have characterized HMIP at the functional and genomic levels. We show that HMIP can complement a yeast knock-out mutant lacking YMIP, demonstrating that HMIP and YMIP are functional homologues. The MIPEP gene spans 57 kb and consists of 19 exons that correlate with the functional domains of HMIP. Primer extension analysis has identified a major transcript of the MIPEP gene expressed differentially and predominantly in tissues with high oxygen consumption, while sequence analysis of ∼2 kb of 5′-flanking DNA has revealed putative Mt1/3/4, NF-κB, and AP-1 elements that may regulate MIPEP expression in these tissues. Using a new polymorphic (CA) n repeat in intron 4, MIPEP has been genetically mapped within a 7-cM interval between markers D13S283 and D13S217 on 13q12. This work provides the basis for molecular analysis of MIPEP in FRDA and possibly other neurodegenerative diseases.

  • Mitochondrial Intermediate Peptidase and the Yeast Frataxin Homolog Together Maintain Mitochondrial Iron Homeostasis in Saccharomyces Cerevisiae
    Human Molecular Genetics, 1999
    Co-Authors: Steven S. Branda, Anne Chew, Zhi Yong Yang, Grazia Isaya
    Abstract:

    Friedreich's ataxia (FRDA) is a neurodegenerative disease typically caused by a deficiency of frataxin, a Mitochondrial protein of unknown function. In Saccharomyces cerevisiae, lack of the yeast frataxin homolog ( YFH1 gene, Yfh1p polypeptide) results in Mitochondrial iron accumulation, suggesting that frataxin is required for Mitochondrial iron homeostasis and that FRDA results from oxidative damage secondary to Mitochondrial iron overload. This hypothesis implies that the effects of frataxin deficiency could be influenced by other proteins involved in Mitochondrial iron usage. We show that Yfh1p interacts functionally with yeast Mitochondrial Intermediate Peptidase ( OCT1 gene, YMIP polypeptide), a metalloprotease required for maturation of ferrochelatase and other iron-utilizing proteins. YMIP is activated by ferrous iron in vitro and loss of YMIP activity leads to Mitochondrial iron depletion, suggesting that YMIP is part of a feedback loop in which iron stimulates maturation of YMIP substrates and this in turn promotes Mitochondrial iron uptake. Accordingly, YMIP is active and promotes Mitochondrial iron accumulation in a mutant lacking Yfh1p ( yfh1 [Delta]), while genetic inactivation of YMIP in this mutant ( yfh1 [Delta] oct1 [Delta]) leads to a 2-fold reduction in Mitochondrial iron levels. Moreover, overexpression of Yfh1p restores Mitochondrial iron homeostasis and YMIP activity in a conditional oct1 ts mutant, but does not affect iron levels in a mutant completely lacking YMIP ( oct1 [Delta]). Thus, we propose that Yfh1p maintains Mitochondrial iron homeostasis both directly, by promoting iron export, and indirectly, by regulating iron levels and therefore YMIP activity, which promotes Mitochondrial iron uptake. This suggests that human MIP may contribute to the functional effects of frataxin deficiency and the clinical manifestations of FRDA.

Brenda D. Wingfield - One of the best experts on this subject based on the ideXlab platform.

  • Characterization of the systems governing sexual and self-recognition in the white rot homobasidiomycete Amylostereum areolatum
    Current Genetics, 2008
    Co-Authors: Magriet A. Nest, Jan Stenlid, Bernard Slippers, Pieter M. Wilken, Rimvis Vasaitis, Michael J. Wingfield, Brenda D. Wingfield
    Abstract:

    This study considered the systems controlling sexual and self-recognition in Amylostereum   areolatum , a homobasidiomycetous symbiont of the Sirex woodwasp. To investigate the structure and organization of these systems in A.   areolatum , we identified a portion of a putative homologue (RAB1) of the pheromone receptor genes of Schizophyllum   commune and Coprinus   cinereus , and a portion of a putative homologue of the S.   commune Mitochondrial Intermediate Peptidase ( mip ) gene. Diagnostic DNA-based assays for mating-type were developed and their application confirmed that the fungus has a heterothallic tetrapolar mating system. Segregation analysis showed that RAB1 is linked to mating-type B, while mip is linked to mating-type A. The results of sexual and vegetative compatibility tests suggest that sexual recognition in A.   areolatum is controlled by two multiallelic mat loci, while self-recognition is controlled by at least two multiallelic het loci. Therefore, despite the association of A.   areolatum with the woodwasp and the unique mixture of sexual and clonal reproduction of the fungus, both recognition systems of the fungus appear to be similar in structure and function to those of other homobasidiomycetes. This is the first report regarding the genes controlling recognition of a homobasidiomycete involved in an obligate mutualistic relationship with an insect.

  • Characterization of the systems governing sexual and self-recognition in the white rot homobasidiomycete Amylostereum areolatum
    Current Genetics, 2008
    Co-Authors: Magriet A. Van Der Nest, Jan Stenlid, Bernard Slippers, Pieter M. Wilken, Rimvis Vasaitis, Michael J. Wingfield, Brenda D. Wingfield
    Abstract:

    This study considered the systems controlling sexual and self-recognition in Amylostereum areolatum, a homobasidiomycetous symbiont of the Sirex woodwasp. To investigate the structure and organization of these systems in A. areolatum, we identified a portion of a putative homologue (RAB1) of the pheromone receptor genes of Schizophyllum commune and Coprinus cinereus, and a portion of a putative homologue of the S. commune Mitochondrial Intermediate Peptidase (mip) gene. Diagnostic DNA-based assays for mating-type were developed and their application confirmed that the fungus has a heterothallic tetrapolar mating system. Segregation analysis showed that RAB1 is linked to mating-type B, while mip is linked to mating-type A. The results of sexual and vegetative compatibility tests suggest that sexual recognition in A. areolatum is controlled by two multiallelic mat loci, while self-recognition is controlled by at least two multiallelic het loci. Therefore, despite the association of A. areolatum with the woodwasp and the unique mixture of sexual and clonal reproduction of the fungus, both recognition systems of the fungus appear to be similar in structure and function to those of other homobasidiomycetes. This is the first report regarding the genes controlling recognition of a homobasidiomycete involved in an obligate mutualistic relationship with an insect.

Jan Stenlid - One of the best experts on this subject based on the ideXlab platform.

  • DNA sequence alignment of MIP gene
    2016
    Co-Authors: Linda T. A. Van Diepen, Åke Olson, Ihrmark Katarina, Jan Stenlid, Timothy Y. James
    Abstract:

    Alignment of coding DNA sequences of the Mitochondrial Intermediate Peptidase gene (MIP), created in MacClade 4.08

  • Extensive Trans-Specific Polymorphism at the Mating Type Locus of the Root Decay Fungus Heterobasidion
    Molecular Biology and Evolution, 2013
    Co-Authors: Linda T. A. Van Diepen, Åke Olson, Jan Stenlid, Katarina Ihrmark, Timothy Y. James
    Abstract:

    Incompatibility systems in which individuals bearing identical alleles reject each other favor the maintenance of a diversity of alleles. Mushroom mating type loci (MAT) encode for dozens or hundreds of incompatibility alleles whose loss from the population is greatly restricted through negative frequency selection, leading to a system of alleles with highly divergent sequences. Here, we use DNA sequences of homeodomain (HD) encoding genes at the MAT locus of five closely related species of the root rot basidiomycete Heterobasidion annosum sensu lato to show that the extended coalescence time of MAT alleles greatly predates speciation in the group, contrasting loci outside of MAT that show allele divergences largely consistent with the species phylogeny with those of MAT, which show rampant trans-species polymorphism. We observe a roughly 6-fold greater genealogical depth and polymorphism of MAT compared with non-MAT that argues for the maintenance of balanced polymorphism for a minimum duration of 24 My based on a molecular-clock calibrated species phylogeny. As with other basidiomycete HD genes, balancing selection appears to be concentrated at the specificity-determining region in the N-terminus of the protein based on identification of codons under selection and the absence of recombination within the region. However, the elevated polymorphism extends into the nonspecificity determining regions as well as a neighboring non-MAT gene, the Mitochondrial Intermediate Peptidase (MIP). In doing so, increased divergence should decrease recombination among alleles and as a by-product create incompatibilities in the functional domains not involved in allele recognition but in regulating sexual development.

  • Characterization of the systems governing sexual and self-recognition in the white rot homobasidiomycete Amylostereum areolatum
    Current Genetics, 2008
    Co-Authors: Magriet A. Nest, Jan Stenlid, Bernard Slippers, Pieter M. Wilken, Rimvis Vasaitis, Michael J. Wingfield, Brenda D. Wingfield
    Abstract:

    This study considered the systems controlling sexual and self-recognition in Amylostereum   areolatum , a homobasidiomycetous symbiont of the Sirex woodwasp. To investigate the structure and organization of these systems in A.   areolatum , we identified a portion of a putative homologue (RAB1) of the pheromone receptor genes of Schizophyllum   commune and Coprinus   cinereus , and a portion of a putative homologue of the S.   commune Mitochondrial Intermediate Peptidase ( mip ) gene. Diagnostic DNA-based assays for mating-type were developed and their application confirmed that the fungus has a heterothallic tetrapolar mating system. Segregation analysis showed that RAB1 is linked to mating-type B, while mip is linked to mating-type A. The results of sexual and vegetative compatibility tests suggest that sexual recognition in A.   areolatum is controlled by two multiallelic mat loci, while self-recognition is controlled by at least two multiallelic het loci. Therefore, despite the association of A.   areolatum with the woodwasp and the unique mixture of sexual and clonal reproduction of the fungus, both recognition systems of the fungus appear to be similar in structure and function to those of other homobasidiomycetes. This is the first report regarding the genes controlling recognition of a homobasidiomycete involved in an obligate mutualistic relationship with an insect.

  • Characterization of the systems governing sexual and self-recognition in the white rot homobasidiomycete Amylostereum areolatum
    Current Genetics, 2008
    Co-Authors: Magriet A. Van Der Nest, Jan Stenlid, Bernard Slippers, Pieter M. Wilken, Rimvis Vasaitis, Michael J. Wingfield, Brenda D. Wingfield
    Abstract:

    This study considered the systems controlling sexual and self-recognition in Amylostereum areolatum, a homobasidiomycetous symbiont of the Sirex woodwasp. To investigate the structure and organization of these systems in A. areolatum, we identified a portion of a putative homologue (RAB1) of the pheromone receptor genes of Schizophyllum commune and Coprinus cinereus, and a portion of a putative homologue of the S. commune Mitochondrial Intermediate Peptidase (mip) gene. Diagnostic DNA-based assays for mating-type were developed and their application confirmed that the fungus has a heterothallic tetrapolar mating system. Segregation analysis showed that RAB1 is linked to mating-type B, while mip is linked to mating-type A. The results of sexual and vegetative compatibility tests suggest that sexual recognition in A. areolatum is controlled by two multiallelic mat loci, while self-recognition is controlled by at least two multiallelic het loci. Therefore, despite the association of A. areolatum with the woodwasp and the unique mixture of sexual and clonal reproduction of the fungus, both recognition systems of the fungus appear to be similar in structure and function to those of other homobasidiomycetes. This is the first report regarding the genes controlling recognition of a homobasidiomycete involved in an obligate mutualistic relationship with an insect.

Timothy Y. James - One of the best experts on this subject based on the ideXlab platform.

  • DNA sequence alignment of MIP gene
    2016
    Co-Authors: Linda T. A. Van Diepen, Åke Olson, Ihrmark Katarina, Jan Stenlid, Timothy Y. James
    Abstract:

    Alignment of coding DNA sequences of the Mitochondrial Intermediate Peptidase gene (MIP), created in MacClade 4.08

  • Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems
    Mycologia, 2013
    Co-Authors: Timothy Y. James, Sheng Sun, Joseph Heitman, Hsiao Che Kuo, Yong-hwan Lee, Fred O. Asiegbu, Åke Olson
    Abstract:

    The process of mating in Basidiomycota is regulated by homeodomain-encoding genes (HD) and pheromones and G protein-coupled pheromone receptor genes (P/R). Whether these genes are actually involved in determining mating type distinguishes mating systems that are considered tetrapolar (two locus) from bipolar (one locus). Polyporales are a diverse group of wood-decay basidiomycetes displaying high variability in mating and decay systems. Many of the bipolar species appear to be brown-rot fungi, and it has been hypothesized that there is a functional basis for this correlation. Here we characterize mating genes in recently sequenced Polyporales and other Agaricomycete genomes. All Agaricomycete genomes encode HD and pheromone receptor genes regardless of whether they are bipolar or tetrapolar. The HD genes are organized into a MAT-HD locus with a high degree of gene order conservation among neighboring genes, with the gene encoding Mitochondrial Intermediate Peptidase consistently syntenic but no linkage to...

  • Extensive Trans-Specific Polymorphism at the Mating Type Locus of the Root Decay Fungus Heterobasidion
    Molecular Biology and Evolution, 2013
    Co-Authors: Linda T. A. Van Diepen, Åke Olson, Jan Stenlid, Katarina Ihrmark, Timothy Y. James
    Abstract:

    Incompatibility systems in which individuals bearing identical alleles reject each other favor the maintenance of a diversity of alleles. Mushroom mating type loci (MAT) encode for dozens or hundreds of incompatibility alleles whose loss from the population is greatly restricted through negative frequency selection, leading to a system of alleles with highly divergent sequences. Here, we use DNA sequences of homeodomain (HD) encoding genes at the MAT locus of five closely related species of the root rot basidiomycete Heterobasidion annosum sensu lato to show that the extended coalescence time of MAT alleles greatly predates speciation in the group, contrasting loci outside of MAT that show allele divergences largely consistent with the species phylogeny with those of MAT, which show rampant trans-species polymorphism. We observe a roughly 6-fold greater genealogical depth and polymorphism of MAT compared with non-MAT that argues for the maintenance of balanced polymorphism for a minimum duration of 24 My based on a molecular-clock calibrated species phylogeny. As with other basidiomycete HD genes, balancing selection appears to be concentrated at the specificity-determining region in the N-terminus of the protein based on identification of codons under selection and the absence of recombination within the region. However, the elevated polymorphism extends into the nonspecificity determining regions as well as a neighboring non-MAT gene, the Mitochondrial Intermediate Peptidase (MIP). In doing so, increased divergence should decrease recombination among alleles and as a by-product create incompatibilities in the functional domains not involved in allele recognition but in regulating sexual development.

  • evolution of the gene encoding Mitochondrial Intermediate Peptidase and its cosegregation with the a mating type locus of mushroom fungi
    Fungal Genetics and Biology, 2004
    Co-Authors: Timothy Y. James, Ursula Kües, Stephen A. Rehner, Rytas Vilgalys
    Abstract:

    The high level of DNA polymorphism at the mating-type loci of mushroom fungi has made the cloning of mating-type genes difficult. As an alternative to strategies that employ sequence conservation, an approach utilizing conserved gene order could facilitate the cloning of A mating-type genes from mushroom fungi. It has been shown that a gene encoding a Mitochondrial Intermediate Peptidase (MIP) is very close (<1 kbp) to the A mating-type locus of two model mushroom species. In this study, the cosegregation of MIP and the A mating-type locus was studied by genotyping progeny of seven additional mushroom species using PCR and genetic crosses. No evidence of any recombination between MIP and the A mating-type locus was detected among all seven species. Phylogenetic analysis of MIP sequences from diverse mushroom species agrees with the current organismal phylogeny, suggesting the sequences are generally orthologous.

  • Evolution of the gene encoding Mitochondrial Intermediate Peptidase and its cosegregation with the A mating-type locus of mushroom fungi.
    Fungal Genetics and Biology, 2004
    Co-Authors: Timothy Y. James, Ursula Kües, Stephen A. Rehner, Rytas Vilgalys
    Abstract:

    The high level of DNA polymorphism at the mating-type loci of mushroom fungi has made the cloning of mating-type genes difficult. As an alternative to strategies that employ sequence conservation, an approach utilizing conserved gene order could facilitate the cloning of A mating-type genes from mushroom fungi. It has been shown that a gene encoding a Mitochondrial Intermediate Peptidase (MIP) is very close (

Magriet A. Nest - One of the best experts on this subject based on the ideXlab platform.

  • Characterization of the systems governing sexual and self-recognition in the white rot homobasidiomycete Amylostereum areolatum
    Current Genetics, 2008
    Co-Authors: Magriet A. Nest, Jan Stenlid, Bernard Slippers, Pieter M. Wilken, Rimvis Vasaitis, Michael J. Wingfield, Brenda D. Wingfield
    Abstract:

    This study considered the systems controlling sexual and self-recognition in Amylostereum   areolatum , a homobasidiomycetous symbiont of the Sirex woodwasp. To investigate the structure and organization of these systems in A.   areolatum , we identified a portion of a putative homologue (RAB1) of the pheromone receptor genes of Schizophyllum   commune and Coprinus   cinereus , and a portion of a putative homologue of the S.   commune Mitochondrial Intermediate Peptidase ( mip ) gene. Diagnostic DNA-based assays for mating-type were developed and their application confirmed that the fungus has a heterothallic tetrapolar mating system. Segregation analysis showed that RAB1 is linked to mating-type B, while mip is linked to mating-type A. The results of sexual and vegetative compatibility tests suggest that sexual recognition in A.   areolatum is controlled by two multiallelic mat loci, while self-recognition is controlled by at least two multiallelic het loci. Therefore, despite the association of A.   areolatum with the woodwasp and the unique mixture of sexual and clonal reproduction of the fungus, both recognition systems of the fungus appear to be similar in structure and function to those of other homobasidiomycetes. This is the first report regarding the genes controlling recognition of a homobasidiomycete involved in an obligate mutualistic relationship with an insect.