NORMAL GENOMIC

• Artal-Sanz M, Tavernarakis N
• Opposing function of mitochondrial prohibitin in aging.
• Aging (Albany NY). 2010; 2: 1004-11
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• While specific signalling cascades involved in aging, such as theinsulin/IGF-1 pathway, are well-described, the actual metabolic changesthey elicit to prolong lifespan remain obscure. Nevertheless, the tuningof cellular metabolism towards maximal survival is the molecular basis oflongevity. The eukaryotic mitochondrial prohibitin complex is amacromolecular structure at the inner mitochondrial membrane, implicatedin several important cellular processes such as mitochondrial biogenesisand function, molecular signalling, replicative senescence, and celldeath. Recent studies inC. elegans have revealed that prohibitindifferentially influences aging by moderating fat metabolism and energyproduction, in response to both intrinsic signalling events and extrinsiccues. These findings indicate that prohibitin is a context-dependentmodulator of longevity. The tight evolutionary conservation and ubiquitousexpression of prohibitin proteins suggest a similar role for themitochondrial prohibitin complex during aging in other organisms.

• Hinderhofer M, Walker CA, Friemel A, Stuermer CA, Moller HM, Reuter A
• Evolution of prokaryotic SPFH proteins.
• BMC Evol Biol. 2009; 9: 10-10
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• BACKGROUND: The SPFH protein superfamily is a diverse family of proteinswhose eukaryotic members are involved in the scaffolding ofdetergent-resistant microdomains. Recently the origin of the SPFH proteinshas been questioned. Instead, convergent evolution has been proposed.However, an independent, convergent evolution of three large prokaryoticand three eukaryotic families is highly unlikely, especially when othermechanisms such as lateral gene transfer which could also explain theirdistribution pattern have not yet been considered.To gain better insightinto this very diverse protein family, we have analyzed the genomes of 497microorganisms and investigated the pattern of occurrence as well as thegenomic vicinity of the prokaryotic SPFH members. RESULTS: According tosequence and operon structure, a clear division into 12 subfamilies wasevident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conservedoperon structure and two additional subfamilies are linked to those threethrough functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsHprotease). Therefore these subgroups most likely share common ancestry.The complex pattern of occurrence among the different phyla is indicativeof lateral gene transfer. Organisms that do not possess a single SPFHprotein are almost exclusively endosymbionts or endoparasites. CONCLUSION:The conserved operon structure and functional similarities suggest that atleast 5 subfamilies that encompass almost 75% of all prokaryotic SPFHmembers share a common origin. Their similarity to the differenteukaryotic SPFH families, as well as functional similarities, suggeststhat the eukaryotic SPFH families originated from different prokaryoticSPFH families rather than one. This explains the difficulties in obtaininga consistent phylogenetic tree of the eukaryotic SPFH members.Phylogenetic evidence points towards lateral gene transfer as one sourceof the very diverse patterns of occurrence in bacterial species.

• Rugarli EI, Langer T
• Translating m-AAA protease function in mitochondria to hereditary spasticparaplegia.
• Trends Mol Med. 2006; 12: 262-9
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• Hereditary spastic paraplegia (HSP) is a genetically heterogeneousneurodegenerative disorder that is characterized by progressive andcell-specific axonal degeneration. An autosomal recessive form of thedisease is caused by mutations in paraplegin, which is a conserved subunitof the ubiquitous and ATP-dependent m-AAA protease in mitochondria. Them-AAA protease carries out protein quality control in the inner membraneof the mitochondria, suggesting a pathogenic role of misfolded proteins inHSP. A recent study demonstrates that the m-AAA protease regulatesribosome assembly and translation within mitochondria by controllingproteolytic maturation of a ribosomal subunit. Here, we will discussimplications of the dual role of the m-AAA protease in protein activationand degradation for mitochondrial dysfunction and axonal degeneration.

• Kaser M, Kambacheld M, Kisters-Woike B, Langer T
• Oma1, a novel membrane-bound metallopeptidase in mitochondria withactivities overlapping with the m-AAA protease.
• J Biol Chem. 2003; 278: 46414-23
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• The integrity of the inner membrane of mitochondria is maintained by amembrane-embedded quality control system that ensures the removal ofmisfolded membrane proteins. Two ATP-dependent AAA proteases withcatalytic sites at opposite membrane surfaces are key components of thisproteolytic system. Here we describe the identification of a novelconserved metallopeptidase that exerts activities overlapping with them-AAA protease and was therefore termed Oma1. Both peptidases are integralparts of the inner membrane and mediate the proteolytic breakdown of amisfolded derivative of the polytopic inner membrane protein Oxa1. Them-AAA protease cleaves off the matrix-exposed C-terminal domain of Oxa1and processively degrades its transmembrane domain. In the absence of them-AAA protease, proteolysis of Oxa1 is mediated in an ATP-independentmanner by Oma1 and a yet unknown peptidase resulting in the accumulationof N- and C-terminal proteolytic fragments. Oma1 exposes its proteolyticcenter to the matrix side; however, mapping of Oma1 cleavage sites revealsclipping of Oxa1 in loop regions at both membrane surfaces. These resultsidentify Oma1 as a novel component of the quality control system in theinner membrane of mitochondria. Proteins homologous to Oma1 are present inhigher eukaryotic cells, eubacteria and archaebacteria, suggesting thatOma1 is the founding member of a conserved family of membrane-embeddedmetallopeptidases.

• Calero M, Whittaker GR, Collins RN
• Yop1p, the yeast homolog of the polyposis locus protein 1, interacts withYip1p and negatively regulates cell growth.
• J Biol Chem. 2001; 276: 12100-12
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• Rab proteins are small GTPases that are essential elements of the proteintransport machinery of eukaryotic cells. Each round of membrane transportrequires a cycle of Rab protein nucleotide binding and hydrolysis. We haverecently characterized a protein, Yip1p, which appears to play a role inRab-mediated membrane transport in Saccharomyces cerevisiae. In thisstudy, we report the identification of a Yip1p-associated protein, Yop1p.Yop1p is a membrane protein with a hydrophilic region at its N terminusthrough which it interacts specifically with the cytosolic domain ofYip1p. Yop1p could also be coprecipitated with Rab proteins from totalcellular lysates. The TB2 gene is the human homolog of Yop1p (Kinzler, K.W., Nilbert, M. C., Su, L.-K., Vogelstein, B., Bryan, T. M., Levey, D. B.,Smith, K. J., Preisinger, A. C., Hedge, P., McKechnie, D., Finniear, R.,Markham, A., Groffen, J., Boguski, M. S., Altschul, S. F., Horii, A.,Ando, H. M., Y., Miki, Y., Nishisho, I., and Nakamura, Y. (1991) Science253, 661-665). Our data demonstrate that Yop1p negatively regulates cellgrowth. Disruption of YOP1 has no apparent effect on cell viability, whileoverexpression results in cell death, accumulation of internal cellmembranes, and a block in membrane traffic. These results suggest thatYop1p acts in conjunction with Yip1p to mediate a common step in membranetraffic.

• Klanner C, Prokisch H, Langer T
• MAP-1 and IAP-1, two novel AAA proteases with catalytic sites on oppositemembrane surfaces in mitochondrial inner membrane of Neurospora crassa.
• Mol Biol Cell. 2001; 12: 2858-69
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• Eukaryotic AAA proteases form a conserved family of membrane-embeddedATP-dependent proteases but have been analyzed functionally only in theyeast Saccharomyces cerevisiae. Here, we have identified two novel membersof this protein family in the filamentous fungus Neurospora crassa, whichwere termed MAP-1 and IAP-1. Both proteins are localized to the innermembrane of mitochondria. They are part of two similar-sized highmolecular mass complexes, but expose their catalytic sites to oppositemembrane surfaces, namely, the intermembrane and the matrix space.Disruption of iap-1 by repeat-induced point mutation caused a slow growthphenotype at high temperature and stabilization of a misfolded innermembrane protein against degradation. IAP-1 could partially substitute forfunctions of its yeast homolog Yme1, demonstrating functionalconservation. However, respiratory growth at 37 degrees C was notrestored. Our results identify two components of the quality controlsystem of the mitochondrial inner membrane in N. crassa and suggest thatAAA proteases with catalytic sites exposed to opposite membrane surfacesare present in mitochondria of all eukaryotic cells.

• Lemaire C, Hamel P, Velours J, Dujardin G
• Absence of the mitochondrial AAA protease Yme1p restores F0-ATPase subunitaccumulation in an oxa1 deletion mutant of Saccharomyces cerevisiae.
• J Biol Chem. 2000; 275: 23471-5
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• The nuclear gene OXA1 encodes a protein located within the mitochondrialinner membrane that is required for the biogenesis of both cytochrome coxidase (Cox) and ATPase. In the absence of Oxa1p, the translocation ofthe mitochondrially encoded subunit Cox2p to the intermembrane space (alsoreferred to as export) is prevented, and it has been proposed that Oxa1pcould be a component of a general mitochondrial export machinery. We haveexamined the role of Oxa1p in light of its relationships with twomitochondrial proteases, the matrix protease Afg3p-Rca1p and theintermembrane space protease Yme1p, by analyzing the assembly and activityof the Cox and ATPase complexes in Deltaoxa1, Deltaoxa1Deltaafg3, andDeltaoxa1Deltayme1 mutants. We show that membrane subunits of bothcomplexes are specifically degraded in the absence of Oxa1p. Neither Afg3pnor Yme1p is responsible for the degradation of Cox subunits. However, theF(0) subunits Atp4p, Atp6p, and Atp17p are stabilized in theDeltaoxa1Deltayme1 double mutant, and oligomycin-sensitive ATPase activityis restored, showing that the increased stability of the ATPase subunitsallows significant translocation and assembly to occur even in the absenceof Oxa1p. These results suggest that Oxa1p is not essential for the exportof ATPase subunits. In addition, although respiratory function isdispensable in Saccharomyces cerevisiae, we show that the simultaneousinactivation of AFG3 and YME1 is lethal and that the essential functiondoes not reside in their protease activity.

• Egan B et al.
• Targeting of tail-anchored proteins to yeast mitochondria in vivo.
• FEBS Lett. 1999; 451: 243-8
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• Tail-anchored proteins are inserted into intracellular membranes via aC-terminal transmembrane domain. The topology of the protein is such thatinsertion must occur post-translationally, since the insertion sequence isnot available for membrane insertion until after translation of thetail-anchored polypeptide is completed. Here, we show that the targetinginformation in one such tail-anchored protein, translocase in the outermitochondrial membrane 22, is contained in a short region flanking thetransmembrane domain. An equivalent region is sufficient to specify thelocalisation of Bcl2 and SNARE proteins to the secretory membranes. Wediscuss the targeting process for directing members of this protein familyto the secretory and mitochondrial membranes in vivo.

• Jacob G, Tellez R, Torres W, Ocasio R, Basilio C, George-Nascimento C
• Proteolysis of mitochondrial-coded and nuclear-coded proteins found inyeast mitochondria.
• Arch Biol Med Exp (Santiago). 1988; 21: 145-50
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• The rate of degradation of radioactive labeled mitochondrial proteinssynthesized both in vitro and in vivo by isolated yeast mitochondria andgrowing yeast cells respectively, has been studied. It was found that thein vitro-synthesized mitochondrial proteins are rapidly degraded by anenergy-dependent proteolytic system. Under the same experimentalconditions the in vivo-synthesized mitochondrial proteins are slowlydegraded to a limited extent by a protease which is slightly inhibited byATP. During this period, the mitochondria are coupled and metabolicallyactive. It is proposed that mitochondria possess an energy-dependentproteolytic system that recognizes as substrates either "abnormal"proteins or unassembled protein subunits encoded in the mitochondrialgenome. An apparently different system, which is independent of energy,seems to be responsible for the slow and limited degradation of "normal"mitochondrial proteins.