PPR (pentatricopeptide repeat) proteins in mammals: important aids to mitochondrial gene expression

2008 ◽  
Vol 416 (1) ◽  
pp. e5-e6 ◽  
Author(s):  
Robert N. Lightowlers ◽  
Zofia M. A. Chrzanowska-Lightowlers

Genes encoding PPR (pentatricopeptide repeat)-containing proteins constitute one of the largest gene families in plants. The majority of these proteins are predicted to target organelles and to bind to RNA. Strikingly, there is a dearth of these proteins in mammals, although genomic searches reveal six candidates, all of which are also predicted to target the mitochondrion. Two of these proteins, POLRMT (the mitochondrial RNA polymerase) and MRPS27, a mitoribosomal protein, are involved in transcription and translation respectively. PTCD1 (pentatricopeptide repeat domain protein 1) and PTCD3 are predicted to be involved in the assembly of respiratory chain complexes, whereas mutations in one other protein, LRPPRC (leucine-rich pentatricopeptide repeat cassette), have been shown to cause defects in the levels of cytochrome c oxidase, the terminal member of the respiratory chain. In this issue of the Biochemical Journal, Xu et al. turn their attention to the remaining candidate, PTCD2. Depletion in a mouse model led to deficiencies of the third complex of the respiratory chain that caused profound ultrastructural changes in the heart. The exact molecular function of PTCD2 remains unclear, but depletion leads to an apparent lack of processing of the mitochondrial transcript encoding apocytochrome b, a critical member of complex III. These data are consistent with PTCD2 playing an important role in the post-transcriptional expression of the mitochondrial genome.

2020 ◽  
Vol 71 (18) ◽  
pp. 5495-5505 ◽  
Author(s):  
Rui Liu ◽  
Shi-Kai Cao ◽  
Aqib Sayyed ◽  
Huan-Huan Yang ◽  
Jiao Zhao ◽  
...  

Abstract C-to-U RNA editing in plant mitochondria requires the participation of many nucleus-encoded factors, most of which are pentatricopeptide repeat (PPR) proteins. There is a large number of PPR proteins and the functions many of them are unknown. Here, we report a mitochondrion-localized DYW-subgroup PPR protein, PPR27, which functions in the editing of multiple mitochondrial transcripts in maize. The ppr27 mutant is completely deficient in C-to-U editing at the ccmFN-1357 and rps3-707 sites, and editing at six other sites is substantially reduced. The lack of editing at ccmFN-1357 causes a deficiency of CcmFN protein. As CcmFN functions in the maturation pathway of cytochrome proteins that are subunits of mitochondrial complex III, its deficiency results in an absence of cytochrome c1 and cytochrome c proteins. Consequently, the assembly of mitochondrial complex III and super-complex I+III2 is decreased, which impairs the electron transport chain and respiration, leading to arrests in embryogenesis and endosperm development in ppr27. In addition, PPR27 was found to physically interact with ZmMORF1, which interacts with ZmMORF8, suggesting that these three proteins may facilitate C-to-U RNA editing via the formation of a complex in maize mitochondria. This RNA editing is essential for complex III assembly and seed development in maize.


2018 ◽  
Vol 29 (7) ◽  
pp. 776-785 ◽  
Author(s):  
Lena Böttinger ◽  
Christoph U. Mårtensson ◽  
Jiyao Song ◽  
Nicole Zufall ◽  
Nils Wiedemann ◽  
...  

Mitochondria are the powerhouses of eukaryotic cells. The activity of the respiratory chain complexes generates a proton gradient across the inner membrane, which is used by the F1FO-ATP synthase to produce ATP for cellular metabolism. In baker’s yeast, Saccharomyces cerevisiae, the cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) associate in respiratory chain supercomplexes. Iron–sulfur clusters (ISC) form reactive centers of respiratory chain complexes. The assembly of ISC occurs in the mitochondrial matrix and is essential for cell viability. The cysteine desulfurase Nfs1 provides sulfur for ISC assembly and forms with partner proteins the ISC-biogenesis desulfurase complex (ISD complex). Here, we report an unexpected interaction of the active ISD complex with the cytochrome bc1 complex and cytochrome c oxidase. The individual deletion of complex III or complex IV blocks the association of the ISD complex with respiratory chain components. We conclude that the ISD complex binds selectively to respiratory chain supercomplexes. We propose that this molecular link contributes to coordination of iron–sulfur cluster formation with respiratory activity.


2020 ◽  
Vol 71 (20) ◽  
pp. 6246-6261 ◽  
Author(s):  
Dawei Dai ◽  
Lifang Jin ◽  
Zhenzhen Huo ◽  
Shumei Yan ◽  
Zeyang Ma ◽  
...  

Abstract Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3585-3585
Author(s):  
Shrivani Sriskanthadevan ◽  
Skrtic Marko ◽  
Bozhena Livak ◽  
Yulia Jitkova ◽  
Rose Hurren ◽  
...  

Abstract Abstract 3585 Recent studies suggest that dysregulated mitochondrial oxygen consumption promotes the growth of AML cells. Therefore, we characterized the structure and metabolic function of the mitochondria in AML and normal G-CSF-mobilized hematopoietic mononuclear cells (PBSCs). Compared to PBSCs, 1o AML cells had increased mitochondrial mass as demonstrated by an increased mitochondrial DNA copy number and increased activity of matrix enzyme citrate synthase. The increased mitochondrial mass observed in 1o AML cells may represent larger mitochondria and/or more numerous mitochondria. Therefore, we evaluated the mitochondria of 1o AML and normal CD34+ hematopoietic cells by electron microscopy. The mitochondria in 1o AML cells were larger in area, but fewer in number compared to normal CD34+ cells. Mitochondria contain the respiratory chain complexes that promote oxidative phosphorylation. Given the dysregulated mitochondrial biogenesis in 1o AML cells, we examined the levels and capacity of the respiratory complexes in 1o AML and normal PBSCs. When normalized for mitochondrial mass, 1o AML cells (n = 12) had reduced activity of respiratory complexes III and IV compared to PBSCs (n = 10) (Mean complex III activity AML vs PBSC: 0.32 ± 0.04 RU vs 0.66 ± 0.11 RU p = 0.0063; Mean complex IV activity AML vs PBSC: 0.13 ± 0.01 RU vs 0.24 ± 0.02 RU, p= 0.0003). We evaluated the capacity of the respiratory complexes in AML cells and PBSCs by treating with increasing concentrations of the complex III inhibitor antimycin, and measuring the changes in oxygen consumption. AML cells displayed heightened sensitivity to the complex III inhibitor and less reserve capacity in the respiratory complex compared to PBSCs (mean concentration of antimycin required to reduce oxygen consumption by 50%: AML (n = 11) vs PBSC (n = 3): 13.7 ± 1.6 nM vs 29.0 ± 2.4 nM; p = 0.0007). AML cell lines were similar to 1o AML cells with decreased basal respiratory complex activity and reserve capacity compared to PBSCs. Given the reduced levels and reserve in the respiratory chain complexes in AML cells, we evaluated the effects of inhibiting mitochondrial protein translation in AML cells and PBSCs. Chemical (tigecycline, and chloramphenicol) and genetic (RNAi knockdown of the EF-Tu) inhibition of mitochondrial translation reduced the levels and function of the respiratory complexes that contain proteins encoded by mitochondrial DNA. Consistent with the reduced reserve capacity, inhibiting mitochondrial translation preferentially reduced oxygen consumption and viability of 1o AML cells and AML cell lines over PBSCs and normal CD34+ cells. To understand the molecular basis for the abnormal mitochondrial biogenesis in 1o AML cells, we measured levels of the NRF-1, TFAM and EF-Tu, genes known to positively regulate mitochondrial biogenesis. Compared to PBSCs, AML samples showed at least a 3-fold increase in mRNA expression of these genes. Myc is a positive regulator of NRF-1, TFAM and EF-Tu. Therefore, we measured levels of myc in 1o AML cells and PBSCs by Q-RT-PCR. Compared to PBSCs, myc was increased in 1o AML cells and positively correlated with expression of NRF-1, TFAM and EF-Tu as well as with mitochondrial mass. To determine whether increased myc expression is functionally related to the increased mitochondrial biogenesis and decreased reserve in respiratory capacity, we employed P493 Burkitt's cells with inducible myc knockdown. P493 cells expressing myc had increased mitochondrial mass, larger mitochondria, and increased basal oxygen consumption compared to the myc knockdown cells. When normalized for mitochondrial mass, myc expressing cells had reduced activity of respiratory complexes III and IV compared to myc knockdown cells. In addition, myc expressing cells had less reserve in respiratory complex III (concentration of antimycin required to reduce oxygen consumption by 50% –+ myc P493 vs –myc P493: 6.580 ± 0.393 nM vs 12.87 ± 1.97 nM p =0.0352). Thus, compared to normal hematopoietic cells, AML cells have greater mitochondrial mass but reduced reserve in their respiratory complexes. As a result of this decreased reserve, AML cells have a heightened sensitivity to inhibition of mitochondrial translation which reduces respiratory chain complex levels and activity. Genetically, the abnormal mitochondrial structure and function appears related to dysregulated myc and its influence on genes promoting increased mitochondrial biogenesis. Disclosures: No relevant conflicts of interest to declare.


2018 ◽  
Vol 60 (2) ◽  
pp. 204-214 ◽  
Author(s):  
Zhongyuan Yin ◽  
Guanghai Yang ◽  
Sisi Deng ◽  
Qiong Wang

Abstract The purpose of this study was to set up a beagle dog model, for radiation-induced lung injury, that would be able to supply fresh lung tissues in the different injury phases for research into oxidative stress levels and mitochondrial gene expression. Blood serum and tissues were collected via CT-guided core needle biopsies from dogs in the various phases of the radiation response over a 40-week period. Levels of reactive oxygen species (ROS) and manganese superoxide dismutase 2 (MnSOD) protein expression in radiation-induced lung injury were determined by in situ immunocytochemistry; malondialdehyde (MDA) content and reductase activity in the peripheral blood were also tested; in addition, the copy number of the mitochondrial DNA and the level of function of the respiratory chain in the lung tissues were assessed. ROS showed dynamic changes and peaked at 4 weeks; MnSOD was mainly expressed in the Type II alveolar epithelium at 8 weeks; the MDA content and reductase activity in the peripheral blood presented no changes; the copy numbers of most mitochondrial genes peaked at 8 weeks, similarly to the level of function of the corresponding respiratory chain complexes; the level of function of the respiratory chain complex III did not peak until 24 weeks, similarly to the level of function of the corresponding gene Cytb. Radiation-induced lung injury was found to be a dynamically changing process, mainly related to interactions between local ROS, and it was not associated with the levels of oxidative stress in the peripheral blood. Mitochondrial genes and their corresponding respiratory chain complexes were found to be involved in the overall process.


2011 ◽  
Vol 441 (1) ◽  
pp. 275-283 ◽  
Author(s):  
Fenghao Xu ◽  
Jane B. L. Addis ◽  
Jessie M. Cameron ◽  
Brian H. Robinson

LRPPRC (leucine-rich pentatricopeptide repeat-containing) has been shown to be essential for the maturation of COX (cytochrome c oxidase), possibly by stabilizing RNA transcripts of COXI, COXII and COXIII genes encoded in mtDNA (mitochondrial DNA). We established a mouse ‘gene-trap’ model using ES cells (embryonic stem cells) in which the C-terminus of LRPPRC has been replaced with a β-geo construct. Mice homozygous for this modification were found to be subject to embryonic lethality, with death before 12.5 dpc (days post-coitum). Biochemical analysis of MEFs (mouse embryonic fibroblasts) isolated from homozygous mutants showed a major decrease in COX activity, with slight reductions in other respiratory chain complexes with mtDNA encoded components. Constructs of LRPPRC containing different numbers of PPRs (pentatricopeptide repeats) were expressed as recombinant proteins and tested for their ability to bind to the COXI mRNA transcript. Full binding required the first 19 PPR motifs. A specific segment of COXI mRNA was identified as the binding target for LRPPRC, encoded by mouse mtDNA nucleotides 5961–6020. These data strongly suggest that LRPPRC is involved in the maturation of COX, and is involved in stabilizing of mitochondrial mRNAs encoding COX transcripts.


2013 ◽  
Vol 25 (2) ◽  
pp. 95-100 ◽  
Author(s):  
Tatiana Barichello ◽  
Lutiana Roque Simões ◽  
Jaqueline S. Generoso ◽  
Mirelle M. Carradore ◽  
Ana Paula Moreira ◽  
...  

BackgroundBacterial meningitis is an infection of the central nervous system characterised by strong inflammatory response. The brain is highly dependent on ATP, and the cell energy is obtained through oxidative phosphorylation, a process which requires the action of various respiratory enzyme complexes and creatine kinase (CK) as an effective buffering system of cellular ATP levels in tissues that consume high energy.ObjectivesEvaluate the activities of mitochondrial respiratory chain complexes I, II, III, IV and CK activity in hippocampus and cortex of the Wistar rat submitted to meningitis byKlebsiella pneumoniae.MethodsAdult Wistar rats received either 10 µl of sterile saline as a placebo or an equivalent volume ofK. pneumoniaesuspension. The animals were killed in different times at 6, 12, 24 and 48 h after meningitis induction. Another group was treated with antibiotic, starting at 16 h and continuing daily until their decapitation at 24 and 48 h after induction.ResultsIn the hippocampus, the meningitis group without antibiotic treatment, the complex I was increased at 24 and 48 h, complex II was increased at 48 h, complex III was inhibited at 6, 12, 24 and 48 h and in complex IV all groups with or without antibiotic treatment were inhibited after meningitis induction, in the cortex there was no alteration.DiscussionAlthough descriptive, our results show that antibiotic prevented in part the changes of the mitochondrial respiratory chain. The meningitis model could be a good research tool to study the biological mechanisms involved in the pathophysiology of theK. pneumoniaemeningitis.


2003 ◽  
Vol 4 (1) ◽  
pp. 37-46 ◽  
Author(s):  
S. Buschlen ◽  
J-M Amillet ◽  
B. Guiard ◽  
A. Fournier ◽  
C. Marcireau ◽  
...  

We have comparedSaccharomyces cerevisiaeglobal gene expression in wild-type and mutants (Δhap2 and Δhap4) of the HAP transcriptional complex, which has been shown to be necessary for growth on respiratory substrates. Several hundred ORFs are under positive or negative control of this complex and we analyse here in detail the effect of HAP on mitochondria. We found that most of the genes upregulated in the wild-type strain were involved in organelle functions, but practically none of the downregulated ones. Nuclear genes encoding the different subunits of the respiratory chain complexes figure in the genes more expressed in the wild-type than in the mutants, as expected, but in this group we also found key components of the mitochondrial translation apparatus. This control of mitochondrial translation may be one of the means of coordinating mitochondrial and nuclear gene expression in elaborating the respiratory chain. In addition, HAP controls the nuclear genes involved in several other mitochondrial processes (import, mitochondrial division) that define the metabolic state of the cell, but not mitochondrial DNA replication and transcription. In most cases, a putative CCAAT-binding site is present upstream of the ORF, while in others no such sites are present, suggesting the control to be indirect. The large number of genes regulated by the HAP complex, as well as the fact that HAP also regulates some putative transcriptional activators of unknown function, place this complex at a hierarchically high position in the global transcriptional regulation of the cell.


2018 ◽  
Author(s):  
Makenzie Saoura ◽  
Christopher A. Powell ◽  
Robert Kopajtich ◽  
Ahmad Alahmad ◽  
Haya H. AL-Balool ◽  
...  

AbstractDysfunction of mitochondrial gene expression, caused by mutations in either the mitochondrial or nuclear genomes, is associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism. For instance, pathogenic mutations have been identified in the genes encoding enzymes involved in the precursor transcript processing, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, which is responsible for endonucleolytic cleavage of the 3’ ends of mitochondrial pre-tRNAs. Here, we report the identification of sixteen novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy and lactic acidosis. We provided further evidence for the pathogenicity of the three previously reported variants by studying the RNase Z activity in an in vitro system and applied this recombinant system to investigate all novel missense variants, confirming the pathogenic role of these new ELAC2 mutations. We also modelled the residues affected by missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the individuals with novel ELAC2 variants have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of hypertrophic cardiomyopathy and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, possibly indicating a functional link between tumorigenesis and mitochondrial RNA metabolism.


2018 ◽  
Vol 115 (12) ◽  
pp. 3024-3029 ◽  
Author(s):  
Karen M. Davies ◽  
Thorsten B. Blum ◽  
Werner Kühlbrandt

We used electron cryo-tomography and subtomogram averaging to investigate the structure of complex I and its supramolecular assemblies in the inner mitochondrial membrane of mammals, fungi, and plants. Tomographic volumes containing complex I were averaged at ∼4 nm resolution. Principal component analysis indicated that ∼60% of complex I formed a supercomplex with dimeric complex III, while ∼40% were not associated with other respiratory chain complexes. The mutual arrangement of complex I and III2 was essentially conserved in all supercomplexes investigated. In addition, up to two copies of monomeric complex IV were associated with the complex I1III2 assembly in bovine heart and the yeast Yarrowia lipolytica, but their positions varied. No complex IV was detected in the respiratory supercomplex of the plant Asparagus officinalis. Instead, an ∼4.5-nm globular protein density was observed on the matrix side of the complex I membrane arm, which we assign to γ-carbonic anhydrase. Our results demonstrate that respiratory chain supercomplexes in situ have a conserved core of complex I and III2, but otherwise their stoichiometry and structure varies. The conserved features of supercomplex assemblies indicate an important role in respiratory electron transfer.


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