The mitochondrial message-specific mRNA protectors Cbp1 and Pet309 are associated in a high-molecular weight complex

Krause, Kirsten; Lopes de Souza, Renata; Roberts, Douglas G.W.; Dieckmann, Carol L.

doi:10.1091/mbc.e04-02-0126

Cited by 60RNA Research and SplicingMitochondrial Function and PathologyRNA and protein synthesis mechanisms

The mitochondrial message-specific mRNA protectors Cbp1 and Pet309 are associated in a high-molecular weight complex

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Krause, Kirsten, Lopes de Souza, Renata, Roberts, Douglas G.W., Dieckmann, Carol L.·2004·Molecular Biology of the Cell

DOI 10.1091/mbc.e04-02-0126PMC PMC420092

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Abstract

In Saccharomyces cerevisiae, the nuclear-encoded protein Cbp1 promotes stability and translation of mitochondrial cytochrome b transcripts through interaction with the 5' untranslated region. Fusion of a biotin binding peptide tag to the C terminus of Cbp1 has now allowed detection in mitochondrial extracts by using peroxidase-coupled avidin. Cbp1 is associated with the mitochondrial membranes when high ionic strength extraction conditions are used. However, the protein is easily solubilized by omitting salt from the extraction buffer, which suggests Cbp1 is loosely associated with the membrane through weak hydrophobic interactions. Gel filtration analysis and blue native PAGE showed that Cbp1 is part of a single 900,000-Da complex. The complex was purified using the biotin tag and a sequence-specific protease cleavage site. In addition to Cbp1, the complex contains several polypeptides of molecular weights between 113 and 40 kDa. Among these, we identified another message-specific factor, Pet309, which promotes the stability and translation of mitochondrial cytochrome oxidase subunit I mRNA. A hypothesis is presented in which the Cbp1-Pet309 complex contains several message-specific RNA binding proteins and links transcription to translation of the mRNAs at the membrane.

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Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation.
“Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation (Krause et al. 2004; Coquille et al. 2014).”
From Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits (2024) · cites this paper as Krause et al. 2004

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Ribosome-binding Proteins Mdm38 and Mba1 Display Overlapping Functions for Regulation of Mitochondrial Translation
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“It was shown that at the inner mitochondrial membrane, Cbp1p was associated with Pet127p—a putative 5#-3# exoribonuclease (Krause et al. 2004).”
Background
Aberrant Translation of CytochromecOxidase Subunit 1 mRNA Species in the Absence of Mss51p in the YeastSaccharomyces cerevisiae
Zambrano, A., Fontanesi, F., Solans, A., de Oliveira, R. L., Fox, T. D., Tzagoloff, A., & Barrientos, A. (2006) · Molecular Biology of the Cell · doi:10.1091/mbc.e06-09-0803 · Cited by 61 · see citing works
“Interactions have also been noted between the transcription factor Nam1p and translational activators, including Pet111p, Pet309p, and Pet494p (Naithani et al., 2003; Krause et al., 2004) raising the possibility that mitochondrial transcription may be coupled to translation.”
Background
Modular biogenesis of mitochondrial respiratory complexes
de Barros, M. H., & McStay, G. P. (2019) · Mitochondrion · doi:10.1016/j.mito.2019.10.008 · Cited by 56 · see citing works
Yeast PPR proteins, watchdogs of mitochondrial gene expression
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“This would be consistent with the observation that Cbp1 interacts with the COX1 translational activator Pet309 (Table 2).(50) Like AEP2, CBP1 is transcribed as a full-length transcript able to encode the normal Cbp1 protein, and a truncated transcript that cannot produce Cbp1.”
Background
In vitro Reconstitution and Characterization of the Yeast Mitochondrial Degradosome Complex Unravels Tight Functional Interdependence
Małecki, M., Jedrzejczak, R. P., Stępień, P. P., & Golik, P. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.06.074 · Cited by 51 · see citing works
Rmd9p Controls the Processing/Stability of Mitochondrial mRNAs and Its Overexpression Compensates for a Partial Deficiency of Oxa1p in Saccharomyces cerevisiae
Nouet, C., Bourens, M., Hlaváček, O., Marsy, S., Lemaire, C., & Dujardin, G. (2006) · Genetics · doi:10.1534/genetics.106.063883 · Cited by 51 · see citing works
“Such a PPR motif was also found in two yeast mitochondrial proteins, Pet309p and Aep3p, that both control stability and translation of single mRNA (Manthey and McEwen 1995; Ellis et al. 2004; Krause et al. 2004).”
Background
Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae
Atkinson, G. C., Kuzmenko, A., Kamenski, P. A., Vysokikh, M. Y., Lakunina, V. A., Tankov, S., Smirnova, E., Soosaar, A., Tenson, T., & Hauryliuk, V. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks272 · Cited by 50 · see citing works
“Aep2p and Cbp1p have representatives across the phylum Ascomycota, although Aspergillus Cbp1ps are very different in sequence.”
The DEAD-box helicase Mss116 plays distinct roles in mitochondrial ribogenesis and mRNA-specific translation
Silva, D. D., Poliquin, S., Zeng, R., Zamudio‐Ochoa, A., Marrero, N., Pérez-Martı́nez, X., Fontanesi, F., & Barrientos, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx426 · Cited by 48 · see citing works
“Pet309 was found to form a complex with other mRNA-specific translational activators, the transcription factor Nam1/Mtf2 and several message-specific RNA-binding proteins, including the RNA polymerase core Rpo41 (61).”
Background
Flow Cross K-function: a bivariate flow analytical method
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Balance between Transcription and RNA Degradation Is Vital forSaccharomyces cerevisiaeMitochondria: Reduced Transcription Rescues the Phenotype of Deficient RNA Degradation
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“RNA processing and translation have been shown to be physically coupled to transcription through a network of protein–protein and protein–RNA interactions (Rodeheffer et al., 2001; Bryan et al., 2002; Krause et al., 2004).”
Background
Inhibition of electron transport chain assembly and function promotes photodynamic killing of Candida
Chabrier‐Roselló, Y., Giesselman, B. R., Andino, F. D. J., Foster, T. H., Mitra, S., & Haidaris, C. G. (2010) · Journal of Photochemistry and Photobiology B Biology · doi:10.1016/j.jphotobiol.2010.03.005 · Cited by 34 · see citing works
“In yeast, a notable characteristic of the mitochondrial gene expression machinery is the close physical association of its components [47].”
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DMR1 (CCM1/YGR150C) of Saccharomyces cerevisiae Encodes an RNA-Binding Protein from the Pentatricopeptide Repeat Family Required for the Maintenance of the Mitochondrial 15S Ribosomal RNA
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COX24 Codes for a Mitochondrial Protein Required for Processing of the COX1 Transcript
de Barros, M. H., Myers, A. M., Driesche, S. V., & Tzagoloff, A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m510778200 · Cited by 29 · see citing works
Systematic screening of nuclear encoded proteins involved in the splicing metabolism of group II introns in yeast mitochondria
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Overexpression of the COX2 translational activator, Pet111p, prevents translation of COX1 mRNA and cytochrome c oxidase assembly in mitochondria of Saccharomyces cerevisiae
Fiori, A., Pérez-Martı́nez, X., & Fox, T. D. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04658.x · Cited by 27 · see citing works
“No evidence for direct interactions between Pet111p and Pet309p were detected in previous studies of translational activator proteins (Naithani et al., 2003; Krause et al., 2004), but this cannot be excluded.”
Background
Saccharomyces cerevisiae translational activator Cbs1p is associated with translationally active mitochondrial ribosomes
Krause‐Buchholz, U., Schöbel, K., Lauffer, S., & Rödel, G. (2005) · Biological Chemistry · doi:10.1515/bc.2005.049 · Cited by 23 · see citing works
Yeast AEP3p Is an Accessory Factor in Initiation of Mitochondrial Translation
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Activation of Yeast Mitochondrial Translation: Who Is in Charge?
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The archaeal exosome localizes to the membrane
Roppelt, V., Hobel, C. F. V., Albers, S., Lassek, C., Schwarz, H., Klug, G., & Evguenieva‐Hackenberg, E. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.05.013 · Cited by 21 · see citing works
“However, hydrophobic interactions of membranes with membrane-associated proteins lacking trans-membrane domains are disturbed under low-salt conditions [20].”
Background
Schizosaccharomyces pombe homologs of the Saccharomyces cerevisiae mitochondrial proteins Cbp6 and Mss51 function at a post-translational step of respiratory complex biogenesis
Kühl, I., Fox, T. D., & Bonnefoy, N. (2012) · Mitochondrion · doi:10.1016/j.mito.2012.02.002 · Cited by 18 · see citing works
“, 1996), and play a role in the topological organization of gene expression at the surface of the inner membrane (Krause et al., 2004; Naithani et al., 2003; Sanchirico et al., 1998b).”
Background
Aep3p-dependent translation of yeast mitochondrialATP8
de Barros, M. H., & Tzagoloff, A. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-11-0775 · Cited by 18 · see citing works
“Pet309p, Atp22p, and Msc6p are examples of yeast mitochondrial PPR proteins involved in the stability and/or translation of mitochondrially encoded RNAs (Krause et al., 2004; Zeng et al., 2007; Moda et al., 2016).”
Background
Yeast mitochondrial protein Pet111p binds directly to two distinct targets in COX2 mRNA, suggesting a mechanism of translational activation
Jones, J. L., Hofmann, K., Cowan, A. T., Temiakov, D., Cramer, P., & Anikin, M. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005355 · Cited by 18 · see citing works
“membrane, Pet111p is associated in a complex, which also includes translational activators specific to COX1, COX3, and COB (10,11).”
Background
Pleiotropic effects of the yeast Sal1 and Aac2 carriers on mitochondrial function via an activity distinct from adenine nucleotide transport
Kucejová, B., Li, L., Wang, X., Giannattasio, S., & Chen, X. J. (2008) · Molecular Genetics and Genomics · doi:10.1007/s00438-008-0342-5 · Cited by 18 · see citing works
“In addition to translational activators that are directly required for eYcient translation of speciWc mRNAs (Barrientos et al. 2004; Fox 1996; Krause et al. 2004; Green-Willms et al. 2001; Steele et al. 1996), defects in other processes Fig.”
Background
Alteration of a Novel Dispensable Mitochondrial Ribosomal Small-Subunit Protein, Rsm28p, Allows Translation of Defective COX2 mRNAs
Williams, E. H., Bsat, N., Bonnefoy, N., Butler, C. A., & Fox, T. D. (2005) · Eukaryotic Cell · doi:10.1128/ec.4.2.337-345.2005 · Cited by 17 · see citing works
“The translational activators appear to both limit (24, 58) and localize (13, 16, 33, 38, 44, 50, 52) translation of mitochondrial mRNAs.”
Background
Analysis of transcription asymmetries along the tRNAE-COB operon: evidence for transcription attenuation and rapid RNA degradation between coding sequences
Krause, K. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh966 · Cited by 15 · see citing works
“Mutant mitochondria were introduced into the strain S150-Bio1/ro by cytoduction (20).”
MethodInfluential
Partial suppression of the respiratory defect of qrs1/her2 glutamyl-tRNA amidotransferase mutants by overexpression of the mitochondrial pentatricopeptide Msc6p
Moda, B. S., Ferreira-Júnior, J. R., & de Barros, M. H. (2016) · Current Genetics · doi:10.1007/s00294-016-0566-6 · Cited by 10 · see citing works
“2007) and Cbp1p activates COB1 translation (Krause et al. 2004).”
Background
Overexpression of MRX9 impairs processing of RNAs encoding mitochondrial oxidative phosphorylation factors COB and COX1 in yeast
Chagas, J. A. C., Soares, M. A. K. M., Franco, L. V. R., & de Barros, M. H. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102214 · Cited by 8 · see citing works
“Cox24p (mS38) is a component of the mitoribosome (84) required for proper COX1 splicing and COX1, COX2, and COX3 translation (14, 22) When we tested the overexpression of MRX9 in some COX mutants, it was clearly more harmful to the mitochondrial protein synthesis of cox24Δ null mutant. n the WT, Mrx9p associated with…”
Background
Mitochondrial Translation in Trypanosomatids
Maslov, D. A., & Agrawal, R. K. (2011) · Nucleic acids and molecular biology · doi:10.1007/978-3-642-28687-2_10 · Cited by 6 · see citing works
Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation
Chicherin, I., Левицкий, С. А., Baleva, M. V., Krasheninnikov, I. A., Patrushev, M. V., & Kamenski, P. A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21103414 · Cited by 5 · see citing works
“It seems that translational activators might function together as a large macromolecular complex; the signs of such complex existence have been previously detected [38].”
Background
Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation
Bridgers, J. B., Carlström, A., Sherpa, D., Couvillion, M. T., Rovšnik, U., Gao, J., Wan, B., Shao, S., Ott, M., & Churchman, L. S. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01726-y · Cited by 6 · see citing works
“Additionally, Cbp1 is found in a high-molecular-weight complex with Pet309, a COX1 TA 52 .”
Revisiting the Yeast PPR Proteins - Application of an Iterative Hidden Markov Model Algorithm Reveals New Members of the Rapidly Evolving Family Research Article
Lipinski, K. A., Puchta, O., Surandranath, V., Kudła, M., & Golik, P. (2011) · Cited by 4 · see citing works
Conserved and Organelle-Specific Molecular Mechanisms of Translation in Mitochondria
Kehrein, K., & Ott, M. (2011) · Springer eBooks · doi:10.1007/978-3-642-22380-8_16 · Cited by 3 · see citing works
Aberrant translation of cytochrome c oxidase subunit 1 mRNA species in the absence of Mss51p in the yeast Saccharomyces cerevisiae
Zambrano, A., Fontanesi, F., Solans, A., de Oliveira, R. L., Fox, T. D., Tzagoloff, A., & Barrientos, A. (2007) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) · Cited by 3 · see citing works
Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits
Wenda, J. M., Drzewicka, K., Mulica, P., Tetaud, E., di Rago, J. P., Golik, P., & Łabędzka-Dmoch, K. (2024) · GENETICS · doi:10.1093/genetics/iyae124 · Cited by 2 · see citing works
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Kinetoplast-Mitochondrial Translation System in Trypanosomatids
Maslov, D. A., & Agrawal, R. K. (2013) · Springer eBooks · doi:10.1007/978-3-642-39426-3_6 · Cited by 2 · see citing works
Insights into the translational activation mechanisms of the COX1 mRNA in yeast mitochondria
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“Proteins were resolved by SDS-PAGE, transferred to PVDF membranes, and detected by immunoblotting with the indicated antibodies.”
Mechanisms and Control of Protein Synthesis in Yeast Mitochondria
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“Additionally, data suggest proteins involved in mitochondrial mRNA stability and translation exist in membrane-bound complexes (Krause et al., 2004) and associate with the mitochondrial RNA polymerase (Rodeheffer et al., 2001).”
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Authors: Krause, K., Lopes de Souza, R., Roberts, D. G. W., & Dieckmann, C. L.
Affiliations: University of Arizona (US)
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721
ORCID: Krause, Kirsten
Dieckmann, Carol L.
Venue: Molecular Biology of the Cell
Publisher: American Society for Cell Biology (ASCB)
Published: 2004-06
Volume: 15
Issue: 6
Pages: 2674-2683
ISSN: 1059-1524 (ISSN-L)
1939-4586
DOI: 10.1091/mbc.e04-02-0126
PMC: PMC420092
OpenAlex: W2026484869
Cited by: 60
References: 62
Citations by year: 2025: 2 · 2024: 1 · 2022: 1 · 2020: 1 · 2019: 3 · 2018: 2 · 2017: 3 · 2016: 1 · 2015: 2 · 2014: 1 · 2013: 3 · 2012: 6
FWCI: 2.13
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Molecular Biology of the Cell (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Deutscher Akademischer Austauschdienst
National Institutes of Health
National Institute of General Medical Sciences (R01GM034893, GM34893)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: CBP1, mitochondrial translation, 5' untranslated region, RNA-binding proteins, high molecular weight protein complexes, transcription-translation coupling, Saccharomyces cerevisiae
MeSH terms: RNA, Mitochondrial, Buffers, Chromatography, Gel, Intracellular Membranes, Membrane Proteins, Molecular Weight, Peptide Initiation Factors, Protein Binding, RNA, Saccharomyces cerevisiae, Salts, Solubility, Sonication, Substrate Specificity, RNA-Binding Proteins, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Mitochondrial Proteins, Saccharomyces cerevisiae Proteins, Multiprotein Complexes

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The mitochondrial message-specific mRNA protectors Cbp1 and Pet309 are associated in a high-molecular weight complex

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