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Hou Y, Zhang W, McGilvray PT, Sobczyk M, Wang T, Weng SHS, Huff A, Huang S, Pena N, Katanski CD, Pan T. Engineered mischarged transfer RNAs for correcting pathogenic missense mutations. Mol Ther 2024; 32:352-371. [PMID: 38104240 PMCID: PMC10861979 DOI: 10.1016/j.ymthe.2023.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023] Open
Abstract
Missense mutations account for approximately 50% of pathogenic mutations in human genetic diseases, and most lack effective treatments. Gene therapies, gene editing, and RNA therapies, including transfer RNA (tRNA) modalities, are common strategies for genetic disease treatments. However, reported tRNA therapies are for nonsense mutations only. It has not been explored how tRNAs can be engineered to correct missense mutations. Here, we describe missense-correcting tRNAs (mc-tRNAs) as a potential therapeutic for correcting pathogenic missense mutations. Mc-tRNAs are engineered tRNAs charged with one amino acid, but read codons of another in translation. We first developed a series of fluorescent protein-based reporters that indicate the successful correction of missense mutations via restoration of fluorescence. We engineered mc-tRNAs that effectively corrected serine and arginine missense mutations in the reporters and confirmed the amino acid substitution by mass spectrometry and mc-tRNA expression by sequencing. We examined the transcriptome response to mc-tRNA expression and found some mc-tRNAs induced minimum transcriptomic changes. Furthermore, we applied an mc-tRNA to rescue a pathogenic CAPN3 Arg-to-Gln mutant involved in LGMD2A. These results establish a versatile pipeline for mc-tRNA engineering and demonstrate the potential of mc-tRNA as an alternative therapeutic platform for the treatment of genetic disorders.
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Affiliation(s)
- Yichen Hou
- Committee on Genomics, Genetics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Marek Sobczyk
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tianxin Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Allen Huff
- Proteomics Platform, University of Chicago, Chicago, IL 60637, USA
| | - Sihao Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Noah Pena
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
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Chertkova RV, Oleynikov IP, Pakhomov AA, Sudakov RV, Orlov VN, Semenova MA, Arutyunyan AM, Ptushenko VV, Kirpichnikov MP, Dolgikh DA, Vygodina TV. Mutant Cytochrome C as a Potential Detector of Superoxide Generation: Effect of Mutations on the Function and Properties. Cells 2023; 12:2316. [PMID: 37759538 PMCID: PMC10528150 DOI: 10.3390/cells12182316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Cytochrome c (CytC) is a single-electron carrier between complex bc1 and cytochrome c-oxidase (CcO) in the electron transport chain (ETC). It is also known as a good radical scavenger but its participation in electron flow through the ETC makes it impossible to use CytC as a radical sensor. To solve this problem, a series of mutants were constructed with substitutions of Lys residues in the universal binding site (UBS) which interact electrostatically with negatively charged Asp and Glu residues at the binding sites of CytC partners, bc1 complex and CcO. The aim of this study was to select a mutant that had lost its function as an electron carrier in the ETC, retaining the structure and ability to quench radicals. It was shown that a mutant CytC with substitutions of five (8Mut) and four (5Mut) Lys residues in the UBS was almost inactive toward CcO. However, all mutant proteins kept their antioxidant activity sufficiently with respect to the superoxide radical. Mutations shifted the dipole moment of the CytC molecule due to seriously changed electrostatics on the surface of the protein. In addition, a decrease in the redox potential of the protein as revealed by the redox titrations of 8Mut was detected. Nevertheless, the CD spectrum and dynamic light scattering suggested no significant changes in the secondary structure or aggregation of the molecules of CytC 8Mut. Thus, a variant 8Mut with multiple mutations in the UBS which lost its ability to electron transfer and saved most of its physico-chemical properties can be effectively used as a detector of superoxide generation both in mitochondria and in other systems.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Ilya P. Oleynikov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Alexey A. Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Roman V. Sudakov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Victor N. Orlov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Marina A. Semenova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Alexander M. Arutyunyan
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Vasily V. Ptushenko
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, M.V. Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, M.V. Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Tatiana V. Vygodina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
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Mamaeva AA, Frolova AY, Kakuev DL, Martynov VI, Deyev SM, Pakhomov AA. Co-expression of different proteins in Escherichia coli using plasmids with identical origins of replication. Biochem Biophys Res Commun 2023; 641:57-60. [PMID: 36521286 DOI: 10.1016/j.bbrc.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
It is generally accepted that the use of two different plasmids with the identical origins of replication in bacteria is not desirable due to their "incompatibility". The utilization of the same bacterial enzymatic apparatus for replication of different plasmids is thought to cause a significant redistribution in favor of one of them. In the present work, examining co-expression of two different fluorescent proteins in Escherichia coli, we have shown that the use of highly homologous plasmids with identical origins of replication and providing resistance to different antibiotics results in high representation of both plasmids in bacteria. Meanwhile, the level of gene expression and the amount of proteins produced may differ and is determined mostly by their sequence rather than by the "incompatibility" of the plasmids.
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Affiliation(s)
- Anastasiia A Mamaeva
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Anastasiya Yu Frolova
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation; A.N.Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Dmitry L Kakuev
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Vladimir I Martynov
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Sergey M Deyev
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Alexey A Pakhomov
- M.M.Shemyakin-Y.A.Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation; A.N.Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russian Federation.
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Pakhomov AA, Pastukhova AA, Tishkin GV, Martynov VI. Transformations of the Chromophore in the Course of Maturation of a Chromoprotein from Actinia equina. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Frolova AY, Pakhomov AA, Martynov VI. Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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