1
|
Lahry K, Datta M, Varshney U. Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view. Mol Microbiol 2024. [PMID: 38410838 DOI: 10.1111/mmi.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.
Collapse
Affiliation(s)
- Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| |
Collapse
|
2
|
Schedler B, Yukhnovets O, Lindner L, Meyer A, Fitter J. The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection. Int J Mol Sci 2023; 24:16379. [PMID: 38003569 PMCID: PMC10671529 DOI: 10.3390/ijms242216379] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.
Collapse
Affiliation(s)
- Benno Schedler
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Lennart Lindner
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Alida Meyer
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
3
|
Kim JM, Seong BL, Jung J. Highly chromophoric dual-terminus labeling of an intrinsically disordered native eukaryotic protein of interest at nanoscale. Int J Biol Macromol 2023:125396. [PMID: 37348577 DOI: 10.1016/j.ijbiomac.2023.125396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
Chemical conjugation of purified proteins of interest (POIs) in Escherichia coli cells is effective for high expression but has limitations for highly chromogenic dual labeling of intrinsically disordered native proteins (IDNPs). Our probes can tag IDNPs using chemical conjugation during protein synthesis and folding while preserving biologically active structures in mammalian cells. We fluorescently labeled IDNPs in mammalian cells using pure fluorescent methionine and ATTO 565-biotin at the N-or C-terminus, respectively. The dual-labeled Tat protein was used as a model for IDNPs in HeLa cells and detected using Ni-NTA beads to estimate its highly chromogenic concentration. We also demonstrated highly chromogenic double labeling of genetically encoded fluorescent-Tat expression in eukaryotic cells using a single fluorescent dye pair with Förster resonance energy transfer (FRET) ratio and two-color correlation analysis. This study aims to solve native POI processing and achieve ultra-sensitive protein folding for biological and ecological applications at the nanoscale.
Collapse
Affiliation(s)
- Jung Min Kim
- Department of Environmental Science and Ecological Engineering, Ojeong Resilience Institute, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02842, Republic of Korea.
| | - Baik Lin Seong
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jinho Jung
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02842, Republic of Korea
| |
Collapse
|
4
|
Remes C, Khawaja A, Pearce SF, Dinan AM, Gopalakrishna S, Cipullo M, Kyriakidis V, Zhang J, Dopico XC, Yukhnovets O, Atanassov I, Firth AE, Cooperman B, Rorbach J. Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria. Nucleic Acids Res 2023; 51:891-907. [PMID: 36629253 PMCID: PMC9881170 DOI: 10.1093/nar/gkac1233] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It has been commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5' leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S), in a manner that requires initiator fMet-tRNAMet binding. In addition, we demonstrate that in human cells and in vitro, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Furthermore, we show that mtIF2 is indispensable for mitochondrial protein synthesis. Our results demonstrate an important evolutionary divergence of the mitochondrial translation system and further our fundamental understanding of a process central to eukaryotic metabolism.
Collapse
Affiliation(s)
- Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Adam M Dinan
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Vasileios Kyriakidis
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Olessya Yukhnovets
- RWTH Aachen, I. Physikalisches Institut (IA), Aachen, Germany
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- STIAS: Stellenbosch Institute for Advanced Study at Stellenbosch University, Marais Rd, Stellenbosch 7600, South Africa
| |
Collapse
|
5
|
Heesink G, Caron C, van Leijenhorst-Groener K, Molenaar R, Gadella TWJ, Claessens MMAE, Blum C. Quantification of Dark Protein Populations in Fluorescent Proteins by Two-Color Coincidence Detection and Nanophotonic Manipulation. J Phys Chem B 2022; 126:7906-7915. [PMID: 36190918 PMCID: PMC9574928 DOI: 10.1021/acs.jpcb.2c04627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Genetically encoded visible fluorescent proteins (VFPs)
are a key
tool used to visualize cellular processes. However, compared to synthetic
fluorophores, VFPs are photophysically complex. This photophysical
complexity includes the presence of non-emitting, dark proteins within
the ensemble of VFPs. Quantitative fluorescence microcopy approaches
that rely on VFPs to obtain molecular insights are hampered by the
presence of these dark proteins. To account for the presence of dark
proteins, it is necessary to know the fraction of dark proteins (fdark) in the ensemble. To date, fdark has rarely been quantified, and different methods
to determine fdark have not been compared.
Here, we use and compare two different methods to determine the fdark of four commonly used VFPs: EGFP, SYFP2,
mStrawberry, and mRFP1. In the first, direct method, we make use of
VFP tandems and single-molecule two-color coincidence detection (TCCD).
The second method relies on comparing the bright state fluorescence
quantum yield obtained by photonic manipulation to the ensemble-averaged
fluorescence quantum yield of the VFP. Our results show that, although
very different in nature, both methods are suitable to obtain fdark. Both methods show that all four VFPs contain
a considerable fraction of dark proteins. We determine fdark values between 30 and 60% for the different VFPs.
The high values for fdark of these commonly
used VFPs highlight that fdark has to
be accounted for in quantitative microscopy and spectroscopy.
Collapse
Affiliation(s)
- Gobert Heesink
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Cécile Caron
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Kirsten van Leijenhorst-Groener
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Robert Molenaar
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Theodorus W J Gadella
- Section of Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94215, 1090 GEAmsterdam, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Christian Blum
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| |
Collapse
|
6
|
Yukhnovets O, Höfig H, Bustorff N, Katranidis A, Fitter J. Impact of Molecule Concentration, Diffusion Rates and Surface Passivation on Single-Molecule Fluorescence Studies in Solution. Biomolecules 2022; 12:biom12030468. [PMID: 35327660 PMCID: PMC8946791 DOI: 10.3390/biom12030468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance energy transfer (smFRET) or two-color coincidence detection (TCCD), the molecule concentration must be set explicitly to targeted values and furthermore needs to be stable over a period of several hours. As a consequence, specific demands must be imposed on the surface passivation of the cover slides during the measurements. The aim of having only one molecule in the detection volume at the time is not only affected by the absolute molecule concentration, but also by the rate of diffusion. Therefore, we discuss approaches to control and to measure absolute molecule concentrations. Furthermore, we introduce an approach to calculate the probability of chance coincidence events and demonstrate that measurements with challenging smFRET samples require a strict limit of maximal sample concentrations in order to produce meaningful results.
Collapse
Affiliation(s)
- Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (O.Y.); (J.F.)
| | - Henning Höfig
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
| | - Nuno Bustorff
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Alexandros Katranidis
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
- Correspondence: (O.Y.); (J.F.)
| |
Collapse
|
7
|
Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
Collapse
Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
| |
Collapse
|
8
|
Bielec K, Bubak G, Kalwarczyk T, Holyst R. Analysis of Brightness of a Single Fluorophore for Quantitative Characterization of Biochemical Reactions. J Phys Chem B 2020; 124:1941-1948. [PMID: 32059107 PMCID: PMC7497653 DOI: 10.1021/acs.jpcb.0c00770] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Intrinsic
molecular brightness (MB) is a number of emitted photons
per second per molecule. When a substrate labeled by a fluorophore
and a second unlabeled substrate form a complex in solution, the MB
of the fluorophore changes. Here we use this change to determine the equilibrium constant (K) for the formation of the complex at pM concentrations.
To illustrate this method, we used a reaction of DNA hybridization,
where only one of the strands was fluorescently labeled. We determined K at the substrate concentrations from 80 pM to 30 nM. We
validated this method against Förster resonance energy transfer
(FRET). This method is much simpler than FRET as it requires only
one fluorophore in the complex with a very small (a f̃ew percent)
change in MB.
Collapse
Affiliation(s)
- Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Grzegorz Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| |
Collapse
|