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Tian S, Zhao G, Lv G, Wu C, Su R, Wang F, Wang Z, Liu Y, Chen N, Li Y. Efficient Fermentative Production of d-Alanine and Other d-Amino Acids by Metabolically Engineered Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8039-8051. [PMID: 38545740 DOI: 10.1021/acs.jafc.4c00914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
d-Amino acids (d-AAs) have wide applications in industries such as pharmaceutical, food, and cosmetics due to their unique properties. Currently, the production of d-AAs has relied on chemical synthesis or enzyme catalysts, and it is challenging to produce d-AAs via direct fermentation from glucose. We observed that Corynebacterium glutamicum exhibits a remarkable tolerance to high concentrations of d-Ala, a crucial characteristic for establishing a successful fermentation process. By optimizing meso-diaminopilmelate dehydrogenases in different C. glutamicum strains and successively deleting l-Ala biosynthetic pathways, we developed an efficient d-Ala fermentation system. The d-Ala titer was enhanced through systems metabolic engineering, which involved strengthening glucose assimilation and pyruvate supply, reducing the formation of organic acid byproducts, and attenuating the TCA cycle. During fermentation in a 5-L bioreactor, a significant accumulation of l-Ala was observed in the broth, which was subsequently diminished by introducing an l-amino acid deaminase. Ultimately, the engineered strain DA-11 produced 85 g/L d-Ala with a yield of 0.30 g/g glucose, accompanied by an optical purity exceeding 99%. The fermentation platform has the potential to be extended for the synthesis of other d-AAs, as demonstrated by the production of d-Val and d-Glu.
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Affiliation(s)
- Siyu Tian
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Gengcheng Lv
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Rui Su
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yuexiang Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
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Kumar P, Sankaranarayanan R. When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis. Nucleic Acids Res 2024; 52:2130-2141. [PMID: 38407292 PMCID: PMC10954443 DOI: 10.1093/nar/gkae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.
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Affiliation(s)
- Pradeep Kumar
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Rajan Sankaranarayanan
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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3
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Kumar P, Roy A, Mukul SJ, Singh AK, Singh DK, Nalli A, Banerjee P, Babu KSD, Raman B, Kruparani SP, Siddiqi I, Sankaranarayanan R. A translation proofreader of archaeal origin imparts multi-aldehyde stress tolerance to land plants. eLife 2024; 12:RP92827. [PMID: 38372335 PMCID: PMC10942605 DOI: 10.7554/elife.92827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Aldehydes, being an integral part of carbon metabolism, energy generation, and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes, i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.
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Affiliation(s)
- Pradeep Kumar
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Ankit Roy
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Shivapura Jagadeesha Mukul
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | | | - Aswan Nalli
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
| | | | | | | | | | - Imran Siddiqi
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
| | - Rajan Sankaranarayanan
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
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4
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Kim RM, Han JH, Lee SM, Kim H, Lim YC, Lee HE, Ahn HY, Lee YH, Ha IH, Nam KT. Chiral plasmonic sensing: From the perspective of light-matter interaction. J Chem Phys 2024; 160:061001. [PMID: 38341778 DOI: 10.1063/5.0178485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/07/2024] [Indexed: 02/13/2024] Open
Abstract
Molecular chirality is represented as broken mirror symmetry in the structural orientation of constituent atoms and plays a pivotal role at every scale of nature. Since the discovery of the chiroptic property of chiral molecules, the characterization of molecular chirality is important in the fields of biology, physics, and chemistry. Over the centuries, the field of optical chiral sensing was based on chiral light-matter interactions between chiral molecules and polarized light. Starting from simple optics-based sensing, the utilization of plasmonic materials that could control local chiral light-matter interactions by squeezing light into molecules successfully facilitated chiral sensing into noninvasive, ultrasensitive, and accurate detection. In this Review, the importance of plasmonic materials and their engineering in chiral sensing are discussed based on the principle of chiral light-matter interactions and the theory of optical chirality and chiral perturbation; thus, this Review can serve as a milestone for the proper design and utilization of plasmonic nanostructures for improved chiral sensing.
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Affiliation(s)
- Ryeong Myeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Hyun Han
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo Min Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeohn Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yae-Chan Lim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hye-Eun Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyo-Yong Ahn
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon Ho Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - In Han Ha
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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5
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Zafar H, Hassan AH, Demo G. Translation machinery captured in motion. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1792. [PMID: 37132456 DOI: 10.1002/wrna.1792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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6
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Kumar P, Babu K, Singh A, Singh D, Nalli A, Mukul S, Roy A, Mazeed M, Raman B, Kruparani S, Siddiqi I, Sankaranarayanan R. Distinct localization of chiral proofreaders resolves organellar translation conflict in plants. Proc Natl Acad Sci U S A 2023; 120:e2219292120. [PMID: 37276405 PMCID: PMC10268278 DOI: 10.1073/pnas.2219292120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.
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Affiliation(s)
- Pradeep Kumar
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Kandhalu Sagadevan Dinesh Babu
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Avinash Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Dipesh Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Aswan Nalli
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shivapura Jagadeesha Mukul
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Ankit Roy
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Mohd Mazeed
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Bakthisaran Raman
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shobha P. Kruparani
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Imran Siddiqi
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
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7
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Li X, Zhang Q, Jian H, Bai S. Chiral implications on Fmoc-dipeptide self-assembly and catalytic kinetics of thermolysin. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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8
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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9
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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10
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Banreti A, Bhattacharya S, Wien F, Matsuo K, Réfrégiers M, Meinert C, Meierhenrich U, Hudry B, Thompson D, Noselli S. Biological effects of the loss of homochirality in a multicellular organism. Nat Commun 2022; 13:7059. [PMID: 36400783 PMCID: PMC9674851 DOI: 10.1038/s41467-022-34516-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Homochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-L-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism's health, we use chiral-selective in vivo assays to detect protein-bound non-L-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a 'heterochirality syndrome' with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
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Affiliation(s)
- Agnes Banreti
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Shayon Bhattacharya
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Frank Wien
- grid.426328.9DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Koichi Matsuo
- grid.257022.00000 0000 8711 3200HiSOR Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Matthieu Réfrégiers
- grid.417870.d0000 0004 0614 8532Centre de Biophysique Moléculaire, CNRS; UPR4301, 45071 Orléans, France
| | - Cornelia Meinert
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Uwe Meierhenrich
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Bruno Hudry
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Damien Thompson
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Stéphane Noselli
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
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11
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Kumar P, Bhatnagar A, Sankaranarayanan R. Chiral proofreading during protein biosynthesis and its evolutionary implications. FEBS Lett 2022; 596:1615-1627. [PMID: 35662005 DOI: 10.1002/1873-3468.14419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/16/2022] [Accepted: 05/29/2022] [Indexed: 11/05/2022]
Abstract
Homochirality of biomacromolecules is a prerequisite for their proper functioning and hence essential for all life forms. This underscores the role of cellular chiral checkpoints in enforcing homochirality during protein biosynthesis. D-aminoacyl-tRNA deacylase (DTD) is an enzyme that performs 'Chirality-based proofreading' to remove D-amino acids mistakenly attached to tRNAs, thus recycling them for further rounds of translation. Paradoxically, owing to its L-chiral rejection mode of action, DTD can remove glycine as well, which is an achiral amino acid. However, this activity is modulated by discriminator base (N73) in tRNA, a unique element that protects the cognate Gly-tRNAGly . Here, we review our recent work showing various aspects of DTD and tRNAGly co-evolution and its key role in maintaining proper translation surveillance in both bacteria and eukaryotes. Moreover, we also discuss two major optimization events on DTD and tRNA that resolved compatibility issues among the archaeal and the bacterial translation apparatuses. Importantly, such optimizations are necessary for the emergence of mitochondria and successful eukaryogenesis.
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Affiliation(s)
- Pradeep Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad, 500007, India
| | - Akshay Bhatnagar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad, 500007, India
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12
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Jani J, Pappachan A. A review on quality control agents of protein translation - The role of Trans-editing proteins. Int J Biol Macromol 2022; 199:252-263. [PMID: 34995670 DOI: 10.1016/j.ijbiomac.2021.12.176] [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: 10/23/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate mischarged tRNAs, which can become lethal to the cells. Accurate protein synthesis necessitates hydrolysis of mischarged tRNAs. Various cis and trans-editing proteins are identified which recognize these mischarged products and correct them by hydrolysis. Trans-editing proteins are homologs of cis-editing domains of aaRS. The trans-editing proteins work in close association with aaRS, Ef-Tu, and ribosome to prevent global mistranslation and ensures correct charging of tRNA. In this review, we discuss the major trans-editing proteins and compared them with their cis-editing counterparts. We also discuss their structural features, biochemical activity and role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India.
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13
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He R, Chen W, Chen H, Zhong Q, Zhang H, Zhang M, Chen W. Antibacterial mechanism of linalool against L. monocytogenes, a metabolomic study. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108533] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Gogoi J, Bhatnagar A, Ann KJ, Pottabathini S, Singh R, Mazeed M, Kuncha SK, Kruparani SP, Sankaranarayanan R. Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria. SCIENCE ADVANCES 2022; 8:eabj7307. [PMID: 35020439 PMCID: PMC8754408 DOI: 10.1126/sciadv.abj7307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/17/2021] [Indexed: 06/09/2023]
Abstract
Mitochondria emerged through an endosymbiotic event involving a proteobacterium and an archaeal host. However, the process of optimization of cellular processes required for the successful evolution and survival of mitochondria, which integrates components from two evolutionarily distinct ancestors as well as novel eukaryotic elements, is not well understood. We identify two key switches in the translational machinery—one in the discriminator recognition code of a chiral proofreader DTD [d-aminoacyl–transfer RNA (tRNA) deacylase] and the other in mitochondrial tRNAGly—that enable the compatibility between disparate elements essential for survival. Notably, the mito-tRNAGly discriminator element is the only one to switch from pyrimidine to purine during the bacteria-to-mitochondria transition. We capture this code transition in the Jakobida, an early diverging eukaryotic clade bearing the most bacterial-like mito-genome, wherein both discriminator elements are present. This study underscores the need to explore the fundamental integration strategies critical for mitochondrial and eukaryotic evolution.
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Affiliation(s)
- Jotin Gogoi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Akshay Bhatnagar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Kezia. J. Ann
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | | | - Raghvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Mohd Mazeed
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Shobha P. Kruparani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB Campus, Uppal Road, Hyderabad 500007, India
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15
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Mazeed M, Singh R, Kumar P, Roy A, Raman B, Kruparani SP, Sankaranarayanan R. Recruitment of archaeal DTD is a key event toward the emergence of land plants. SCIENCE ADVANCES 2021; 7:7/6/eabe8890. [PMID: 33536220 PMCID: PMC7857688 DOI: 10.1126/sciadv.abe8890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/16/2020] [Indexed: 06/09/2023]
Abstract
Streptophyte algae emerged as a land plant with adaptations that eventually led to terrestrialization. Land plants encounter a range of biotic and abiotic stresses that elicit anaerobic stress responses. Here, we show that acetaldehyde, a toxic metabolite of anaerobic stress, targets and generates ethyl adducts on aminoacyl-tRNA, a central component of the translation machinery. However, elongation factor thermo unstable (EF-Tu) safeguards l-aminoacyl-tRNA, but not d-aminoacyl-tRNA, from being modified by acetaldehyde. We identified a unique activity of archaeal-derived chiral proofreading module, d-aminoacyl-tRNA deacylase 2 (DTD2), that removes N-ethyl adducts formed on d-aminoacyl-tRNAs (NEDATs). Thus, the study provides the molecular basis of ethanol and acetaldehyde hypersensitivity in DTD2 knockout plants. We uncovered an important gene transfer event from methanogenic archaea to the ancestor of land plants. While missing in other algal lineages, DTD2 is conserved from streptophyte algae to land plants, suggesting its role toward the emergence and evolution of land plants.
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Affiliation(s)
- Mohd Mazeed
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Raghvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Pradeep Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad 500007, India
| | - Ankit Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Bakthisaran Raman
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Shobha P Kruparani
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad 500007, India
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16
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Guo F, Liang Q, Zhang M, Chen W, Chen H, Yun Y, Zhong Q, Chen W. Antibacterial Activity and Mechanism of Linalool against Shewanella putrefaciens. Molecules 2021; 26:molecules26010245. [PMID: 33466475 PMCID: PMC7796449 DOI: 10.3390/molecules26010245] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 11/26/2022] Open
Abstract
The demand for reduced chemical preservative usage is currently growing, and natural preservatives are being developed to protect seafood. With its excellent antibacterial properties, linalool has been utilized widely in industries. However, its antibacterial mechanisms remain poorly studied. Here, untargeted metabolomics was applied to explore the mechanism of Shewanella putrefaciens cells treated with linalool. Results showed that linalool exhibited remarkable antibacterial activity against S. putrefaciens, with 1.5 µL/mL minimum inhibitory concentration (MIC). The growth of S. putrefaciens was suppressed completely at 1/2 MIC and 1 MIC levels. Linalool treatment reduced the membrane potential (MP); caused the leakage of alkaline phosphatase (AKP); and released the DNA, RNA, and proteins of S. putrefaciens, thus destroying the cell structure and expelling the cytoplasmic content. A total of 170 differential metabolites (DMs) were screened using metabolomics analysis, among which 81 species were upregulated and 89 species were downregulated after linalool treatment. These DMs are closely related to the tricarboxylic acid (TCA) cycle, glycolysis, amino acid metabolism, pantothenate and CoA biosynthesis, aminoacyl-tRNA biosynthesis, and glycerophospholipid metabolism. In addition, linalool substantially affected the activity of key enzymes, such as succinate dehydrogenase (SDH), pyruvate kinase (PK), ATPase, and respiratory chain dehydrogenase. The results provided some insights into the antibacterial mechanism of linalool against S. putrefaciens and are important for the development and application of linalool in seafood preservation.
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Affiliation(s)
- Fengyu Guo
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Qiong Liang
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
| | - Ming Zhang
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
| | - Wenxue Chen
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Haiming Chen
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Yonghuan Yun
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Qiuping Zhong
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
- Correspondence: (Q.Z.); (W.C.)
| | - Weijun Chen
- College of Food Science and Technology, Hainan University, Haikou 570228, China; (F.G.); (Q.L.); (M.Z.); (W.C.); (H.C.); (Y.Y.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
- Correspondence: (Q.Z.); (W.C.)
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17
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Eis PS, Huang N, Langston JW, Hatchwell E, Schüle B. Loss-of-Function NUBPL Mutation May Link Parkinson's Disease to Recessive Complex I Deficiency. Front Neurol 2020; 11:555961. [PMID: 33224084 PMCID: PMC7667465 DOI: 10.3389/fneur.2020.555961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/28/2020] [Indexed: 02/01/2023] Open
Abstract
In an unbiased genome-wide screen for copy number variants (CNVs) on a cohort of Parkinson's disease (PD) patients, we identified in one patient a complex chromosomal rearrangement involving the nucleotide binding protein-like (NUBPL) gene on chromosome 14q12. We noted that mutations in the NUBPL gene had been reported as causing autosomal recessive (AR) mitochondrial Complex I (CI) deficiency in children. The precise breakpoints of the rearrangement in our PD case were found to be identical to those described in a patient with AR CI deficiency who also harbored a second pathogenic mutation in NUBPL. Mitochondrial dysfunction has long been considered a strong contributor to PD, and there is substantial evidence that decreased CI activity plays a central role in PD pathogenesis. We hypothesize that pathogenic NUBPL variants may increase the risk for PD analogous to variants in the glucosylceramidase beta (GBA) gene that increase the risk of developing PD in heterozygous carriers.
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Affiliation(s)
- Peggy S Eis
- Population Bio, Inc., New York, NY, United States
| | - Neng Huang
- Valley Parkinson Clinic, Los Gatos, CA, United States
| | - J William Langston
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Eli Hatchwell
- Population Bio, UK, Begbroke, Oxfordshire, United Kingdom
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
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18
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Violi JP, Bishop DP, Padula MP, Steele JR, Rodgers KJ. Considerations for amino acid analysis by liquid chromatography-tandem mass spectrometry: A tutorial review. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Kuncha SK, Venkadasamy VL, Amudhan G, Dahate P, Kola SR, Pottabathini S, Kruparani SP, Shekar PC, Sankaranarayanan R. Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia. eLife 2020; 9:58118. [PMID: 32463355 PMCID: PMC7302879 DOI: 10.7554/elife.58118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions. The first animals evolved around 750 million years ago from single-celled ancestors that were most similar to modern-day organisms called the Choanoflagellates. As animals evolved they developed more complex body plans consisting of multiple cells organized into larger structures known as tissues and organs. Over time cells also evolved increased levels of molecules called reactive oxygen species, which are involved in many essential cell processes but are toxic at high levels. Animal cells also contain more types of molecules known as transfer ribonucleic acids, or tRNAs for short, than Choanoflagellate cells and other single-celled organisms. These molecules deliver building blocks known as amino acids to the machinery that produces new proteins. To ensure the proteins are made correctly, it is important that tRNAs deliver specific amino acids to the protein-building machinery in the right order. Each type of tRNA usually only pairs with a specific type of amino acid, but sometimes the enzymes involved in this process can make mistakes. Therefore, cells contain proofreading enzymes that help remove incorrect amino acids on tRNAs. One such enzyme – called ATD – is only found in animals. Experiments in test tubes reported that ATD removes an amino acid called alanine from tRNAs that are supposed to carry threonine, but its precise role in living cells remained unclear. To address this question, Kuncha et al. studied proofreading enzymes in human kidney cells. The experiments showed that, in addition to ATD, a second enzyme known as ThrRS was also able to correct alanine substitutions for threonines on tRNAs. However, reactive oxygen species inactivated the proofreading ability of ThrRS, suggesting ATD plays an essential role in correcting errors in cells containing high levels of reactive oxygen species. These findings suggest that as organisms evolved multiple cells and the levels of tRNA and oxidative stress increased, this led to the appearance of a new proofreading enzyme. Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals. The next step following on from this work will be to understand the role of ATD in the cells of organs that are known to have particularly high levels of reactive oxygen species, such as testis and ovaries.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | | | - Priyanka Dahate
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sankara Rao Kola
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - P Chandra Shekar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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20
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Hobbs C, Řezanka P, Řezanka M. Cyclodextrin‐Functionalised Nanomaterials for Enantiomeric Recognition. Chempluschem 2020; 85:876-888. [DOI: 10.1002/cplu.202000187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/29/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher Hobbs
- Department of Nanomaterials in Natural SciencesInstitute for Nanomaterials, Advanced Technologies and InnovationTechnical University of Liberec Studentská 1402/2 461 17 Liberec Czech Republic
| | - Pavel Řezanka
- Department of Analytical ChemistryUniversity of Chemistry and Technology Prague Technická 5 166 28 Prague 6 Czech Republic
| | - Michal Řezanka
- Department of Nanomaterials in Natural SciencesInstitute for Nanomaterials, Advanced Technologies and InnovationTechnical University of Liberec Studentská 1402/2 461 17 Liberec Czech Republic
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21
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Janzen E, Blanco C, Peng H, Kenchel J, Chen IA. Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution. Chem Rev 2020; 120:4879-4897. [PMID: 32011135 PMCID: PMC7291351 DOI: 10.1021/acs.chemrev.9b00620] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The ability of enzymes,
including ribozymes, to catalyze side reactions
is believed to be essential to the evolution of novel biochemical
activities. It has been speculated that the earliest ribozymes, whose
emergence marked the origin of life, were low in activity but high
in promiscuity, and that these early ribozymes gave rise to specialized
descendants with higher activity and specificity. Here, we review
the concepts related to promiscuity and examine several cases of highly
promiscuous ribozymes. We consider the evidence bearing on the question
of whether de novo ribozymes would be quantitatively
more promiscuous than later evolved ribozymes or protein enzymes.
We suggest that while de novo ribozymes appear to
be promiscuous in general, they are not obviously more promiscuous
than more highly evolved or active sequences. Promiscuity is a trait
whose value would depend on selective pressures, even during prebiotic
evolution.
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Affiliation(s)
- Evan Janzen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Huan Peng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Josh Kenchel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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