1
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Sedlmayr VL, Luger M, Pittenauer E, Marchetti-Deschmann M, Kronlachner L, Limbeck A, Raunjak P, Quehenberger J, Spadiut O. Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula. Extremophiles 2024; 28:36. [PMID: 39060419 PMCID: PMC11282131 DOI: 10.1007/s00792-024-01348-0] [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: 03/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.
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Affiliation(s)
- Viktor Laurin Sedlmayr
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Maximilian Luger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Ernst Pittenauer
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | | | - Laura Kronlachner
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Andreas Limbeck
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Philipp Raunjak
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Julian Quehenberger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria.
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2
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Prosdocimi F, de Farias ST. Major evolutionary transitions before cells: A journey from molecules to organisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:11-24. [PMID: 38971326 DOI: 10.1016/j.pbiomolbio.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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3
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Rousseau M, Oulavallickal T, Williamson A, Arcus V, Patrick WM, Hicks J. Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus. Nucleic Acids Res 2024; 52:3924-3937. [PMID: 38421610 DOI: 10.1093/nar/gkae149] [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: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
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Affiliation(s)
- Meghan Rousseau
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Tifany Oulavallickal
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Adele Williamson
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Vic Arcus
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Joanna Hicks
- Te Huataki Waiora School of Health, The University of Waikato, Hamilton 3216, New Zealand
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4
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A multiple primers-mediated exponential rolling circle amplification strategy for highly sensitive detection of T4 polynucleotide kinase and T4 DNA ligase activity. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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5
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Arbab S, Ullah H, Khan MIU, Khattak MNK, Zhang J, Li K, Hassan IU. Diversity and distribution of thermophilic microorganisms and their applications in biotechnology. J Basic Microbiol 2021; 62:95-108. [PMID: 34878177 DOI: 10.1002/jobm.202100529] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/16/2021] [Accepted: 11/27/2021] [Indexed: 11/07/2022]
Abstract
Hot springs ecosystem is the most ancient continuously inhabited ecosystem on earth which harbors diverse thermophilic bacteria and archaea distributed worldwide. Life in extreme environments is very challenging so there is a great potential biological dark matter and their adaptation to harsh environments eventually producing thermostable enzymes which are very vital for the welfare of mankind. There is an enormous need for a new generation of stable enzymes that can endure harsh conditions in industrial processes and can either substitute or complement conventional chemical processes. Here, we review at the variety and distribution of thermophilic microbes, as well as the different thermostable enzymes that help them survive at high temperatures, such as proteases, amylases, lipases, cellulases, pullulanase, xylanases, and DNA polymerases, as well as their special properties, such as high-temperature stability. We have documented the novel isolated thermophilic and hyperthermophilic microorganisms, as well as the discovery of their enzymes, demonstrating their immense potential in the scientific community and in industry.
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Affiliation(s)
- Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Muhammad I U Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Muhammad N K Khattak
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Inam Ul Hassan
- Department of Microbiology, Hazara University, Manshera, Pakistan
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6
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Williamson A, Leiros HKS. Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res 2020; 48:8225-8242. [PMID: 32365176 PMCID: PMC7470946 DOI: 10.1093/nar/gkaa307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
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Affiliation(s)
- Adele Williamson
- School of Science, University of Waikato, Hamilton 3240, New Zealand.,Department of Chemistry, UiT The Arctic University of Norway, Tromsø N-9037, Norway
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7
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Berg K, Leiros I, Williamson A. Temperature adaptation of DNA ligases from psychrophilic organisms. Extremophiles 2019; 23:305-317. [DOI: 10.1007/s00792-019-01082-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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8
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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9
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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10
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Amir M, Kumar V, Dohare R, Islam A, Ahmad F, Hassan MI. Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family. J Evol Biol 2018; 31:1903-1917. [PMID: 30267552 DOI: 10.1111/jeb.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/28/2022]
Abstract
The cold shock domain (CSD) belongs to the oligosaccharide/oligonucleotide-binding fold superfamily which is highly conserved from prokaryotes to higher eukaryotes, and appears to function as RNA chaperones. CSD is involved in diverse cellular processes, including adaptation to low temperatures, nutrient stress, cellular growth and developmental processes. Structural Classification of Proteins (SCOP) database broadly classifies OB fold proteins into 18 different superfamilies, including nucleic acid-binding superfamily (NAB). The NAB is further divided into 17 families together with cold shock DNA-binding protein family (CSDB). The CSDB have more than 240 000 sequences in UniProt database consisting of 32 domains including CSD. Among these domains, CSD is the second largest sequence contributor (> 40 398 sequences). Herein, we have systematically analysed the relative abundance and distribution of CSD proteins based on sequences, structures, repeats and gene ontology (GO) molecular functions in all domains of life. Analysis of sequence distribution suggesting that CSDs are largely found in bacteria (83-94%) with single CSD repeat. However, repeat distribution in eukaryota varies from 1 to 5 in combination with other auxiliary domain that makes CSD proteins functionally more diverse compared to the bacterial counterparts. Further, analysis of repeats distributions on evolutionary scale suggest that existence of CSD in multiple repeats is mainly driven through speciation, gene shuffling and gene duplication events.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Amity Institute of Neuropsychology & Neurosciences, Amity University Noida, UP, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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11
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Becker HF, Héliou A, Djaout K, Lestini R, Regnier M, Myllykallio H. High-throughput sequencing reveals circular substrates for an archaeal RNA ligase. RNA Biol 2017; 14:1075-1085. [PMID: 28277897 DOI: 10.1080/15476286.2017.1302640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.
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Affiliation(s)
- Hubert F Becker
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,b Sorbonne Universités, UPMC Univ Paris 06 , 4 Place Jussieu, Paris , France
| | - Alice Héliou
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Kamel Djaout
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Roxane Lestini
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Mireille Regnier
- c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Hannu Myllykallio
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
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12
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Kumar S, Arumugam N, Permaul K, Singh S. Chapter 5 Thermostable Enzymes and Their Industrial Applications. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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13
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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