1
|
Pan J, Singh A, Hanning K, Hicks J, Williamson A. A role for the ATP-dependent DNA ligase lig E of Neisseria gonorrhoeae in biofilm formation. BMC Microbiol 2024; 24:29. [PMID: 38245708 PMCID: PMC10799422 DOI: 10.1186/s12866-024-03193-9] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND The ATP-dependent DNA ligase Lig E is present as an accessory DNA ligase in numerous proteobacterial genomes, including many disease-causing species. Here we have constructed a genomic Lig E knock-out in the obligate human pathogen Neisseria gonorrhoeae and characterised its growth and infection phenotype. RESULTS This demonstrates that N. gonorrhoeae Lig E is a non-essential gene and its deletion does not cause defects in replication or survival of DNA-damaging stressors. Knock-out strains were partially defective in biofilm formation on an artificial surface as well as adhesion to epithelial cells. In addition to in vivo characterisation, we have recombinantly expressed and assayed N. gonorrhoeae Lig E and determined the crystal structure of the enzyme-adenylate engaged with DNA substrate in an open non-catalytic conformation. CONCLUSIONS These findings, coupled with the predicted extracellular/ periplasmic location of Lig E indicates a role in extracellular DNA joining as well as providing insight into the binding dynamics of these minimal DNA ligases.
Collapse
Affiliation(s)
- Jolyn Pan
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Avi Singh
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Kyrin Hanning
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Joanna Hicks
- School of Health, University of Waikato, Hamilton, New Zealand
| | - Adele Williamson
- School of Science, University of Waikato, Hamilton, New Zealand.
| |
Collapse
|
2
|
Buckley RJ, Lou‐Hing A, Hanson KM, Ahmed NR, Cooper CDO, Bolt EL. Escherichia coli DNA repair helicase Lhr is also a uracil-DNA glycosylase. Mol Microbiol 2023; 120:298-306. [PMID: 37452011 PMCID: PMC10953399 DOI: 10.1111/mmi.15123] [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: 01/16/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
DNA glycosylases protect genetic fidelity during DNA replication by removing potentially mutagenic chemically damaged DNA bases. Bacterial Lhr proteins are well-characterized DNA repair helicases that are fused to additional 600-700 amino acids of unknown function, but with structural homology to SecB chaperones and AlkZ DNA glycosylases. Here, we identify that Escherichia coli Lhr is a uracil-DNA glycosylase (UDG) that depends on an active site aspartic acid residue. We show that the Lhr DNA helicase activity is functionally independent of the UDG activity, but that the helicase domains are required for fully active UDG activity. Consistent with UDG activity, deletion of lhr from the E. coli chromosome sensitized cells to oxidative stress that triggers cytosine deamination to uracil. The ability of Lhr to translocate single-stranded DNA and remove uracil bases suggests a surveillance role to seek and remove potentially mutagenic base changes during replication stress.
Collapse
Affiliation(s)
| | - Anna Lou‐Hing
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Karl M. Hanson
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Nadia R. Ahmed
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Christopher D. O. Cooper
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
- CHARM Therapeutics LtdB900 Babraham Research CampusCambridgeUK
| | - Edward L. Bolt
- School of Life SciencesUniversity of NottinghamNottinghamUK
| |
Collapse
|
3
|
Rzoska-Smith E, Stelzer R, Monterio M, Cary SC, Williamson A. DNA repair enzymes of the Antarctic Dry Valley metagenome. Front Microbiol 2023; 14:1156817. [PMID: 37125210 PMCID: PMC10140301 DOI: 10.3389/fmicb.2023.1156817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.
Collapse
Affiliation(s)
- Elizabeth Rzoska-Smith
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
| | - Ronja Stelzer
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
| | - Maria Monterio
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen C. Cary
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, New Zealand
| | - Adele Williamson
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Adele Williamson,
| |
Collapse
|
4
|
Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Catalysts 2021. [DOI: 10.3390/catal12010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of HR in Archaea, the helicase-promoting branch migration is not fully understood. Previous biochemical studies identified three candidates for archaeal helicase promoting branch migration in vitro: Hjm/Hel308, PINA, and archaeal long helicase related (aLhr) 2. However, there is no direct evidence of their involvement in HR in vivo. Here, we identified a novel helicase encoded by Saci_0814, isolated from the thermophilic crenarchaeon Sulfolobus acidocaldarius; the helicase dissociated a synthetic HJ. Notably, HR frequency in the Saci_0814-deleted strain was lower than that of the parent strain (5-fold decrease), indicating that Saci_0814 may be involved in HR in vivo. Saci_0814 is classified as an aLhr1 under superfamily 2 helicases; its homologs are conserved among Archaea. Purified protein produced in Escherichia coli showed branch migration activity in vitro. Based on both genetic and biochemical evidence, we suggest that aLhr1 is involved in HR and may function as a branch migration helicase in S. acidocaldarius.
Collapse
|
5
|
Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase. Biomolecules 2021; 11:biom11070950. [PMID: 34206878 PMCID: PMC8301817 DOI: 10.3390/biom11070950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.
Collapse
|
6
|
Warren GM, Wang J, Patel DJ, Shuman S. Oligomeric quaternary structure of Escherichia coli and Mycobacterium smegmatis Lhr helicases is nucleated by a novel C-terminal domain composed of five winged-helix modules. Nucleic Acids Res 2021; 49:3876-3887. [PMID: 33744958 PMCID: PMC8053096 DOI: 10.1093/nar/gkab145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium smegmatis Lhr (MsmLhr; 1507-aa) is the founder of a novel clade of bacterial helicases. MsmLhr consists of an N-terminal helicase domain (aa 1–856) with a distinctive tertiary structure (Lhr-Core) and a C-terminal domain (Lhr-CTD) of unknown structure. Here, we report that Escherichia coli Lhr (EcoLhr; 1538-aa) is an ATPase, translocase and ATP-dependent helicase. Like MsmLhr, EcoLhr translocates 3′ to 5′ on ssDNA and unwinds secondary structures en route, with RNA:DNA hybrid being preferred versus DNA:DNA duplex. The ATPase and translocase activities of EcoLhr inhere to its 877-aa Core domain. Full-length EcoLhr and MsmLhr have homo-oligomeric quaternary structures in solution, whereas their respective Core domains are monomers. The MsmLhr CTD per se is a homo-oligomer in solution. We employed cryo-EM to solve the structure of the CTD of full-length MsmLhr. The CTD protomer is composed of a series of five winged-helix (WH) modules and a β-barrel module. The CTD adopts a unique homo-tetrameric quaternary structure. A Lhr-CTD subdomain, comprising three tandem WH modules and the β-barrel, is structurally homologous to AlkZ, a bacterial DNA glycosylase that recognizes and excises inter-strand DNA crosslinks. This homology is noteworthy given that Lhr is induced in mycobacteria exposed to the inter-strand crosslinker mitomycin C.
Collapse
Affiliation(s)
- Garrett M Warren
- Molecular Biology and Structural Biology Programs, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Juncheng Wang
- Molecular Biology and Structural Biology Programs, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dinshaw J Patel
- Molecular Biology and Structural Biology Programs, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology and Structural Biology Programs, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
7
|
Ghosh S, Ejaz A, Repeta L, Shuman S. Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3'-PO4 and 3'-OH termini. Nucleic Acids Res 2021; 49:1023-1032. [PMID: 33367848 PMCID: PMC7826289 DOI: 10.1093/nar/gkaa1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.
Collapse
Affiliation(s)
- Shreya Ghosh
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anam Ejaz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lucas Repeta
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
8
|
Mechanistic insights into Lhr helicase function in DNA repair. Biochem J 2021; 477:2935-2947. [PMID: 32706021 PMCID: PMC7437997 DOI: 10.1042/bcj20200379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022]
Abstract
The DNA helicase Large helicase-related (Lhr) is present throughout archaea, including in the Asgard and Nanoarchaea, and has homologues in bacteria and eukaryotes. It is thought to function in DNA repair but in a context that is not known. Our data show that archaeal Lhr preferentially targets DNA replication fork structures. In a genetic assay, expression of archaeal Lhr gave a phenotype identical to the replication-coupled DNA repair enzymes Hel308 and RecQ. Purified archaeal Lhr preferentially unwound model forked DNA substrates compared with DNA duplexes, flaps and Holliday junctions, and unwound them with directionality. Single-molecule FRET measurements showed that binding of Lhr to a DNA fork causes ATP-independent distortion and base-pair melting at, or close to, the fork branchpoint. ATP-dependent directional translocation of Lhr resulted in fork DNA unwinding through the ‘parental’ DNA strands. Interaction of Lhr with replication forks in vivo and in vitro suggests that it contributes to DNA repair at stalled or broken DNA replication.
Collapse
|
9
|
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: 13] [Impact Index Per Article: 3.3] [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.
Collapse
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
| | | |
Collapse
|
10
|
Zhou L, Jiao X, Liu S, Hao M, Cheng S, Zhang P, Wen Y. Functional DNA-based hydrogel intelligent materials for biomedical applications. J Mater Chem B 2020; 8:1991-2009. [DOI: 10.1039/c9tb02716e] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multifunctional intelligent DNA hydrogels have been reviewed for many biomedical applications.
Collapse
Affiliation(s)
- Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology
- School of Chemistry and Biological Engineering
- University of Science and Technology Beijing
- Beijing
- China
| | - Xiangyu Jiao
- Beijing Key Laboratory for Bioengineering and Sensing Technology
- School of Chemistry and Biological Engineering
- University of Science and Technology Beijing
- Beijing
- China
| | - Songyang Liu
- Department of Orthopaedics and Trauma
- Peking University People's Hospital
- Beijing
- China
| | - Mingda Hao
- Beijing Key Laboratory for Bioengineering and Sensing Technology
- School of Chemistry and Biological Engineering
- University of Science and Technology Beijing
- Beijing
- China
| | - Siyang Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology
- School of Chemistry and Biological Engineering
- University of Science and Technology Beijing
- Beijing
- China
| | - Peixun Zhang
- Department of Orthopaedics and Trauma
- Peking University People's Hospital
- Beijing
- China
| | - Yongqiang Wen
- Beijing Key Laboratory for Bioengineering and Sensing Technology
- School of Chemistry and Biological Engineering
- University of Science and Technology Beijing
- Beijing
- China
| |
Collapse
|
11
|
|
12
|
Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
Collapse
Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
13
|
Ejaz A, Goldgur Y, Shuman S. Activity and structure of Pseudomonas putida MPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster. J Biol Chem 2019; 294:7931-7941. [PMID: 30894417 DOI: 10.1074/jbc.ra119.008049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/20/2019] [Indexed: 02/04/2023] Open
Abstract
A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are as follows: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-β-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here, we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 Å resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp33, His35, Asp78, Asn112, His124, His146, and His158 A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the β sandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-à-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.
Collapse
Affiliation(s)
| | - Yehuda Goldgur
- Structural Biology Programs, Sloan Kettering Institute, New York, New York 10065
| | | |
Collapse
|
14
|
Boël G, Danot O, de Lorenzo V, Danchin A. Omnipresent Maxwell's demons orchestrate information management in living cells. Microb Biotechnol 2019; 12:210-242. [PMID: 30806035 PMCID: PMC6389857 DOI: 10.1111/1751-7915.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.
Collapse
Affiliation(s)
- Grégory Boël
- UMR 8261 CNRS‐University Paris DiderotInstitut de Biologie Physico‐Chimique13 rue Pierre et Marie Curie75005ParisFrance
| | - Olivier Danot
- Institut Pasteur25‐28 rue du Docteur Roux75724Paris Cedex 15France
| | - Victor de Lorenzo
- Molecular Environmental Microbiology LaboratorySystems Biology ProgrammeCentro Nacional de BiotecnologiaC/Darwin n° 3, Campus de Cantoblanco28049MadridEspaña
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
- The School of Biomedical SciencesLi Kashing Faculty of MedicineHong Kong University21, Sassoon RoadPokfulamSAR Hong Kong
| |
Collapse
|