Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation

Autor: Céline Loot, Aleksandra Nivina, Guillaume Cambray, Rocío López-Igual, Jose Antonio Escudero, Didier Mazel
Přispěvatelé: Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Université Paris Descartes - Paris 5 (UPD5), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Fondation pour la Recherche Medicale [DBF20160635736, FDT20150532465], Agence Nationale de la Recherche [ANR-10-LABX-62-IBEID, ANR-12-BLAN-DynamINT], FP7 People: Marie-Curie Actions [IEF-ICADIGE], Consejeria de Educacion, Juventud y Deporte, Comunidad de Madrid [2016-T1/BIO-1105], Seventh Framework Programme [PLASWIRES], FP7Health [EVOTAR], ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-12-BSV3-0015,DynamINT,Recombination des cassettes d'intégron: dynamique in vivo et in vitro(2012), European Project: 612146,EC:FP7:ICT,FP7-ICT-2013-10,PLASWIRES(2013), European Project: 282004,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,EVOTAR(2011), Plasticité du Génome Bactérien, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Universidad Complutense de Madrid [Madrid] (UCM), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Fondation pour la Recherche Médicale. Grant Numbers: DBF20160635736, FDT20150532465Agence Nationale de la Recherche. Grant Numbers: ANR‐10‐LABX‐62‐IBEID, ANR‐12‐BLAN‐DynamINTFP7 People: Marie‐Curie Actions. Grant Number: IEF‐ICADIGEConsejería de Educación, Juventud y Deporte, Comunidad de Madrid. Grant Number: 2016‐T1/BIO‐1105Seventh Framework Programme. Grant Number: PLASWIRESParis Descartes University‐Sorbonne Paris CitéCentre National de la Recherche Scientifique. Grant Number: UMR3525École Doctorale Frontières du VivantFP7Health. Grant Number: EVOTAR, European Project: 303022,EC:FP7:PEOPLE,FP7-PEOPLE-2011-IEF,ICADIGE(2012)
Rok vydání: 2017
Předmět:
Models
Molecular
synonymous genes
0301 basic medicine
Biotecnología
MESH: Integrases
[SDV.BIO]Life Sciences [q-bio]/Biotechnology
Protein Conformation
[SDV]Life Sciences [q-bio]
Evolutionary landscape
Microbiología
Applied Microbiology and Biotechnology
mRNA secondary structure
Synthetic biology
MESH: Protein Conformation
MESH: Directed Molecular Evolution
Degeneracy (biology)
Protein secondary structure
ComputingMilieux_MISCELLANEOUS
Genetics
Biología molecular
MESH: Integrons
MESH: Protein Biosynthesis
Synonymous substitution
algorithme
MESH: Models
Molecular
Biotechnology
multi-objective particle swarm optimization (mopso)
030106 microbiology
Bioengineering
Computational biology
Biology
03 medical and health sciences
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
optimized gene
Allele
Gene
Integrases
DNA design
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular biology
recombination
Evolvability
Evolución
synthèse d'adn
recombinaison
030104 developmental biology
Protein Biosynthesis
integrons
synthetic biology
Directed Molecular Evolution
Zdroj: Biotechnology and Bioengineering
Biotechnology and Bioengineering, 2018, 115 (1), pp.184-191. ⟨10.1002/bit.26450⟩
Biotechnology and Bioengineering, Wiley, 2018, 115 (1), pp.184-191. ⟨10.1002/bit.26450⟩
ISSN: 0006-3592
1097-0290
DOI: 10.1002/bit.26450
Popis: Synthetic DNA design needs to harness the many information layers embedded in a DNA string. We previously developed the Evolutionary Landscape Painter (ELP), an algorithm that exploits the degeneracy of the code to increase protein evolvability. Here, we have used ELP to recode the integron integrase gene (intI1) in two alternative alleles. Although synonymous, both alleles yielded less IntI1 protein and were less active in recombination assays than intI1. We spliced the three alleles and mapped the activity decrease to the beginning of alternative sequences. Mfold predicted the presence of more stable secondary structures in the alternative genes. Using synonymous mutations, we decreased their stability and recovered full activity. Following a design-build-test approach, we have now updated ELP to consider such structures and provide streamlined alternative sequences. Our results support the possibility of modulating gene activity through the ad hoc design of 5′ secondary structures in synthetic genes. This article is protected by copyright. All rights reserved
Databáze: OpenAIRE
Externí odkaz: