Systematic genome engineering approaches to investigate mutational effects and evolutionary processes

Nyerges Ákos József
Systematic genome engineering approaches to investigate mutational effects and evolutionary processes.
PhD, University of Szeged.

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Abstract in foreign language

To address the shortcomings of currently available genome editing and in vivo directed evolution techniques, we have developed a plasmid-based method for broad-host-range genome engineering (pORTMAGE), and based on pORTMAGE, a method for in vivo directed evolution. This new method, termed DIvERGE (directed evolution with random genomic mutations) allows the systematic multiplex mutagenesis of long genomic segments. DIvERGE has numerous advantages over the alternative techniques, including (I) the possibility to target multiple, user-defined genomic regions; (II) it has a broad and controllable mutagenesis spectrum for each nucleotide position; (III) it allows of up to a million-fold increase in mutation rate at the target sequence; (IV) it enables multiple rounds of mutagenesis and selection in a fast and continuous manner; (V) it is applicable to a wide range of enterobacterial species without the need for prior genomic modification(s); (VI) it avoids off-target mutagenesis, and (VII) it is also cost-effective as it relies on soft-randomized oligos which can easily be manufactured at a modest cost. In summary, DIvERGE offers a versatile solution for high-precision directed evolution at multiple loci in their native genomic context. Due to these favorable characteristics, DIvERGE is especially well-suited to study bacterial evolution leading to antibiotic resistance.

Item Type: Thesis (PhD)
Creators: Nyerges Ákos József
Hungarian title label: Rendszerszintű genommérnöki vizsgálatok az evolúciós folyamatok tanulmányozására
Title of the thesis in foreign language: Systematic genome engineering approaches to investigate mutational effects and evolutionary processes
Divisions: Doctoral School of Biology
Discipline label: természettudományok > biológiai tudományok
Defence date label: 2019. March 18.
Uncontrolled Keywords: Synthetic biology, genome engineering, antibiotic resistance, directed evolution
Item ID: 10051
Date Deposited: 2019. Jan. 09. 19:28
Last Modified: 2019. Apr. 30. 10:48
Depository no.: B 6501
Supervisor label:
Supervisor Supervisor scientific name label
Dr. Pál Csaba
tudományos főmunkatárs, PhD, Szegedi Biológiai Kutatóközpont Magyar Tudományos Akadémia
Reviewer label:
Reviewer name label Reviewer scientific name label
Dr. Rákhely Gábor
Dr. Olasz Ferenc
PhD, tanszékvezető egyetemi docens, SZTE TTIK Biotechnológiai Tanszék
PhD, intézetigazgató, NAIK Mezőgazdasági Biotechnológiai Kutatóintézet
President label:
President name label President scientific name label
Dr. Vágvölgyi Csaba
DSc, tanszékvezető egyetemi tanár, SZTE TTIK Mikrobiológiai Tanszék
Member label:
Member name label Member scientific name label
Dr. Somogyvári Ferenc
Dr. Sinka Rita
PhD, egyetemi docens, SZTE ÁOK Orvosi Vegytani Intézet
PhD, adjunktus, SZTE TTIK Genetikai Tanszék
Defence/Citable status: Not Defended. (Do not cite until it has not assigned DOI number!)

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