scholarly journals A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger

2016 ◽  
Vol 198 (9) ◽  
pp. 861-868 ◽  
Author(s):  
Jing Niu ◽  
Mark Arentshorst ◽  
Felix Seelinger ◽  
Arthur F. J. Ram ◽  
Jean Paul Ouedraogo
Keyword(s):  
Aspergillus Niger ◽  
Gene Deletion ◽  
Deletion Mutants ◽  
Multiple Gene

Pleiotropic drug-resistance attenuated genomic library improves elucidation of drug mechanisms

2015 ◽  
Vol 11 (11) ◽  
pp. 3129-3136 ◽  
Author(s):  
Namal V. C. Coorey ◽  
James H. Matthews ◽  
David S. Bellows ◽  
Paul H. Atkinson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Mechanism Of Action ◽  
Gene Deletion ◽  
Genomic Library ◽  
Deletion Mutants ◽  
Pleiotropic Drug Resistance ◽  
Genome Wide

Identifying Saccharomyces cerevisiae genome-wide gene deletion mutants that confer hypersensitivity to a xenobiotic aids the elucidation of its mechanism of action (MoA).

scholarly journals Large-scale Phenotypic Profiling of Gene Deletion Mutants in Candida glabrata

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (14) ◽  
Author(s):  
Fabian Istel ◽  
Tobias Schwarzm�ller ◽  
Michael Tscherner ◽  
Karl Kuchler
Keyword(s):  
Candida Glabrata ◽  
Large Scale ◽  
Gene Deletion ◽  
Deletion Mutants

scholarly journals Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

2020 ◽  
Vol 48 (8) ◽  
pp. 4585-4600
Author(s):  
Gabriel A Suárez ◽  
Kyle R Dugan ◽  
Brian A Renda ◽  
Sean P Leonard ◽  
Lakshmi Suryateja Gangavarapu ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Single Gene ◽  
Acinetobacter Baylyi ◽  
Gene Deletions ◽  
Multiple Gene ◽  
Transposon Insertion ◽  
A Genome ◽  
Acinetobacter Baylyi Adp1 ◽  
Transposon Insertion Sequencing ◽  
Improved Methods

Abstract One goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 18 successful multiple-gene deletions ranged in size from 21 to 183 kb and collectively accounted for 23.4% of its genome. The success of each multiple-gene deletion attempt could only be partially predicted on the basis of an existing collection of viable ADP1 single-gene deletion strains and a new transposon insertion sequencing (Tn-Seq) dataset that we generated. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.

Revelation of molecular basis for chromium toxicity by phenotypes of Saccharomyces cerevisiae gene deletion mutants

Metallomics ◽  
2016 ◽  
Vol 8 (5) ◽  
pp. 542-550 ◽  
Author(s):  
Adam J. Johnson ◽  
Filip Veljanoski ◽  
Patrick. J. O'Doherty ◽  
Mohammad S. Zaman ◽  
Gayani Petersingham ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Basis ◽  
Gene Deletion ◽  
Deletion Mutants ◽  
Chromium Toxicity

scholarly journals Siderophores Are Not Involved in Fe(III) Solubilization during Anaerobic Fe(III) Respiration by Shewanella oneidensis MR-1

2010 ◽  
Vol 76 (8) ◽  
pp. 2425-2432 ◽  
Author(s):  
Christine M. Fennessey ◽  
Morris E. Jones ◽  
Martial Taillefert ◽  
Thomas J. DiChristina
Keyword(s):  
Electron Acceptor ◽  
Gene Deletion ◽  
Shewanella Oneidensis ◽  
Nitrilotriacetic Acid ◽  
Organic Ligands ◽  
Aerobic Respiration ◽  
Deletion Mutants ◽  
Wild Type ◽  
Voltammetric Techniques ◽  
Wide Range

ABSTRACT Shewanella oneidensis MR-1 respires a wide range of anaerobic electron acceptors, including sparingly soluble Fe(III) oxides. In the present study, S. oneidensis was found to produce Fe(III)-solubilizing organic ligands during anaerobic Fe(III) oxide respiration, a respiratory strategy postulated to destabilize Fe(III) and produce more readily reducible soluble organic Fe(III). In-frame gene deletion mutagenesis, siderophore detection assays, and voltammetric techniques were combined to determine (i) if the Fe(III)-solubilizing organic ligands produced by S. oneidensis during anaerobic Fe(III) oxide respiration were synthesized via siderophore biosynthesis systems and (ii) if the Fe(III)-siderophore reductase was required for respiration of soluble organic Fe(III) as an anaerobic electron acceptor. Genes predicted to encode the siderophore (hydroxamate) biosynthesis system (SO3030 to SO3032), the Fe(III)-hydroxamate receptor (SO3033), and the Fe(III)-hydroxamate reductase (SO3034) were identified in the S. oneidensis genome, and corresponding in-frame gene deletion mutants were constructed. ΔSO3031 was unable to synthesize siderophores or produce soluble organic Fe(III) during aerobic respiration yet retained the ability to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. ΔSO3034 retained the ability to synthesize siderophores during aerobic respiration and to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. These findings indicate that the Fe(III)-solubilizing organic ligands produced by S. oneidensis during anaerobic Fe(III) oxide respiration are not synthesized via the hydroxamate biosynthesis system and that the Fe(III)-hydroxamate reductase is not essential for respiration of Fe(III)-citrate or Fe(III)-nitrilotriacetic acid (NTA) as an anaerobic electron acceptor.

scholarly journals Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

2008 ◽  
Vol 9 (9) ◽  
pp. R140 ◽  
Author(s):  
Evan S Snitkin ◽  
Aimée M Dudley ◽  
Daniel M Janse ◽  
Kaisheen Wong ◽  
George M Church ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Deletion Mutants ◽  
Yeast Gene ◽  
Model Driven

scholarly journals Functional profiling inStreptococcus mutans: construction and examination of a genomic collection of gene deletion mutants

2015 ◽  
Vol 30 (6) ◽  
pp. 474-495 ◽  
Author(s):  
R.G. Quivey ◽  
E.J. Grayhack ◽  
R.C. Faustoferri ◽  
C.J. Hubbard ◽  
J.D. Baldeck ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Deletion Mutants ◽  
Functional Profiling

scholarly journals Markerless Multiple-Gene-Deletion System for Streptococcus mutans

2008 ◽  
Vol 74 (7) ◽  
pp. 2037-2042 ◽  
Author(s):  
Anirban Banerjee ◽  
Indranil Biswas
Keyword(s):  
Dental Caries ◽  
Streptococcus Mutans ◽  
Genetic Background ◽  
Double Mutant ◽  
Gene Deletion ◽  
Low Ph ◽  
Gene Deletions ◽  
Multiple Gene ◽  
Modified Method ◽  
Oxidative Agents

ABSTRACT Inactivation or selective modification is essential to elucidate the putative function of a gene. The present study describes an improved Cre-loxP-based method for markerless multiple gene deletion in Streptococcus mutans, the principal etiological agent of dental caries. This modified method uses two mutant loxP sites, which after recombination creates a double-mutant loxP site that is poorly recognized by Cre recombinase, facilitating multiple gene deletions in a single genetic background. The effectiveness of this modified strategy was demonstrated by the construction of both single and double gene deletions at the htrA and clpP loci on the chromosome of Streptococcus mutans. HtrA and ClpP play key roles in the processing and maturation of several important proteins, including many virulence factors. Deletion of these genes resulted in reducing the organism's ability to withstand exposure to low pH and oxidative agents. The method described here is simple and efficient and can be easily implemented for multiple gene deletions with S. mutans and other streptococci.

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