The “Italian” Barley Genetic Mutant Collection: Conservation, Development of New Mutants and Use

The diagnostic and therapeutic agent gallium offers multiple clinical and commercial uses including the treatment of cancer and the localization of tumors, among others. Further, this metal has been proven to be an effective antimicrobial agent against a number of microbes. Despite the latter, the fundamental mechanisms of gallium action have yet to be fully identified and understood. To further the development of this antimicrobial, it is imperative that we understand the mechanisms by which gallium interacts with cells. As a result, we screened the Escherichia coli Keio mutant collection as a means of identifying the genes that are implicated in prolonged gallium toxicity or resistance and mapped their biological processes to their respective cellular system. We discovered that the deletion of genes functioning in response to oxidative stress, DNA or iron–sulfur cluster repair, and nucleotide biosynthesis were sensitive to gallium, while Ga resistance comprised of genes involved in iron/siderophore import, amino acid biosynthesis and cell envelope maintenance. Altogether, our explanations of these findings offer further insight into the mechanisms of gallium toxicity and resistance in E. coli.

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Screening the yeast deletant mutant collection for hypersensitivity and hyper-resistance to sorbate, a weak organic acid food preservative

Yeast ◽

10.1002/yea.1141 ◽

2004 ◽

Vol 21 (11) ◽

pp. 927-946 ◽

Cited By ~ 50

Author(s):

Mehdi Mollapour ◽

Dahna Fong ◽

Krishna Balakrishnan ◽

Nicholas Harris ◽

Suzanne Thompson ◽

...

Keyword(s):

Organic Acid ◽

Food Preservative ◽

Weak Organic Acid ◽

Mutant Collection

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A Novel Saccharomyces cerevisiae FG Nucleoporin Mutant Collection for Use in Nuclear Pore Complex Functional Experiments

G3 Genes|Genome|Genetics ◽

10.1534/g3.115.023002 ◽

2015 ◽

Vol 6 (1) ◽

pp. 51-58 ◽

Cited By ~ 4

Author(s):

Rebecca L. Adams ◽

Laura J. Terry ◽

Susan R. Wente

Keyword(s):

Saccharomyces Cerevisiae ◽

Nuclear Pore Complex ◽

Nuclear Pore ◽

Mutant Collection

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The Identification of Genetic Determinants of Methanol Tolerance in Yeast Suggests Differences in Methanol and Ethanol Toxicity Mechanisms and Candidates for Improved Methanol Tolerance Engineering

Journal of Fungi ◽

10.3390/jof7020090 ◽

2021 ◽

Vol 7 (2) ◽

pp. 90

Author(s):

Marta N. Mota ◽

Luís C. Martins ◽

Isabel Sá-Correia

Keyword(s):

Dna Repair ◽

Regulatory Networks ◽

Fatty Acid Biosynthesis ◽

Methylotrophic Yeast ◽

Genetic Determinants ◽

Methanol Tolerance ◽

Yeast Strains ◽

Starting Point ◽

Ethanol Toxicity ◽

Mutant Collection

Methanol is a promising feedstock for metabolically competent yeast strains-based biorefineries. However, methanol toxicity can limit the productivity of these bioprocesses. Therefore, the identification of genes whose expression is required for maximum methanol tolerance is important for mechanistic insights and rational genomic manipulation to obtain more robust methylotrophic yeast strains. The present chemogenomic analysis was performed with this objective based on the screening of the Euroscarf Saccharomyces cerevisiae haploid deletion mutant collection to search for susceptibility phenotypes in YPD medium supplemented with 8% (v/v) methanol, at 35 °C, compared with an equivalent ethanol concentration (5.5% (v/v)). Around 400 methanol tolerance determinants were identified, 81 showing a marked phenotype. The clustering of the identified tolerance genes indicates an enrichment of functional categories in the methanol dataset not enriched in the ethanol dataset, such as chromatin remodeling, DNA repair and fatty acid biosynthesis. Several genes involved in DNA repair (eight RAD genes), identified as specific for methanol toxicity, were previously reported as tolerance determinants for formaldehyde, a methanol detoxification pathway intermediate. This study provides new valuable information on genes and potential regulatory networks involved in overcoming methanol toxicity. This knowledge is an important starting point for the improvement of methanol tolerance in yeasts capable of catabolizing and copying with methanol concentrations present in promising bioeconomy feedstocks, including industrial residues.

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Tnt1 retrotransposon as an efficient tool for development of an insertional mutant collection of Lotus japonicus

In Vitro Cellular & Developmental Biology - Plant ◽

10.1007/s11627-016-9768-3 ◽

2016 ◽

Vol 52 (3) ◽

pp. 338-347 ◽

Cited By ~ 3

Author(s):

Anelia Iantcheva ◽

Miglena Revalska ◽

Grigor Zehirov ◽

Irina Boycheva ◽

Kevin Magne ◽

...

Keyword(s):

Lotus Japonicus ◽

Efficient Tool ◽

Insertional Mutant ◽

Mutant Collection ◽

Tnt1 Retrotransposon

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An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1

10.1101/2020.02.06.936690 ◽

2020 ◽

Cited By ~ 3

Author(s):

Adithi R. Varadarajan ◽

Raymond N. Allan ◽

Jules D. P. Valentin ◽

Olga E. Castañeda Ocampo ◽

Vincent Somerville ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Antibiotic Resistance ◽

Biofilm Formation ◽

Soft Lithography ◽

Flow Chamber ◽

Model System ◽

Secretion Systems ◽

Phenotypic Data ◽

Biofilm Growth ◽

Mutant Collection

AbstractPseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance.Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and missed genes by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq datasets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth. Experiments conducted across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated both known and novel genes involved in biofilm growth and antibiotic resistance identified in screens of the mutant collection. Differential protein expression data from planktonic cells versus biofilm confirmed upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type six secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance and resistance evolution.

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Abstract 347: Zebrafish Insertional Cardiac (ZIC) Mutants: a Living Genomic Resource for Cardiac Biology

Circulation Research ◽

10.1161/res.113.suppl_1.a347 ◽

2013 ◽

Vol 113 (suppl_1) ◽

Author(s):

Weibin Liu ◽

Yonghe Ding ◽

Beninio Gore ◽

Stephen C Ekker ◽

Xiaolei Xu

Keyword(s):

Insertional Mutagenesis ◽

Cardiac Development ◽

Adult Stage ◽

Current Status ◽

Phenotypic Analysis ◽

Specific Expression ◽

Cardiac Gene ◽

Genomic Resource ◽

And Function ◽

Mutant Collection

The human genome encodes about 20,000 genes and only a fraction of them are expressed in the heart. We hypothesized that annotation of this category of genes may facilitate our understanding of cardiac development and function. Recently, we reported a pilot insertional mutagenesis screening in zebrafish to annotate cardiac gene functions using a gene-break transposon (GBT). It demonstrated the feasibility of generation of a Zebrafish Insertional Cardiac (ZIC) mutant collection by screening gene expression in the embryonic heart. Here, we report an alternative strategy to identify cardiac mutants based on adult heart expression, and explore the application of expanded ZIC lines for understanding cardiac biology. From 203 GBT lines, we identified 34 lines with detectable expression in the dissected adult hearts. Various expression levels of the tagged genes were detected in embryonic hearts. Based on their tissue-specific expression, the candidate ZIC lines can be grouped into myocardium lines, endocardium lines, or both. Based on their subcellular expression, myocardium ZIC lines can be further categorized into sarcomeric lines, mitochondrial lines, and/or nucleic lines. Phenotypic analysis is being conducted to identify recessive mutants including embryonic lethal lines. We will present the current status of our ZIC collection, and discuss its application as a genomic resource platform for elucidating cardiac biology. Our data suggest that ~15% genes in the whole genome might have detectable cardiac expression. The sensitivity of screening for cardiac genes at adult stage is higher than that at embryonic stage (34/203 versus 18/322). We plan to expand the ZIC collection by screening 1,000 GBT lines that are being generated at Mayo Clinic. It is expected that this living mutant collection of cardiac genes will open doors to systematic annotation of novel cardiac genes and forward cardiac mutagenesis screening.

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