Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Yeast Strains and Media
2.2. Genomic DNA Extraction
2.3. Whole-Genome Sequencing
2.4. Whole-Genome Sequencing Data Analysis
2.5. RNA Extraction and cDNA Generation
2.6. qPCR
2.7. Statistical Analyses and Code Availability
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
Abbreviations
PGC | Peterhof Genetic Collection |
WGS | Whole genome sequencing |
eRF1/eRF3 | eukaryotic release factor 1/3 |
5-FOA | 5-fluoroorotic acid |
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Strajn | Genotype | References | Sequencing Data |
---|---|---|---|
U-1A-D1628 | MATα ade1-14(UGA) trp1-289(UAG) | [11] | [24] |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP45::HIS3MX [pRS316-SUP45] | |||
L-1A-D1628 | MATα ade1-14(UGA) trp1-289(UAG) | [11] | This work |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP45::HIS3MX [pRS315-SUP45] | |||
nL-1A-D1628 | MATα ade1-14(UGA) trp1-289(UAG) | [11] | This work |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP45::HIS3MX [pRS315-sup45-n] | |||
U-14-D1690 | MATα ade1-14(UGA) trp1-289(UAG) | This work | This work |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP35::HIS3MX [pRSU2] | |||
L-14-D1690 | MATα ade1-14(UGA) trp1-289(UAG) | This work | This work |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP35::HIS3MX [pRSU1] | |||
nL-14-D1690 | MATα ade1-14(UGA) trp1-289(UAG) | This work | This work |
his3-Δ200 lys2 ura3-52 leu2-3,112 | |||
SUP35::HIS3MX [pRSU1-n] | |||
1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | [28]; This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B | |||
101-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup45-101 | |||
102-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup45-102 | |||
104-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup45-104 | |||
105-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup45-105 | |||
107-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [11] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup45-107 | |||
222-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | [29] |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-222 | |||
203-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-203 | |||
218-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-218 | |||
240-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-240 | |||
244-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-244 | |||
260-1B-D1606 | MATα ade1-14(UGA) his7-1(UAA) | [12] | This work |
lys9-A21(UAA) trp1-289(UAG) ura3-52 | |||
leu2–3,112 gal10-1B sup35-260 |
Plasmid | Description (Selectable Marker, Promoter, Gene) | References |
---|---|---|
pRS316-SUP45 | URA3, PSUP45, SUP45 | [30] |
pRS315-SUP45 | LEU2, PSUP45, SUP45 | [30] |
pRS315-sup45-101 | LEU2, PSUP45, sup45-101 (G796T) (E266[UAA]) | [11] |
pRS315-sup45-102 | LEU2, PSUP45, sup45-102 (T159A) (Y53[UAA]) | [11] |
pRS315-sup45-104 | LEU2, PSUP45, sup45-104 (T848A) (L283[UAA]) | [11] |
pRS315-sup45-105 | LEU2, PSUP45, sup45-105 (G1153T) (E385[UAA]) | [11] |
pRS315-sup45-107 | LEU2, PSUP45, sup45-107 (T950G) (L317[UGA]) | [11] |
pRSU2 | URA3, PSUP35, SUP35 | [25] |
pRSU1 | LEU2, PSUP35, SUP35 | [25] |
pRSU1-21 | LEU2, PSUP35, sup35-21 (C1264T) (Q422[UAA]) | [12] |
pRSU1-74 | LEU2, PSUP35, sup35-74 (C388E) (Q130[UAA]) | [12] |
pRSU1-218 | LEU2, PSUP35, sup35-218 (G541T) (E181[UAA]) | [12] |
pRSU1-240 | LEU2, PSUP35, sup35-240 (C166T) (Q56[UAA]) | [12] |
No. | Primer Name | Target Gene | Sequences |
---|---|---|---|
1 | bla_F | bla | ATAAATCTGGAGCCGGTGAG |
2 | bla_R | bla | CTACGATACGGGAGGGCTTA |
3 | SUP45_F | SUP45 | CGATCCAAGACTAGCATGTAAG |
4 | SUP45_R | SUP45 | CTTGAACATACTTGACATTGGC |
5 | SUP35_F | SUP35 | ACAACAAGGTAACAACAGATACC |
6 | SUP35_R | SUP35 | GGATTGAATTGCTGCTGATAAC |
7 | ACT1_F | ACT1 | TAACGGTTCTGGTATGTGTAAAGC |
8 | ACT1_R | ACT1 | GCTTCATCACCAACGTAGGAGTC |
9 | F-ADH1-RT | ADH1 | CAAGTCGTCAAGTCCATCTC |
10 | R-ADH1-RT | ADH1 | GTAGACAAGCCGACAACCT |
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Maksiutenko, E.M.; Barbitoff, Y.A.; Matveenko, A.G.; Moskalenko, S.E.; Zhouravleva, G.A. Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes. Genes 2021, 12, 2019. https://0-doi-org.brum.beds.ac.uk/10.3390/genes12122019
Maksiutenko EM, Barbitoff YA, Matveenko AG, Moskalenko SE, Zhouravleva GA. Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes. Genes. 2021; 12(12):2019. https://0-doi-org.brum.beds.ac.uk/10.3390/genes12122019
Chicago/Turabian StyleMaksiutenko, Evgeniia M., Yury A. Barbitoff, Andrew G. Matveenko, Svetlana E. Moskalenko, and Galina A. Zhouravleva. 2021. "Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes" Genes 12, no. 12: 2019. https://0-doi-org.brum.beds.ac.uk/10.3390/genes12122019