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| Status |
Public on Nov 02, 2020 |
| Title |
YAMAT-seq of mature tRNA pools in the bacterium Pseudomonas fluorescens SBW25 and derivatives |
| Organism |
Pseudomonas fluorescens |
| Experiment type |
Other
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| Summary |
Mature tRNA pools were measured using an adaptation of Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq) (Shigematsu et al., 2017) in nine strains derived from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing the single-copy serCGA gene by genetic engineering, and (ii) duplicating the serTGA gene during a subsequent, compensatory evolution experiment. We found that (i) results in the loss of tRNA-Ser(CGA) from the mature tRNA pool, and (ii) results in a 2-fold higher expression of tRNA-Ser(UGA). tRNA-Ser(UGA) presumably substitutes for tRNA-Ser(CGA) by wobble base pairing to translate codon 5'-UCG-3'.
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| Overall design |
Three replicates of nine strains: SBW25, delserCGA-1, delserCGA-2, W1-L, M1-L, M2-L, M2-Lop, M3-L, M4-L
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| Contributor(s) |
Gallie J, Ayan GB, Park H |
| Citation(s) |
33124983 |
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| Submission date |
Feb 05, 2020 |
| Last update date |
Nov 24, 2020 |
| Contact name |
Jenna Gallie |
| E-mail(s) |
gallie@evolbio.mpg.de
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| Organization name |
Max Planck Institute for Evolutionary Biology
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| Street address |
August-Thienemann Strasse 2
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| City |
Ploen |
| ZIP/Postal code |
24306 |
| Country |
Germany |
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| Platforms (1) |
| GPL28120 |
NextSeq 550 (Pseudomonas fluorescens) |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA604919 |
| SRA |
SRP247350 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144791_aligned_read_numbers.xlsx |
36.0 Kb |
(ftp)(http) |
XLSX |
| GSE144791_deseq2_comparisons.xlsx |
225.4 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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