The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
- Department of Genetics, Rutgers University, United States
- Robert Wood Johnson Medical School, Rutgers University, United States
- Waksman Institute, Rutgers University, United States
- Human Genetics Institute of New Jersey, Rutgers University, United States
Figures
Figure 1 with 3 supplements
Parallel changes in mRNA abundances.
(A) Schematic diagram of the experimental setup. (B) Pairwise Pearson correlations based on (where transcripts per million [TPM] is the mean from replicates) separated by comparisons between …
Figure 1—figure supplement 1
Sequencing data statistics.
(A) The average number of reads aligned per gene using Kallisto for each library. The color scheme remains the same in panels B and D. (B) Distributions of mapped and deduplicated read counts per …
Figure 1—figure supplement 2
Magnitude and variation in mRNA fold-changes across evolved lines.
(A) Distributions of all mRNA fold-changes (using DESeq2) in each line. Lines with a mutator phenotype are in red. (B) The number of differentially expressed genes (DEGs) (DESeq2 ) in each line. (C…
Figure 1—figure supplement 3
Comparison of expression changes between this study and Cooper et al., 2003.
(A) The direction and magnitude of expression changes in genes identified as differentially expressed in Cooper et al., 2003, study and the direction of changes for those genes in our dataset. While …
Figure 2 with 2 supplements
Evolved lines are larger in cell size and carry more mRNAs.
(A) All evolved lines are larger than the ancestral strain. Distributions of cellular volume as determined by phase-contrast microscopy and assuming sphero-cylindrical shape of Escherichia coli …
Figure 2—figure supplement 1
Relationship between cellular features and cell volume.
(A) Comparison of median volumes of each evolved line from this manuscript to estimates of cellular volumes from Grant et al., 2021. (B) Relationship between median cell volumes of all cells …
Figure 2—figure supplement 2
Absolute changes in mRNA abundances per CFU across all evolved lines.
(A) Abundances of spike-in RNA control oligos are correlated with their estimates in sequencing data. Linear models relating the number of molecules of each ERCC control sequence added to their …
Figure 3 with 1 supplement
Changes in gene expression at the translational level.
(A) Translational changes are correlated with transcriptional changes. The relationship between RNA-seq and Ribo-seq fold-changes in Ara+1 (see Figure 3—figure supplement 1A for all evolved lines). …
Figure 3—figure supplement 1
Relationship between RNAseq and riboseq fold-changes for all evolved lines.
(A) The relationship between RNA-seq fold-changes and Ribo-seq fold-changes in evolved lines.
Figure 4 with 2 supplements
Parallel changes in biological processes and pathways.
(A) Parallel changes in biological processes and pathways. The top 10 KEGG pathways that were significantly altered () based on RNA-seq data. Enrichment score represents the degree to which a …
Figure 4—figure supplement 1
Parallel changes in biological processes and pathways based on Ribo-seq data.
(A) Parallel changes in biological processes and pathways. The top 10 KEGG pathways that were significantly altered () based on Ribo-seq data. Enrichment score represents the degree to which a …
Figure 4—figure supplement 2
GO and other functional analyses of differentially expressed genes.
(A) The top 10 GO biological process categories that were significantly altered (Fisher’s exact test ≤ 0.05). White spaces indicate that the category was not significantly altered in that line. (B) …
Figure 5 with 1 supplement
Mutations in transcriptional regulators lead to parallel changes in gene expression.
RNA-seq fold-changes for genes belonging to (A) maltose-transport/metabolism and (B) nicotinamide adenine dinucleotide (NAD) biosynthesis. Gene names in each category are colored based on their …
Figure 5—figure supplement 1
Link between mutations and expression changes for other gene sets.
(A–F) Mutations in transcriptional regulators lead to parallel changes in gene expression (RNA-seq). Gene names in each category are colored based on their operon membership. Transcription factors …
Additional files
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Supplementary file 1
Results of the kallisto alignment for all samples.
Counts in this file were first rounded, and new transcripts per million (TPM) were calculated based on rounded counts. This file was generated using ‘data_cleaning.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/data_processing).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp1-v2.zip
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Supplementary file 2
Results from DESeq2 for all samples.
Generated from ‘DESeq2.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp2-v2.csv
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Supplementary file 3
Quantifications from our optical microscopy.
This table is supplied and is not generated from the code.
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp3-v2.csv
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Supplementary file 4
Our colony-forming unit (CFU) numbers.
This table is supplied and is not generated from the code.
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp4-v2.csv
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Supplementary file 5
Amounts of ERCC spike-ins added to each sample and their abundance in the sequencing libraries.
This table is supplied and is not generated from the code.
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp5-v2.csv
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Supplementary file 6
Measures of mRNA abundance per colony-forming unit (CFU).
Generated from ‘absolute_counts.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp6-v2.csv
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Supplementary file 7
Results from riborex.
Generated from ‘riborex.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp7-v2.csv
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Supplementary file 8
Calculated genome-wide codon densities.
Generated from ‘codon_specific_densities.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp8-v2.csv
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Supplementary file 9
KEGG search results.
Generated from ‘kegg_analysis.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp9-v2.csv
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Supplementary file 10
GO search results.
Generated from ‘go.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp10-v2.csv
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Supplementary file 11
Pathway perturbation score (PPS) calculations.
Generated from ‘manual_pps.Rmd’ (https://github.com/shahlab/LTEE_gene_expression_2/tree/main/code/analysis).
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp11-v2.csv
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Supplementary file 12
Mmutation data for our clones as downloaded from https://barricklab.org/shiny/LTEE-Ecoli/.
This file is supplied and not generated from the code or can be downloaded from the website.
- https://cdn.elifesciences.org/articles/81979/elife-81979-supp12-v2.csv
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MDAR checklist
- https://cdn.elifesciences.org/articles/81979/elife-81979-mdarchecklist1-v2.pdf
