|
| Status |
Public on Mar 28, 2018 |
| Title |
Evolutionary Convergence of Pathway-specific Enzyme Expression Stoichiometry |
| Organisms |
Caulobacter vibrioides; Bacillus subtilis subsp. subtilis str. 168; Escherichia coli str. K-12 substr. MG1655; Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 |
| Experiment type |
Other
|
| Summary |
Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. Yet, it remains unexplored whether the relative abundance of coregulated proteins requires precise tuning. Here we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. Using end-enriched RNA-sequencing (Rend-seq) with single-nucleotide resolution, we found that many bacterial gene clusters encoding conserved pathways have undergone massive divergence in transcript abundance and architectures via remodeling of internal promoters and terminators. Remarkably, these evolutionary changes are compensated post-transcriptionally to maintain preferred stoichiometry of protein synthesis rates. Even more strikingly, in eukaryotic budding yeast, functionally analogous proteins that arose independently from bacterial counterparts also evolved to convergent in-pathway expression. The broad requirement for exact protein stoichiometries despite regulatory divergence provides an unexpected principle for building biological pathways both in nature and for synthetic activities.
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| Overall design |
Three ribosome profiling datasets (two in Bacillus subtilis and one in Vibrio natriegens). Eighteen Rend-seq data sets (Esherichia coli, Bacillus subtilis, Vibrio natriegens, and Caulobacter crescentus, including mutants and different library preparations).
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| |
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| Contributor(s) |
Lalanne J, Taggart JC, Guo MS, Herzel L, Schieler A, Li G |
| Citation(s) |
29606352 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R00 GM105913 |
Probing the function of translational pausing in bacterial protein synthesis |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Gene-Wei Li |
| R35 GM124732 |
Evolution and Regulation of Bacterial Proteome Composition |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Gene-Wei Li |
|
| Submission date |
Feb 22, 2017 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Jean-Benoit Lalanne |
| E-mail(s) |
lalannej@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Jay Shendure
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platforms (7)
|
| GPL15010 |
Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655) |
| GPL15205 |
Illumina HiSeq 2000 (Bacillus subtilis subsp. subtilis str. 168) |
| GPL21117 |
Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655) |
| GPL21796 |
Illumina NextSeq 500 (Bacillus subtilis subsp. subtilis str. 168) |
| GPL23093 |
Illumina HiSeq 2000 (Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759) |
| GPL24555 |
Illumina NextSeq 500 (Caulobacter vibrioides) |
| GPL24556 |
Illumina NextSeq 500 (Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759) |
|
| Samples (21)
|
| GSM2500125 |
Bacillus_subtilis_ribosome_profiling_LB |
| GSM2500126 |
Vibrio_natriegens_ribosome_profiling_MOPS_comp_3NaCl |
| GSM2500127 |
Bacillus_subtilis_WT_Rend_seq_LB_25s_frag_pooled |
| GSM2500128 |
Bacillus_subtilis_WT_Rend_seq_LB_50s_frag |
| GSM2500129 |
Bacillus_subtilis_WT_Rend_seq_LB_100s_frag |
| GSM2500130 |
Bacillus_subtilis_WT_Rend_seq_LB_200s_frag |
| GSM2500131 |
Escherichia_coli_WT_Rend_seq_MOPS_comp_25s_frag_pooled |
| GSM2500132 |
Bacillus_subtilis_rho_Rend_seq_LB_25s_frag_pooled |
| GSM2500133 |
Bacillus_subtilis_pnpA_Rend_seq_LB_105s_frag_1 |
| GSM2500134 |
Bacillus_subtilis_pnpA_Rend_seq_LB_105s_frag_2 |
| GSM2500135 |
Bacillus_subtilis_rph_Rend_seq_LB_105s_frag |
| GSM2500136 |
Bacillus_subtilis_rnr_Rend_seq_LB_105s_frag |
| GSM2500137 |
Bacillus_subtilis_yhaM_Rend_seq_LB_105s_frag |
| GSM2971248 |
Bacillus_subtilis_Delta_sU_ylqC_yqlD_ribosome_profiling_LB |
| GSM2971249 |
Vibrio_natriegens_Rend_seq_MOPS_comp_3NaCl_25s_frag |
| GSM2971250 |
Bacillus_subtilis_WT_Rend_seq_5_exo_LB_25s_frag_pooled |
| GSM2971251 |
Caulobacter_crescentus_Rend_seq_PYE_25s_frag |
| GSM2971252 |
Escherichia_coli_WT_Rend_seq_5_exo_MOPS_comp_25s_frag |
| GSM2971253 |
Escherichia_coli_pnp_Rend_seq_MOPS_comp_25s_frag |
| GSM2971254 |
Escherichia_coli_rnb_Rend_seq_MOPS_comp_25s_frag |
| GSM2971255 |
Bacillus_subtilis_pnpA_Rend_seq_LB_25s_frag |
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| Relations |
| BioProject |
PRJNA376419 |
| SRA |
SRP100536 |
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