This vignette runs the code to make the plots from the following paper first published by Springer Nature:
Dick JM. 2022. A thermodynamic model for water activity and redox potential in evolution and development. Journal of Molecular Evolution 90(2): 182–199. doi: 10.1007/s00239-022-10051-7
Use this link for full-text access to a view-only version of the paper: https://rdcu.be/cITho. A preprint of the paper is available on bioRxiv at doi: 10.1101/2021.01.29.428804.
On 2023-12-18, Figure 3a was modified from the original publication to use chemical metrics computed from the sum of amino acid compositions of proteins in each gene age category. The original publication used mean values of pre-computed chemical metrics for all proteins in each gene age category. The tables of chemical metrics for all proteins were removed to save space in the current version of the package; they remain available in the Zenodo archive up to JMDplots version 1.2.18 (https://doi.org/10.5281/zenodo.8207128). Compared to the original publication, the summation of amino acid compositions gives greater weight to longer proteins. The lines shift somewhat because of this revision, but the overall trends are unchanged.
This vignette was compiled on 2024-03-11 with JMDplots 1.2.19-11, CHNOSZ 2.1.0-5, and canprot 1.1.2-39.
To reduce running time, the plots in this vignette are made with 99 bootstrap replicates. To reproduce the plots in the paper, the value of boot.R
in the function calls below should be changed to 999.
Data source: UniProt reference protoemes (https://uniprot.org).
Data sources: Phylostrata are from Trigos et al. (2017). Consensus gene ages are from Liebeskind et al. (2016).
Data sources: a Consensus gene ages are from Liebeskind et al. (2016). Divergence times of human lineage are from Kumar et al. (2017). b Amino acid compositions of homology groups for Pfam domains are from James et al. (2020) and James et al. (2021).
Data sources: Blood plasma and subcellular redox potentials (EGSH) are from Jones and Sies (2015) and Schwarzländer et al. (2016).
Data source: Transcriptomic and proteomic data are from Futo et al. (2021).
Data sources: a Whole-organism water content is from Church and Robertson (1966). b Stoichiometric hydration state of proteins is calculated in this study using proteomic data from Casas-Vila et al. (2017). d ZC and nH2O of differentially expressed proteins in embryos and adult flies is calculated in this study using proteomic data from Fabre et al. (2019).
## Total number of genes: 17318
## Total gene count in each phylostratum:
##
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
## 1761 4675 283 1986 1191 1116 319 2773 554 526 591 764 126 241 377 35
## Genes not mapped to UniProt: 169
## Unmapped genes in each phylostratum:
##
## 1 2 3 4 5 6 7 8 9 10 12 13 14 15 16
## 7 10 1 2 2 3 2 6 2 5 3 3 21 92 10
## C H N O S
## LYSC_CHICK 613 959 193 185 10
## [1] 0.01631321
## protein organism ref abbrv chains Ala Cys Asp Glu Phe Gly His Ile Lys
## 6 LYSC CHICK UniProt P00698 1 12 8 7 2 3 12 1 6 6
## Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr
## 6 8 2 14 2 3 11 10 7 6 6 3
## 6
## 0.01631321
## Per-residue chemical formula of LYSC_CHICK
## [1] "C4.752H7.434N1.496O1.434S0.078"
## Stoichiometry of formation reaction
## coeff name formula
## 3508 1.0000 LYSC_residue C4.752H7.434N1.496O1.434S0.078
## 1723 -0.5144 glutamine C5H10N2O3
## 1724 -0.3892 glutamic acid C5H9NO4
## 1721 -0.0780 cysteine C3H7NO2S
## 1 0.8794 water H2O
## 2679 0.4713 oxygen O2
## logK of formation reaction (25 °C, 1 bar)
## [1] -39.84
## logQ of formation reaction (logfO2 = -70, logaH2O = 0)
## [1] -29.33
## log(K/Q)
## [1] -10.52
TPPG17_file <- "extdata/evdevH2O/phylostrata/TPPG17.csv.xz"
LMM16_file <- "extdata/evdevH2O/phylostrata/LMM16.csv.xz"
TPPG17 <- read.csv(system.file(TPPG17_file, package = "JMDplots"), as.is = TRUE)
LMM16 <- read.csv(system.file(LMM16_file, package = "JMDplots"), as.is = TRUE)
UniProt_IDs <- na.omit(intersect(TPPG17$Entry, LMM16$UniProt))
length(UniProt_IDs)
## [1] 16723
Data sources: Trigos et al. (2017) (TPPG17
) and Liebeskind et al. (2016) (LMM16
).
Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant J-Y, Butter F. 2017. The developmental proteome of Drosophila melanogaster. Genome Research 27(7): 1273–1285. doi: 10.1101/gr.213694.116
Church RB, Robertson FW. 1966. A biochemical study of the growth of Drosophila melanogaster. Journal of Experimental Zoology 162(3): 337–351. doi: 10.1002/jez.1401620309
Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. 2019. Comparison of Drosophila melanogaster embryo and adult proteome by SWATH-MS reveals differential regulation of protein synthesis, degradation machinery, and metabolism modules. Journal of Proteome Research 18(6): 2525–2534. doi: 10.1021/acs.jproteome.9b00076
Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, et al. 2021. Embryo-like features in developing Bacillus subtilis biofilms. Molecular Biology and Evolution 38(1): 31–47. doi: 10.1093/molbev/msaa217
James JE, Willis SM, Nelson PG, Weibel C, Kosinski LJ, Masel J. 2021. Universal and taxon-specific trends in protein sequences as a function of age. eLife 10: e57347. doi: 10.7554/eLife.57347
James J, Willis S, Nelson P, Weibel C, Kosinski L, Masel J. 2020. Data from: Universal and taxon-specific trends in protein sequences as a function of age. Figshare. doi: 10.6084/m9.figshare.12037281.v1
Jones DP, Sies H. 2015. The redox code. Antioxidants & Redox Signaling 23(9): 734–746. doi: 10.1089/ars.2015.6247
Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: A resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 34(7): 1812–1819. doi: 10.1093/molbev/msx116
Liebeskind BJ, McWhite CD, Marcotte EM. 2016. Towards consensus gene ages. Genome Biology and Evolution 8(6): 1812–1823. doi: 10.1093/gbe/evw113
Schwarzländer M, Dick TP, Meyer AJ, Morgan B. 2016. Dissecting redox biology using fluorescent protein sensors. Antioxidants & Redox Signaling 24(13): 680–712. doi: 10.1089/ars.2015.6266
Trigos AS, Pearson RB, Papenfuss AT, Goode DL. 2017. Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. Proceedings of the National Academy of Sciences 114(24): 6406–6411. doi: 10.1073/pnas.1617743114