yeast: Composition, Localization, and Abundances of Proteins in Yeast

Description

Retrieve the amino acid compositions of one or more proteins from Saccharomyces cerevisiae and get localizations and abundances reported by the YeastGFP project.

Usage

yeast.aa(protein = NULL)
  yeastgfp(location, exclusive = TRUE)

Arguments

protein

character, name of protein

location

character, name of subcellular location (compartment)

exclusive

logical, report only proteins exclusively localized to a compartment?

Value

For yeast.aa, a data frame, or list of data frames, containing the amino acid composition(s) of the specified protein(s) in the format of thermo$protein.

For yeastgfp, a list with elements named protein (names of proteins) and abundance (counts or concentrations without any conversion from the units in the data file). If location is NULL, yeastgfp returns the names of all known locations, and if the length of location is >1, the protein and abundance values are lists of the results for each location.

Details

yeast.aa retrieves the amino acid composition(s) of the indicated proteins in Saccharomyces cerevisiae. The calculation depends on the data file extdata/protein/Sce.csv.xz, which contains the amino acid compositions of the proteins. The protein argument should be a vector or a list of vectors of one or more SGD IDs, Open Reading Frame (ORF) or gene names that are found in these files. The output data frame contains rows with NA compositions for names that are not matched.

yeastgfp returns the identities and abundances of proteins with the requested subcellular localization(s) (specified in location) using data from the YeastGFP project that is stored in extdata/abundance/yeastgfp.csv.xz. If exclusive is FALSE, the function grabs all proteins that are localized to a compartment even if they are also localized to other compartments. If exclusive is TRUE (the default), only those proteins that are localized exclusively to the requested compartments are identified, unless there are no such proteins, then the non-exclusive localizations are used (applies to the bud localization).

References

Boer, V. M., de Winde, J. H., Pronk, J. T. and Piper, M. D. W. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278, 3265--3274. https://doi.org/10.1074/jbc.M209759200

Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J.-M. and Pronk, J. T. (2005) Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J. Biol. Chem. 280, 437--447. https://doi.org/10.1074/jbc.M410573200

Examples

Run this code

# NOT RUN {
# the first few names in UniProt for "aminotransferase yeast"
genes <- c("AATC", "ARO8", "BCA1", "AMPL", "BCA2", "ARO9")
# the corresponding ORF names
ORF <- c("YLR027C", "YGL202W", "YHR208W", "YKL103C", "YJR148W", "YHR137W")
# we only match two of them by gene name, but all by ORF name
aa <- yeast.aa(genes)
aa <- yeast.aa(ORF)
# what are their formulas and average oxidation states of carbon
protein.formula(aa)
ZC(protein.formula(aa))

## potential fields for overall protein compositions 
## transcriptionally induced and repressed in aerobic
## and anaerobic carbon limitation
## (experiments of Tai et al., 2005)
# the activities of ammonium and sulfate used here
# are similar to the non-growth-limiting concentrations
# used by Boer et al., 2003
basis(c("glucose", "H2O", "NH4+", "hydrogen", "SO4-2", "H+"),
  c(-1, 0, -1.3, 999, -1.4, -7))
# the names of the experiments in TBD+05.csv
expt <- c("Clim.aerobic.down", "Clim.aerobic.up",
  "Clim.anaerobic.down", "Clim.anaerobic.up")
file <- system.file("extdata/abundance/TBD+05.csv", package="CHNOSZ")
dat <- read.csv(file, as.is=TRUE)
# yeast.aa: get the amino acid compositions
# aasum: average them together
for(thisexpt in expt) {
  p <- dat$protein[dat[, thisexpt]]
  aa <- yeast.aa(p)
  aa <- aasum(aa, average=TRUE, protein=thisexpt)
  add.protein(aa)
}
species(expt, "Sce")
a <- affinity(C6H12O6=c(-30, 0), H2=c(-20, 0))
d <- diagram(a, normalize=TRUE, fill=NULL)
title(main=paste("Formation potential of proteins associated with\n",
  "transcriptional response to carbon limitation in yeast"))
# the affinity of formation favors the proteins upregulated 
# by carbon limitation at low chemical potentials of C6H12O6 ...
stopifnot(c(d$predominant[1,1], d$predominant[1,128])==grep("up", expt))
# ... and favors proteins downregulated by aerobic conditions
# at high hydrogen fugacities
stopifnot(c(d$predominant[128, 128], d$predominant[128, 1])==grep("down", expt))

## overall oxidation state of proteins exclusively localized 
## to cytoplasm of S. cerevisiae with/without abundance weighting
y <- yeastgfp("cytoplasm")
aa <- yeast.aa(y$protein)
aaavg <- aasum(aa, average=TRUE)
ZC(protein.formula(aaavg))
# the average composition weighted by abundance
waaavg <- aasum(aa, abundance=y$abundance, average=TRUE)
ZC(protein.formula(waaavg))
# }

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