gradH2O: Signatures of salinity gradients in the chemical composition...

In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

Signatures of salinity gradients in the chemical composition of proteins

Description

Plots from the paper by Dick et al. (2020).

Usage

  gradH2O0()
  gradH2O1(pdf = FALSE)
  gradH2O2(pdf = FALSE)
  gradH2O3(pdf = FALSE, vars = "H2O-ZC")
  gradH2O4(pdf = FALSE, var = NULL)
  gradH2O5(pdf = FALSE)
  gradH2O6(pdf = FALSE)
  gradH2O7(pdf = FALSE)
  NifProteomes()

Arguments

pdf	logical, make a PDF file?
vars	character, variables to plot (passed to pcomp)
var	character, variable to plot (passed to mplot)

Details

This table gives a brief description of each function.

gradH2O0	Number of reactions for each amino acid in E. coli metabolic reconstruction (no plot)
gradH2O1	Comparison of different sets of basis species
gradH2O2	Schematic of \nH2O and \Zc calculations
gradH2O3	\nH2O-\Zc scatterplots for redox gradients and the Baltic Sea
gradH2O4	\nH2O for Baltic Sea metagenome and metatranscriptome in different size fractions
gradH2O5	\nH2O-\Zc for freshwater, marine, and hypersaline environments
gradH2O6	\nH2O-\Zc and GRAVY-pI plots for Baltic Sea and Rodriguez-Brito et al. data
gradH2O7	Differential gene and protein expression; time-course experiments and NaCl or organic solutes

NifProteomes, which is used in gradH2O3, calculates the mean and standard deviation of \Zc and \nH2O for proteomes encoding different homologs of nitrogenase (Nif-D, Nif-C, Nif-B, or Nif-A), as listed by Poudel et al. (2018). The organisms are limited to those that have at least 1000 RefSeq protein sequences, and any duplicated organism names are removed.

Files in extdata/gradH2O

Table_S1.xlsx

Accession numbers used and sequence processing statistics for salinity gradients.

Table_S2.xlsx

Accession numbers used and sequence processing statistics for redox gradients.

MGP.rds

Amino acid compositions sampled from metagenomically derived protein sequences, generated as described in gradox.

mkrds.R

Script to make the RDS files from multiple CSV files produced by the “ARAST” workflow.

reaction_equations.csv

Equations for metabolic reactions in E. coli from the ‘⁠reactions_GPRs⁠’ worksheet from Supplementary Information 1 of Feist et al. (2007). This is used in gradH2O0.

AAbasis.csv, AAbasis.R

Slopes and R-squared values for linear models of \nH2O-\Zc and \nO2-\Zc for all combinations of basis species including \H2O, \O2, and 3 amino acids or \H2O, \O2, 2 amino acids, and acetic acid. AAbasis.R is the script used to make the CSV file.

References

Dick JM, Yu M and Tan J (2020) Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences. Biogeosciences 17, 6145–6162. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5194/bg-17-6145-2020")}

Feist AM et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/msb4100155")}

Poudel S et al. (2018) Electron transfer to nitrogenase in different genomic and metabolic backgrounds. J. Bacteriol. 200, e00710.1038/ismej.2010.157-17. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1128/JB.00757-17")}

Rodriguez-Brito B et al. (2010) Viral and microbial community dynamics in four aquatic environments. ISME J. 4, 739–751. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ismej.2010.1")}

See Also

The script for processing proteomes of Nif-encoding genomes has been moved to utogig.

Examples

# Make Figs. 1 and 2
gradH2O1()
gradH2O2()

# list ZC and nH2O of proteomes for Nif-encoding genomes
NifProteomes()

jedick/JMDplots documentation built on April 12, 2025, 1:35 p.m.