mjenergy: Energy release during protein synthesis at ultramafic-hosted...
In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

mjenergy

R Documentation

Energy release during protein synthesis at ultramafic-hosted hydrothermal systems

Description

Plots from the paper by Dick and Shock (2021). Affinities are calculated for each protein in the Methanocaldococcus jannaschii (Mj) proteome. Amino acid compositions are taken from the file UP000000805_243232.csv.xz (see JMDplots-package).

Usage

  mjenergy1(pdf = FALSE)
  mjenergy2(pdf = FALSE)
  mjenergy3(pdf = FALSE, write.csv = FALSE)
  calc_affinity(T = 85, protein = "CSG_METJA")
  mjenergy_Table_S3()
  mjenergy_Dataset_S1(write.csv = FALSE)

Arguments

`pdf`	logical, make a PDF file?
`T`	numeric, temperature in \degC
`protein`	character, protein name used in CHNOSZ (see `pinfo`)
`write.csv`	logical, save a CSV file with the calculation results?

Details

This table gives a brief description of each plotting function.

`mjenergy1`	Affinities for methanogenesis and amino acid synthesis
`mjenergy2`	ZC of amino acids vs frequency in the Mj proteome
`mjenergy3`	Affinities of overall synthesis of proteins in the Mj proteome

calc_affinity calculates and prints the affinity for amino acid synthesis and polymerization for a single protein at temperature T. The default arguments correspond to the example calculation discussed in the paper (CSG_METJA at 85 \degC).

The files described below correspond to Tables S1 and S2 in the supporting information for the paper. mjenergy_Table_S3 outputs the amino acid synthesis reactions that are listed in Table S3. mjenergy_Dataset_S1 outputs the UniProt accession number, elemental composition, sequence length, and \Zc for each protein in the Mj proteome. Use mjenergy_Dataset_S1(write.csv = TRUE) to instead save the results in a file named ‘⁠Dataset_S1.csv⁠’, which corresponds to Dataset S1 in the paper.

Use mjenergy3(write.csv = TRUE) to save the affinities (MJ / mol protein) in two files named ‘⁠Dataset_S2.csv⁠’ and ‘⁠Dataset_S3.csv⁠’ for Rainbow and Endeavor vent fields. The column names are fluid temperatures (\degC) and the rownames are UniProt accession numbers of the proteins. Regardless of the value of write.csv, mjenergy returns the affinities of the proteins invisibly in a list with two elements named ‘⁠Rainbow⁠’ and ‘⁠Endeavor⁠’

Files in extdata/mjenergy

SC10_Rainbow.csv: Values of temperature (\degC), pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas (2010).
SC10_Endeavor.csv: Values of temperature (\degC), pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Endeavor field (Juan de Fuca Ridge), taken from Shock and Canovas (2010).

References

Shock E and Canovas P (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161–192. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1468-8123.2010.00277.x")}

Dick JM and Shock EL (2021) The release of energy during protein synthesis at ultramafic-hosted submarine hydrothermal ecosystems. J. Geophys. Res.: Biogeosciences 126, e2021JG006436. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1029/2021JG006436")}