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Retrieve tRNA aminoacylation identity elements

Source: R/identity.R
identity_elements.Rd

Returns experimentally validated identity elements (determinants and antideterminants) for tRNA aminoacylation, based on data from Giege & Eriani (2023). Elements are defined per amino acid family using Sprinzl numbering.

Usage

identity_elements(
  organism,
  amino_acid = NULL,
  type = c("both", "determinant", "antideterminant")
)

Arguments

organism

Character string specifying the organism name (e.g., "Escherichia coli", "Saccharomyces cerevisiae", "Homo sapiens"). Use identity_organisms() to list supported organisms.

amino_acid

Optional character vector of 3-letter amino acid codes to filter by (e.g., "Ala", "Arg"). If NULL (default), returns elements for all amino acids.

type

Which element types to return: "both" (default), "determinant", or "antideterminant".

Value

A tibble with columns:

  • amino_acid: 3-letter amino acid code

  • domain: evolutionary domain ("Bacteria" or "Eukarya")

  • sprinzl_pos: Sprinzl position number (integer; NA for structural determinants like the long variable arm; -1 for the His G\(_{-1}\) position)

  • nucleotide: expected base (A/C/G/U, or NA if variable)

  • region: tRNA structural region name

  • type: "determinant" or "antideterminant"

  • strength: "strong" or "weak" (determinants only)

  • pair_pos: partner Sprinzl position for base pairs (NA for single-nucleotide elements)

  • pair_type: "wc" or "wobble" (NA for unpaired)

  • against_aars: aaRS blocked (antideterminants only)

  • universal: TRUE if conserved across all domains

  • description: human-readable description

References

Giege R, Eriani G (2023). "The tRNA identity landscape for aminoacylation and beyond." Nucleic Acids Research, 51(4), 1528–1570. doi:10.1093/nar/gkad007

Examples

# All identity elements for E. coli
identity_elements("Escherichia coli")
#> # A tibble: 135 × 12
#>    amino_acid domain   sprinzl_pos nucleotide region     type  strength pair_pos
#>    <chr>      <chr>          <int> <chr>      <chr>      <chr> <chr>       <int>
#>  1 Ala        Bacteria          73 A          discrimin… dete… strong         NA
#>  2 Ala        Bacteria           3 G          acceptor_… dete… strong         70
#>  3 Ala        Bacteria          70 U          acceptor_… dete… strong          3
#>  4 Ala        Bacteria           4 G          acceptor_… dete… weak           69
#>  5 Ala        Bacteria          69 C          acceptor_… dete… weak            4
#>  6 Ala        Bacteria          20 G          d_arm      dete… weak           NA
#>  7 Arg        Bacteria          73 NA         discrimin… dete… strong         NA
#>  8 Arg        Bacteria           2 G          acceptor_… dete… weak           71
#>  9 Arg        Bacteria          71 C          acceptor_… dete… weak            2
#> 10 Arg        Bacteria           3 C          acceptor_… dete… weak           70
#> # ℹ 125 more rows
#> # ℹ 4 more variables: pair_type <chr>, against_aars <chr>, universal <lgl>,
#> #   description <chr>

# Ala determinants only
identity_elements("Escherichia coli", amino_acid = "Ala",
  type = "determinant")
#> # A tibble: 6 × 12
#>   amino_acid domain   sprinzl_pos nucleotide region      type  strength pair_pos
#>   <chr>      <chr>          <int> <chr>      <chr>       <chr> <chr>       <int>
#> 1 Ala        Bacteria          73 A          discrimina… dete… strong         NA
#> 2 Ala        Bacteria           3 G          acceptor_s… dete… strong         70
#> 3 Ala        Bacteria          70 U          acceptor_s… dete… strong          3
#> 4 Ala        Bacteria           4 G          acceptor_s… dete… weak           69
#> 5 Ala        Bacteria          69 C          acceptor_s… dete… weak            4
#> 6 Ala        Bacteria          20 G          d_arm       dete… weak           NA
#> # ℹ 4 more variables: pair_type <chr>, against_aars <chr>, universal <lgl>,
#> #   description <chr>