Codon Usage

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Mesoplasma florum, like many Mollicutes, utilize TGA for tryptophan instead of for a stop codon [1] This, hypothetically, will prevent any genes from Mesoplasma florum from being expressed in E coli, therefore lowering the toxicity of the genome as a BAC.


Codon usage table from the Codon Usage Database[2].

fields: [triplet] [frequency: per thousand] ([number])
UUU F 0.81 41.9 ( 10293)  UCU S 0.17 14.6 (  3585)  UAU Y 0.78 29.3 (  7191)  UGU C 0.85  5.2 (  1275)
UUC F 0.19  9.7 (  2391)  UCC S 0.00  0.4 (    92)  UAC Y 0.22  8.0 (  1972)  UGC C 0.15  0.9 (   228)
UUA L 0.71 64.0 ( 15736)  UCA S 0.34 30.2 (  7413)  UAA * 0.81  2.2 (   551)  UGA W 0.96 10.1 (  2489)
UUG L 0.08  7.2 (  1765)  UCG S 0.01  0.8 (   206)  UAG * 0.19  0.5 (   132)  UGG W 0.04  0.4 (   101)

CUU L 0.12 10.9 (  2682)  CCU P 0.37  9.4 (  2306)  CAU H 0.73  9.0 (  2211)  CGU R 0.83  4.1 (   998)
CUC L 0.00  0.2 (    52)  CCC P 0.03  0.6 (   157)  CAC H 0.27  3.4 (   836)  CGC R 0.06  0.3 (    67)
CUA L 0.08  6.9 (  1690)  CCA P 0.57 14.3 (  3516)  CAA Q 0.95 28.7 (  7058)  CGA R 0.11  0.5 (   128)
CUG L 0.01  0.7 (   182)  CCG P 0.03  0.8 (   203)  CAG Q 0.05  1.6 (   404)  CGG R 0.01  0.0 (     6)

AUU I 0.88 59.8 ( 14701)  ACU T 0.42 22.6 (  5558)  AAU N 0.77 55.4 ( 13612)  AGU S 0.17 15.3 (  3752)
AUC I 0.12  8.0 (  1968)  ACC T 0.02  1.1 (   274)  AAC N 0.23 16.9 (  4161)  AGC S 0.04  3.8 (   935)
AUA M 0.58 31.5 (  7748)  ACA T 0.55 29.5 (  7243)  AAA K 0.91 88.4 ( 21721)  AGA S 0.25 22.2 (  5448)
AUG M 0.42 23.0 (  5660)  ACG T 0.02  0.9 (   211)  AAG K 0.09  8.6 (  2110)  AGG S 0.01  0.8 (   194)

GUU V 0.65 39.3 (  9660)  GCU A 0.47 25.6 (  6297)  GAU D 0.83 44.4 ( 10918)  GGU G 0.47 25.0 (  6147)
GUC V 0.02  1.4 (   344)  GCC A 0.04  2.1 (   522)  GAC D 0.17  9.0 (  2203)  GGC G 0.03  1.9 (   461)
GUA V 0.28 17.2 (  4237)  GCA A 0.46 25.2 (  6198)  GAA E 0.91 66.3 ( 16303)  GGA G 0.43 23.3 (  5717)
GUG V 0.04  2.6 (   632)  GCG A 0.04  2.1 (   519)  GAG E 0.09  6.3 (  1543)  GGG G 0.06  3.5 (   848)

http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=265311&aa=5&style=N


Codon usage table from OpenWetWare compromise table [3]

AmAcid    Codon     Number/mf /1000/mf  mf/ec codons
Gly       GGG              848      3.45  0.12
Gly       GGA             5717     23.26  0.26
Gly       GGT             6147     25.01  0.49
Gly       GGC              461      1.88  0.13

Glu       GAG             1543      6.28  0.17
Glu       GAA            16303     66.34  0.83
Asp       GAT            10918     44.43  0.74
Asp       GAC             2203      8.96  0.26  

Val       GTG              632      2.57  0.15
Val       GTA             4237     17.24  0.25
Val       GTT             9660     39.31  0.52
Val       GTC              344       1.4  0.08

Ala       GCG              519      2.11  0.15
Ala       GCA             6198     25.22  0.38
Ala       GCT             6297     25.62  0.34
Ala       GCC              522      2.12  0.13

Arg       AGG              194      0.79  0.05
Arg       AGA             5448     22.17  0.33
Ser       AGT             3752     15.27  0.23
Ser       AGC              935       3.8  0.16

Lys       AAG             2110      8.59  0.15
Lys       AAA            21721     88.38  0.85
Asn       AAT            13612     55.39  0.62
Asn       AAC             4161     16.93  0.38

Met       ATG             5660     23.03  1.0
Ile       ATA             7748     31.53  0.17
Ile       ATT            14701     59.82  0.62
Ile       ATC             1968      8.01  0.21

Thr       ACG              211      0.86  0.10
Thr       ACA             7243     29.47  0.38
Thr       ACT             5558     22.62  0.38
Thr       ACC              274      1.11  0.14

Trp       TGG             2590     10.54  1.0
End       TGA                0         0  0
Cys       TGT             1275      5.19  0.68
Cys       TGC              228      0.93  0.32

End       TAG              132      0.54  0.14
End       TAA              551      2.24  0.86
Tyr       TAT             7191     29.26  0.68
Tyr       TAC             1972      8.02  0.32

Leu       TTG             1765      7.18  0.16
Leu       TTA            15736     64.03  0.48
Phe       TTT            10293     41.88  0.70
Phe       TTC             2391      9.73  0.30

Ser       TCG              206      0.84  0.05
Ser       TCA             7413     30.16  0.29
Ser       TCT             3585     14.59  0.22
Ser       TCC               92      0.37  0.05

Arg       CGG                6      0.02  0
Arg       CGA              128      0.52  0.06
Arg       CGT              998      4.06  0.44
Arg       CGC               67      0.27  0.12

Gln       CAG              404      1.64  0.24
Gln       CAA             7058     28.72  0.76
His       CAT             2211         9  0.65
His       CAC              836       3.4  0.35

Leu       CTG              182      0.74  0.11
Leu       CTA             1690      6.88  0.08
Leu       CTT             2682     10.91  0.17
Leu       CTC               52      0.21  0

Pro       CCG              203      0.83  0.16
Pro       CCA             3516     14.31  0.44
Pro       CCT             2306      9.38  0.32
Pro       CCC              157      0.64  0.08




Interestingly enough, Bacillus subtilis also can decode TGA as tryptophan at a low frequency[4]. It appears that the Firmicutes have drifted to decode UGA codons. Due to genome reduction, this has drifted Mollicutes to using TGA as the main tryptophan codon.

Mollicute TGA.jpg

Image above shows phylogenetic relationship between Firmicutes and Mollicutes[5].

References

  1. Todd Lowe, Patricia Chan. Genomic tRNA Database. "tRNAscan-SE Analysis of Mesoplasma florum L1". [1]
  2. Codon Usage Database. "Mesoplasma florum L1 [gbbct]: 683 CDS's (245761 codons)". [2]
  3. Tom Knight 2007. "Mesoplasma florum:Codon usage". OpenWetWare. [3]
  4. PS Lovett et al (1991). "UGA can be decoded as tryptophan at low efficiency in Bacillus subtilis". Journal of Bacteriology. [4]
  5. Kenro Oshima, Kensaku Maejima and Shigetou Namba - Front. Microbiol., 14 August 2013 / doi: 10.3389/fmicb.2013.00230, CC BY 3.0, [5]