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. 2020 Oct 30;9:e57947. doi: 10.7554/eLife.57947

Figure 1. The tRNA gene set and serine translation system in P. fluorescens SBW25.

(A) Genomic location of the 66 canonical (grey arrows) and one non-canonical (cysGCA-2; black arrow) tRNA genes. Four tRNA genes encode seryl-tRNAs (red arrows). One of these, serCGA, is predicted to encode a non-essential tRNA type. Six other tRNA genes encoding the remaining five non-essential tRNA types (green arrows). Replication origin and terminus are indicated. (B) The predicted translational relationship between seryl-tRNAs and serine codons. The six theoretically possible seryl-tRNA anticodons are listed on the left (red = present in SBW25, grey = absent, * = theoretically capable of translating codon UCG), and six cognate codons are listed in column 2. Connections signify a theoretical match (solid black lines = Watson Crick pairing; black dotted lines = wobble pairing through post-transcriptional modification; grey dotted line = G:U wobble pairing). Columns 3 and 4 list codon use as a percentage of serine and all codons, respectively (Chan and Lowe, 2016). Anticodons and codons are 5'→3'.

Figure 1.

Figure 1—figure supplement 1. Predicted structure and function of tRNA types tRNA-Ser(CGA) and tRNA-Ser(UGA) in P. fluorescens SBW25.

Figure 1—figure supplement 1.

(A) Gene sequences for P. fluorescens SBW25 serCGA (top), P. fluorescens SBW25 serTGA (middle), and hypothetical serCGA (serTGA backbone with a single point mutation to a CGA anticodon; see Discussion). Colour highlights indicate various parts of each tRNA, with the base pairing (stem) components in each region underlined (blue = acceptor stem, green = D stem/loop, grey = anticodon stem/loop, yellow = anticodon, pink = variable region, turquoise = TψC stem/loop). Bold letters in serCGA indicate 36 nucleotide differences from serTGA. (B) Predicted mature tRNA structures for the tRNA sequences in panel A, using tRNAscan-SE v2.0 (Chan and Lowe, 2019). The predicted CmoA/B/M mediated post-transcriptional modification U34→cmo5U34 is also shown in tRNA-Ser(UGA). (C) Cartoon depicting translation of serine codons: canonical base pairing occurred between tRNA-Ser(CGA) and UCG, and wobble base pairing is occurring between post-transcriptionally modified tRNA-Ser(UGA) and codons UCA and UCG.