Anticodon table of the chloroplast genome and identification of putative quadruplet anticodons in chloroplast tRNAs

Abstract

The chloroplast genome of 5959 species was analyzed to construct the anticodon table of the chloroplast genome. Analysis of the chloroplast transfer ribonucleic acid (tRNA) revealed the presence of a putative quadruplet anticodon containing tRNAs in the chloroplast genome. The tRNAs with putative quadruplet anticodons were UAUG, UGGG, AUAA, GCUA, and GUUA, where the GUUA anticodon putatively encoded tRNAAsn. The study also revealed the complete absence of tRNA genes containing ACU, CUG, GCG, CUC, CCC, and CGG anticodons in the chloroplast genome from the species studied so far. The chloroplast genome was also found to encode tRNAs encoding N-formylmethionine (fMet), Ile2, selenocysteine, and pyrrolysine. The chloroplast genomes of mycoparasitic and heterotrophic plants have had heavy losses of tRNA genes. Furthermore, the chloroplast genome was also found to encode putative spacer tRNA, tRNA fragments (tRFs), tRNA-derived, stress-induced RNA (tiRNAs), and the group I introns. An evolutionary analysis revealed that chloroplast tRNAs had evolved via multiple common ancestors and the GC% had more influence toward encoding the tRNA number in the chloroplast genome than the genome size.

Tuning tRNAs for improved translation

“…Such quadruplet decoding, or “programmed frameshifts,” occur in nature, often with an extended 8-base anticodon loop as opposed to the canonical 7-base loop ( Riyasaty and Atkins, 1968 ; Riddle and Roth, 1970 ; Yourno and Kohno, 1972 ; Riddle and Carbon, 1973 ; Bossi and Smith, 1984 ; Farabaugh, 1996 ; Moore et al, 2000a ; Walker and Fredrick, 2006 ; Atkins and Björk, 2009 ; Mohanta et al, 2023 ). Many experiments have since demonstrated that inserting a single nucleotide into the anticodon loop of a tRNA to create an 8-base anticodon results in moderate quadruplet decoding in vitro and in vivo, especially in combination with engineered synthetases ( Curran and Yarus, 1987 ; Ma et al, 1993 ; Hohsaka et al, 1996 ; Hohsaka et al, 1999 ; Hohsaka et al, 2001 ; Moore et al, 2000b ; Magliery et al, 2001 ; O’Connor, 2002 ; Ohtsuki et al, 2005 ; Taki et al, 2006 ; Wan et al, 2010 ; Chatterjee et al, 2012 ; Hankore et al, 2019 ; Dunkelmann et al, 2020 ; Dunkelmann et al, 2021 ; DeBenedictis et al, 2022 ).…”