Recognition of tRNAs with a long variable arm by aminoacyl-tRNA synthetases

Abstract

In prokaryotic cells three tRNA species, tRNASer, tRNALeu and tRNATyr, possess a long variable arm of 11–20 nucleotides (type 2 tRNA) rather than usual 4 or 5 nucleotides (type 1 tRNA). In this review we have summarized the results of our research on the structural basis for recognition and discrimination of type 2 tRNAs by Thermus thermophilus seryl-, tyrosyl- and leucyl-tRNA synthetases (SerRS, TyrRS and LeuRS) obtained by X-ray crystallography and chemical probing tRNA in solution. Crystal structures are now known of all three aminoacyl-tRNA synthetases complexed with type 2 tRNAs and the different modes of tRNA recognition represented by these structures will be discussed. In particular, emphasis will be given to the results on recognition of characteristic shape of type 2 tRNAs by cognate synthetases. In tRNASer, tRNATyr and tRNALeu the orientation of the long variable arm with respect to the body of the tRNA is different and is controlled by different packing of the core. In the case of SerRS the N-terminal domain and in the case of TyrRS, the C-terminal domain, bind to the characteristic long variable arm of the cognate RNA, thus recognizing the unique shape of the tRNA. The core of T. thermophilus tRNALeu has several layers of unusual base-pairs, which are revealed by the crystal structure of tRNALeu complexed with T. thermophilus LeuRS and by probing a ligand-free tRNA by specific chemical reagents in solution. In the crystal structure of the LeuRS-tRNALeu complex the unique D-stem structure is recognized by the C-terminal domain of LeuRS and these data are in good agreement with those obtained in solution. LeuRS has canonical class I mode of tRNA recognition, approaching the tRNA acceptor stem from the D-stem and minor groove of the acceptor stem side. SerRS also has canonical class II mode of tRNA recognition and approaches tRNASer from opposite, variable stem and major groove of acceptor stem site. And finally, TyrRS in strong contrast to canonical class I system has class II mode of tRNA recognition

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

“…All tRNAs(CCU) are also missing the extra arm that characterizes Ser-tRNA (Bilokapić et al. 2009; Tukalo et al. 2013), confirming their Ala-tRNA identity.…”

“…(1998), McClain and Foss (1988), and Musier-Forsyth et al. (1991). b TFAM, respectively, predicted a Trp-tRNA and a Met-tRNA identity for tRNA(CCU) in B. minor and T. obliquus , see supplementary table S2 of the Supplementary Material online. c Tukalo et al. (2013), Asahara et al.…”

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

“…All tRNAs(CCU) are also missing the extra arm that characterizes Ser-tRNA (Bilokapić et al. 2009; Tukalo et al. 2013), confirming their Ala-tRNA identity.…”

“…(1998), McClain and Foss (1988), and Musier-Forsyth et al. (1991). b TFAM, respectively, predicted a Trp-tRNA and a Met-tRNA identity for tRNA(CCU) in B. minor and T. obliquus , see supplementary table S2 of the Supplementary Material online. c Tukalo et al. (2013), Asahara et al.…”

Transfer RNAs with novel cloverleaf structures

“…As predicted, the two G-1 tRNA1 species were aminoacylated by E. coli HisRS, even more efficiently than E. coli tRNA His , despite the Thr GGU anticodon (Figure 4B ). The GUG triplet at positions 35–37 (but not the anticodon positions 34–36 in tRNA His ) of the two G-1 tRNA1 species might have been recognized by HisRS ( 35 – 37 ). Interestingly, the two G-1 tRNA1 species did not insert His in response to the ACC Thr codon at position 2 in a sfGFP variant gene in E. coli .…”

Identification of Common Genes and Pathways Underlying Imatinib and Nilotinib Treatment in CML: a Bioinformatics Study

“…Tukalo et al demonstrated the overexpression of seryl-tRNA synthetase (SARS or SerRS) in nearly half of the kidney cancer samples, however, two of samples showed slight reduction. In 38% of colon cancer samples, marked reduction in SARS expression levels were observed [22]. In another research, it has been revealed that, SARS expression levels was downregulated in approximately 80% of the prostate cancer cases and deemed to have clinical value in prostate carcer diagnosis [24].…”

“…Numerous lines of evidence demonstrated critical role of the aminoacyl-tRNA synthetases (ARSs) in different cancers [22,23]. The expression pro les of ARSs can be considered as a prognostic marker in cancers, since they are involved in overall patient survival [23].…”

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

“…All tRNAs(CCU) are also missing the extra arm that characterizes Ser-tRNA (Bilokapić et al. 2009; Tukalo et al. 2013), confirming their Ala-tRNA identity.…”

“…(1998), McClain and Foss (1988), and Musier-Forsyth et al. (1991). b TFAM, respectively, predicted a Trp-tRNA and a Met-tRNA identity for tRNA(CCU) in B. minor and T. obliquus , see supplementary table S2 of the Supplementary Material online. c Tukalo et al. (2013), Asahara et al.…”

Transfer RNAs with novel cloverleaf structures

“…As predicted, the two G-1 tRNA1 species were aminoacylated by E. coli HisRS, even more efficiently than E. coli tRNA His , despite the Thr GGU anticodon (Figure 4B ). The GUG triplet at positions 35–37 (but not the anticodon positions 34–36 in tRNA His ) of the two G-1 tRNA1 species might have been recognized by HisRS ( 35 – 37 ). Interestingly, the two G-1 tRNA1 species did not insert His in response to the ACC Thr codon at position 2 in a sfGFP variant gene in E. coli .…”

Identification of Common Genes and Pathways Underlying Imatinib and Nilotinib Treatment in CML: a Bioinformatics Study

“…Tukalo et al demonstrated the overexpression of seryl-tRNA synthetase (SARS or SerRS) in nearly half of the kidney cancer samples, however, two of samples showed slight reduction. In 38% of colon cancer samples, marked reduction in SARS expression levels were observed [22]. In another research, it has been revealed that, SARS expression levels was downregulated in approximately 80% of the prostate cancer cases and deemed to have clinical value in prostate carcer diagnosis [24].…”

“…Numerous lines of evidence demonstrated critical role of the aminoacyl-tRNA synthetases (ARSs) in different cancers [22,23]. The expression pro les of ARSs can be considered as a prognostic marker in cancers, since they are involved in overall patient survival [23].…”

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

“…All tRNAs(CCU) are also missing the extra arm that characterizes Ser-tRNA (Bilokapić et al. 2009; Tukalo et al. 2013), confirming their Ala-tRNA identity.…”

“…(1998), McClain and Foss (1988), and Musier-Forsyth et al. (1991). b TFAM, respectively, predicted a Trp-tRNA and a Met-tRNA identity for tRNA(CCU) in B. minor and T. obliquus , see supplementary table S2 of the Supplementary Material online. c Tukalo et al. (2013), Asahara et al.…”

Transfer RNAs with novel cloverleaf structures

“…As predicted, the two G-1 tRNA1 species were aminoacylated by E. coli HisRS, even more efficiently than E. coli tRNA His , despite the Thr GGU anticodon (Figure 4B ). The GUG triplet at positions 35–37 (but not the anticodon positions 34–36 in tRNA His ) of the two G-1 tRNA1 species might have been recognized by HisRS ( 35 – 37 ). Interestingly, the two G-1 tRNA1 species did not insert His in response to the ACC Thr codon at position 2 in a sfGFP variant gene in E. coli .…”

Identification of Common Genes and Pathways Underlying Imatinib and Nilotinib Treatment in CML: a Bioinformatics Study

“…Tukalo et al demonstrated the overexpression of seryl-tRNA synthetase (SARS or SerRS) in nearly half of the kidney cancer samples, however, two of samples showed slight reduction. In 38% of colon cancer samples, marked reduction in SARS expression levels were observed [22]. In another research, it has been revealed that, SARS expression levels was downregulated in approximately 80% of the prostate cancer cases and deemed to have clinical value in prostate carcer diagnosis [24].…”

“…Numerous lines of evidence demonstrated critical role of the aminoacyl-tRNA synthetases (ARSs) in different cancers [22,23]. The expression pro les of ARSs can be considered as a prognostic marker in cancers, since they are involved in overall patient survival [23].…”