Interaction of Human Phenylalanyl-tRNA Synthetase with Specific tRNA According to Thiophosphate Footprinting

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I. A. Vasil’eva¹, E. A. Semenova², and N. A. Moor^1*

¹Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva 8, 630090 Novosibirsk, Russia; fax: (383) 333-3677; E-mail: moor@niboch.nsc.ru

²Novosibirsk State University, ul. Pirogova 2, 630090 Novosibirsk, Russia

^* To whom correspondence should be addressed.

Received June 23, 2008; Revision received July 10, 2008

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The interaction of human cytoplasmic phenylalanyl-tRNA synthetase (an enzyme with yet unknown 3D-structure) with homologous tRNA^Phe under functional conditions was studied by footprinting based on iodine cleavage of thiophosphate-substituted tRNA transcripts. Most tRNA^Phe nucleotides recognized by the enzyme in the anticodon (G34), anticodon stem (G30–C40, A31–U39), and D-loop (G20) have effectively or moderately protected phosphates. Other important specificity elements (A35 and A36) were found to form weak nonspecific contacts. The D-stem, T-arm, and acceptor stem are also among continuous contacts of the tRNA^Phe backbone with the enzyme, thus suggesting the presence of additional recognition elements in these regions. The data indicate that mechanisms of interaction between phenylalanyl-tRNA synthetases and specific tRNAs are different in prokaryotes and eukaryotes.

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KEY WORDS: nucleoside-5′-O-(1-thiotriphosphate), tRNA^Phe, human phenylalanyl-tRNA synthetase, footprinting

DOI: 10.1134/S0006297909020084

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