Contribution of Eutrema salsugineum Cold Shock Domain Structure to the Interaction with RNA

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V. V. Taranov^1#, N. E. Zlobin^1#, K. I. Evlakov¹, A. O. Shamustakimova^1,a*, and A. V. Babakov^1,b

¹All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia

^# These authors contributed equally to this work.

^* To whom correspondence should be addressed.

Received June 5, 2018; Revision received July 24, 2018

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Plant cold shock domain proteins (CSDPs) are DNA/RNA-binding proteins. CSDPs contain the conserved cold shock domain (CSD) in the N-terminal part and a varying number of the CCHC-type zinc finger (ZnF) motifs alternating with glycine-rich regions in the C-terminus. CSDPs exhibit RNA chaperone and RNA-melting activities due to their nonspecific interaction with RNA. At the same time, there are reasons to believe that CSDPs also interact with specific RNA targets. In the present study, we used three recombinant CSDPs from the saltwater cress plant (Eutrema salsugineum) – EsCSDP1, EsCSDP2, EsCSDP3 with 6, 2, and 7 ZnF motifs, respectively, and showed that their nonspecific interaction with RNA is determined by their C-terminal fragments. All three proteins exhibited high affinity to the single-stranded regions over four nucleotides long within RNA oligonucleotides. The presence of guanine in the single- or double-stranded regions was crucial for the interaction with CSDPs. Complementation test using E. coli BX04 cells lacking four cold shock protein genes (ΔcspA, ΔcspB, ΔcspE, ΔcspG) revealed that the specific binding of plant CSDPs with RNA is determined by CSD.

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KEY WORDS: Eutrema salsugineum, Arabidopsis thaliana, cold shock domain proteins, cold shock domain, zinc fingers, RNA–protein interaction

DOI: 10.1134/S000629791811007X

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