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Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids

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Abstract

This review summarizes the features of cold shock domain (CSD) proteins in the context of their interactions with nucleic acids and describes similarities and differences in the structure of cold shock proteins of prokaryotes and CSD proteins of eukaryotes with special emphasis on the functions related to the RNA/DNA-binding ability of these proteins. The mechanisms and specificity of their interaction with nucleic acids in relation to the growing complexity of protein domain structure are described, as well as various complexes of the mammalian Y-box binding protein 1 (YB-1) with nucleic acids (filaments, globules, toroids). The role of particular amino acid residues in the binding of nitrogenous bases and the sugar-phosphate backbone of nucleic acids is emphasized. The data on the nucleic acid sequences recognized by the Y-box binding proteins are systematized. Post-translational modifications of YB-1, especially its phosphorylation, affect the recognition of specific sequences in the promoter regions of various groups of genes by YB-1 protein. The data on the interaction of Lin28 protein with let-7 miRNAs are summarized. The features of the domain structure of plant CSD proteins and their effect on the interaction with nucleic acids are discussed.

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Abbreviations

a.a.:

amino acid residue

A/P:

domain, alanine/ proline-rich domain

CRS:

cytoplasmic retention site

CSD:

cold shock domain

CSP:

cold shock protein

CTD:

C-terminal domain

dsDNA:

double-stranded DNA

(m)RNP:

(messenger) ribonucleoprotein

NLS:

nuclear localization signal

ssDNA:

single-stranded DNA

ssRNA:

single-stranded RNA

UTR:

untranslated region

YB-1:

Y-box binding protein 1

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Acknowledgements.

The authors thank E. V. Serebrova for the help in the manuscript preparation.

Funding

Funding. This study was performed within the State Assignment no. 0574-2019-0001 and supported in part (section “YB proteins”) by the Russian Science Foundation (project 19-74-20129).

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Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia

    K. S. Budkina, S. V. Kononova & L. P. Ovchinnikov

  2. All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia

    N. E. Zlobin & A. V. Babakov

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  1. K. S. Budkina
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  2. N. E. Zlobin
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  3. S. V. Kononova
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  4. L. P. Ovchinnikov
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  5. A. V. Babakov
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Correspondence to L. P. Ovchinnikov.

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Compliance with ethical norms. This article does not contain any studies with human participants or animals performed by any of the authors.

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Conflict of interest. The authors declare no conflict of interest.

Russian Text © The Author(s), 2020, published in Uspekhi Biologicheskoi Khimii, 2020, Vol. 60, pp. 3–42.

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Budkina, K.S., Zlobin, N.E., Kononova, S.V. et al. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. Biochemistry Moscow 85 (Suppl 1), 1–19 (2020). https://doi.org/10.1134/S0006297920140011

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  • DOI: https://doi.org/10.1134/S0006297920140011

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