Cellular nucleic acid binding protein binds G‐rich single‐stranded nucleic acids and may function as a nucleic acid chaperone

Abstract

Cellular nucleic acid binding protein (CNBP) is a small single-stranded nucleic acid binding protein made of seven Zn knuckles and an Arg-Gly rich box. CNBP is strikingly conserved among vertebrates and was reported to play broad-spectrum functions in eukaryotic cells biology. Neither its biological function nor its mechanisms of action were elucidated yet. The main goal of this work was to gain further insights into the CNBP biochemical and molecular features. We studied Bufo arenarum CNBP (bCNBP) binding to single-stranded nucleic acid probes representing the main reported CNBP putative targets. We report that, although bCNBP is able to bind RNA and single-stranded DNA (ssDNA) probes in vitro, it binds RNA as a preformed dimer whereas both monomer and dimer are able to bind to ssDNA. A systematic analysis of variant probes shows that the preferred bCNBP targets contain unpaired guanosine-rich stretches. These data expand the knowledge about CNBP binding stoichiometry and begins to dissect the main features of CNBP nucleic acid targets. Besides, we show that bCNBP presents a highly disordered predicted structure and promotes the annealing and melting of nucleic acids in vitro. These features are typical of proteins that function as nucleic acid chaperones. Based on these data, we propose that CNBP may function as a nucleic acid chaperone through binding, remodeling, and stabilizing nucleic acids secondary structures. This novel CNBP biochemical activity broadens the field of study about its biological function and may be the basis to understand the diverse ways in which CNBP controls gene expression.

Dissecting CNBP, a Zinc-Finger Protein Required for Neural Crest Development, in Its Structural and Functional Domains

“…[14][15][16][17] The nucleic acid chaperone activity may allow CNBP to control transcriptional processes through chromatin structure remodeling of promoter regions and/or translational processes by affecting RNA structures that finally modulate the action of specific trans-acting factors. 18 Amino acid sequence analysis of the CNBP family reveals the presence of two remarkable structural features (Fig. 1).…”

Arginine methylation of the cellular nucleic acid binding protein does not affect its subcellular localization but impedes RNA binding

“…It is also present in the ITAF complex promoting cap-independent translation [6]. It binds to G-rich single-stranded nucleic acid and may function as a nucleic acid chaperone [7]. CNBP is highly conserved among human, mouse, rat, chicken, Xenopus species and fish [8].…”

Targeting G-Quadruplex DNA with Small Molecules

“…Single-stranded DNA viral genomes and telomeric DNA circles are known exceptions to this rule. [6] The thermodynamic and kinetic barriers of duplex dissociation, a prerequisite for singlestranded DNA folding, might be off-set in part or in whole by single-stranded DNA binding proteins, [7] chaperones, [8,9] smallmolecule binding, [10][11][12] and/or negative supercoiling. [12][13][14][15][16] Polypurine-polypyrimidine tracts and other repetitive sequences can form nonduplex and/or higher-order chromatin structures possibly related to a wide variety of biological activities.…”

“…[22] But much faster rates of folding have been observed when G-quadruplex DNA was imbedded in a molecular matrix at temperatures slightly below the T m (k f ~1.0 s -1 ). [43] Molecular crowding, [44] synthetic and endogenous chaperones, [8][9][10][11][12] and dehydrating conditions inside the nucleus might also accelerate the rates of G-quadruplex formation in vivo. [22] Due to the self-complementary nature of duplex DNA, approximately 370'000 Crich motifs (C 3+ N 1-7 ) 4+ (where C = cytosine and N = any base) are present in the human genome.…”