Cold-Shock Domains—Abundance, Structure, Properties, and Nucleic-Acid Binding

Abstract

The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.

β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis

“…Soluble β-barrels can have a chromophore that determines their optical properties. They can bind and transport small hydrophobic molecules with high affinity (lipocalins), bind the superoxide radical anion in the active center, activate cell surface receptors, participate in protein storage defense from pathogens, and perform other functions [ 37 , 38 , 39 , 40 , 41 , 42 , 43 ].…”

“…Another representative of amyloidogenic β-barrels is the cold-shock domain (CSD), which is present in bacterial cold-shock proteins (CSPs) and Y-box proteins of eukaryotes. This domain consists of five antiparallel β-strands folded into a barrel [ 38 ]. Proteins containing the CSD bind single-stranded nucleic acids [ 38 ], thus acting as mRNA chaperones and participating in the regulation of transcription and translation [ 75 , 76 ].…”

Is It Possible to Create Antimicrobial Peptides Based on the Amyloidogenic Sequence of Ribosomal S1 Protein of P. aeruginosa?

“…OB-fold is a β-barrel including five antiparallel β-strands and a single α-helix. This fold is capable of performing a wide range of biological processes: control of RNA splicing, DNA repair, regulation of transcription, and many other functions [43,44]. The S1 domain can be found in different living organisms, and the number of S1 domains can vary from one to 15 [45].…”

Expert annotation and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) highlight the role of cold shock proteins in dormancy exit

“…Altogether our results clearly indicate that CSPs are major TFs of the rust life cycle with a role associated to dormancy exit and basidia differentiation. In other eukaryotes a variety of functions have been assigned to CSPs (Heinemann and Roske, 2021). A next challenge will be to determine whether each of the three MlpCSP genes exhibit some specificity or show functional redundancy in the regulation of subsequent cellular processes.…”

“…CSD proteins (CSPs) are mainly associated with cold adaptation and they function as RNA chaperone with a role in RNA secondary structure stability during cold stress (Chaikam and Karlson, 2010). The structures of CSPs provided evidence for a global conservation of the CSD between prokaryotes and eukaryotes (Chaikam and Karlson, 2010;Heinemann and Roske, 2021) with two consensus RNA-binding motifs (RNP1 and RNP2) mediating RNA binding activity and enhancing the RNA affinity (Landsman, 1992;Nakaminami et al, 2006).…”