Structure and Function of Cold Shock Proteins in Archaea

Abstract

Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal thermophiles and hyperthermophiles. In bacteria, Csps are small, nucleic acid binding proteins involved in a variety of cellular processes, such as transcription. In this study, archaeal Csp function was assessed by examining the ability of csp genes from psychrophilic and mesophilic Euryarchaeota and Crenarchaeota to complement a cold-sensitive growth defect in Escherichia coli. In addition, an archaeal gene with a cold shock domain (CSD) fold but little sequence identity to Csps was also examined. Genes encoding Csps or a CSD structural analog from three psychrophilic archaea rescued the E. coli growth defect. The three proteins were predicted to have a higher content of solvent-exposed basic residues than the noncomplementing proteins, and the basic residues were located on the nucleic acid binding surface, similar to their arrangement in E. coli CspA. The M. frigidum Csp was purified and found to be a single-domain protein that folds by a reversible two-state mechanism and to exhibit a low conformational stability typical of cold-adapted proteins. Moreover, M. frigidum Csp was characterized as binding E. coli single-stranded RNA, consistent with its ability to complement function in E. coli. The studies show that some Csp and CSD fold proteins have retained sufficient similarity throughout evolution in the Archaea to be able to function effectively in the Bacteria and that the function of the archaeal proteins relates to cold adaptation. The initial biochemical analysis of M. frigidum Csp has developed a platform for further characterization and demonstrates the potential for expanding molecular studies of proteins from this important archaeal stenopsychrophile.

gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16

“…The Escherichia coli strain BX04 is a quadruple deletion mutant that lacks four CSPs (CspA, B, E, and G), and is thus cold sensitive. Numerous CSPs from bacteria and archaea, as well as eukaryotic Y-box proteins, have been shown to complement the cold sensitivity of BX04, presumably due to their ability to act as RNA chaperones (Nakaminami et al 2006;Giaquinto et al 2007;Kim et al 2007). To determine whether RBP16 acts as an RNA chaperone in an in vivo context, we asked if it can complement cold sensitivity in the BX04 cells.…”

RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution

“…The cold-induced proteins include a family of proteins named major cold shock proteins (CSPs). They are ubiquitous proteins in the domain of Eubacteria and Archaea (Graumann and Marahiel 1998;Giaquinto et al 2007). CSPs appear to serve various cellular functions in the context of stress response, but they are not antifreeze proteins.…”

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

“…These include genes involved in diverse cellular processes (e.g. metabolism, replication, transposases) and that have a range of ER values (ER2,6;ER3,7;ER4,11;ER5,6). The ER2 genes were archaeal DNA polymerase II small subunit, F 420 H 2 dehydrogenase subunit J and four pyrrolysine-containing methyltransferases.…”

“…Four proteins from M. burtonii were assigned ER1 as they have been experimentally characterized; elongation factor 2 (Mbur_1171) [5], two proteins involved in formation of the compatible solute glycosylglycerate, glucosyl-3-phosphoglycerate synthase (Mbur_0737) [6] and glucosyl-3-phosphoglycerate phosphatase (Mbur_0736) [6], and a protein with a cold shock domain that complements a cold sensitive defect in E. coli (Mbur_1438) [7] and appears to form part of the archaeal exosome [29]. Forty-two percent of proteins in the M. burtonii genome had strong (ER2) or moderate (ER3) similarity to experimentally characterized proteins from other organisms, and 32% of the proteins had similarity to protein domains or families but no experimentally characterized homolog (ER4) ( Table SI1).…”