An Introduction to RNA Helicases: Superfamilies, Families, and Major Themes

Jankowsky, Eckhard; Fairman-Williams, Margaret E.

doi:10.1039/9781849732215-00001

Cited by 18 publications

(24 citation statements)

References 143 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the case of Ski2-like helicases, sequence analysis has identified two RecA domains containing 12 conserved sequence motifs. [1][2][3][4][5] The Mtr4 and Ski2 structures confirm that the RecA domains (designated here as RecA1 and RecA2) adopt structures and sequence motif arrangements similar to that observed in other SF2 helicases (Fig. 1).…”

Section: Common Architecture Of Ski2-like Helicasessupporting

confidence: 50%

See 1 more Smart Citation

Ski2-like RNA helicase structures

Johnson

Jackson

2013

RNA Biology

View full text Add to dashboard Cite

Section: Common Architecture Of Ski2-like Helicasessupporting

confidence: 50%

“…[1][2][3][4][5] A distinctive feature of these helicases is their large size, spanning 120-225 kDa in S. cerevisiae. Named for their founding member, Ski2, [6][7][8][9] Ski2-like RNA helicases play important roles in RNA degradation, processing and splicing pathways.…”

mentioning

confidence: 99%

Ski2-like RNA helicase structures

Johnson

Jackson

2013

RNA Biology

View full text Add to dashboard Cite

“…The majority of the human RNA-binding DexD/H helicases, 42 members, belong to the DEAD box class, while the others are DEAH and DExH Ski-like helicases (named after its founding member Ski2p) (la Cruz et al 1999). DExD/H RNA helicases belong to the SF2 helicase superfamily and contain NTPase characteristic Walker A and B motifs; their seven helicase signature motifs extend over ~400 amino acids (Tanner and Linder 2001; Rocak and Linder 2004; Pyle 2008; Jankowsky and Fairman-Williams 2010; Fairman-Williams et al 2010). The helicases are differentiated by their catalytic core residues Asp-Glu-Ala-Asp for DEAD box helicases, and Asp-Glu-Ala/x- His for the related DEAH box and Ski2-like helicases.…”

Section: Structural Analysis Of Rna-binding Domainsmentioning

confidence: 99%

“…DExD/H RNA helicases generally lack substrate specificity, or even affinity, towards RNA and DNA. This allows them to promiscuously unwind and remodel a broad range of targets, but also requires their association with cofactors that give specificity and affinity for their targets (Rocak and Linder 2004; Jankowsky and Fairman-Williams 2010). While most members of DExD/H helicases are involved in mRNA-related processes, in particular splicing, they play essential roles in diverse PTGR pathways such as transcriptional regulation, rRNA and tRNA maturation, viral defense, miRNA RISC loading, translation initiation, RNA export, and degradation (Rocak and Linder 2004; Fukuda et al 2007; Pyle 2008; Jankowsky 2011; Linder and Jankowsky 2011; Martin et al 2013; Schmidt and Butler 2013; Fullam and Schröder 2013).…”

Section: Structural Analysis Of Rna-binding Domainsmentioning

confidence: 99%

Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease

Gerstberger

Hafner

Ascano

et al. 2014

Advances in Experimental Medicine and Biology

125

104

View full text Add to dashboard Cite

RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.

show abstract

“…Recently, a novel SF2 helicase named Archaea-specific helicase (ASH) was reported, which is specific to Euryarchaeota, with the exception of Thermoproteales and Archaeoglobales (21). SF2 helicases, which unwind DNA duplexes from unpaired 3= or 5= ends, contain highly conserved nucleoside triphosphate (NTP) substrate-or metal-binding motifs, such as Walker A and Walker B motifs (22)(23)(24)(25). T. kodakarensis possesses several SF2 genes in its genome (26).…”

mentioning

confidence: 99%

Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR

Fujiwara

Kawato

Kato

et al. 2016

Appl Environ Microbiol

View full text Add to dashboard Cite

DNA/RNA helicases, which are enzymes for eliminating hydrogen bonds between bases of DNA/DNA, DNA/RNA, and RNA/ RNA using the energy of ATP hydrolysis, contribute to various biological activities. In the present study, the Euryarchaeota-specific helicase EshA (TK0566) from the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-EshA) was obtained as a recombinant form, and its enzymatic properties were examined. Tk-EshA exhibited maximal ATPase activity in the presence of RNA at 80°C. Unwinding activity was evaluated with various double-stranded DNAs (forked, 5= overhung, 3= overhung, and blunt end) at 50°C. Tk-EshA unwound forked and 3= overhung DNAs. These activities were expected to unwind the structured template and to peel off misannealed primers when Tk-EshA was added to a PCR mixture. To examine the effect of Tk-EshA on PCR, various target DNAs were selected, and DNA synthesis was investigated. When 16S rRNA genes were used as a template, several misamplified products (noise DNAs) were detected in the absence of Tk-EshA. In contrast, noise DNAs were eliminated in the presence of Tk-EshA. Noise reduction by Tk-EshA was also confirmed when Taq DNA polymerase (a family A DNA polymerase, PolI type) and KOD DNA polymerase (a family B DNA polymerase, ␣ type) were used for PCR. Misamplified bands were also eliminated during toxA gene amplification from Pseudomonas aeruginosa DNA, which possesses a high GC content (69%). Tk-EshA addition was more effective than increasing the annealing temperature to reduce misamplified DNAs during toxA amplification. Tk-EshA is a useful tool to reduce noise DNAs for accurate PCR. IMPORTANCEPCR is a technique that is useful for genetic diagnosis, genetic engineering, and detection of pathogenic microorganisms. However, troubles with nonspecific DNA amplification often occur from primer misannealing. In order to achieve a specific DNA amplification by eliminating noise DNAs derived from primer misannealing, a thermostable Euryarchaeota-specific helicase (Tk-EshA) was included in the PCR mixture. The addition of Tk-EshA has reduced noise DNAs in PCR.

show abstract

An Introduction to RNA Helicases: Superfamilies, Families, and Major Themes

Cited by 18 publications

References 143 publications

Ski2-like RNA helicase structures

Ski2-like RNA helicase structures

Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease

Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR

Contact Info

Product

Resources

About