Autoinhibition of human dicer by its internal helicase domain

Dicer, a member of the ribonuclease III family of enzymes, processes double-stranded RNA substrates into ∼ 21- to 27-nt products that trigger sequence-directed gene silencing by RNA interference. Although the mechanism of RNA recognition and length-specific cleavage by Dicer has been established, the way in which dicing activity is regulated is unclear. Here, we show that the N-terminal domain of human Dicer, which is homologous to DExD/H-box helicases, substantially attenuates the rate of substrate cleavage. Deletion or mutation of this domain activates human Dicer in both single- and multiple-turnover assays. The catalytic efficiency (k_cat/K_m) of the deletion construct is increased by 65-fold over that exhibited by the intact enzyme. Kinetic analysis shows that this activation is almost entirely due to an enhancement in k_cat. Modest stimulation of catalysis by the full-length Dicer enzyme was observed in the presence of the TAR-RNA binding protein, which physically interacts with the DExD/H-box domain. These results suggest that the DExD/H-box domain likely disrupts the functionality of the Dicer active site until a structural rearrangement occurs, perhaps upon assembly with its molecular partners.     

Key Amino Acid Residues Responsible for the Color of Green and Yellow Fluorescent Proteins from the Coral Polyp Zoanthus sp.

Site-directed mutagenesis was used to study the structural basis of color diversity of fluorescent proteins by the example of two closely related proteins from one organism (coral polyp Zoanthus sp.), one of which produces green and the other, yellow fluorescence. As a result, the following conversions of emission colors were performed: from yellow to green, from yellow to a dual color (yellow and green), and from green to yellow. The saltatory character of the spectral transitions and the manifestation of the dual-color fluorescence suggest that chemically different fluorophores are responsible for the green and yellow fluorescence. The simultaneous presence of three residues, Gly63, Lys65, and Asp68, is necessary for the efficient formation of the yellow rather than green fluorophore.     

Bacillus subtilis YkuK protein is distantly related to RNase H

In addition to one hypothetical viral sequence from Bacteriophage KVP40, the PfamA family of unknown function DUF458 (Pfam Accession No. PF04308) encompasses several uncharacterized bacterial proteins including Bacillus subtilis YkuK protein. Using Meta-BASIC, a highly sensitive method for detection of distant similarity between proteins, we assign DUF458 family members to the ribonuclease H-like (RNase H-like) superfamily. DUF458 sequences maintain all core secondary structure elements of RNase H-like fold and share several conserved, presumably active site residues with RNase HI, including an invariant DDE motif. In addition to providing a model structure for a previously uncharacterized protein family, this finding suggests that DUF458 proteins function as nucleases. The unusual phyletic pattern, together with a presence of DUF458 in several thermophilic organisms, may suggest a potential role of these proteins in DNA repair in stressful conditions such as an extreme heat or other stress that causes spore formation.     

Crystal structure of bacterial cytotoxic necrotizing factor CNFY reveals molecular building blocks for intoxication

Cytotoxic necrotizing factors (CNFs) are bacterial single‐chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three‐dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full‐length Yersinia pseudotuberculosis CNF_Y. CNF_Y consists of five domains (D1–D5), and by integrating structural and functional data, we demonstrate that D1–3 act as export and translocation module for the catalytic unit (D4–5) and for a fused β‐lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP‐ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4–5 fragment. This liberates D5 from a semi‐blocked conformation in full‐length CNF_Y, leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad‐specificity protein delivery tool.     

盐单胞菌DSM 16354T中新型耐盐基因的克隆及解析*

目的: 嗜盐菌分布广泛且适应能力极强,为加强对嗜盐菌耐盐机制的探索与研究,从盐单胞菌Halomonas alkaliphila DSM 16354^T中筛选出潜在的与耐盐有关的基因,对其进行生物信息学分析,并验证相关蛋白的生理功能。方法: 利用基因文库筛选和功能互补相结合的方法,通过与大肠杆菌(Escherichia coli)盐敏感缺陷株KNabc(ΔnhaA、ΔnhaB、ΔchaA)的耐盐功能互补实验,筛选出具有耐盐功能的蛋白编码基因,并通过荧光猝灭恢复实验测定蛋白的逆向转运活性以及底物亲和力。结果: 筛选得到两个具有耐盐功能的蛋白编码基因,生物信息学分析结果表明该基因编码来自于DUF1538(domain of unknown function with No.1538 family)家族功能未知的膜蛋白,分别命名为duf1和duf2。系统发育树分析结果表明,来自盐单胞菌DSM 16354^T中的DUF1、DUF2属于一个独立的分支,预测这两个蛋白可能是DUF1538家族转运蛋白的新成员。对DUF1和DUF2的生理功能进行分析,发现duf1和duf2单独表达时均不具有耐盐碱能力,而共同表达时则表现出显著的耐盐碱功能,表明DUF1和DUF2两个亚基共同支持了蛋白的耐盐碱功能。蛋白的逆向转运测定活性结果表明双组份蛋白DUF1-2具有Na⁺(Li⁺、K⁺)/H⁺逆向转运活性。结论: 筛选得到的基因duf1和duf2共同表达时具有盐碱耐受功能以及逆向转运蛋白活性,这为筛选出新的DUF1538家族转运蛋白基因和进一步探究DUF1538家族转运蛋白功能奠定了基础。     

Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function

Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri, the first structural representative from this protein domain family. We demonstrate that the structure of VF0530 adopts a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. Moreover, gel shift binding data indicate a potential dsDNA binding role for VF0530.     

Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction

Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an α-β-β-β-α topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal α helix of DUF283 runs cross over the C-terminal α helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.