A novel nuclear DNA helicase with high specific activity from Pisum sativum catalytically translocates in the 3'-->5' direction

Functional characterization of PeIF5B as eIF5B homologue from Pisum sativum

We earlier reported 'PeIF5B' as a novel factor from Pisum sativum that has sequence similarity to eIF5B (S. Rasheedi, S. Ghosh, M. Suragani et al., P. sativum contains a factor with strong homology to eIF5B, Gene 399 (2007) 144-151). The main aim of the present study was to perform functional characterization of PeIF5B as an eIF5B homologue from plant system. PeIF5B shows binding to Met - tRNA(f)(Met), hydrolyses GTP and interacts with ribosomes. In vivo growth complementation analysis shows that PeIF5B partially complements its yeast homologue. Interestingly, PeIF5B mainly localizes in the nucleus as confirmed by nuclear localization signal (NLS) prediction, confocal imaging and immunoblots of cellular fractions. Similar to the yeast eIF5B but unlike the human orthologue, PeIF5B is an intron-less gene. This study highlights PeIF5B's role as a functional eIF5B homologue possibly participating in nuclear translation in plant system.

DNA helicase 3.6.4.12

EC number

 3.6.4.12

Systematic name

 ATP phosphohydrolase (DNA helix unwinding)

Recommended name

 DNA helicase

Synonyms

 3’ to 5’ DNA helicase <28> [35]

 3’-5’ DNA helicase <11> [55]

 3’-5’ PfDH <11> [55]

 5’ to 3’ DNA helicase <26,27> [19,42]

 AvDH1 <47> [37]

 BACH1 helicase <19> [34]

 BLM <3> [28]

 BLM protein <3> [28]

 BRCA1-associated C-terminal helicase <19> [34]

 BcMCM <8> [52]

 CeWRN-1 <43> [9]

 DDX25 <3,48> [36]

 DNA helicase 120 <7> [15]

 DNA helicase A <4> [8]

 DNA helicase E <5> [44]

 DNA helicase II <9> [7]

 DNA helicase III <4> [27]

 DNA helicase RECQL5β <44> [17]

 DNA helicase VI <3> [45]

 Dbp9p <46> (<46> a member of the DEAD box protein family [24]) [24]

 DmRECQ5 <1> [50]

 DnaB helicase <29> [23]

 E1 helicase <17> [58]

 GRTH/DDX25 <3,48> [36]

 HCoV SF1 helicase <23> [3]

 HCoV helicase <23> [3]

 HDH IV <3> [45]

 Hel E <5> [44]

 Hmi1p <40> [60]

 MCM helicase <6,5,38> [43,54]

 MCM protein <6,35> [43]

 MER3 helicase <22> [30]

 MER3 protein <22> [30]

 MPH1 <28> [35]

 NS3 <12,50> (<12,50> ambiguous [38,65,66]) [38,65,66]

 NS3 NTPase/helicase <14> (<14> ambiguous [67]) [67]

 NS3 protein <12> (<12> ambiguous [63]) [63]

 NTPase/helicase <12,16> (<12> ambiguous [61]) [61,64]

 PDH120 <7> [15]

 PIF1 <33> [51]

 PIF1 helicase <33> [51,53]

 PcrA <37> [20]

 PcrA helicase <37,41,49> [20,21,39]

 PcrASpn <41> [21]

 PfDH A <11> [55]

 Pfh1p <27> [42]

 RECQ5 <1> [49,50]

 RECQ5 helicase <1> (<1> small isoform [49]) [49]

 RECQL5b <44> [17]

 REcQ <31> [13]

 RSF1010 RepA <30> [5]

 RecG <45> [6]

 RecQ helicase <32> [56]

 RecQsim <32> [56]

 Rep52 <24> [40]

 Rrm3p <26> [19]

 Sgs1 <36> [29]

 Sgs1 DNA helicase <36> [29]

 TWINKLE <21> [33]

 Tth UvrD <20> [16]

 UvrD <20,42> [16,22]

 UvrD helicase <39> [18]

 WRN <18> [31]

 WRN RecQ helicase <18> [12]

 WRN helicase <18> [12]

 WRN protein <18> [12]

 WRN-1 RecQ helicase <43> [9]

 Werner Syndrome helicase <18> [31]

 Werner syndrome RecQ helicase <18> [12]

 dheI I <1> [46]

 dnaB <29> [23]

 hPif1 <33> [53]

 helicase DnaB <2> [10]

 helicase II <25> [25]

 helicase PcrA <49> [39]

 helicase UvrD <20> [16]

 helicase domain of bacteriophage T7 gene 4 protein <10> [47]

 non structural protein 3 <12> (<12> ambiguous [61,62]) [61,62]

 nonstructural protein 3 <12,14,50,51> (<12,14,50> ambiguous [38,63,65,66,67]; <51> ambigous [4]) [4,38,63,65,66,67]

 protein NS3 <12> (<12> ambiguous [62]) [62]

 scHelI <4> [26]

 urvD <25> [25]

A novel dual Dbp5/DDX19 homologue from Plasmodium falciparum requires Q motif for activity

Helicases are ubiquitous essential enzymes which have significant role in the nucleic acid metabolism. Using in silico approaches in the recent past we have identified a number of helicases in the Plasmodium falciparum genome. In the present study we report purification and detailed characterization of a novel helicase from P. falciparum. Our results indicate that this helicase is a homologue of Dbp5 and DDX19 from yeast and human, respectively. The biochemical characterization shows that it contains DNA and RNA unwinding, nucleic acid dependent ATPase and RNA binding activities. It is interesting to note that this enzyme can unwind DNA duplexes in both 5' to 3' and 3' to 5' directions. Using truncated derivatives we further show that Q motif is essentially required for all of its activities. These studies should make an important contribution in understanding the enzymes involved in nucleic acid metabolism in the parasite.

Plasmodium falciparum DNA helicase 60. dsRNA- and antibody-mediated inhibition of malaria parasite growth and downregulation of its enzyme activities by DNA-interacting compounds

Helicases are ubiquitous enzymes that play important roles in all types of DNA transaction in the cells. Recently we have reported the characterization of the first DEAD-box helicase [Plasmodium falciparum DNA helicase 60 (PfDH60)] from Plasmodium falciparum and have shown that it is a unique, dual bipolar helicase expressed in a stage-specific manner. In this study, we show the further characterization of PfDH60. For analyzing the significance of this enzyme in parasite growth, we studied the effect of dsRNA and specific antibodies on growth of the parasite. The studies indicate that the parasite cultures treated with PfDH60 dsRNA exhibited approximately 50% growth inhibition when compared with either untreated cultures or cultures treated with unrelated dsRNA. It was interesting to note that purified immunoglobulins against PfDH60 induced approximately 62% inhibition of in vitro growth of P. falciparum and that this inhibitory effect was associated with morphologic damage to the parasite. DNA-interacting compounds inhibit DNA helicase and ssDNA-dependent ATPase activities of PfDH60. Of various compounds tested, only actinomycin, daunorubicin, ethidium bromide, netropsin and nogalamycin were able to inhibit the enzyme activities of PfDH60, with apparent IC50 values for helicase inhibition of 0.8, 0.3, 2.0, 1.2 and 1.5 microm, respectively. It may be proposed that these compounds form a complex with DNA and specifically inhibit helicases due to obstruction in the translocation of the enzyme. These compounds also inhibited parasite growth in culture. This is the first study to show inhibition of growth of the parasite by the dsRNA of a helicase, and most probably this is due to interference with cognate mRNA expression.

The Gly-Arg-rich C-terminal domain of pea nucleolin is a DNA helicase that catalytically translocates in the 5'- to 3'-direction

Nucleolin is a major nucleolar phosphoprotein of exponentially growing eukaryotic cells. Here we report the cloning, purification, and characterization of the C-terminal glycine/arginine-rich (GAR) domain of pea nucleolin. The purified recombinant protein (17 kDa) shows ATP-/Mg(2+)-dependent DNA helicase and ssDNA-/Mg(2+)-dependent ATPase activities. The enzyme unwinds DNA in the 5'- to 3'-direction, which is the first report in plant for this directional activity. It unwinds forked/non-forked DNA with equal efficiency. The anti-nucleolin antibodies immunodepleted the activities of the enzyme. The DNA interacting ligands nogalamycin, daunorubicin, actinomycin C1, and ethidium bromide were inhibitory to DNA unwinding (with K(i) values of 0.40, 2.21, 8.0, and 9.0 microM, respectively) and ATPase (with K(i) values of 0.43, 1.65, 4.6, and 7.0 microM, respectively) activities of the enzyme. This study confirms that the unwinding and ATPase activities of pea nucleolin resided in the GAR domain. This study should make important contribution to our better understanding of DNA transaction in plants, mechanism of DNA unwinding, and the mechanism by which these ligands can disturb genome integrity.