Putative DEAD and DExH-box RNA helicases families in Entamoeba histolytica

Marchat, Laurence A.; Orozco, Esther; Guillén, Nancy; Weber, Christian; López-Camarillo, César

doi:10.1016/j.gene.2008.07.042

Cited by 15 publications

(24 citation statements)

References 57 publications

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“…To provide a schematic graphical overview of DEAD-box sequence motif conservation, we performed a multiple sequence alignment for each motif and then used the WebLogo software to obtain a precise description of sequence similarity [37,38] (Figure 1 - inset). Analysis of regions separating each pair of consecutive motifs was consistent with the reported low sequence but high length conservation (Figure 1) [33,34]. The DEAD-box family has an N-terminal length ranging from 2 to 233 amino acids and a C-terminal length from 29 to 507 amino acids, but lack any additional domain described in other DEAD-box proteins (Figure 1) [39].…”

Section: Resultssupporting

confidence: 74%

Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts

et al. 2012

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BackgroundRegulation of surface antigenic variation in Giardia lamblia is controlled post-transcriptionally by an RNA-interference (RNAi) pathway that includes a Dicer-like bidentate RNase III (gDicer). This enzyme, however, lacks the RNA helicase domain present in Dicer enzymes from higher eukaryotes. The participation of several RNA helicases in practically all organisms in which RNAi was studied suggests that RNA helicases are potentially involved in antigenic variation, as well as during Giardia differentiation into cysts.ResultsAn extensive in silico analysis of the Giardia genome identified 32 putative Super Family 2 RNA helicases that contain almost all the conserved RNA helicase motifs. Phylogenetic studies and sequence analysis separated them into 22 DEAD-box, 6 DEAH-box and 4 Ski2p-box RNA helicases, some of which are homologs of well-characterized helicases from higher organisms. No Giardia putative helicase was found to have significant homology to the RNA helicase domain of Dicer enzymes. Additionally a series of up- and down-regulated putative RNA helicases were found during encystation and antigenic variation by qPCR experiments. Finally, we were able to recognize 14 additional putative helicases from three different families (RecQ family, Swi2/Snf2 and Rad3 family) that could be considered DNA helicases.ConclusionsThis is the first comprehensive analysis of the Super Family 2 helicases from the human intestinal parasite G. lamblia. The relative and variable expression of particular RNA helicases during both antigenic variation and encystation agrees with the proposed participation of these enzymes during both adaptive processes. The putatives RNA and DNA helicases identified in this early-branching eukaryote provide initial information regarding the biological role of these enzymes in cell adaptation and differentiation.

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Section: Resultssupporting

confidence: 74%

Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts

et al. 2012

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“…In the common eukaryotic ancestor, a bona fide DEAD-box RNA helicase underwent a gene duplication event, thereby creating two paralogous copies of the helicase gene. Considering that all DEAD-box RNA helicases share the same conserved sequence motifs and are thus likely paralogs, multiple independent helicase gene duplication events must have occurred (Aubourg et al 1999;Marchat et al 2008). Over the course of evolutionary time, selective pressures maintained the helicase function of one copy while the second copy, which became Utp25, underwent progressive sequence divergence and eventual loss of most helicase motifs.…”

Section: Discussionmentioning

confidence: 99%

The DEAD-box RNA helicase-like Utp25 is an SSU processome component

Charette

Baserga²

2010

RNA

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The SSU processome is a large ribonucleoprotein complex consisting of the U3 snoRNA and at least 43 proteins. A database search, initiated in an effort to discover additional SSU processome components, identified the uncharacterized, conserved and essential yeast nucleolar protein YIL091C/UTP25 as one such candidate. The C-terminal DUF1253 motif, a domain of unknown function, displays limited sequence similarity to DEAD-box RNA helicases. In the absence of the conserved DEAD-box sequence, motif Ia is the only clearly identifiable helicase element. Since the yeast homolog is nucleolar and interacts with components of the SSU processome, we examined its role in pre-rRNA processing. Genetic depletion of Utp25 resulted in slowed growth. Northern analysis of pre-rRNA revealed an 18S rRNA maturation defect at sites A 0 , A 1 , and A 2 . Coimmunoprecipitation confirmed association with U3 snoRNA and with Mpp10, and with components of the t-Utp/UtpA, UtpB, and U3 snoRNP subcomplexes. Mutation of the conserved motif Ia residues resulted in no discernable temperaturesensitive or cold-sensitive growth defects, implying that this motif is dispensable for Utp25 function. A yeast two-hybrid screen of Utp25 against other SSU processome components revealed several interacting proteins, including Mpp10, Utp3, and Utp21, thereby identifying the first interactions among the different subcomplexes of the SSU processome. Furthermore, the DUF1253 domain is required and sufficient for the interaction of Utp25 with Utp3. Thus, Utp25 is a novel SSU processome component that, along with Utp3, forms the first identified interactions among the different SSU processome subcomplexes.

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“…It was reported that the N-or C-terminal flanking region other than the helicase core domain could be related to its subcellular localization and its proper function (Aubourg et al, 1999;Marchat et al, 2008). PSORT (http://psort.ims.u-tokyo.ac.jp/form.html) analysis of the deduced amino acid sequences of GmRH revealed the presence of the bipartite nuclear targeting sequence (28-69 aa), implying the possibility of the GmRH protein to be localized in the nucleus with 93% probability (Fig.…”

Section: Nuclear Localization Of Gmrh-gfp Protein In Protoplastsmentioning

confidence: 99%