An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA

DEAD box proteins share several highly conserved motifs including the characteristic Asp-Glu-Ala-Asp (D-E-A-D in the amino acid single-letter code) motif and have established or putative ATP-dependent RNA helicase activity. These proteins are implicated in a range of cellular processes that involve regulation of RNA function, including translation initiation, RNA splicing and ribosome assembly. Here we describe the isolation and characterization of an embryonic RNA helicase gene, ERH, which maps to mouse chromosome 1 and encodes a new member of the DEAD box family of proteins. The predicted ERH protein shows high sequence similarity to the testes-specific mouse PL10 and to the maternally acting Xenopus An3 helicase proteins. The ERH expression profile is similar, to that of An3, which localizes to the animal hemisphere of oocytes and is abundantly expressed in the embryo. ERH is expressed in oocytes and is a ubiquitous mRNA in the 9 days-post-conception embryo, and at later stages of development shows a more restricted pattern of expression in brain and kidney. The similarities in sequence and in expression profile suggest that ERH is the murine equivalent of the Xenopus An3 gene, and we propose that ERH plays a role in translational activation of mRNA in the oocyte and early embryo.

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Investigation of a Novel Salt Stress-Responsive Pathway Mediated by Arabidopsis DEAD-Box RNA Helicase Gene AtRH17 Using RNA-Seq Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms21051595 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1595 ◽

Cited By ~ 1

Author(s):

Hye-Yeon Seok ◽

Linh Vu Nguyen ◽

Doai Van Nguyen ◽

Sun-Young Lee ◽

Yong-Hwan Moon

Keyword(s):

Salt Stress ◽

Stress Tolerance ◽

Stress Responses ◽

Rna Helicase ◽

Rna Seq ◽

Salt Stress Tolerance ◽

Salt Stress Condition ◽

Dead Box ◽

Helicase Gene ◽

Upregulated Genes

Previously, we reported that overexpression of AtRH17, an Arabidopsis DEAD-box RNA helicase gene, confers salt stress-tolerance via a pathway other than the well-known salt stress-responsive pathways. To decipher the salt stress-responsive pathway in AtRH17-overexpressing transgenic plants (OXs), we performed RNA-Sequencing and identified 397 differentially expressed genes between wild type (WT) and AtRH17 OXs. Among them, 286 genes were upregulated and 111 genes were downregulated in AtRH17 OXs relative to WT. Gene ontology annotation enrichment and KEGG pathway analysis showed that the 397 upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Taken together, our results suggest that a high AtRH17 expression confers salt stress-tolerance through a novel salt stress-responsive pathway involving nine genes, other than the well-known ABA-dependent and ABA-independent pathways.

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Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs

Biochemical Society Transactions ◽

10.1042/bst20170095 ◽

2017 ◽

Vol 45 (6) ◽

pp. 1313-1321 ◽

Cited By ~ 27

Author(s):

Benjamin Gilman ◽

Pilar Tijerina ◽

Rick Russell

Keyword(s):

Conformational Changes ◽

Protein Complexes ◽

Rna Helicase ◽

Conformational Transitions ◽

Messenger Rnas ◽

Base Pairs ◽

Dead Box ◽

Evolutionarily Conserved ◽

Partially Unfolded ◽

Rna Protein Complexes

Structured RNAs and RNA–protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how their distinct mechanisms enable DEAD-box proteins to disrupt RNA base pairs on the surfaces of structured RNAs and RNPs, while some DEAH-box proteins are adept at disrupting base pairs in the interior of RNPs. Proteins from these families use these mechanisms to chaperone folding and promote rearrangements of structured RNAs and RNPs, including the spliceosome, and may use related mechanisms to maintain cellular messenger RNAs in unfolded or partially unfolded conformations.

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RNA Helicase Mediates Competitive Fitness of Listeria monocytogenes on the Surface of Cantaloupe

Horticulturae ◽

10.3390/horticulturae4040040 ◽

2018 ◽

Vol 4 (4) ◽

pp. 40 ◽

Cited By ~ 1

Author(s):

Robert Price ◽

Cameron Parsons ◽

Sophia Kathariou

Keyword(s):

Listeria Monocytogenes ◽

Foodborne Pathogen ◽

Rna Helicase ◽

Relative Fitness ◽

Competitive Fitness ◽

Growth And Survival ◽

Dead Box ◽

Helicase Gene ◽

Genetic Features ◽

Flagellum Biosynthesis

Listeria monocytogenes is a foodborne pathogen that is implicated in numerous outbreaks of disease (listeriosis) via fresh produce. The genetic features of L. monocytogenes that allow adherence and growth on produce remain largely uncharacterized. In this study, two non-motile transposon mutants were characterized for attachment, growth, and survival on the surface of cantaloupe rind. One of the mutants, L1E4, harbored a single transposon insertion in a DEAD-box RNA helicase gene (lmo0866 homolog), while the other, M1A5, harbored an insertion in a gene from a flagellum biosynthesis and chemotaxis gene cluster (lmo0694 homolog). When inoculated alone, neither mutant was significantly impaired in growth or survival on the surface of cantaloupe at either 25 or 37 °C. However, when co-inoculated with the wildtype parental strain, the RNA helicase mutant L1E4 had a clear competitive disadvantage, while the relative fitness of M1A5 was not noticeably impacted. Genetic complementation of L1E4 with the intact RNA helicase gene restored relative fitness on cantaloupe. The findings suggest that the DEAD-box RNA helicase encoded by the lmo0866 homolog is critical for relative fitness of L. monocytogenes on cantaloupe. Mutant L1E4 was pleiotropic, being not only non-motile but also cold-sensitive and with reduced hemolytic activity, warranting further studies to elucidate the role of this helicase in the competitive fitness of L. monocytogenes on produce.

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p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts.

Molecular and Cellular Biology ◽

10.1128/mcb.11.3.1326 ◽

1991 ◽

Vol 11 (3) ◽

pp. 1326-1333 ◽

Cited By ~ 87

Author(s):

R D Iggo ◽

D J Jamieson ◽

S A MacNeill ◽

J Southgate ◽

J McPheat ◽

...

Keyword(s):

Simian Virus 40 ◽

Rna Helicase ◽

Simian Virus ◽

T Antigen ◽

Functional Roles ◽

Dead Box ◽

Helicase Gene ◽

P68 Rna Helicase ◽

Living Organisms ◽

Yeast Genes

The human p68 protein is an RNA-dependent ATPase and RNA helicase which was first identified because of its immunological cross-reaction with a viral RNA helicase, simian virus 40 large T antigen. It belongs to a recently discovered family of proteins (DEAD box proteins) that share extensive regions of amino acid sequence homology, are ubiquitous in living organisms, and are involved in many aspects of RNA metabolism, including splicing, translation, and ribosome assembly. We have shown by immunofluorescent microscopy that mammalian p68, which is excluded from the nucleoli during interphase, translocates to prenucleolar bodies during telophase. We have cloned 55% identical genes from both Schizosaccharomyces pombe and Saccharomyces cerevisiae and shown that they are essential in both yeasts. The human and yeast genes contain a large intron whose position has been precisely conserved. In S. cerevisiae, the intron is unusual both because of its size and because of its location near the 3' end of the gene. We discuss possible functional roles for such an unusual intron in an RNA helicase gene.

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p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts

Molecular and Cellular Biology ◽

10.1128/mcb.11.3.1326-1333.1991 ◽

1991 ◽

Vol 11 (3) ◽

pp. 1326-1333

Author(s):

R D Iggo ◽

D J Jamieson ◽

S A MacNeill ◽

J Southgate ◽

J McPheat ◽

...

Keyword(s):

Simian Virus 40 ◽

Rna Helicase ◽

Simian Virus ◽

T Antigen ◽

Functional Roles ◽

Dead Box ◽

Helicase Gene ◽

P68 Rna Helicase ◽

Living Organisms ◽

Yeast Genes

The human p68 protein is an RNA-dependent ATPase and RNA helicase which was first identified because of its immunological cross-reaction with a viral RNA helicase, simian virus 40 large T antigen. It belongs to a recently discovered family of proteins (DEAD box proteins) that share extensive regions of amino acid sequence homology, are ubiquitous in living organisms, and are involved in many aspects of RNA metabolism, including splicing, translation, and ribosome assembly. We have shown by immunofluorescent microscopy that mammalian p68, which is excluded from the nucleoli during interphase, translocates to prenucleolar bodies during telophase. We have cloned 55% identical genes from both Schizosaccharomyces pombe and Saccharomyces cerevisiae and shown that they are essential in both yeasts. The human and yeast genes contain a large intron whose position has been precisely conserved. In S. cerevisiae, the intron is unusual both because of its size and because of its location near the 3' end of the gene. We discuss possible functional roles for such an unusual intron in an RNA helicase gene.

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A multigene locus containing the Manx and bobcat genes is required for development of chordate features in the ascidian tadpole larva

Development ◽

10.1242/dev.126.8.1643 ◽

1999 ◽

Vol 126 (8) ◽

pp. 1643-1653 ◽

Cited By ~ 2

Author(s):

B.J. Swalla ◽

M.A. Just ◽

E.L. Pederson ◽

W.R. Jeffery

Keyword(s):

Gene Locus ◽

Single Copy ◽

Rna Helicase ◽

Untranslated Regions ◽

Cdna Clones ◽

Gene Complex ◽

Coding Region ◽

Dead Box ◽

Dorsal Neural Tube ◽

Alternatively Spliced

The Manx gene is required for the development of the tail and other chordate features in the ascidian tadpole larva. To determine the structure of the Manx gene, we isolated and sequenced genomic clones from the tailed ascidian Molgula oculata. The Manx gene contains 9 exons and encodes both major and minor Manx mRNAs, which differ in the length of their 5′ untranslated regions. The coding region of the single-copy bobcat gene, which encodes a DEAD-box RNA helicase, is embedded within the first Manx intron. The organization of the bobcat and Manx transcription units was determined by comparing genomic and cDNA clones. The Manx-bobcat gene locus has an unusual organization in which a non-coding first exon is alternatively spliced at the 5′ end of two different mRNAs. The bobcat and Manx genes are expressed coordinately during oogenesis and embryogenesis, but not during spermatogenesis, in which bobcat mRNA accumulates independently of Manx mRNA. Similar to Manx, zygotic bobcat transcripts accumulate in the embryonic primordia responsible for generating chordate features, including the dorsal neural tube and notochord, are downregulated during embryogenesis in the tailless species Molgula occulta and are upregulated in M. occulta X M. oculata hybrids, which restore these chordate features. Antisense experiments indicate that zygotic bobcat expression is required for development of the same suite of chordate features as Manx. The results show that the Manx-bobcat gene complex has a role in the development of chordate features in ascidian tadpole larvae.

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Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3.

Molecular and Cellular Biology ◽

10.1128/mcb.17.3.1354 ◽

1997 ◽

Vol 17 (3) ◽

pp. 1354-1365 ◽

Cited By ~ 69

Author(s):

P L Weaver ◽

C Sun ◽

T H Chang

Keyword(s):

Saccharomyces Cerevisiae ◽

Slow Growth ◽

Rna Helicase ◽

Amino Terminus ◽

Ribosomal Biogenesis ◽

Rrna Processing ◽

Ribosomal Subunits ◽

Rnase Mrp ◽

Dead Box ◽

Evolutionarily Conserved

In Saccharomyces cerevisiae, ribosomal biogenesis takes place primarily in the nucleolus, in which a single 35S precursor rRNA (pre-rRNA) is first transcribed and sequentially processed into 25S, 5.8S, and 18S mature rRNAs, leading to the formation of the 40S and 60S ribosomal subunits. Although many components involved in this process have been identified, our understanding of this important cellular process remains limited. Here we report that one of the evolutionarily conserved DEAD-box protein genes in yeast, DBP3, is required for optimal ribosomal biogenesis. DBP3 encodes a putative RNA helicase, Dbp3p, of 523 amino acids in length, which bears a highly charged amino terminus consisting of 10 tandem lysine-lysine-X repeats ([KKX] repeats). Disruption of DBP3 is not lethal but yields a slow-growth phenotype. This genetic depletion of Dbp3p results in a deficiency of 60S ribosomal subunits and a delayed synthesis of the mature 25S rRNA, which is caused by a prominent kinetic delay in pre-rRNA processing at site A3 and to a lesser extent at sites A2 and A0. These data suggest that Dbp3p may directly or indirectly facilitate RNase MRP cleavage at site A3. The direct involvement of Dbp3p in ribosomal biogenesis is supported by the finding that Dbp3p is localized predominantly in the nucleolus. In addition, we show that the [KKX] repeats are dispensable for Dbp3p's function in ribosomal biogenesis but are required for its proper localization. The [KKX] repeats thus represent a novel signaling motif for nuclear localization and/or retention.

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