Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.

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Dual-level autoregulation of the E. coli DeaD RNA helicase via mRNA stability and Rho-dependent transcription termination

10.1101/2020.04.19.049098 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sandeep Ojha ◽

Chaitanya Jain

Keyword(s):

Mrna Stability ◽

Transcription Termination ◽

Rna Helicase ◽

Feedback Mechanism ◽

Helicase Activity ◽

Coding Region ◽

E Coli ◽

Negative Feedback Mechanism ◽

Dead Box ◽

Rna Remodeling

ABSTRACTDEAD-box proteins (DBPs) are RNA remodeling factors associated with RNA helicase activity that are found in nearly all organisms. Despite extensive studies on the mechanisms used by DBPs to regulate RNA function, very little is known about how DBPs themselves are regulated. In this work, we have analyzed the expression and regulation of DeaD/CsdA, the largest of the DBPs in Escherichia coli (E. coli). We show that deaD transcription initiates 838 nts upstream of the start of the coding region. We have also found that DeaD is autoregulated through a negative feedback mechanism that operates both at the level of mRNA stability and Rho-dependent transcription termination, and this regulation is dependent upon the 5’ untranslated region (5’ UTR). These findings suggest that DeaD might be regulating the conformation of its own mRNA through its RNA helicase activity to facilitate ribonuclease and Rho access to its 5’UTR.

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Faculty Opinions recommendation of The DEAD-box RNA helicase Vad1 regulates multiple virulence-associated genes in Cryptococcus neoformans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1024704.293704 ◽

2005 ◽

Author(s):

Herb Arst

Keyword(s):

Cryptococcus Neoformans ◽

Rna Helicase ◽

Dead Box ◽

The Dead

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Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

Journal of Bacteriology ◽

10.1128/jb.00135-17 ◽

2017 ◽

Vol 199 (13) ◽

Cited By ~ 15

Author(s):

Angel A. Aguirre ◽

Alexandre M. Vicente ◽

Steven W. Hardwick ◽

Daniela M. Alvelos ◽

Ricardo R. Mazzon ◽

...

Keyword(s):

Low Temperature ◽

Caulobacter Crescentus ◽

Immunoblot Analysis ◽

Rna Helicase ◽

Rnase E ◽

Rna Helicases ◽

Content Type ◽

Dead Box ◽

Rna Degradosome ◽

The Dead

ABSTRACT In diverse bacterial lineages, multienzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic Gram-negative bacterium Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below those optimum for growth. Phenotype analyses of rhlE, rhlB, and rhlE rhlB mutant strains show that RhlE is important for cell fitness at low temperature and its role may not be substituted by RhlB. Transcriptional and translational fusions of rhlE to the lacZ reporter gene and immunoblot analysis of an epitope-tagged RhlE indicate that its expression is induced upon temperature decrease, mainly through posttranscriptional regulation. RNase E pulldown assays show that other proteins, including the transcription termination factor Rho, a second DEAD-box RNA helicase, and ribosomal protein S1, also associate with the degradosome at low temperature. The results suggest that the RNA degradosome assembly can be remodeled with environmental change to alter its repertoire of helicases and other accessory proteins. IMPORTANCE DEAD-box RNA helicases are often present in the RNA degradosome complex, helping unwind secondary structures to facilitate degradation. Caulobacter crescentus is an interesting organism to investigate degradosome remodeling with change in temperature, because it thrives in freshwater bodies and withstands low temperature. In this study, we show that at low temperature, the cold-induced DEAD-box RNA helicase RhlE is recruited to the RNA degradosome, along with other helicases and the Rho protein. RhlE is essential for bacterial fitness at low temperature, and its function may not be complemented by RhlB, although RhlE is able to complement for rhlB loss. These results suggest that RhlE has a specific role in the degradosome at low temperature, potentially improving adaptation to this condition.

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The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR

Antiviral Research ◽

10.1016/j.antiviral.2013.09.002 ◽

2013 ◽

Vol 100 (2) ◽

pp. 487-499 ◽

Cited By ~ 33

Author(s):

Chen Li ◽

Ling-ling Ge ◽

Peng-peng Li ◽

Yue Wang ◽

Ming-xia Sun ◽

...

Keyword(s):

Japanese Encephalitis Virus ◽

Virus Replication ◽

Japanese Encephalitis ◽

Rna Helicase ◽

Encephalitis Virus ◽

Positive Regulator ◽

Dead Box ◽

The Dead

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Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.97.24.13080 ◽

2000 ◽

Vol 97 (24) ◽

pp. 13080-13085 ◽

Cited By ~ 187

Author(s):

J. M. Caruthers ◽

E. R. Johnson ◽

D. B. McKay

Keyword(s):

Crystal Structure ◽

Rna Helicase ◽

Initiation Factor ◽

Dead Box

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The embryonic RNA helicase gene (ERH): a new member of the DEAD box family of RNA helicases

Biochemical Journal ◽

10.1042/bj3080839 ◽

1995 ◽

Vol 308 (3) ◽

pp. 839-846 ◽

Cited By ~ 15

Author(s):

J Sowden ◽

W Putt ◽

K Morrison ◽

R Beddington ◽

Y Edwards

Keyword(s):

Expression Profile ◽

Sequence Similarity ◽

Rna Helicase ◽

Chromosome 1 ◽

Rna Helicases ◽

High Sequence Similarity ◽

Dead Box ◽

Isolation And Characterization ◽

Helicase Gene ◽

The Dead

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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