DbpA is a region‐specific RNA helicase

Moore, Anthony F. T.; Gentry, Riley C.; Koculi, Eda

doi:10.1002/bip.23001

Cited by 6 publications

(14 citation statements)

References 38 publications

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“…Due to this multiplicity in the interactions between the separate regions, the structural importance of the L2 linker had escaped attention. Interestingly, an elongation of the L2 linker by 23 unstructured amino acids only slightly reduced the helicase activity of DbpA ( 24 ). This can be explained by our finding that the L2 linker is only partially folded ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Despite the known interaction between HP92 of the 23S rRNA and the RRM the precise role of DbpA during ribosome maturation remains unclear ( 18 , 24 ). In that light, our results provide additional insights and identify the ssRNA region preceding H90 (nt ∼2,501 to 2,508) as the binding site for the helicase core.…”

Section: Discussionmentioning

confidence: 99%

“…The spacer length (3 or 11 nt) depends on whether the duplex is located 5′ or 3′ to HP92, a finding that can be explained by a fixed orientation of the RNA substrate with respect to the helicase core (16). On the other hand, there is also support for the structural independence of core and RRM domain for YxiN and DbpA based on smallangle X-ray scattering data (23) and enzymatic experiments for a DbpA mutant with an elongated L2 linker (24). Single-molecule fluorescence resonance energy transfer (smFRET) experiments indicate a repositioning of the RRM relative to the core domains upon binding of HP92 (21,25).…”

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confidence: 94%

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Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome

Wurm

Glowacz

Sprangers

2021

Proc. Natl. Acad. Sci. U.S.A.

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The adenosine triphosphate (ATP)-dependent DEAD-box RNA helicase DbpA from Escherichia coli functions in ribosome biogenesis. DbpA is targeted to the nascent 50S subunit by an ancillary, carboxyl-terminal RNA recognition motif (RRM) that specifically binds to hairpin 92 (HP92) of the 23S ribosomal RNA (rRNA). The interaction between HP92 and the RRM is required for the helicase activity of the RecA-like core domains of DbpA. Here, we elucidate the structural basis by which DbpA activity is endorsed when the enzyme interacts with the maturing ribosome. We used nuclear magnetic resonance (NMR) spectroscopy to show that the RRM and the carboxyl-terminal RecA-like domain tightly interact. This orients HP92 such that this RNA hairpin can form electrostatic interactions with a positively charged patch in the N-terminal RecA-like domain. Consequently, the enzyme can stably adopt the catalytically important, closed conformation. The substrate binding mode in this complex reveals that a region 5′ to helix 90 in the maturing ribosome is specifically targeted by DbpA. Finally, our results indicate that the ribosome maturation defects induced by a dominant negative DbpA mutation are caused by a delayed dissociation of DbpA from the nascent ribosome. Taken together, our findings provide unique insights into the important regulatory mechanism that modulates the activity of DbpA.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 94%

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Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome

Wurm

Glowacz

Sprangers

2021

Proc. Natl. Acad. Sci. U.S.A.

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“… 3 Based on their in vitro RNA unwinding activity, many DEAD-box proteins are believed to serve as RNA chaperones. 9 − 12 The investigations of how the catalytic activity of DDX3X is regulated is important both for the understanding of its precise role in important cellular processes and for the design and development of potential therapeutic agents that target the DDX3X protein.…”

Section: Introductionmentioning

confidence: 99%

Interactions of the C-Terminal Truncated DEAD-Box Protein DDX3X With RNA and Nucleotide Substrates

2021

Self Cite

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DDX3X is a human DEAD-box RNA helicase implicated in many important cellular processes. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. The ancillary domains of DEAD-box RNA helicases have been shown to modulate their interactions with RNA and nucleotide substrates. Here, with the goal of understanding the role of N- and C-terminal domains of DDX3X on the DDX3X catalytic activity, we examined the interactions of RNA substrates and nucleotides with a DDX3X construct possessing the entire N-terminal domain and the catalytic core but lacking 80 residues from its C-terminal domain. Next, we compared our results with previously investigated DDX3X constructs. Our data show that the C-terminal truncated DDX3X does not bind to a blunt-ended double-helix RNA. This conclusion agrees with the data obtained on the wild-type LAF-1 protein, the DDX3X ortholog in Caenorhabditis elegans , and disagrees with the data obtained on the minimally active DDX3X construct, which misses 131 residues from its N-terminal domain and 80 residues from its C-terminal domain. The minimally active DDX3X construct was able to bind to the blunt-ended RNA construct. Combined, the previous studies and our results indicate that the N-terminal of DDX3X modulates the choice of DDX3X–RNA substrates. Furthermore, a previous study showed that the wild-type DDX3X construct hydrolyzes all four nucleotides and deoxynucleotides, both in the presence and absence of RNA. The C-terminal truncated DDX3X investigated here hydrolyzes only cytidine triphosphate (CTP) in the absence of RNA and CTP, adenosine triphosphate (ATP), and deoxyribose adenosine triphosphate (dATP) in the presence of RNA. Hence, the C-terminal truncated DDX3X has a more stringent nucleotide specificity than wild-type DDX3X.

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“…DNA‐binding protein A (dbpA)/ZO‐1‐associated nucleic acid‐binding protein is encoded by the gene Ybx3 (Frankel et al, 2005), which is a member of the cold shock protein superfamily containing a highly conserved nucleic acid‐binding motif called the cold shock domain (Li et al, 1997). The conserved cold shock domain enables dbpA to directly or indirectly bind with DNA and RNA, acting as a transcription and translation factor (Moore, Gentry, & Koculi, 2017). It has been reported that dbpA bound and inhibited the expression of cyclin‐dependent kinase 5 (Cdk5), meanwhile, dbpA protein interacts with the cyclin‐dependent kinase 4 (Cdk4) and suppressed the activity of Cdk4/cyclin D1 enzyme (Moorthamer, Zumstein‐Mecker, & Chaudhuri, 1999).…”

Section: Introductionmentioning

confidence: 99%

Knockdown of DNA‐binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/β‐catenin/Chk1 pathway

Tong

Wang

et al. 2020

Cell Biology International

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DNA‐binding protein A (dbpA) is reported to be upregulated in many cancers and associated with tumor progress. The present study aimed to investigate the role of dbpA in 5‐fluorouracil (5‐FU)‐resistant and oxaliplatin (L‐OHP)‐resistant colorectal cancer (CRC) cells. We found that 5‐FU and L‐OPH treatment promoted the expression of dbpA. Enhanced dbpA promoted the drug resistance of SW620 cells to 5‐FU and L‐OHP. DbpA knockdown inhibited cell proliferation, induced cell apoptosis, and cell cycle arrested in SW620/5‐FU and SW620/L‐OHP cells. Besides, dbpA short hairpin RNA (shRNA) enhanced the cytotoxicity of 5‐FU and L‐OHP to SW620/5‐FU and SW620/L‐OHP cells. Meanwhile, dbpA shRNA inhibited the activation of the Wnt/β‐catenin pathway that induced by 5‐FU stimulation in SW620/5‐FU cells. Activation of the Wnt/β‐catenin pathway or overexpression of checkpoint kinase 1 (Chk1) abrogated the promoting effect of dbpA downregulation on 5‐FU sensitivity of CRC cells. Importantly, downregulation of dbpA suppressed tumor growth and promoted CRC cells sensitivity to 5‐FU in vivo. Our study indicated that the knockdown of dbpA enhanced the sensitivity of CRC cells to 5‐FU via Wnt/β‐catenin/Chk1 pathway, and DbpA may be a potential therapeutic target to sensitize drug resistance CRC to 5‐FU and L‐OHP.

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DbpA is a region‐specific RNA helicase

Cited by 6 publications

References 38 publications

Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome

Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome

Interactions of the C-Terminal Truncated DEAD-Box Protein DDX3X With RNA and Nucleotide Substrates

Knockdown of DNA‐binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/β‐catenin/Chk1 pathway

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