ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor

Cai, Rujie; Price, Ian R.; Ding, Fang; Wu, Feifei; Chen, Ting; Zhang, Yunlong; Liu, Guangfeng; Jardine, Paul J.; Lu, Changrui; Ke, Ailong

doi:10.1093/nar/gkz692

Cited by 10 publications

(13 citation statements)

References 60 publications

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“…Furthermore, protein factors may also impact bcd quaternary structure. This multimerization mechanism and the ability to form more than one type of multimer is reminiscent of the bacteriophage ø29 prohead RNA (pRNA), discussed below [ 110 , 111 , 112 , 113 ] ( Figure 2 c).…”

Section: Dimerization-mediated Mrna Localizationmentioning

confidence: 99%

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Bou‐Nader

Zhang

2020

Molecules

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In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing (“kissing”) interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.

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Section: Dimerization-mediated Mrna Localizationmentioning

confidence: 99%

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Bou‐Nader

Zhang

2020

Molecules

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“…THF-II riboswitch has a relatively simple secondary structure compared to the first THF riboswitch, THF-I, which is similar to the SAM-VI riboswitch class [ 23 ]. Previous studies showed that ligand binding usually causes global conformation changes, usually involving alternative base paring, as shown by SAXS scattering and/or chemical probing data [ 45 , 46 , 47 , 48 , 49 ]. Generally, apo RNA has usually a larger Rg compared to the ligand-bound RNA.…”

Section: Discussionmentioning

confidence: 99%

The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes

Liu

Zhang

Chen

et al. 2022

IJMS

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Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2′-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.

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“…To begin to design tRNA-antiterminator fusion for crystallization, we first sought to minimize the structure. Our starting point was the full-length antiterminator from the G. kaustophilus tRNA Gly T-box riboswitch that has been the model for most of our previous work [5,[30][31][32]49,59]. The G. kaustophilus antiterminator resembles canonical antiterminators with a proximal helix, broken by a single-stranded bulge that contains the tRNA UCCA tail recognition sequence, UGGA and a distal helix capped by a loop.…”

Section: Challenges In Crystallizing the Trna/t-box Antiterminator Co...mentioning

confidence: 99%

“…Our choice to use tRNA as a crystallization chaperone is based on prior knowledge that tRNA folds robustly strong evolutionary pressure to conserve its structure; the inspection of other tRNA crystal structures revealed strong and predictable crystal contacts and engineered tRNA fusions have shown drastically improved folding and stability when expressed in vivo [26][27][28][29]. We have previously employed tRNA fusions to determine the structure prohead RNA (pRNA) domain II structure [30,31]. We hypothesized that we could use an engineered tRNA scaffold to assist the crystallization of the usually dynamic T-box antiterminator and to potentially select tRNA acceptorantiterminator interactions in crystals.…”

Section: Introductionmentioning

confidence: 99%

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch

Grigg

Price

2022

Crystals

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RNAs are prone to misfolding and are often more challenging to crystallize and phase than proteins. Here, we demonstrate that tRNA fusion can streamline the crystallization and structure determination of target RNA molecules. This strategy was applied to the T-box riboswitch system to capture a dynamic interaction between the tRNA 3′-UCCA tail and the T-box antiterminator, which senses aminoacylation. We fused the T-box antiterminator domain to the tRNA anticodon arm to capture the intended interaction through crystal packing. This approach drastically improved the probability of crystallization and successful phasing. Multiple structure snapshots captured the antiterminator loop in an open conformation with some resemblance to that observed in the recent co-crystal structures of the full-length T box riboswitch–tRNA complex, which contrasts the resting, closed conformation antiterminator observed in an earlier NMR study. The anticipated tRNA acceptor–antiterminator interaction was captured in a low-resolution crystal structure. These structures combined with our previous success using prohead RNA–tRNA fusions demonstrates tRNA fusion is a powerful method in RNA structure determination.

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ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor

Cited by 10 publications

References 60 publications

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch

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