High resolution structure of hexameric herpesvirus DNA-packaging motor elucidates revolving mechanism and ends 20-year fervent debate

Guo, Peixuan

doi:10.1007/s13238-020-00714-w

Cited by 7 publications

(5 citation statements)

References 33 publications

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“…DNA packaging is characteristic of double-stranded DNA (dsDNA) viruses including phage [ 36 ]. This mechanism is composed of two key components including the portal protein, which affects the procapsid assembly and provides an interface for tail attachment or assembly, and the terminase influencing the phage genome packing into the phage head.…”

Section: Resultsmentioning

confidence: 99%

Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

et al. 2021

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Vibrio campbellii is an emerging aquaculture pathogen that causes luminous vibriosis in farmed shrimp. Although prophages in various aquaculture pathogens have been widely reported, there is still limited knowledge regarding prophages in the genome of pathogenic V. campbellii. Here, we describe the full-genome sequence of a prophage named HY01, induced from the emerging shrimp pathogen V. campbellii HY01. The phage HY01 was induced by mitomycin C and was morphologically characterized as long tailed phage. V. campbellii phage HY01 is composed of 41,772 bp of dsDNA with a G+C content of 47.45%. A total of 60 open reading frames (ORFs) were identified, of which 31 could be predicted for their biological functions. Twenty seven out of 31 predicted protein coding regions were matched with several encoded proteins of various Enterobacteriaceae, Pseudomonadaceae, Vibrionaceae, and other phages of Gram-negative bacteria. Interestingly, the comparative genome analysis revealed that the phage HY01 was only distantly related to Vibrio phage Va_PF430-3_p42 of fish pathogen V. anguillarum but differed in genomic size and gene organization. The phylogenetic tree placed the phage together with Siphoviridae family. Additionally, a survey of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers revealed two matching sequences between phage HY01 genome and viral spacer sequence of Vibrio spp. The spacer results combined with the synteny results suggest that the evolution of V. campbellii phage HY01 is driven by the horizontal genetic exchange between bacterial families belonging to the class of Gammaproteobacteria.

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Section: Resultsmentioning

confidence: 99%

Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

et al. 2021

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“…[3][4][5] Such an action offers several advantages to the revolution mechanism compared with the rotation mechanism, including avoiding supercoiling that requires the work of topoisomerase enzymes to correct. [6,7] The double-strand (ds)DNA-packaging motors of prokaryotic cells and their viruses that pack the genomes against an accumulating internal pressure in an entropically unfavorable manner have evolved common structures and mechanisms. [8][9][10][11] Among these, the motor of bacteriophage phi29 was the first to be constructed as a defined in vitro system.…”

Section: Introductionmentioning

confidence: 99%

“…[ 3–5 ] Such an action offers several advantages to the revolution mechanism compared with the rotation mechanism, including avoiding supercoiling that requires the work of topoisomerase enzymes to correct. [ 6,7 ]…”

Section: Introductionmentioning

confidence: 99%

Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces

2023

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Investigations of the parallel architectures of biomotors in both prokaryotic and eukaryotic systems suggest a similar revolving mechanism in the use of ATP to drive translocation of the lengthy double‐stranded (ds)DNA genomes. This mechanism is exemplified by the dsDNA packaging motor of bacteriophage phi29 that operates through revolving but not rotating dsDNA to “Push through a one‐way valve”. This unique and novel revolving mechanism discovered in phi29 DNA packaging motor was recently reported in other systems including the dsDNA packaging motor of herpesvirus, the dsDNA ejecting motor of bacteriophage T7, the plasmid conjugation machine TraB in Streptomyces, the dsDNA translocase FtsK of gram‐negative bacteria, and the genome‐packaging motor in mimivirus. These motors exhibit an asymmetrical hexameric structure for transporting the genome via an inch‐worm sequential action. This review intends to delineate the revolving mechanism from a perspective of conformational changes and electrostatic interactions. In phi29, the positively charged residues Arg‐Lys‐Arg in the N‐terminus of the connector bind the negatively charged interlocking domain of pRNA. ATP binding to an ATPase subunit induces the closed conformation of the ATPase. The ATPase associates with an adjacent subunit to form a dimer facilitated by the positively charged arginine finger. The ATP‐binding induces a positive charging on its DNA binding surface via an allostery mechanism and thus the higher affinity for the negatively charged dsDNA. ATP hydrolysis induces an expanded conformation of the ATPase with a lower affinity for dsDNA due to the change of the surface charge, but the (ADP+Pi)‐bound subunit in the dimer undergoes a conformational change that repels dsDNA. The positively charged lysine rings of the connector attract dsDNA stepwise and periodically to keep its revolving motion along the channel wall, thus maintaining the one‐way translocation of dsDNA without reversal and sliding out. The finding of the presence of the asymmetrical hexameric architectures of many ATPases that use the revolving mechanism may provide insights into the understanding of translocation of the gigantic genomes including chromosomes in complicated systems without coiling and tangling to speed up dsDNA translocation and save energy.

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“…The gene product 16 (gp16) of bacteriophage phi29 has long been employed to study the sequential process in ring-shaped ATPases (Figure ). ,, Based on the sequence and structural analysis, the R-finger of gp16 was determined to be Arg146, after the α4 helix. WA and WB residues are also located near the R-finger with a sequence of GXXGXGKS/T 8 and hhhhDE, respectively.…”

Section: Introductionmentioning

confidence: 99%

Identification of Arginine Finger as the Starter of the Biomimetic Motor in Driving Double-Stranded DNA

Liang

Guo

2021

ACS Nano

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Nanomotors in nanotechnology may be as important as cars in daily life. Biomotors are nanoscale machines ubiquitous in living systems to carry out ATP-driven activities such as walking, breathing, blinking, mitosis, replication, transcription, and trafficking. The sequential action in an asymmetrical hexamer by a revolving mechanism has been confirmed in dsDNA packaging motors of phi29, herpesviruses, bacterial dsDNA translocase FtsK, and Streptomyces TraB for conjugative dsDNA transfer. These elaborate, delicate, and exquisite ring structures have inspired scientists to design biomimetics in nanotechnology. Many multisubunit ATPase rings generate force via sequential action of multiple modules, such as the Walker A, Walker B, P-loop, arginine finger, sensors, and lid. The chemical to mechanical energy conversion usually takes place in sequential order. It is commonly believed that ATP binding triggers such conversion, but how the multimodule motor starts the sequential process has not been explicitly investigated. Identification of the starter is of great significance for biomimetic motor fabrication. Here, we report that the arginine finger is the starter of the motor. Only one amino acid residue change in the arginine finger led to the impediment and elimination of all following steps. Without the arginine finger, the motor failed to assemble, bind ATP, recruit DNA, or hydrolyze ATP and was eventually unable to package DNA. However, the loss of ATPase activity due to an inactive arginine finger can be rescued by an arginine finger from the adjacent subunit of Walker A mutant through trans-complementation. Taken together, we demonstrate that the formation of dimers triggered by the arginine finger initiates the motor action rather than the general belief of initiation by ATP binding.

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High resolution structure of hexameric herpesvirus DNA-packaging motor elucidates revolving mechanism and ends 20-year fervent debate

Cited by 7 publications

References 33 publications

Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces

Identification of Arginine Finger as the Starter of the Biomimetic Motor in Driving Double-Stranded DNA

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