Regulation of phage lambda packaging motor-DNA interactions: Nucleotide independent and dependent gripping and friction
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Curated by eLife
eLife assessment
This fundamental study has major implications that can be paradigm-shifting for our understanding of how the phage lambda DNA motor works and what the precise roles of the TerS and TerL proteins in the motor complex are. The experiments are exceptionally well done, providing compelling evidence for the conclusion of the authors.
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Abstract
Many dsDNA viruses utilize ATP-powered “terminase” motors to package their genomes into procapsid shells. Here we use a single-molecule DNA grip/slip assay with rapid solution exchange to probe effects of nucleotide binding/dissociation in phage lambda motors containing both the large (TerL) and small (TerS) terminase subunits. Both subunits are required for packaging in vivo, but for some viruses (e.g., phages T4, HK97) packaging can be measured in vitro with only the catalytic TerL subunit. TerS facilitates initiation of packaging in vivo, but it has remained unclear if it plays any role during translocation. Surprisingly we measure frequent DNA gripping and high motor-DNA friction even in the absence of nucleotide. Such behavior was not observed in phage T4 motors containing only TerL, for which motor-DNA interactions were measured to be much weaker and significant gripping and friction was only observed with nucleotide present. For the lambda TerL/TerS holoenzyme, binding of nucleotide (ATP analogs or ADP) further increases gripping and friction, indicating there are both nucleotide independent and dependent interactions. Our findings suggest that TerS plays an important role in motor processivity, and that ATP-independent DNA gripping explains pausing observed during lambda packaging. We propose TerS acts as a “sliding clamp” to limit back slipping when TerL loses grip. Additionally, we show that the lambda packaging complex has a “DNA end clamp” mechanism that prevents the viral genome from completely exiting the capsid once packaging has initiated.
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Author Response
Reviewer #1 (Public Review):
Summary:
In this work, the authors use an OT setup to measure the DNA gripping and DNA slipping dynamics of phage lambda terminase motor interaction with DNA. They discover major differences in the dynamics of these two events, in comparison to the phage T4 motor, which they previously investigated. They attribute these differences to the presence of the TerS (small terminase) subunit of the motor complex of phage lambda in addition to the TerL (large terminase) subunit in phage, while in T4 only the TerL subunit is present. By exposing the stalled phage lambda procapsid-DNA complex (stalled with ATP-gammaS) to solutions containing 1) no nucleotide, 2) poorly hydrolyzed ATP, and 3) ADP, they found that the gripping persistence is strongest with ATP, weaker with ADP, and weakest with no …
Author Response
Reviewer #1 (Public Review):
Summary:
In this work, the authors use an OT setup to measure the DNA gripping and DNA slipping dynamics of phage lambda terminase motor interaction with DNA. They discover major differences in the dynamics of these two events, in comparison to the phage T4 motor, which they previously investigated. They attribute these differences to the presence of the TerS (small terminase) subunit of the motor complex of phage lambda in addition to the TerL (large terminase) subunit in phage, while in T4 only the TerL subunit is present. By exposing the stalled phage lambda procapsid-DNA complex (stalled with ATP-gammaS) to solutions containing 1) no nucleotide, 2) poorly hydrolyzed ATP, and 3) ADP, they found that the gripping persistence is strongest with ATP, weaker with ADP, and weakest with no nucleotide. This demonstrates nucleotide-dependent DNA gripping and friction of the motor. However, both persistence of gripping and friction are dramatically stronger than in the T4 TerL motor, due to the presence of the TerS subunit. While TerS was believed to be essential for the initiation of packaging in vivo, its role during DNA translocation was unclear. This study reveals the key role played by TerS in DNA gripping and DNA-motor friction, highlighting its role in DNA translocation where TerS acts as a "sliding clamp".
The study also provides a method to investigate factors affecting the stability of the initiation complex in viral packaging motors.
Strengths:
The experiments are well carried out and the conclusions are justified. These findings are of great significance and advance our understanding of viral motor function in the DNA packaging process and packaging dynamics.
Weaknesses:
While the collected OT data is quantitative, therefore is no further quantitative analysis of the motor packaging dynamics with regard to different motor subunit functions and the presence of nucleotides.
We thank the reviewer for the feedback and we will address the additional recommendations in a revised manuscript. Regarding the comment about quantitative analysis of the packaging dynamics, we emphasize that the present study focuses only on analysis of the grip/slip dynamics in the absence of ATP, since we have already studied the packaging dynamics (DNA translocation dynamics) with ATP in prior studies (refs 34, 35, 39-43). Note that in the present paper we do relate the present studies to these prior studies (such as on p. 7-8 regarding the mechanism of DNA gripping/release during translocation, on p. 8 regarding the finding that the T4 motor (without TerS) exhibits more frequent slipping during packaging, and on p. 8-9 regarding the cause of pauses during packaging).
Reviewer #2 (Public Review):
Summary:
In their paper Rawson et al investigate the nanomechanical properties of the lambda bacteriophage packaging motor in terms of its ability to allow either the slippage of DNA out of the capsid or exerting a grip on the DNA, thereby preventing the slipping. They use a fascinatingly elegant single-molecule biophysics approach, in which gentle forces, generated and controlled by optical tweezers, are used to pull on the DNA molecule about to be packaged by the virus. A microfluidic device is then used to change the nucleotide environment of the reaction, so that the packaging motor can be investigated in its nucleotide-free (apo), ADP-, and non-hydrolyzable ATP-analog-bound states. The authors show that the apo state is dominated by DNA slippage which is impeded by friction. The slippage is stochastically halted by gripping stages. In ADP the DNA-gripped state becomes overwhelming, resulting in a much slowed DNA slippage. In non-hydrolyzable ATP analogs, the DNA slippage is essentially halted and the gripped state becomes exclusive. The authors also show that the slipping and gripping states are controlled not only by nucleotides but also by the force exerted on DNA. Altogether, DNA transport through/by the lambda-phage packaging motor is regulated by nucleotides and mechanical force. Furthermore, the authors document an intriguingly interesting DNA end-clamping mechanism that prevents the DNA from slipping entirely out of the capsid, which would make the packaging process inefficient even on the statistical level. The authors claim that their findings are likely related to the function of a small terminase subunit (TerS) in the lambda-phage motor, which may act as a sliding clamp.
Strengths:
Altogether this is a very elegantly executed, thought-provoking, and interesting work with numerous significant practical implications. The paper is well-written and nicely documented.
Weaknesses:
There are really no major weaknesses, apart from a few minor issues detailed below in my recommendations.
We thank the reviewer for the feedback and we will address the minor issues in a revised manuscript.
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eLife assessment
This fundamental study has major implications that can be paradigm-shifting for our understanding of how the phage lambda DNA motor works and what the precise roles of the TerS and TerL proteins in the motor complex are. The experiments are exceptionally well done, providing compelling evidence for the conclusion of the authors.
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Reviewer #1 (Public Review):
Summary:
In this work, the authors use an OT setup to measure the DNA gripping and DNA slipping dynamics of phage lambda terminase motor interaction with DNA. They discover major differences in the dynamics of these two events, in comparison to the phage T4 motor, which they previously investigated. They attribute these differences to the presence of the TerS (small terminase) subunit of the motor complex of phage lambda in addition to the TerL (large terminase) subunit in phage, while in T4 only the TerL subunit is present. By exposing the stalled phage lambda procapsid-DNA complex (stalled with ATP-gammaS) to solutions containing 1) no nucleotide, 2) poorly hydrolyzed ATP*, and 3) ADP, they found that the gripping persistence is strongest with ATP*, weaker with ADP, and weakest with no nucleotide. This …Reviewer #1 (Public Review):
Summary:
In this work, the authors use an OT setup to measure the DNA gripping and DNA slipping dynamics of phage lambda terminase motor interaction with DNA. They discover major differences in the dynamics of these two events, in comparison to the phage T4 motor, which they previously investigated. They attribute these differences to the presence of the TerS (small terminase) subunit of the motor complex of phage lambda in addition to the TerL (large terminase) subunit in phage, while in T4 only the TerL subunit is present. By exposing the stalled phage lambda procapsid-DNA complex (stalled with ATP-gammaS) to solutions containing 1) no nucleotide, 2) poorly hydrolyzed ATP*, and 3) ADP, they found that the gripping persistence is strongest with ATP*, weaker with ADP, and weakest with no nucleotide. This demonstrates nucleotide-dependent DNA gripping and friction of the motor. However, both persistence of gripping and friction are dramatically stronger than in the T4 TerL motor, due to the presence of the TerS subunit. While TerS was believed to be essential for the initiation of packaging in vivo, its role during DNA translocation was unclear. This study reveals the key role played by TerS in DNA gripping and DNA-motor friction, highlighting its role in DNA translocation where TerS acts as a "sliding clamp".The study also provides a method to investigate factors affecting the stability of the initiation complex in viral packaging motors.
Strengths:
The experiments are well carried out and the conclusions are justified. These findings are of great significance and advance our understanding of viral motor function in the DNA packaging process and packaging dynamics.Weaknesses:
While the collected OT data is quantitative, therefore is no further quantitative analysis of the motor packaging dynamics with regard to different motor subunit functions and the presence of nucleotides. -
Reviewer #2 (Public Review):
Summary:
In their paper Rawson et al investigate the nanomechanical properties of the lambda bacteriophage packaging motor in terms of its ability to allow either the slippage of DNA out of the capsid or exerting a grip on the DNA, thereby preventing the slipping. They use a fascinatingly elegant single-molecule biophysics approach, in which gentle forces, generated and controlled by optical tweezers, are used to pull on the DNA molecule about to be packaged by the virus. A microfluidic device is then used to change the nucleotide environment of the reaction, so that the packaging motor can be investigated in its nucleotide-free (apo), ADP-, and non-hydrolyzable ATP-analog-bound states. The authors show that the apo state is dominated by DNA slippage which is impeded by friction. The slippage is …Reviewer #2 (Public Review):
Summary:
In their paper Rawson et al investigate the nanomechanical properties of the lambda bacteriophage packaging motor in terms of its ability to allow either the slippage of DNA out of the capsid or exerting a grip on the DNA, thereby preventing the slipping. They use a fascinatingly elegant single-molecule biophysics approach, in which gentle forces, generated and controlled by optical tweezers, are used to pull on the DNA molecule about to be packaged by the virus. A microfluidic device is then used to change the nucleotide environment of the reaction, so that the packaging motor can be investigated in its nucleotide-free (apo), ADP-, and non-hydrolyzable ATP-analog-bound states. The authors show that the apo state is dominated by DNA slippage which is impeded by friction. The slippage is stochastically halted by gripping stages. In ADP the DNA-gripped state becomes overwhelming, resulting in a much slowed DNA slippage. In non-hydrolyzable ATP analogs, the DNA slippage is essentially halted and the gripped state becomes exclusive. The authors also show that the slipping and gripping states are controlled not only by nucleotides but also by the force exerted on DNA. Altogether, DNA transport through/by the lambda-phage packaging motor is regulated by nucleotides and mechanical force. Furthermore, the authors document an intriguingly interesting DNA end-clamping mechanism that prevents the DNA from slipping entirely out of the capsid, which would make the packaging process inefficient even on the statistical level. The authors claim that their findings are likely related to the function of a small terminase subunit (TerS) in the lambda-phage motor, which may act as a sliding clamp.Strengths:
Altogether this is a very elegantly executed, thought-provoking, and interesting work with numerous significant practical implications. The paper is well-written and nicely documented.Weaknesses:
There are really no major weaknesses, apart from a few minor issues detailed below in my recommendations. -
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