The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity

Claudia J. Barahona, L. Emilia Basantes, Kassidy J. Tompkins, Desirae M. Heitman, Barbara I. Chukwu, Juan Sanchez, Jonathan L. Sanchez, Niloofar Ghadirian, Chad K. Park, Nancy C Horton

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.

Original languageEnglish (US)
JournalJournal of virology
Volume93
Issue number5
DOIs
StatePublished - Mar 1 2019

Fingerprint

DNA Cleavage
Enzymes
enzymes
DNA
Virus Diseases
Streptomyces griseus
Type II Site Specific Deoxyribonucleases
enzyme activation
Bacteria
bacteria
restriction endonucleases
Enzyme Activation
infection
bacteriophages
Bacteriophages
Antiviral Agents
cells
enzyme activity
mutation
kinetics

Keywords

  • antiphage mechanism
  • enzyme kinetics
  • enzyme mechanism
  • filament forming enzymes
  • kinetic simulations
  • phage infection
  • protein structure-function
  • restriction endonuclease

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

The Need for Speed : Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. / Barahona, Claudia J.; Basantes, L. Emilia; Tompkins, Kassidy J.; Heitman, Desirae M.; Chukwu, Barbara I.; Sanchez, Juan; Sanchez, Jonathan L.; Ghadirian, Niloofar; Park, Chad K.; Horton, Nancy C.

In: Journal of virology, Vol. 93, No. 5, 01.03.2019.

Research output: Contribution to journalArticle

Barahona, CJ, Basantes, LE, Tompkins, KJ, Heitman, DM, Chukwu, BI, Sanchez, J, Sanchez, JL, Ghadirian, N, Park, CK & Horton, NC 2019, 'The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity', Journal of virology, vol. 93, no. 5. https://doi.org/10.1128/JVI.01647-18
Barahona, Claudia J. ; Basantes, L. Emilia ; Tompkins, Kassidy J. ; Heitman, Desirae M. ; Chukwu, Barbara I. ; Sanchez, Juan ; Sanchez, Jonathan L. ; Ghadirian, Niloofar ; Park, Chad K. ; Horton, Nancy C. / The Need for Speed : Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. In: Journal of virology. 2019 ; Vol. 93, No. 5.
@article{bc1126110f7e4456b45a793b5e2c8d56,
title = "The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity",
abstract = "Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.",
keywords = "antiphage mechanism, enzyme kinetics, enzyme mechanism, filament forming enzymes, kinetic simulations, phage infection, protein structure-function, restriction endonuclease",
author = "Barahona, {Claudia J.} and Basantes, {L. Emilia} and Tompkins, {Kassidy J.} and Heitman, {Desirae M.} and Chukwu, {Barbara I.} and Juan Sanchez and Sanchez, {Jonathan L.} and Niloofar Ghadirian and Park, {Chad K.} and Horton, {Nancy C}",
year = "2019",
month = "3",
day = "1",
doi = "10.1128/JVI.01647-18",
language = "English (US)",
volume = "93",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "5",

}

TY - JOUR

T1 - The Need for Speed

T2 - Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity

AU - Barahona, Claudia J.

AU - Basantes, L. Emilia

AU - Tompkins, Kassidy J.

AU - Heitman, Desirae M.

AU - Chukwu, Barbara I.

AU - Sanchez, Juan

AU - Sanchez, Jonathan L.

AU - Ghadirian, Niloofar

AU - Park, Chad K.

AU - Horton, Nancy C

PY - 2019/3/1

Y1 - 2019/3/1

N2 - Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.

AB - Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.

KW - antiphage mechanism

KW - enzyme kinetics

KW - enzyme mechanism

KW - filament forming enzymes

KW - kinetic simulations

KW - phage infection

KW - protein structure-function

KW - restriction endonuclease

UR - http://www.scopus.com/inward/record.url?scp=85061869658&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85061869658&partnerID=8YFLogxK

U2 - 10.1128/JVI.01647-18

DO - 10.1128/JVI.01647-18

M3 - Article

C2 - 30518649

AN - SCOPUS:85061869658

VL - 93

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 5

ER -