PacBio amplicon sequencing method to measure pilin antigenic variation frequencies of Neisseria gonorrhoeae

Egon A. Ozer, Lauren L. Prister, Shaohui Yin, Billy H. Ward, Stanimir Ivanov, H. Steven Seifert*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection.

Original languageEnglish (US)
Article numbere00562-19
JournalmSphere
Volume4
Issue number5
DOIs
StatePublished - Jan 1 2019

Fingerprint

Fimbriae Proteins
Antigenic Variation
Neisseria gonorrhoeae
Genes
Gene Conversion
Software
Macrophages
Infection

Keywords

  • antigenic variation, Pacific Biosciences sequencing, amplicon sequencing, gene diversification

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Ozer, Egon A. ; Prister, Lauren L. ; Yin, Shaohui ; Ward, Billy H. ; Ivanov, Stanimir ; Seifert, H. Steven. / PacBio amplicon sequencing method to measure pilin antigenic variation frequencies of Neisseria gonorrhoeae. In: mSphere. 2019 ; Vol. 4, No. 5.
@article{dc5d8c649ed940498327b4deee510a1a,
title = "PacBio amplicon sequencing method to measure pilin antigenic variation frequencies of Neisseria gonorrhoeae",
abstract = "Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection.",
keywords = "antigenic variation, Pacific Biosciences sequencing, amplicon sequencing, gene diversification",
author = "Ozer, {Egon A.} and Prister, {Lauren L.} and Shaohui Yin and Ward, {Billy H.} and Stanimir Ivanov and Seifert, {H. Steven}",
year = "2019",
month = "1",
day = "1",
doi = "10.1128/mSphere.00562-19",
language = "English (US)",
volume = "4",
journal = "mSphere",
issn = "2379-5042",
publisher = "American Society for Microbiology",
number = "5",

}

PacBio amplicon sequencing method to measure pilin antigenic variation frequencies of Neisseria gonorrhoeae. / Ozer, Egon A.; Prister, Lauren L.; Yin, Shaohui; Ward, Billy H.; Ivanov, Stanimir; Seifert, H. Steven.

In: mSphere, Vol. 4, No. 5, e00562-19, 01.01.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - PacBio amplicon sequencing method to measure pilin antigenic variation frequencies of Neisseria gonorrhoeae

AU - Ozer, Egon A.

AU - Prister, Lauren L.

AU - Yin, Shaohui

AU - Ward, Billy H.

AU - Ivanov, Stanimir

AU - Seifert, H. Steven

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection.

AB - Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection.

KW - antigenic variation, Pacific Biosciences sequencing, amplicon sequencing, gene diversification

UR - http://www.scopus.com/inward/record.url?scp=85072923199&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85072923199&partnerID=8YFLogxK

U2 - 10.1128/mSphere.00562-19

DO - 10.1128/mSphere.00562-19

M3 - Article

C2 - 31578246

AN - SCOPUS:85072923199

VL - 4

JO - mSphere

JF - mSphere

SN - 2379-5042

IS - 5

M1 - e00562-19

ER -