Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species

View ORCID ProfileGiulia Orazi, View ORCID ProfileAlan J. Collins, Rachel J. Whitaker
doi: https://doi.org/10.1101/2021.12.16.473053
Giulia Orazi
aCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Giulia Orazi
  • For correspondence: gorazi@illinois.edu rwhitakr@illinois.edu
Alan J. Collins
aCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alan J. Collins
Rachel J. Whitaker
aCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
bDepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: gorazi@illinois.edu rwhitakr@illinois.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

ABSTRACT

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one other, primarily via transformation and homologous recombination, and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from other prophages and MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus.

IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus, and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) have been identified and characterized in Neisseria species. In this study, we identified a large number of candidate phages integrated within the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Figures 7 and 8 were revised.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted February 03, 2022.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species
Giulia Orazi, Alan J. Collins, Rachel J. Whitaker
bioRxiv 2021.12.16.473053; doi: https://doi.org/10.1101/2021.12.16.473053
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species
Giulia Orazi, Alan J. Collins, Rachel J. Whitaker
bioRxiv 2021.12.16.473053; doi: https://doi.org/10.1101/2021.12.16.473053

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3700)
  • Biochemistry (7818)
  • Bioengineering (5692)
  • Bioinformatics (21335)
  • Biophysics (10601)
  • Cancer Biology (8202)
  • Cell Biology (11969)
  • Clinical Trials (138)
  • Developmental Biology (6783)
  • Ecology (10424)
  • Epidemiology (2065)
  • Evolutionary Biology (13905)
  • Genetics (9729)
  • Genomics (13104)
  • Immunology (8168)
  • Microbiology (20064)
  • Molecular Biology (7875)
  • Neuroscience (43163)
  • Paleontology (321)
  • Pathology (1281)
  • Pharmacology and Toxicology (2266)
  • Physiology (3362)
  • Plant Biology (7250)
  • Scientific Communication and Education (1316)
  • Synthetic Biology (2012)
  • Systems Biology (5549)
  • Zoology (1133)