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Title: Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species

Abstract

The Francisella genus includes several recognized species, additional potential species, and other representatives that inhabit a range of incredibly diverse ecological niches, but are not closely related to the named species. Francisella species have been obtained from a wide variety of clinical and environmental sources; documented species include highly virulent human and animal pathogens, fish pathogens, opportunistic human pathogens, tick endosymbionts, and free-living isolates inhabiting brackish water. While more than 120 Francisella genomes have been sequenced to date, only a few contain plasmids, and most of these appear to be cryptic, with unknown benefit to the host cell. We have identified several putative cryptic plasmids in the sequenced genomes of three Francisella novicida and F. novicida-like strains (TX07-6608, AZ06-7470, DPG_3A-IS) and two new Francisella species (F. frigiditurris CA97-1460 and F. opportunistica MA06-7296). These plasmids were compared to each other and to previously identified plasmids from other Francisella species. Some of the plasmids encoded functions potentially involved in replication, conjugal transfer and partitioning, environmental survival (transcriptional regulation, signaling, metabolism), and hypothetical proteins with no assignable functions. In conclusion, genomic and phylogenetic comparisons of these new plasmids to the other known Francisella plasmids revealed some similarities that add to our understanding ofmore » the evolutionary relationships among the diverse Francisella species.« less

Authors:
ORCiD logo [1];  [2];  [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. US Food and Drug Administration, Silver Spring, MD (United States). Office of Laboratory Science and Safety
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; US Department of Homeland Security (DHS)
OSTI Identifier:
1394974
Report Number(s):
LA-UR-17-23160
Journal ID: ISSN 1932-6203
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 12; Journal Issue: 8; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biological Science

Citation Formats

Challacombe, Jean Faust, Pillai, Segaran, and Kuske, Cheryl R. Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species. United States: N. p., 2017. Web. doi:10.1371/journal.pone.0183554.
Challacombe, Jean Faust, Pillai, Segaran, & Kuske, Cheryl R. Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species. United States. doi:10.1371/journal.pone.0183554.
Challacombe, Jean Faust, Pillai, Segaran, and Kuske, Cheryl R. Thu . "Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species". United States. doi:10.1371/journal.pone.0183554. https://www.osti.gov/servlets/purl/1394974.
@article{osti_1394974,
title = {Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species},
author = {Challacombe, Jean Faust and Pillai, Segaran and Kuske, Cheryl R.},
abstractNote = {The Francisella genus includes several recognized species, additional potential species, and other representatives that inhabit a range of incredibly diverse ecological niches, but are not closely related to the named species. Francisella species have been obtained from a wide variety of clinical and environmental sources; documented species include highly virulent human and animal pathogens, fish pathogens, opportunistic human pathogens, tick endosymbionts, and free-living isolates inhabiting brackish water. While more than 120 Francisella genomes have been sequenced to date, only a few contain plasmids, and most of these appear to be cryptic, with unknown benefit to the host cell. We have identified several putative cryptic plasmids in the sequenced genomes of three Francisella novicida and F. novicida-like strains (TX07-6608, AZ06-7470, DPG_3A-IS) and two new Francisella species (F. frigiditurris CA97-1460 and F. opportunistica MA06-7296). These plasmids were compared to each other and to previously identified plasmids from other Francisella species. Some of the plasmids encoded functions potentially involved in replication, conjugal transfer and partitioning, environmental survival (transcriptional regulation, signaling, metabolism), and hypothetical proteins with no assignable functions. In conclusion, genomic and phylogenetic comparisons of these new plasmids to the other known Francisella plasmids revealed some similarities that add to our understanding of the evolutionary relationships among the diverse Francisella species.},
doi = {10.1371/journal.pone.0183554},
journal = {PLoS ONE},
number = 8,
volume = 12,
place = {United States},
year = {2017},
month = {8}
}

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Works referenced in this record:

Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032 T , Isolated from Air-Conditioning Systems in China
journal, March 2015

  • Svensson, Daniel; Öhrman, Caroline; Bäckman, Stina
  • Genome Announcements, Vol. 3, Issue 2
  • DOI: 10.1128/genomeA.00024-15

Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS
journal, September 2015

  • Johnson, Shannon L.; Minogue, Timothy D.; Daligault, Hajnalka E.
  • Genome Announcements, Vol. 3, Issue 5
  • DOI: 10.1128/genomeA.01046-15

Genetic Organization of the Francisella Plasmid pFNL10
journal, November 2001

  • Pomerantsev, Andrei P.; Golovliov, Igor R.; Ohara, Yoshiro
  • Plasmid, Vol. 46, Issue 3
  • DOI: 10.1006/plas.2001.1548

Francisella tularensis subsp. novicida isolated from a human in Arizona
journal, January 2009

  • Birdsell, Dawn N.; Stewart, Tasha; Vogler, Amy J.
  • BMC Research Notes, Vol. 2, Issue 1
  • DOI: 10.1186/1756-0500-2-223

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009


Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009


Circular genome visualization and exploration using CGView
journal, October 2004


Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources
journal, January 2012

  • Siddaramappa, Shivakumara; Challacombe, Jean F.; Petersen, Jeannine M.
  • BMC Genomics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2164-13-422

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013

  • Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2474

Plasmids foster diversification and adaptation of bacterial populations in soil
journal, November 2012


Common Ancestry and Novel Genetic Traits of Francisella novicida-Like Isolates from North America and Australia as Revealed by Comparative Genomic Analyses
journal, June 2011

  • Siddaramappa, Shivakumara; Challacombe, Jean F.; Petersen, Jeannine M.
  • Applied and Environmental Microbiology, Vol. 77, Issue 15
  • DOI: 10.1128/AEM.00337-11

Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment
journal, March 1998

  • Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.175

Cryptic plasmids in Helicobacter pylori: putative functions in conjugative transfer and microcin production
journal, September 2004

  • Höfler, Claudia; Fischer, Wolfgang; Hofreuter, Dirk
  • International Journal of Medical Microbiology, Vol. 294, Issue 2-3
  • DOI: 10.1016/j.ijmm.2004.06.021

Solexa Ltd
journal, June 2004


Francisella halioticida sp. nov., a pathogen of farmed giant abalone (Haliotis gigantea) in Japan: Francisella halioticida sp. nov.
journal, October 2011


Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes
journal, February 2008


Plasmid rolling-circle replication: highlights of two decades of research
journal, March 2005


The bacterial ParA-ParB partitioning proteins
journal, October 2001


Outbreak of Francisella novicida Bacteremia Among Inmates at a Louisiana Correctional Facility
journal, June 2014

  • Brett, M. E.; Respicio-Kingry, L. B.; Yendell, S.
  • Clinical Infectious Diseases, Vol. 59, Issue 6
  • DOI: 10.1093/cid/ciu430

Mobility of Plasmids
journal, August 2010

  • Smillie, C.; Garcillan-Barcia, M. P.; Francia, M. V.
  • Microbiology and Molecular Biology Reviews, Vol. 74, Issue 3
  • DOI: 10.1128/MMBR.00020-10

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998


The involvement of host replication proteins and of specific origin sequences in the in vitro replication of miniplasmid Rl DNA
journal, January 1986

  • Ortega, Sagrario; Lanka, Erich; Diaz, Ramon
  • Nucleic Acids Research, Vol. 14, Issue 12
  • DOI: 10.1093/nar/14.12.4865

Biological Diversity of Prokaryotic Type IV Secretion Systems
journal, November 2009

  • Alvarez-Martinez, C. E.; Christie, P. J.
  • Microbiology and Molecular Biology Reviews, Vol. 73, Issue 4
  • DOI: 10.1128/MMBR.00023-09

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
journal, June 2010


Cryptic plasmid pFNL10 from Francisella novicida -like F6168: The base of plasmid vectors for Francisella tularensis
journal, March 1996


Where does bacterial replication start? Rules for predicting the oriC region
journal, July 2004


The development of tools for diagnosis of tularemia and typing of Francisella tularensis
journal, December 2004


Tandem repeats finder: a program to analyze DNA sequences
journal, January 1999


How Many Bootstrap Replicates Are Necessary?
journal, March 2010

  • Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
  • Journal of Computational Biology, Vol. 17, Issue 3
  • DOI: 10.1089/cmb.2009.0179

ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008

  • Butler, J.; MacCallum, I.; Kleber, M.
  • Genome Research, Vol. 18, Issue 5
  • DOI: 10.1101/gr.7337908

Comparative analyses of a putative Francisella conjugative element
journal, March 2014

  • Siddaramappa, Shivakumara; Challacombe, Jean F.; Petersen, Jeannine M.
  • Genome, Vol. 57, Issue 3
  • DOI: 10.1139/gen-2013-0231

Nicking by transesterification: the reaction catalysed by a relaxase
journal, September 1997


Confidence Limits on Phylogenies: an Approach Using the Bootstrap
journal, July 1985


A classification scheme for mobilization regions of bacterial plasmids
journal, February 2004

  • Francia, M. Victoria; Varsaki, Athanasia; Garcillán-Barcia, M. Pilar
  • FEMS Microbiology Reviews, Vol. 28, Issue 1
  • DOI: 10.1016/j.femsre.2003.09.001

Francisella guangzhouensis sp. nov., isolated from air-conditioning systems
journal, April 2013

  • Qu, P. -H.; Chen, S. -Y.; Scholz, H. C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 10
  • DOI: 10.1099/ijs.0.049916-0

Comparing thousands of circular genomes using the CGView Comparison Tool
journal, January 2012


Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes
journal, October 2013

  • Brown, Celeste J.; Sen, Diya; Yano, Hirokazu
  • Applied and Environmental Microbiology, Vol. 79, Issue 24
  • DOI: 10.1128/AEM.02252-13

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

Francisella infections in farmed and wild aquatic organisms
journal, January 2011


Environmental Survey for Four Pathogenic Bacteria and Closely Related Species Using Phylogenetic and Functional Genes*
journal, May 2006


Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae
journal, March 2016

  • Larson, Marilynn A.; Nalbantoglu, Ufuk; Sayood, Khalid
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 3
  • DOI: 10.1099/ijsem.0.000855

Detection of Diverse New Francisella-Like Bacteria in Environmental Samples
journal, September 2005


Genome Sequencing of 18 Francisella Strains To Aid in Assay Development and Testing: TABLE 1 
journal, April 2015

  • Johnson, Shannon L.; Daligault, Hajnalka E.; Davenport, Karen W.
  • Genome Announcements, Vol. 3, Issue 2
  • DOI: 10.1128/genomeA.00147-15

DNA Processing Reactions in Bacterial Conjugation
journal, June 1995


Consed: a graphical editor for next-generation sequencing
journal, August 2013


Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation
journal, April 1997

  • Cabezón, E.; Sastre, J. Ignacio; Cruz, F. de la
  • Molecular and General Genetics MGG, Vol. 254, Issue 4
  • DOI: 10.1007/s004380050432

Occurrence of Francisella piscicida in farmed and wild Atlantic cod, Gadus morhua L., in Norway
journal, July 2008


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

The Sequence Alignment/Map format and SAMtools
journal, June 2009


Genome sequence and phenotypic analysis of a first German Francisella sp. isolate (W12-1067) not belonging to the species Francisella tularensis
journal, January 2014

  • Rydzewski, Kerstin; Schulz, Tino; Brzuszkiewicz, Elzbieta
  • BMC Microbiology, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2180-14-169

Bacterial plasmids: replication of extrachromosomal genetic elements encoding resistance to antimicrobial compounds
journal, January 1999

  • Actis, Luis, A.
  • Frontiers in Bioscience, Vol. 4, Issue 1-3
  • DOI: 10.2741/Actis

Cutaneous Infection Caused by a Novel Francisella sp.
journal, July 2013

  • Respicio-Kingry, L. B.; Byrd, L.; Allison, A.
  • Journal of Clinical Microbiology, Vol. 51, Issue 10
  • DOI: 10.1128/JCM.01105-13

AT-rich region and repeated sequences – the essential elements of replication origins of bacterial replicons
journal, March 2012


Isolation and Characterization of a Novel Francisella sp. from Human Cerebrospinal Fluid and Blood
journal, May 2008

  • Kugeler, K. J.; Mead, P. S.; McGowan, K. L.
  • Journal of Clinical Microbiology, Vol. 46, Issue 7
  • DOI: 10.1128/JCM.00698-08

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