Complete Genome Sequence of Yersinis pestis Strains Antiqua and Nepa1516: Evidence of Gene Reduction in an Emerging Pathogen

Journal Article · Sun Jan 01 04:00:00 EST 2006 · Journal of Bacteriology

DOI:https://doi.org/10.1128/JB.00124-06· OSTI ID:978221

Chain, Patrick S ^[1]; Hu, Ping ^[2]; Malfatti, Stephanie ^[3]; Radnedge, Lyndsay ^[3]; Larimer, Frank W ^[1]; Vergez, Lisa ^[3]; Worsham, Patricia ^[4]; Chu, May C ^[5]; Anderson, Gary L ^[2]

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1. ORNL
2. Lawrence Berkeley National Laboratory (LBNL)
3. Lawrence Livermore National Laboratory (LLNL)
4. U.S. Army Medical Research Institute of Infectious Diseases
5. Centers for Disease Control and Prevention

Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the ''classical'' antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 978221
• Journal Information: Journal of Bacteriology, Journal Name: Journal of Bacteriology Journal Issue: 12 Vol. 188; ISSN JOBAAY; ISSN 0021-9193
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
BACTERIA
DISTRIBUTION
GENES
GENETICS
NUCLEOTIDES
PATHOGENS
STRAINS
VIRULENCE