The bacteria genus Streptococcus includes some of the most important human pathogens, causing a wide range of different disease, and inflicting significant morbidity and mortality throughout the world. Our long term goal is to reach a thorough understanding of the molecular specifics correlated with adaptive differences within and between the pathogenic taxa of the genus Streptococcus. Our central hypothesis is that many loci, sites within loci, and noncoding functional elements, identified as being under lineage specific, or positive selection pressure, in our evolutionary analyses, will be key loci involved in the colonization, persistence, survival, and propensity to cause disease in these pathogenic streptococci.
The specific aims of this proposal can be summarized as follows: 1. Generate and annotate genome sequence data for 9 species of Streptococcus within the Pyogenes, and Mutans groups, chosen such that they will yield various sister group comparisons involving important human pathogens, and construct a Streptococcus Genome Browser for presentation of data and associated comparative genomic analyses. 2. Assess the role of positive selection and lateral gene transfer in the diversification of the genomes of the species within the different Streptococcus groups. 3. Collect comparative sequence data of species specific, putative virulence, and core genes, across strains of the same species, for the purpose of analyzing selection pressure and demographic history, employing new population genetic based methods developed by us, as well as additional methods developed as part of this project. 4. Employing new methods developed by us, as well as additional methods developed as part of this project, conduct a comprehensive survey of noncoding functional elements in the Streptococcus Pyogenes, Mutans, and Mitis groups. 5. Based on the results arising from the selection analyses, and identification of noncoding functional elements, create gene knockout and site specific mutants for S. mutans, and assay the phenotypic effects. The fundamental data on comparative genomics and molecular adaptation, arising from this project, will serve as a framework for the development of novel therapeutic and preventative strategies for pathogenic species of Streptococcus. The results from these evolutionary analyses will serve as a guide for future follow-up, cause- effect experimentation, and the Streptococcus Genome Browser will serve as a valuable resource to the scientific community by displaying results of in vitro and in vivo studies of associations between sequence and function.

Public Health Relevance

This project will yield a great deal of fundamental information regarding the molecular details of how Streptococcus pathogens are adapted to their human hosts. This information will in turn be a valuable asset to the development of novel therapeutic and preventative strategies for these pathogenic bacteria.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI073368-05
Application #
8291319
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
GU, Xin-Xing
Project Start
2008-07-01
Project End
2014-06-30
Budget Start
2012-07-01
Budget End
2014-06-30
Support Year
5
Fiscal Year
2012
Total Cost
$385,385
Indirect Cost
$103,046
Name
Cornell University
Department
Veterinary Sciences
Type
Schools of Veterinary Medicine
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Richards, Vincent P; Palmer, Sara R; Pavinski Bitar, Paulina D et al. (2014) Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol 6:741-53
Zeng, Lin; Choi, Sang Chul; Danko, Charles G et al. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One 8:e60465
Cornejo, Omar E; Lefebure, Tristan; Bitar, Paulina D Pavinski et al. (2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol 30:881-93
Kim, Jeong Nam; Stanhope, Michael J; Burne, Robert A (2013) Core-gene-encoded peptide regulating virulence-associated traits in Streptococcus mutans. J Bacteriol 195:2912-20
Palmer, Sara R; Miller, James H; Abranches, Jacqueline et al. (2013) Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLoS One 8:e61358
Suzuki, Haruo; Lefebure, Tristan; Bitar, Paulina Pavinski et al. (2012) Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. BMC Genomics 13:38
Suzuki, Haruo; Stanhope, Michael J (2012) Functional bias of positively selected genes in Streptococcus genomes. Infect Genet Evol 12:274-7
Suzuki, Haruo; Lefebure, Tristan; Hubisz, Melissa Jane et al. (2011) Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol 3:168-85
Richards, Vincent P; Lang, Ping; Bitar, Paulina D Pavinski et al. (2011) Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect Genet Evol 11:1263-75