Our research is driven by an interest in bacterial pathogenesis and its relationship with microbial physiology, structure, and genetics. Borrelia burgdorferi (which causes Lyme disease) and Treponema pallidum (the causative agent of syphilis) are spirochetes that cause chronic, multisystemic diseases. These organisms can invade almost any tissue and survive and cause disease in the host for years to decades, and thus serve as excellent models for the study of persistent, invasive pathogens. In the case of B. burgdorferi, molecular genetic techniques such as transposon mutagenesis (including signature tagged mutagenesis), PCR, Luminex®-based high-throughput screening procedures, and reverse genomics are being utilized in combination with infectivity studies to identify genes and gene products required for infectivity in a mouse model. Thus far, we have identified and characterized the vls antigenic variation of B. burgdorferi, an elaborate mechanism similar to the Variable Major Protein system of relapsing fever borreliae. In addition, we have determined that the linear plasmids lp25 (and its encoded gene pncA) and lp28-1 are required for full virulence of B. burgdorferi during infection in mice. We are currently taking a global approach to identify additional genes encoding virulence determinants important in the pathogenesis of Lyme disease, as well as genes required for vls recombination and immune evasion. Little is known about T. pallidum due to the inability to culture the organism continuously in vitro. In collaboration with Dr. George Weinstock and the Institute of Genomic Research in Rockville, Md., the complete sequence analysis of the 1.14 megabase chromosome of T. pallidum was completed in 1998; the genome sequences of several related subspecies and strains have also been determined using second generation sequencing approaches. The sequence of the 2.84 megabase genome of Treponema denticola, an oral spirochete involved in periodontal disease, was published in April 2004. We are currently applying ‘functional genomics’ to the elucidation metabolism, structure, and pathogenic mechanisms of these spirochetes. In addition, cryo-electron tomography, a relatively new electron microscopy technique that creates 3D images of bacteria, is being utilized in collaborative studies with Dr. Jun Liu to elucidate the architecture of the flagellar motor and other structural elements of these organisms.