Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma (σ) factor cascade, the Hk1/Rrp1 twocomponent system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or finetuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by highthroughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each. caister.com/cimb 223 Curr. Issues Mol. Biol. Vol. 42 Curr. Issues Mol. Biol. 42: 223-266. caister.com/cimb Gene Regulation and Transcriptomics Samuels et al.Figure 2. A model of the RpoN-RpoS σ factor cascade. During tick feeding and mammalian infection, environmental and host signals activate the RpoN-RpoS σ factor cascade. Activation of RpoN requires phosphorylation of Rrp2 and accumulation of BosR. Rrp2 is the sole prokaryotic enhancer-binding protein present in B. burgdorferi that is required for RpoN (σ 54 ) activation. Phosphorylation of Rrp2 not only is required for RpoN-RpoS activation, but also is indispensable for cell survival, presumably replication. Levels of BosR respond to environmental signals and accumulation of BosR activates rpoS at its RpoN-dependent promoter via an unknown mechanism. BadR represses rpoS transcription by directly binding near the RpoN-dependent promoter region. In addition to the major rpoS mRNA species transcribed from the RpoN-dependent promoter, a longer rpoS transcript is produced at low cell density from an RpoN-independent promoter located within the upstream flgJ gene. The sRNA DsrABb regulates the efficiency of long rpoS mRNA species translation in response to temperature. DDB18 can regulate RpoS (σ S ) levels at the post-transcriptional level. Accumulation of rpoS transcript leads to the production of OspC, DbpA, DbpB, BBK32, and other mammalian infection-associated proteins.