The endospores of Bacillus anthracis are the infectious particles of anthrax. Spores are dormant bacterial morphotypes able to withstand harsh environments for decades, which contributes to their ability to be formulated and dispersed as a biological weapon. We monitored gene expression in B. anthracis during growth and sporulation using full genome DNA microarrays and matched the results against a comprehensive analysis of the mature anthrax spore proteome. A large portion (ϳ36%) of the B. anthracis genome is regulated in a growth phase-dependent manner, and this regulation is marked by five distinct waves of gene expression as cells proceed from exponential growth through sporulation. The identities of more than 750 proteins present in the spore were determined by multidimensional chromatography and tandem mass spectrometry. Comparison of data sets revealed that while the genes responsible for assembly and maturation of the spore are tightly regulated in discrete stages, many of the components ultimately found in the spore are expressed throughout and even before sporulation, suggesting that gene expression during sporulation may be mainly related to the physical construction of the spore, rather than synthesis of eventual spore content. The spore also contains an assortment of specialized, but not obviously related, metabolic and protective proteins. These findings contribute to our understanding of spore formation and function and will be useful in the detection, prevention, and early treatment of anthrax. This study also highlights the complementary nature of genomic and proteomic analyses and the benefits of combining these approaches in a single study.Entry of Bacillus anthracis spores into the host from the environment, or by events brought about by human design, is the initial event of anthrax infections (8). Vegetative bacilli are not believed to be the disease contagion for any form of anthrax. The route of spore entry into the host dictates the specific pathology and severity of the disease; e.g., cutaneous anthrax is generally far less severe than either the gastrointestinal or inhalational form (8). Endospores are produced in response to nutrient deprivation via an alternative developmental cascade by two known genera of gram-positive bacteria, Clostridium and Bacillus (34). During sporulation, vegetative metabolism is minimized, and a series of alternative sigma factors are sequentially expressed and activated to coordinate the expression of mRNAs responsible for spore development (22).Mature spores are metabolically inactive and have a highly ordered structure. This structure provides the protection required for survival over long periods, even in the face of harsh environmental conditions (48). Spore germination, outgrowth, and initiation of a vegetative cycle occur when small molecules, often nutrients and/or ions, are sensed in the context of aqueous environments. B. anthracis spores recognize specific signals provided by the local environment of a mammalian host and rapidly germinate when ass...