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This chapter represents a summary of the findings from the strain 8081 whole genome sequence and the associated microarray analysis. Section 1 & 2 provide an introduction to the species and an overview of the general features of the genome. Section 3 identifies important regions within the genome which highlight important differences in gene function that separate the three pathogenic s. Section 4 describes genomic loci conferring important, species-specific, metabolic and virulence traits. Section 5 details extensive microarray data to provide an overview of species-specific core gene functions and important insights into the intra-species differences between the high, low and non-pathogenic biotypes.

Unlike the classical strains, members of an atypical group of from Central Asia, denominated subspecies (also known as one of several pestoides types), are distinguished by a number of characteristics including their ability to ferment rhamnose and melibiose, their lack of the small plasmid encoding the plasminogen activator () and pesticin, and their exceptionally large variants of the virulence plasmid pMT (encoding murine toxin and capsular antigen).

Sequencing of genes and comparison of the deduced amino acid sequences from ten strains belonging mostly to the group of atypical rhamnose-positive isolates (non- subspecies or pestoides group) showed that the LcrV proteins analyzed could be classified into five sequence types. This classification was based on major amino acid polymorphisms among LcrV proteins in the four “hot points” of the protein sequences. Some additional minor polymorphisms were found throughout these sequence types. The “hot points” corresponded to amino acids 18 (Lys → Asn), 72 (Lys → Arg), 273 (Cys → Ser), and 324-326 (Ser-Gly-Lys → Arg) in the LcrV sequence of the reference strain CO92. One possible explanation for polymorphism in amino acid sequences of LcrV among different strains is that strain-specific variation resulted from adaptation of the plague pathogen to different rodent and lagomorph hosts.

ERIC (Enteropathogen Resource Information Center) is one of the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers for Biodefense and Emerging/Re-emerging Infectious Disease. ERIC serves as a comprehensive information resource for five related pathogens: , , diarrheagenic , spp., and spp. ERIC integrates genomics, proteomics, biochemical and microbiological information to facilitate the interpretation and understanding of ERIC pathogens and select related non-pathogens for the advancement of diagnostics, therapeutics, and vaccines.

This review is based on the opening lecture I was honored to give during the 9 International Symposium on Yersinia in Lexington, Kentucky in October 2006. I present some topics that have been close to my interest during the past 25 years with some historical anecdotes. For example, how detection of intervening sequences in rDNA genes resulted in development of microbial diagnostic applications. How the adhesin YadA was detected and named and what do we know of its function now? What was the first pseudogene sequenced in ? I will also discuss lipopolysaccharide, bacteriophages and serum resistance mechanisms which we have worked on lately.

Most Gram negative pathogens express surface located fibrillar organelles that are used for adhesion to host epithelia and/or for protection. The assembly of many such organelles is managed by a highly conserved periplasmic chaperone/usher assembly pathway. During the last few years, considerable progress has been made in understanding how periplasmic chaperones mediate folding, targeting, and assembly of F1 antigen subunits into the F1 capsular antigen. In particular, structures representing snapshots of several of the steps involved in assembly have allowed us to begin to draw a detailed molecular-level picture of F1 assembly specifically, and of chaperone/usher-mediated assembly in general. Here, a brief summary of these new results will be presented.

Disruption of lipopolysaccharide (LPS) biosynthesis genes in an epidemiologically significant strain showed that the ability to synthesize the full inner core of the LPS is crucial for resistances to the bactericidal action of antimicrobial peptides and to complement- mediated serum killing. Resistance to polymyxin B also requires a high content of the cationic sugar, 4-amino-4-deoxy-L-arabinose, in lipid A.

, the causative agent of plague, is a gram-negative pathogen that evolved from 1,500-20,000 years ago (Achtman et al. 1999). Plague has ravaged human populations for centuries and continues to occur in outbreaks throughout the world (Cantor 2001; Perry and Fetherston 1997). is usually transmitted by fleas that have fed on infected rodents prior to biting their human hosts. A number of virulence factors have been described in that contribute to disease including the 70-kb Yop-encoding plasmid pCD1 (Cornelis et al 1998), plasminogen activator (Sodeinde et al. 1992), iron acquisition functions (Brubaker et al 1965) and a surface-localized adhesin pH 6 antigen (Lindler et al 1990).

Extensive data in a wide range of organisms point to the importance of polyamine homeostasis for growth. The two most common polyamines found in bacteria are putrescine and spermidine. The investigation of polyamine function in bacteria has revealed that they are involved in a number of functions other than growth, which include incorporation into the cell wall and biosynthesis of siderophores. They are also important in acid resistance and can act as a free radical ion scavenger. More recently it has been suggested that polyamines play a potential role in signaling cellular differentiation in . Polyamines have also been shown to be essential in biofilm formation in . The pleiotropic nature of polyamines has made their investigation difficult, particularly in discerning any specific effect from more global growth effects. Here we describe key developments in the investigation of the function of polyamines in bacteria that have revealed new roles for polyamines distinct from growth. We describe the bacterial genes necessary for biosynthesis and transport, with a focus on . Finally we review a novel role for polyamines in the regulation of biofilm development in and provide evidence that the investigation of polyamines in may provide a model for understanding the mechanism through which polyamines regulate biofilm formation.

The variables carriage of pCD, CO2 tension, exogenous ATP, L-glutamate, Mg2+, Na+, pH, source of energy, and temperature are known to modulate the low calcium response of . The role of these effectors and the basis of their interactions are defined here with emphasis on known -specific missense mutations in glucose 6- phosphate dehydrogenase and aspartase, which preclude use of the hexose monophosphate pathway and prevent efficient catabolism of L-glutamic acid, respectively. A physiological Ca2+-deficient rescue scenario is provided that permits essentially full-scale growth of virulent (<0.1 mM Na+ and 25 mM L-glutamate at pH 6.5) with expression of pCD-encoded virulence effectors and their attendant type III secretion system. Multiplication in this environment indicates that Ca2+ prevents innate toxicity of Na+. However, Na+ actually promotes growth in Ca2+-deficient medium at pH 9.0 due to the evident action of Na+- translocating NADH-ubiquinone oxidoreductase. Another Ca2+-deficient rescue scenario (100 mM Na+ and 25 mM L-glutamate at pH 5.5) permitted growth while downregulating pCD-encoded functions. A consequence of the abrupt Na+-mediated bacteriostasis typical of aspartase-deficient is conversion of L-glutamate to L-aspartate with release of the latter into culture supernatant fluids. Occurrence of this event would radically alter the equilibrium of host amino acid pools thereby contributing to enhanced lethality.