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Chapter 13 : Functional Genomics of

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Abstract:

This chapter addresses how genomic sciences are revealing why is such an effective caries pathogen in humans. Recognizing the importance of central metabolism and acid production in pathogenesis by , many laboratories began functional studies in the post-genomic era with a focus on gene regulation, stress tolerance, and biofilm formation. The AtlA protein of does not share substantial primary sequence homology with many other proteins in the databases, so AtlA may be a good target for novel therapeutics. A variety of other examples can be cited of how functional genomics revealed new properties of . The translation of environmental stimuli into changes in gene expression in bacteria frequently involves two-component signal transduction systems (TCSs) consisting of a membrane-bound sensor histidine kinase (HK) and a cytoplasmic response regulator (RR). A common theme that emerged from these studies is that has streamlined its genome by using pathways to cope with environmental insults to regulate a variety of virulence attributes. The expression of fruA is inducible by its substrates and is sensitive to carbon catabolite repression (CCR)-inducing reagents, including glucose, fructose, and mannose. Galactose gives the least repression of CCR-sensitive genes in . In a study, only one strain of , UA159, was tested, and although it was able to reach the intracellular compartment in very low numbers, the fate of UA159 in the host cytoplasm, as well as the consequences of invasion for the host cell, was not investigated.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13

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Two-Component Signal Transduction Systems
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Figures

Image of FIGURE 1
FIGURE 1

Schematic diagram of PCR-ligation-mutation strategy. The flanking 5′ and 3′ regions of the target gene (A) are amplified via PCR with gene-specific primers (black triangles) containing restriction sites engineered at the 3′ end of the 5′ fragment and the 5′ end of the 3′ fragment (#1). Following proper restriction enzyme digestions (#2), these fragments are ligated to a selective marker (M) that is released from a plasmid (#3). The ligation mix is then used directly to transform As a result of double-crossover homologous recombination (#4) between the 5′ and 3′ regions on the chimeric DNA fragment and the respective chromosomal loci, mutants that have the targeted gene replaced by the selective marker (#5) can be isolated on agar plates containing proper antibiotics.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 2
FIGURE 2

Schematic diagram of BrpA and AtlA. (A) BrpA. N, putative N-terminal transmembrane domain; LCP, region (residues 80 to 238) that shows some similarity to the LytR/CpsA/Psr family of proteins; Sr, serine/threonine-rich C terminus. (B) AtlA. Region 1 is a cleavable signal peptide at an alanine residue at position 18. The shaded regions indicated by number 2 represent a series of repeats at amino acid positions 208 to 347 and 502 to 641. Region 3 spans amino acid residues 774 to 886 and places AtlA in the glycoside hydrolase family 25 (lysozyme) of proteins.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 3
FIGURE 3

Scanning electron microscopic analysis of biofilms by BrpA-deficient strains. Biofilms of wild-type UA159 (panels 1 and 3) and the BrpAdeficient mutant TW14 (panels 2 and 4) were allowed to grow for 24 h on hydroxylapatite disks that were deposited in 24-well cell culture clusters in semidefined biofilm medium ( ) with 20 mM glucose (panels 1 and 2) or sucrose (panels 3 and 4) as the supplemental carbohydrate source. Data presented here are representative of three independent experiments.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 4
FIGURE 4

Genomic organization of the , and TCS operons in UA159. TCSs primarily consist of a membrane-bound sensor HK (gray), a cytoplasmic RR (black), and, in certain cases, an additional component (dotted), such as , or The HK autophosphorylated in response to a specific stimulus activates the RR by transfer of the phosphate group (P) to the RR.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 5
FIGURE 5

(p)ppGpp metabolism in UA159. (A) Schematic representation of the , and loci in the UA159 genome. (or ) encodes a bifunctional (p)ppGpp synthetase/hydrolase enzyme, and and code for (p)ppGpp synthetases. codes for an RR, and encodes the HK of a TCS. , and code for hypothetical proteins of unknown function. , and are predicted to encode -tyrosyl-tRNA deacylase, ATP-NAD kinase, large-subunit pseudouridine synthase E, and phosphotransacetylase, respectively. Arrows indicate the direction of transcription. (B) Growth curves of UA159, JLT1 (∆), and JLQ1 (∆) in FMC (chemically defined medium) lacking leucine or valine. The results are representative of at least four independent experiments. OD, optical density at 600 nm.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 6
FIGURE 6

Schematic model of carbon catabolite repression in as represented by the regulation of the system. Small open hexagons represent sugars, as indicated by G (glucose), F (fructose), and M (mannose). Phosphoryl groups are depicted as circles with the letter P inside, and proteins are represented by various shapes with writing beside or inside them. Lines with a bar at the end represent negative regulation.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Image of FIGURE 7
FIGURE 7

Transmission electron micrograph of HCAEC harboring OMZ175 (Bratthall serotype ). Medium was removed and the cells were fixed in paraformaldehyde/glutaraldehyde and postfixed with osmium tetroxide. Cells (arrows) are readily observed in multiple vacuoles in this view. Cells can also be found free in the cytoplasm (data not shown) later in the invasion process.

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13
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Tables

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TABLE 1

Summary of selected stress-related genes required for acid tolerance and biofilm formation

Citation: Burne R, Abranches J, Ahn S, Lemos J, Wen Z, Zeng L. 2011. Functional Genomics of , p 185-204. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch13

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