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Chapter 39 : 39 Genomics and Proteomics of Foodborne Microorganisms

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Abstract:

Foods are teeming with microorganisms that may be innocuous, pathogenic threats, spoilage agents, or beneficial microorganisms driving fermentations or acting as biocontrol agents. This chapter outlines the basic concepts underlying genomics, proteomics, and associated technologies. With the number of completely sequenced bacterial genomes increasing rapidly, one powerful approach to defining unique or conserved gene content and understanding how microorganisms evolved is comparative genomics, via an in silico analysis. The discipline of functional genomics deals with defining the roles of genes in their appropriate organisms. This chapter utilizes comparative and functional genomics and proteomics to demonstrate the role of SpaC in mucin binding and potentially its importance to the retention of some lactobacilli in the gastrointestinal tract. The principles behind DNA microarray technology make it very applicable to many different uses that include comparative genomics and global gene expression analysis. While the details of the Gad system were elucidated primarily by experiments in , genomics and bioinformatics have enabled researchers to identify and study the effects of these genes in other organisms. The contribution of genome sequencing and functional genomics has greatly facilitated our understanding of the pathogenicity of . Differences between the pathogenic and nonpathogenic species appear most strongly in the secretory proteome.

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.1
Figure 39.1

dNTP (top) has a 3′ hydroxyl present on the deoxyribose that ddNTP (bottom) does not. This stops DNA strand growth because DNA polymerase no longer has a way to connect the bases in the growing strand. doi:10.1128/9781555818463.ch39f1

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.2
Figure 39.2

(a) Schematic representation of 454 GS FLX pyrosequencing. Oligonucleotide adapters are ligated to fragmented DNA and immobilized to the surface of microscopic beads before PCR amplification in an oil-water droplet emulsion. Beads are isolated in picoliter wells and incubated with dNTPs, DNA polymerase, and beads bearing enzymes for the chemiluminescent reaction. Incorporation of a nucleotide into the complementary strand releases pyrophosphate, which is used to produce ATP. This, in turn, provides the energy for the generation of light. The light emitted is recorded as an image for analysis. (b) SOLiD sample preparation is similar to that of 454 pyrosequencing. After amplification, the beads are immobilized onto a custom substrate. A primer that is complementary to the adapter sequence (green), random oligonucleotides with known 3´ dinucleotides, and a corresponding fluorophore are hybridized sequentially along the sequence, and image data are collected. After five repeats, the complementary strand is melted away and a new primer is added to the adapter sequence, ending at a position one nucleotide upstream of the previous primer. Second-strand synthesis is repeated, allowing two-color encoding and double reading of each of the target nucleotides. Repeats of these cycles ensure that nucleotides in the gap between known dinucleotides are read. Knowledge of the first base in the adapter reveals the dinucleotide, using the color-space scheme. In other words, knowing that the last adapter nucleotide is T and the color is red means that the first base to be sequenced must be A. Knowing that the first base is A and the color is green means that the next base must be C, and so on. (c) For Solexa GA sequencing, adapters are ligated onto DNA and used to anchor the fragments to a prepared substrate. Fold-back PCR results in isolated spots of DNA of a large enough quantity that the amassed fluorophore can be detected. Terminator nucleotides and DNA polymerase are then used to create cDNA. Images are collected at the end of each cycle before the terminator is removed. (d) Heliscope sequencing immobilizes unamplified DNA with ligated adapters to a substrate. Each species of dNTP with a bright fluorophore attached is used sequentially to create second-strand DNA; a “virtual terminator” prevents the inclusion of more than one nucleotide per strand and cycle, and background signal is reduced by removal of “used” fluorophore at the start of each cycle. (e) The new sequencing method developed by Pacific Biosciences occurs in zeptoliter wells that contain an immobilized DNA polymerase. DNA and dNTPs are added for synthesis. Fluorophores are cleaved from the complementary strand as it grows and diffuse away, allowing single nucleotides to be read. Continuous detection of fluorescence in the detection volume and high dNTP concentration allow extremely fast and long reading. Adapted by permission from Macmillan Publishers Ltd., , vol. 57, copyright 2009. doi:10.1128/9781555818463.ch39f2

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.3
Figure 39.3

KEGG pathway map and predicted enzymes for folate metabolism in Pathway intermediates and reaction products are shown with EC numbers for enzymes that catalyze these reactions. Those catalytic activities encoded in the genome are highlighted in green. doi:10.1128/9781555818463.ch39f3

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.4
Figure 39.4

Genome atlas of WCFS1. The predicted origin of replication is shown at the top. The outer to inner circles show (i) positive-strand ORFs (red); (ii) negative-strand ORFs (blue); (iii) GC-skew (green); (iv) G+C content (black); (v) prophage-related functions (green) and -like elements (purple); and (vi) rRNA gene operons (black) and tRNA-encoding genes (red). Reprinted from Kleerebezem et al. ( ) with permission. doi:10.1128/9781555818463.ch39f4

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.5
Figure 39.5

Comparison of the region containing the virulence gene cluster of and the homologous regions of the and genomes. Open blue boxes and arrows, orthologs among the three genomes; solid red boxes and arrows, virulence gene cluster; solid yellow boxes and arrows, genes absent from . (A) Scheme generated by GenomeScout (LION Bioscience). (B) Enlargement of the region containing the virulence gene cluster. Reprinted from Glaser et al. ( ). doi:10.1128/9781555818463.ch39f5

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.6
Figure 39.6

Plasmid insertion into a gene through homologous recombination for inactivation of gene function. The phenotype of the mutant can then be analyzed to investigate the function of the gene. doi:10.1128/9781555818463.ch39f6

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.7
Figure 39.7

A replacement or deletion mutant can be created by first cloning two noncontiguous portions of a gene into an integration vector. The vector integrates into a targeted gene within one region of homology (black or light gray regions). Excision of the plasmid from the integrant structure can occur in a manner that either resolves the original gene (wild type) or leaves the deleted version. Points of resolution at steps A, B, C, or D will result in various combinations, as illustrated. doi:10.1128/9781555818463.ch39f7

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.8
Figure 39.8

Identification of pili in GG by immunogold electron microscopy. GG was grown to stationary phase, treated with anti-SpaC serum, labeled with protein A-conjugated gold particles (10 nm), negatively stained, and examined by transmission electron microscopy. (A) High-resolution electron micrograph showing multiple pili and an isometric bacteriophage (black arrow). Also included is a panel inset adjusted for heightened contrast and darkness to highlight the pilus ultrastructure (white arrow). (B) Electron micrograph showing pili clustered at the cell poles. (Bars: A, 200 nm; B, 500 nm.) Reprinted from Kankainen et al. ( ) with permission. doi:10.1128/9781555818463.ch39f8

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.9
Figure 39.9

Microarrays. Probes are PCR amplified from clones in a library or from genomic DNA using gene-specific primers. Individual amplicons are purified and spotted onto glass slides. Total RNA is labeled from both a test sample and a reference sample using fluorescent dyes and allowed to hybridize to the probes on the array. The array is then visualized using a laser scanner that generates color images that are overlaid and compared for intensity and source. Reprinted with permission from Duggan et al. ( ). doi:10.1128/9781555818463.ch39f9

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.10
Figure 39.10

Proteomic methods. (A) 2D-PAGE-MS. First dimension: proteins are separated based on isoelectric point (pI) using IEF. Proteins migrate along a pH gradient until they reach their pI, at which point they carry no net charge and stop migrating. Second dimension: proteins are further separated according to molecular weight using SDS-PAGE. Gels are stained to identify protein bands. Individual spots (red circles) are excised from the gel, trypsin digested, and sequenced using MS/MS. (B) Protein expression profiling. By overlaying images of 2D-PAGE gels, comparisons can be made between the proteomes of different organisms or differences in protein expression of a single organism under different conditions. Downregulated (dotted red circles) and upregulated (blue circles) proteins can be visualized. Printed with permission from Phillips and Bogyo ( ). doi:10.1128/9781555818463.ch39f10

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.11
Figure 39.11

GadA and GadB catalyze the exchange of the α-carboxyl of glutamate for a proton in the environment, leading to the creation of a molecule of carbon dioxide and one molecule of GABA. GadC is an antiporter that expels GABA from the cell and imports fresh glutamate. doi:10.1128/9781555818463.ch39f11

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Image of Figure 39.12
Figure 39.12

The EvgA/S circuit of acid resistance regulation is dependent on a histidine protein kinase (EvgS), which senses an environmental change causing it to activate its corresponding response regulator (EvgA), which is then able to act as a transcriptional regulator. The regulation follows a pathway to produce GadE, which ultimately induces the transcription of GadA/BC ( Fig. 39.11 ). doi:10.1128/9781555818463.ch39f12

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Figure 39.13

BSHs catalyze the hydrolysis of the peptide bond between the amino acid and the cholesterol-derived backbone of the bile salt. doi:10.1128/9781555818463.ch39f13

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39
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Tables

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Table 39.1

Microorganisms of foodborne significance with completed or in-progress genome sequencing projects

Citation: Douglas G, Pfeiler E, Duong T, Klaenhammer T. 2013. 39 Genomics and Proteomics of Foodborne Microorganisms, p 975-996. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch39

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