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Chapter 15 : Functional Genomics of Lactic Acid Bacteria

Authors: Tri Duong1, Todd R. Klaenhammer2
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Affiliations: 1: Genomic Sciences Graduate Program, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695; 2: Dept. of Food, Bioprocessing and Nutrition Sciences, and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695
Content Type: Monograph
Publication Year: 2008

Category: Clinical Microbiology

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Abstract:

The lactic acid bacteria (LAB) are a diverse group of microorganisms related by their common metabolic and physiological characteristics and named for the major end product of their primary metabolism. Major advances have been made in the genomic characterization of the LAB. A number of LAB genomes have been sequenced and are publicly available, while more genomes are being sequenced. This chapter lists genome features of sequenced LAB. While genomic analyses of LAB have identified features important for the functionality of the organisms in bioprocessing and health, further characterization of genes and gene products remains important for understanding cell physiology, metabolic and signaling networks, and molecular interactions of LAB with their environments. This information is rapidly providing a mechanistic understanding of these microorganisms and identifying important gene sets critical to their functionality. An understanding of genes directing important metabolic pathways combined with the tools available for the inactivation of undesirable genes and overexpression of existing or novel genes will certainly aid in the production of important food ingredients or food products with improved flavor and nutritional properties. Because of their acid tolerance, record of safety, and ability to modulate the immune system, considerable interest has developed for using LAB as live vectors for the delivery of vaccines and other biotherapeutics to the intestinal mucosa.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Functional Genomics of Lactic Acid Bacteria
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Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
/content/10.1128/9781555815462.ch15.ch15fig01
Figure 1
A phylogenetic tree of constructed on the basis of concatenated alignments of genes encoding four subunits of the DNA-dependent RNA polymerase. Reprinted from ( ) with permission of the publisher.
10.1128/9781555815462/ch15fig1_thmb.gif
10.1128/9781555815462/ch15fig1.gif
Image of Figure 1
Figure 1

A phylogenetic tree of constructed on the basis of concatenated alignments of genes encoding four subunits of the DNA-dependent RNA polymerase. Reprinted from ( ) with permission of the publisher.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Figure 2
Synteny between and genomes. axis, position on genome (unit, mega-base pairs); axis, position on genome (unit, megabase pairs). 0, replication origin. Dots indicate windows of significant protein similarity by BLAST scores. Adapted from ( ) with permission of the publisher.
10.1128/9781555815462/ch15fig2_thmb.gif
10.1128/9781555815462/ch15fig2.gif
Image of Figure 2
Figure 2

Synteny between and genomes. axis, position on genome (unit, mega-base pairs); axis, position on genome (unit, megabase pairs). 0, replication origin. Dots indicate windows of significant protein similarity by BLAST scores. Adapted from ( ) with permission of the publisher.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Figure 3
A comparison of the gene contents of 20 strains. Strains are indicated on the left. Gene content is indicated in a rectangle mapping onto the WCFS1 genome sequence: the presence (no line) and absence (black line) of fragments are indicated. The upper rectangle, labeled “missing,” shows in black the fragments of the genome that were not spotted on the microarray. Sum of distances indicates genotypic variation mapping onto the loci of the WCFS1 genome. The lower panel shows the base deviation index along the chromosome of WCFS1. A phylogenetic tree of the strains compared is shown on the left. Reprinted from the ( ) with permission of the publisher.
10.1128/9781555815462/ch15fig3_thmb.gif
10.1128/9781555815462/ch15fig3.gif
Image of Figure 3
Figure 3

A comparison of the gene contents of 20 strains. Strains are indicated on the left. Gene content is indicated in a rectangle mapping onto the WCFS1 genome sequence: the presence (no line) and absence (black line) of fragments are indicated. The upper rectangle, labeled “missing,” shows in black the fragments of the genome that were not spotted on the microarray. Sum of distances indicates genotypic variation mapping onto the loci of the WCFS1 genome. The lower panel shows the base deviation index along the chromosome of WCFS1. A phylogenetic tree of the strains compared is shown on the left. Reprinted from the ( ) with permission of the publisher.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Figure 4
(A) Chemical structures of intermediates and end products in the tetrahydrofolate and folate biosynthesis pathways. Thick arrows indicate enzymatic reactions that are controlled in metabolic engineering experiments. (B) Schematic representation of folate biosynthesis genes in encodes a bifunctional protein. Hatched arrows represent genes involved in folate biosynthesis, black arrows represent genes involved in folate biosynthesis that are overexpressed by metabolic engineering, and white arrows represent genes that are not expected to be involved in folate biosynthesis. Reprinted from ( ) with permission of the publisher.
10.1128/9781555815462/ch15fig4_thmb.gif
10.1128/9781555815462/ch15fig4.gif
Image of Figure 4
Figure 4

(A) Chemical structures of intermediates and end products in the tetrahydrofolate and folate biosynthesis pathways. Thick arrows indicate enzymatic reactions that are controlled in metabolic engineering experiments. (B) Schematic representation of folate biosynthesis genes in encodes a bifunctional protein. Hatched arrows represent genes involved in folate biosynthesis, black arrows represent genes involved in folate biosynthesis that are overexpressed by metabolic engineering, and white arrows represent genes that are not expected to be involved in folate biosynthesis. Reprinted from ( ) with permission of the publisher.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Figure 5
Schematic diagram of a replacement strategy. Gray lines represent target areas for recombination, thick black lines represent nontarget chromosome fragments, and thin black lines represent the exchange vector. 1, 2, and 3 represent PCR primer pairs. Stages include the following: (1) introduction of the nonreplicative vector; (2) 5′ crossover event, facilitated by erythromycin (Em) selection; (3) second crossover event in the absence of Em; (4) acquisition of desired transgenic chromosome organization. , human IL-10 gene; , thymidylate synthase gene. Reprinted from ( ) with permission from Macmillan Publishers Ltd.
10.1128/9781555815462/ch15fig5_thmb.gif
10.1128/9781555815462/ch15fig5.gif
Image of Figure 5
Figure 5

Schematic diagram of a replacement strategy. Gray lines represent target areas for recombination, thick black lines represent nontarget chromosome fragments, and thin black lines represent the exchange vector. 1, 2, and 3 represent PCR primer pairs. Stages include the following: (1) introduction of the nonreplicative vector; (2) 5′ crossover event, facilitated by erythromycin (Em) selection; (3) second crossover event in the absence of Em; (4) acquisition of desired transgenic chromosome organization. , human IL-10 gene; , thymidylate synthase gene. Reprinted from ( ) with permission from Macmillan Publishers Ltd.

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
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Tables

Functional Genomics of Lactic Acid Bacteria
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Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15
/content/10.1128/9781555815462.ch15.ch15table01
Table 1
Features of sequenced LAB genomes
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Table 1

Features of sequenced LAB genomes

Citation: Duong T, Klaenhammer T. 2008. Functional Genomics of Lactic Acid Bacteria, p 193-204. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch15

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