Full text loading...
Chapter 15 : Functional Genomics of Lactic Acid Bacteria
Category: Clinical Microbiology
Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase
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.
A phylogenetic tree of Lactobacillales constructed on the basis of concatenated alignments of genes encoding four subunits of the DNA-dependent RNA polymerase. Reprinted from Journal of Bacteriology ( Makarova and Koonin, 2007 ) with permission of the publisher.
Synteny between L. bulgaricus and L. acidophilus genomes. x axis, position on L. bulgaricus genome (unit, mega-base pairs); y axis, position on L. acidophilus genome (unit, megabase pairs). 0, replication origin. Dots indicate windows of significant protein similarity by BLAST scores. Adapted from Proceedings of the National Academy of Sciences of the United States of America ( van de Guchte et al., 2006 ) with permission of the publisher.
A comparison of the gene contents of 20 L. plantarum strains. Strains are indicated on the left. Gene content is indicated in a rectangle mapping onto the L. plantarum 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 L. plantarum WCFS1. A phylogenetic tree of the strains compared is shown on the left. Reprinted from the Journal of Bacteriology ( Molenaar et al., 2005 ) with permission of the publisher.
(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 L. lactis. folKE 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 Applied and Environmental Microbiology ( Sybesma et al., 2003 ) with permission of the publisher.
Schematic diagram of a thyA 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. hIL10, human IL-10 gene; thyA, thymidylate synthase gene. Reprinted from Nature Biotechnology ( Steidler et al., 2003 ) with permission from Macmillan Publishers Ltd.
Features of sequenced LAB genomes