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Transport Capabilities of Eleven Gram-Positive Bacteria: Comparative Genomic Analyses

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Transport Capabilities of Eleven Gram-Positive Bacteria: Comparative Genomic Analyses View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1768 (2007) 1342–1366 www.elsevier.com/locate/bbamem Review Transport capabilities of eleven gram-positive bacteria: Comparative genomic analyses Graciela L. Lorca 1,2, Ravi D. Barabote 1, Vladimir Zlotopolski, Can Tran, Brit Winnen, Rikki N. Hvorup, Aaron J. Stonestrom, Elizabeth Nguyen, ⁎ Li-Wen Huang, David S. Kim, Milton H. Saier Jr. Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA Received 5 October 2006; received in revised form 29 December 2006; accepted 7 February 2007 Available online 17 February 2007 Abstract The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G+C lactic acid bacteria and two high G+C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to 18% of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes. Our studies reveal unique characteristics of the lactic acid bacteria such as the universal presence of genes encoding mechanosensitive channels, competence systems and large numbers of sugar transporters of the phosphotransferase system. The analyses lead to important physiological predictions regarding the preferred signalling and metabolic activities of these industrially important bacteria. © 2007 Elsevier B.V. All rights reserved. Keywords: Lactic acid bacteria; Transport proteins; Genomic analyses; Energetics Contents 1. Introduction ............................................................. 1343 2. Computer methods ......................................................... 1344 3. Genome statistics .......................................................... 1345 4. Transporter classification ...................................................... 1345 ⁎ Corresponding author. Tel.: +1 858 534 4084; fax: +1 858 534 7108. E-mail address: [email protected] (M.H. Saier). 1 These two authors contributed equally to the work reported. 2 Current address: Department of Microbiology and Cell Science, University of Florida, Museum Road 1052, Gainesville, FL 32611, USA. 0005-2736/$ - see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.bbamem.2007.02.007 G.L. Lorca et al. / Biochimica et Biophysica Acta 1768 (2007) 1342–1366 1343 5. Organismal representation ......................................................1345 6. Topological distribution among Transport Proteins (TPs) ......................................1347 7. Classes of TPs in the 11 organisms .................................................1348 8. Channel-forming proteins.......................................................1353 9. Secondary carrier superfamilies....................................................1354 9.1. MFS (2.A.1)..........................................................1354 9.2. GPH (2.A.2)..........................................................1354 9.3. APC (2.A.3) ..........................................................1354 9.4. RND (2.A.6)..........................................................1355 9.5. DMT (2.A.7) .........................................................1355 9.6. SSS (2.A.21) .........................................................1355 9.7. MOP (2.A.66) .........................................................1355 10. Smaller families of secondary carriers ................................................1355 10.1. Divalent cations .......................................................1355 10.2. Monovalent cations .....................................................1355 10.3. Anions ............................................................1356 10.4. Amino acids and peptides ..................................................1356 10.5. Nucleobases and nucleosides.................................................1356 11. Primary active transporters ......................................................1356 11.1. The ABC superfamily (3.A.1) ................................................1356 11.2. P-type ATPases (3.A.3) ...................................................1358 11.3. Macromolecular secretion systems ..............................................1358 11.4. Na+-translocating organocarboxylate decarboxylases.....................................1358 12. The Phosphotransferase System (PTS) ................................................1358 13. Transmembrane electron transport systems ..............................................1359 14. Auxiliary transport proteins......................................................1359 15. Poorly characterized transporters ...................................................1359 16. Conclusions..............................................................1360 Acknowledgments ..............................................................1363 References..................................................................1363 1. Introduction Lactobacillus casei, Lactobacillus gasseri, Lactobacillus acid- ophilus, and Bifidobacterium longum, in addition to being Membrane transport systems catalyze the uptake of essential useful in the food industry, are natural inhabitants of the human nutrients, ions and metabolites, as well as the expulsion of toxic gastrointestinal (GI) tract where they synthesize probiotic-like compounds, cell envelope macromolecules, secondary metabo- substances. These compounds stimulate the immune system, lites and the end products of metabolism. Transporters also provide key nutrients and promote the development of a healthy participate in energy generation and interconversion, and they organism [5]. allow communication between cells and their environments. The Lactic Acid Bacterial Genomics Consortium has Transport is therefore essential to virtually every aspect of life. recently carried out genome sequencing of eleven Gram- Many Gram-positive bacteria are important in the food positive bacterial species [8,9]. The initial shotgun sequencing industry (see Table 1). These bacteria are used for the was conducted at the Joint Genome Institute in Walnut Creek, fermentation of vegetables and fruits, for the conversion of CA, and genome closure was achieved subsequently [9]. Nine dairy products into cheeses and yogurt, and for the preparation of the sequenced bacteria are low G+C Gram-positive lactic of beer and wine. A key feature of lactic acid bacteria (LABs) acid bacteria (LABs) (Pediococcus pentosaceus, L. brevis, L. when grown in laboratory growth media that lack hematin and casei, L. delbruekii, L. gasseri, Lactococcus lactis, subspecies related compounds is the inability to synthesize porphyrin (e.g., cremoris, S. thermophilus, Leuconostoc mesenteroides and heme). Consequently, LABs grown under these conditions are Oenococcus oeni) while two of them (B. longum and Brevi- devoid of “true” catalase activity and cytochromes. They lack bacterium linens) are high G+C Gram-positive bacteria. These electron transfer chains and rely on fermentation (i.e., substrate bacteria exhibit considerable diversity with respect to their level phosphorylation) for the generation of energy. However if ecological habitats, being found in milk, meat, plants, the GI hematin is added to the growth medium, catalase and tracts of humans and other animals, and elsewhere (see Table 1). cytochromes may be formed, in some cases resulting in They also differ with respect to their carbohydrate metabolic respiration [1–3]. pathways (Table 2). Little is known about the transport Some LABs are both useful and harmful. For example, capabilities of these important organisms. Lactobacillus brevis promotes both the preparation and the In this review we report comprehensive analyses of the spoilage of beer [4]. Other Gram-positive bacteria, such as transport capabilities encoded within the eleven Gram-positive
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