Transport capabilities of eleven gram-positive bacteria: comparative genomic analyses.
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.
Lorca
Graciela L
GL
Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
Barabote
Ravi D
RD
Zlotopolski
Vladimir
V
Tran
Can
C
Winnen
Brit
B
Hvorup
Rikki N
RN
Stonestrom
Aaron J
AJ
Nguyen
Elizabeth
E
Huang
Li-Wen
LW
Kim
David S
DS
Saier
Milton H
MH
D001692:Biological Transport / Q000235:genetics / Q000502:physiology; D002352:Carrier Proteins / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000378:metabolism; D008660:Metabolism / Q000235:genetics*; D010802:Phylogeny; D015398:Signal Transduction / Q000235:genetics*; D013045:Species Specificity
D002352:Carrier Proteins