Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays

Abstract

The transport and catabolic machinery involved in carbohydrate utilization by Lactobacillus acidophilus was characterized genetically by using whole-genome cDNA microarrays. Global transcriptional profiles were determined for growth on glucose, fructose, sucrose, lactose, galactose, trehalose, raffinose, and fructooligosaccharides. Hybridizations were carried out by using a roundrobin design, and microarray data were analyzed with a two-stage mixed model ANOVA. Differentially expressed genes were visualized by hierarchical clustering, volcano plots, and contour plots. Overall, only 63 genes (3% of the genome) showed a >4-fold induction. Specifically, transporters of the phosphoenolpyruvate: sugar transferase system were identified for uptake of glucose, fructose, sucrose, and trehalose, whereas ATP-binding cassette transporters were identified for uptake of raffinose and fructooligosaccharides. A member of the LacS subfamily of galactosidepentose hexuronide translocators was identified for uptake of galactose and lactose. Saccharolytic enzymes likely involved in the metabolism of monosaccharides, disaccharides, and polysaccharides into substrates of glycolysis were also found, including enzymatic machinery of the Leloir pathway. The transcriptome appeared to be regulated by carbon catabolite repression. Although substrate-specific carbohydrate transporters and hydrolases were regulated at the transcriptional level, genes encoding regulatory proteins CcpA, Hpr, HprK͞P, and EI were consistently highly expressed. Genes central to glycolysis were among the most highly expressed in the genome. Collectively, microarray data revealed that coordinated and regulated transcription of genes involved in sugar uptake and metabolism is based on the specific carbohydrate provided. L. acidophilus's adaptability to environmental conditions likely contributes to its competitive ability for limited carbohydrate sources available in the human gastrointestinal tract.ATP-binding cassette ͉ carbon catabolite repression ͉ fructooligosaccharide ͉ galactoside-pentose hexuronide

Transcriptional and functional analysis of galactooligosaccharide uptake bylacSinLactobacillus acidophilus

“…No genetic loci involved with carbohydrate metabolism were identified from the list of genes induced by glucose, suggesting that glucose is transported by the constitutively expressed mannose/glucose phospho-enolpyruvate-dependent phosphotransferase system (PEP-PTS) transporter (LBA0452, LBA0454-LBA0456), as suggested previously (26). The transcription analysis indicated that the lac operon in L. acidophilus NCFM is solely responsible for the metabolism of GOS and potentially other lactose-derived galactosides, because the gene induction profile of GOS is comparable to the lactose-induced lac gene expression pattern (26).…”

“…The transcription analysis indicated that the lac operon in L. acidophilus NCFM is solely responsible for the metabolism of GOS and potentially other lactose-derived galactosides, because the gene induction profile of GOS is comparable to the lactose-induced lac gene expression pattern (26). It also indicates that regulation occurs at the transcriptional level, likely depending upon HPr (ptsH, LBA0639), CcpA (ccpA, LBA0431), and HPrK/P (ptsK, LBA0676), all of which are encoded in the L. acidophilus NCFM genome (23) and as previously proposed for carbohydrate utilization in L. acidophilus NCFM (26).…”

“…The L. acidophilus NCFM genome was recently sequenced to reveal that the molecular machinery responsible for carbohydrate uptake and catabolism in NCFM accounts for 17% of the genes present in the genome (23). Broad carbohydrate utilization of L. acidophilus NCFM was demonstrated and included transporters for trehalose (24), fructooligosaccharides (25), and several other mono-, di-, and trisaccharides (26).…”

Substrate-driven gene expression in Roseburia inulinivorans : Importance of inducible enzymes in the utilization of inulin and starch

“…The Bacillus subtilis genome encodes 15 PTS proteins with different sugar specificities (31), one of which is also adjacent to a 1-pfk enzyme. PTS transport systems are linked with uptake of monomeric substrates, whereas ABC transport systems are required for the transport of larger substrates, as shown for L. acidophilus (29). Sucrose-use clusters, including PTSII transporter systems that are up-regulated during growth on sucrose or FOS, have been identified in C. beijerinckii (30), C. acetobutylicum (32), and L. plantarum (23).…”

“…2). The gene encoding the fructofuranosidase-linked ABC transport protein was induced strongly during growth on longer-chain inulin substrates, whereas the PTSI had maximum induction on fructose, reflecting the different transport capabilities of these two systems (29).…”