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Journal of Bacteriology, November 2005, p. 7267-7282, Vol. 187, No. 21
0021-9193/05/$08.00+0     doi:10.1128/JB.187.21.7267-7282.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in the Hyperthermophilic Bacterium Thermotoga maritima{dagger}

Shannon B. Conners, Clemente I. Montero, Donald A. Comfort, Keith R. Shockley,{ddagger} Matthew R. Johnson, Swapnil R. Chhabra,§ and Robert M. Kelly*

Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905

Received 28 April 2005/ Accepted 27 July 2005


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ABSTRACT
 
Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, ß-xylan, and ß-glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.


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INTRODUCTION
 
Thermotoga maritima, a hyperthermophilic anaerobe with an optimal growth temperature of 80°C, has been found in diverse high-temperature locations and is capable of using a wide variety of simple and complex carbohydrate substrates for growth. The complexity of its carbohydrate utilization strategies, revealed by genome sequencing (48) and through previous work (11, 12, 47, 51), is surprising, given the primitive features of this microorganism. Considerable genomic plasticity has been observed even within the Thermotoga genus, with respect to the gene content of carbohydrate active enzymes and transporter subunits, which may to some extent relate to lateral gene transfer events (48, 49). Despite the range of sugar-active enzymes found within T. maritima MSB8 genome (Table S1 in the supplemental material)(6, 9, 10, 23, 27, 34, 35, 37, 38, 39, 42, 45, 46, 54, 70, 71), a PTS (phosphoenolpyruvate-dependent phosphotransferase system) similar to those used by other species for preferential uptake of selected sugars is apparently absent (48). No homologs of the PTS components EI and HPr (phosphocarrier proteins) and no sugar-specific EII sugar transporter subunits have been identified in the Thermotogales. Homologs of PTS-associated transcriptional regulators are found in T. maritima MSB8 but have not been implicated in global transcriptional regulation of sugar uptake. Whereas catabolite repression by glucose has been demonstrated for Thermotoga neapolitana (78), a mechanism for the global regulation of sugar utilization remains to be identified within the Thermotoga genus.

The importance of carbohydrates as carbon and energy sources for T. maritima is reflected by the disproportionate number of ABC (for ATP-binding cassettes) transporters that are found within T. maritima relative to its genome size (56). These ABC transporters can be classified into large families of sugar transporters and peptide (Opp, oligopeptide; Dpp, dipeptide) transporters, although it has been suggested that both types may participate in the uptake of simple and complex sugars in T. maritima (11, 12, 28). Attempts to annotate the functional specificity of these transporters using computational tools have been largely unsuccessful (59) due to the phylogenetic distance between homologs in T. maritima and model bacteria. In fact, several sets of T. maritima "oligopeptide" transporters are more closely related to archaeal sugar transporters (15, 29) than characterized bacterial peptide transporters and may have arrived in the T. maritima lineage through lateral gene transfer (48). Presumably, subsequent duplication and divergence events generated paralogous sets of transporter gene subfamilies with different sugar-binding specificities. Determining the apparent specificities of each system and associated transcriptional regulators or hydrolases is a key step in testing this hypothesis. Most members of the LacI (lactose repressor) family of carbohydrate-responsive transcriptional regulators in T. maritima cannot be easily assigned into known functional classes using a subset of protein sites (44). Similarly, the specificities of the multiple T. maritima homologs of the XylR (xylose repressor) family regulators cannot be determined from sequence homology alone. The presence of these genes nearby sets of ABC transporters suggests that they may play a regulatory role in uptake and utilization of different carbohydrates. Genetic systems enabling knockouts or in vivo overexpression studies of genes are currently lacking for T. maritima, as well as for the majority of sequenced bacterial genomes, which now number ~180 complete and >300 in progress (4). Clearly, alternative complementary methodologies are necessary for performing large-scale functional predictions for expanded protein families in organisms such as T. maritima, which lack genetic tools.

Transcriptional analysis has proven to be a useful tool for the annotation of members of expanded gene families in a number of genomes. Such approaches have been instrumental in revealing biological pathways (41) and suggesting likely functions for individual genes, operons, or multiple members of related families of glycoside hydrolases, transporters, and regulatory proteins (3, 5, 76). Previous studies in T. maritima to examine carbohydrate-related gene expression utilized Northern blots to examine transcription of selected hydrolases during growth on glucan- and mannan-based polysaccharides (12). Work with a full genome array comparing gene expression patterns of T. maritima on glucose, maltose, and lactose further underscored the relevance of this approach in the absence of a genetic system for this organism (51) and guided subsequent biochemical studies, which suggested divergence of transporter substrates for two members of the maltose-binding protein family (47). Efforts using a targeted cDNA microarray demonstrated an expanded methodology for predicting carbohydrate-related gene expression in T. maritima (11). In the present study, a comprehensive analysis of genome-wide expression patterns during growth on 14 monosaccharide and polysaccharide substrates (Table 1) was undertaken with the goal of suggesting sugar specificities for transport systems and putative regulators of unknown specificity found within the genome. Similar expression-based strategies could prove useful in improving genome annotation in other species of bacteria and archaea whose genomes have been sequenced but which also lack genetic systems.


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  		TABLE 1. Carbon sources used in this studya


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MATERIALS AND METHODS
 
Growth of T. maritima and RNA isolation. Cultures of T. maritima MSB8 were grown in artificial seawater using optical density measurements and epifluorescence microscopic cell density enumeration, as described previously (12). Growth substrates glucose, mannose, arabinose, rhamnose, ribose, xylose, ß-xylan (birchwood), laminarin (Laminaria digitata), and starch (potato) were obtained from Sigma (St. Louis, MO). Galactomannan (carob), glucomannan (konjac), and ß-glucan (barley) were obtained from Megazyme (Wicklow, Ireland), and pustulan (U. papullosa) was obtained from Calbiochem (San Diego, CA). These growth substrates were prepared as described previously (12). Substrate purities as provided by the manufacturers varied from 95 to 99%. All carbohydrate growth substrates were included in the medium at a final concentration of 0.25% (wt/vol). To ensure minimum carryover between substrates, cells were grown for at least six passes on each carbon source using a 0.5% (vol/vol) starting inoculum before obtaining the growth curves. Isolation of total RNA from T. maritima was performed on cells that were grown until early- to mid-exponential phase on the various growth substrates, using a protocol described previously (18).

Microarray protocols. A T. maritima cDNA microarray was constructed and utilized by using methodologies discussed previously (11, 24). Hybridizations were carried out for 18 h according to modified TIGR protocols described elsewhere (11, 20, 21). Hybridized slides were scanned on a Perkin-Elmer ExpressLite Scanner (Perkin-Elmer) and quantitated by using ScanArray 2.1 (Perkin-Elmer).

Mixed model analyses of microarray data. Replication of treatments, arrays, dyes, and cDNA spots allowed the use of analysis of variance (26, 83) models for data analysis. A loop design was constructed (Fig. 1), and reciprocal labeling utilized for all samples to estimate dye effects for each treatment. Scanarray spot intensities were imported into SAS (SAS Institute, Cary, NC) and flagged low-intensity or low-quality spots were removed before further analysis. After local background subtraction and log transformation of spot intensities, a linear normalization analysis of variance model (83) was used to estimate global variation in the form of fixed effects (dye [D], treatment [T]), random effects (array [A], spot A [S]), and random error by using the model log2(yijklmn) = µ + Ai + Dj + Tk + Ai(Sl) + {varepsilon}ijklm. A gene-specific analysis of variance model was used to partition the remaining variation into gene-specific effects using the model rijklmn = µ + Ai + Dj +Tk + Ai (Sl) + {varepsilon}ijklm. Least-squares mean estimates of gene-specific treatment effects were examined by using hierarchical clustering in JMP (SAS Institute), and histograms in Excel (Microsoft) were used to visualize expression patterns for specific contiguous genomic locations. A subset of samples included in this analysis represented biological repeats of conditions examined previously with an array including a targeted subset of T. maritima genes (11). The correlations between the two sets of least-squares mean estimates of gene-specific treatment effects for genes in common between both arrays (n = 262) were as follows: galactomannan, barley glucan, and glucose, r ≥ 0.78; and starch and mannose, r ≥ 0.62. An examination of fold changes for genes most highly differentially expressed between selected pairs of treatments (e.g., barley and starch) revealed good agreement between gene lists, although the full genome array used here resulted in more conservative estimates of fold changes than the targeted array used previously (11). Unless otherwise noted, original gene annotations have been checked against the COG database at the National Center for Biotechnology Information (NCBI) (74) and the Conserved Domain Database at the NCBI (40). Information on the magnitude and statistical significance of the fold changes for all of the genes included on the array may be found online (http://www.che.ncsu.edu/extremophiles/page5.html).



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  		FIG. 1. Loop design used for the study of carbon source utilization of T. maritima in the present study. The arrowheads correspond to the Cy5 channel, and the dotted arrow ends correspond to the Cy3 channel. Abbreviations for sugar names used in subsequent expression histograms are shown in parentheses.

Prediction of transcriptional regulator binding sites and promoters. Consensus binding sequences for LacI and XylR family proteins were taken from the literature (32, 61). The Web-based RSA Tools was used to extract the 300 bases upstream of every gene in the T. maritima genome, and the RSA Tools DNA Pattern Search was used to identify matches to regulator consensus sequences with two or fewer mismatches (77). Pattern searches with more degenerate matches were identified by using the program FuzzNuc from the EMBOSS software suite (60).

Construction of phylogenetic trees. Protein sequences were obtained from GenBank Batch Entrez and aligned with CLUSTAL X (75). In an attempt to draw information from sequence homology between related T. maritima proteins, phylogenetic analysis was constructed separately for Opp/Dpp ABC transporter subunits (substrate-binding proteins, ATP-binding proteins, and permeases), other predicted sugar transporter subunits, LacI family regulators and XylR family regulators of T. maritima using MEGA2 (30). For the T. maritima Opp/Dpp family proteins, the topologies of individual phylogenetic trees for the substrate-binding proteins, ATP-binding subunits, and permease proteins showed consistent relationships among operons for three methods (neighbor-joining, minimum evolution, and maximum parsimony) (63, 65, 69). A consensus tree is shown in Fig. 3.





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  		FIG. 3. Pentose-responsive loci of T. maritima. Predicted {sigma}A promoters are represented by arrows. Substrate-binding proteins are outlined in bold and boxed. Spacing between genes is less than 30 bases unless indicated otherwise. (A) A T. maritima locus which responds to the pentose sugars ribose, arabinose, and xylose contains genes for the utilization of the simple sugar D-ribose, a likely ribose transport system, and other genes likely to participate in the pentose phosphate pathway. (B) An arabinose utilization locus contains genes for the conversion of arabinose into D-xylulose-5-P. (C) Predicted pathway for the hydrolysis, transport and utilization of xylan, xylose, ribose, and arabinose by T. maritima. Extracellular enzymes responsible for polysaccharide hydrolysis are shown, as well as periplasmic binding proteins, membrane-embedded permeases, associated ATP-binding subunits, and intracellular hydrolases. References for hydrolases shown in the pathway are listed in Table S2 in the supplemental material.


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RESULTS
 
Expression results for selected T. maritima ABC transporters. Figure 2 summarizes the genomic locations and microarray expression results for selected sets of genes in the T. maritima genome. These include ABC-type bacterial carbohydrate uptake transporters from the two main families, CUT1 and CUT2 (64), as well as members of the Opp/Dpp ABC transporter family. Expression data are also shown for associated hydrolases and putative transcriptional regulators. Based on these results, predictions of transporter specificities are shown in Table 2, along with a summary of specificities predicted by previous work.



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  		FIG. 2. Circular representation of the T. maritima genome showing locations of known carbohydrate transport proteins and Opp/Dpp family ABC transporter components. Least-squares mean estimates (see Materials and Methods) of transcript levels corrected for systematic errors are shown for selected operons whose carbohydrate specificity is predicted in this study. In this context, red and green denote transcript levels above (red) and below (green) the mean expression across all genes, where "0" represents the mean rather than no expression. Oligopeptide transporter subunits are represented in black, CUT1 transporter subunits are represented in gray, and CUT2 transporter subunits are represented in white.


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  		TABLE 2. List of predicted or confirmed sugar transport systems of T. maritima

CUT1 ABC transport systems. CUT1 transporters with substrate-binding proteins related to maltose-binding proteins include maltose transporter subunits (TM1836 and TM1839 and TM1202 to TM1204) recently shown to have different expression patterns and varied transport capabilities (47, 51, 80). Expression patterns during growth in the presence of other carbohydrates that were examined did not reveal new information about the specificity of a third related set of transport proteins for which no substrate has yet been suggested (TM0418 to TM0422) (Table 2).

The CUT1 permeases and substrate-binding proteins encoded by TM0810 to TM0813 are found with genes whose functions relate to breakdown of N-acetylglucosamine polysaccharides. However, growth of T. maritima in the presence of the ß-1,4-N-acetylglucosamine polymer chitin was similar to control cultures, a finding consistent with a lack of differential expression of this locus. Sequence similarity searches suggest that T. maritima lacks an identifiable chitinase and might instead utilize chitin in the presence of neighboring species capableof chitin hydrolysis. Alternatively, transcription of these genes may be higher in the presence of N-acetylglucosamine or another N-acetylglucosamine-containing oligosaccharide found in the natural environment of T. maritima.

CUT2 transport systems. The two CUT2 transporters found in T. maritima are comprised of a substrate-binding protein, a single permease subunit presumed to form a homodimer in the functional transporter and a fusion protein consisting of two nucleotide-binding domains. Previously, we observed the upregulation of the LacI family gene TM0949 and the predicted ribokinase TM0960 during growth on xylose (11). Computational analysis of LacI regulators has determined that TM0949 is most similar to RbsR, a negative regulator of ribose uptake (17). Here, several genes within the TM0949-to-TM0960 gene string were upregulated during growth on xylose, ribose and arabinose (Fig. 3A), including rbsABCD homologs not examined previously by Chhabra et al. (11). From expression results alone, it is unclear whether this system can import multiple pentose sugars or whether transcription of the genes is triggered by the interconversion of xylose or arabinose to ribose via the pentose phosphate pathway (Fig. 3C). Two strong matches to a LacI family consensus binding site are arrayed consecutively upstream of the ribokinase TM0960 (Table S2 in the supplemental material), and a predicted rho-independent terminator located downstream of TM0949 is the only identifiable terminator within the gene cluster (Fig. 3A) (16). Similar to observations of other transport systems of T. maritima discussed below, the putative binding protein of this transport set (TM0958) was more highly upregulated than other transporter components.

Expression results shown here suggest several clarifications of T. maritima genome annotation and the T. maritima pentose phosphate pathway as predicted by sequence similarity in the KEGG database (25). The predicted KEGG pathway identifies an RpiB homolog responsible for the interconversion of ribulose-5-phosphate to ribose-5-phosphate as TM1080, which was detected at similar levels on all substrates (data not shown). However, expression results and sequence similarity suggest TM0951 as a possible candidate for a second, inducible ribose-5-phosphate isomerase. Two nearby transketolase subunits (TM0953 and TM0954) previously annotated as frameshifts are detected at higher levels during growth on xylose, ribose, and arabinose, a finding consistent with their proposed role in the T. maritima pentose phosphate pathway (Fig. 3C). Although TM0952 is annotated as a glycerol kinase, a second T. maritima glycerol kinase homolog (TM1430, GK2) shares greater sequence identity with Bacillus subtilis glpK (66% identity over 479 amino acids versus 45% identity over 487 amino acids) and colocalizes with other glycerol utilization genes. Both TM0952 and TM1430 belong to the FGGY family of carbohydrate kinases, which also include xylulokinases, fucokinases, and gluconokinases (Pfam00370). TM0116, a predicted T. maritima xylulokinase, is found within a distant operon (see below) but was not observed to be differentially expressed on any sugar substrate examined here (data not shown). Given the lack of additional glycerol utilization genes nearby TM0952, a role for the encoded protein as an inducible xylulokinase should be considered.

Two hypothetical proteins of unknown function within the TM0949-to-TM0960 locus are also differentially expressed. The functions of these proteins remain unclear, but their upregulation during growth on multiple pentoses suggests a plausible role in pentose uptake or catabolism. TM0950, which is related to a hypothetical protein in Lactobacillus johnsonii (LJ1257), contains no known domains. However, LJ1257 is located in a gene cluster with similar composition to the T. maritima pentose-responsive locus, including a putative sugar isomerase (LJ1064), a LacI family regulator (LJ1265), N- and C-terminal transketolase subunits (LJ1266-1267), and an FGGY family sugar kinase.

Homologs to the RbsABC ABC transporter subunits bearing 40 to 52% identity to the T. maritima homologs are found together in the genome of the hyperthermophile Thermoanaerobacter tencongensis (2) with a putative N-acetylglucosamine kinase (TTE0216) classified into COG2971 in the clusters of orthologous groups of proteins database (COG) (74). A related T. maritima protein (TM1280) was expressed much more highly during growth of T. maritima on xylose than on any other sugar examined. The expression of TM1280 was >30-fold higher during growth on xylose than on the ß-(1,4)-linked xylose polymer xylan. The annotation for sugar specificity of this putative kinase is apparently drawn from a distantly related human N-acetylglucosamine kinase (22), since the specificities of closely related microbial homologs have not yet been determined.

The second T. maritima CUT2 transport set is found with the XylR family regulator TM0110. Despite the lack of an rbsD cytoplasmic sugar-binding homolog, genes homologous to rbsABC are all present. Transcripts of TM0110 were detected at higher levels during growth on xylose compared to all other substrates tested here except laminarin, although other genes within this gene string were not significantly differentially expressed between xylose and any other sugar. Unlike the xylose catabolic genes of many model organisms, the characterized T. maritima xylose isomerase (TM1667) (1) is not found with the predicted xylulokinase (TM0116). This separation might reflect a broader physiological specificity of the TM1667 enzyme, which has also been used in the conversion of glucose to fructose (1) or may reflect differential regulation of the two activities in response to different xylose-containing substrates.

In addition to genes within the TM0949-to-TM0960 locus described above, other T. maritima genes also respond to the simple sugar L-arabinose, including a characterized L-arabinose isomerase (TM0276) (33), an {alpha}-L-arabinofuranosidase (TM0281), an uncharacterized conserved protein (TM0280), and a homolog to the protein araM from the B. subtilis arabinose utilization operon (66) (Fig. 3B). Located upstream of these genes is a LacI family regulator, TM0275, which is most similar to AraR from a Geobacillus stearothermophilus arabinose cluster (Table S2 in the supplemental material). Sugar ABC permease subunits TM0278 and TM0279 do not show strong differential regulation and, together with a frameshifted substrate-binding protein (TM0277), suggest a nonfunctional transporter.

Sequence analysis of Opp/Dpp transporters subunits in T. maritima. Taken together, the well-documented ability of T. maritima to use complex carbohydrates and the lack of annotated polysaccharides transporters suggested novel oligosaccharide transporters yet to be identified in the T. maritima genome. The high degree of identity between the Dpp/Opp family cellobiose transporter of P. furiosus and a likely cellobiose transporter of T. maritima (29) has raised the possibility that additional related transporters of T. maritima might transport oligosaccharides. The phylogeny of Opp/Dpp transport subunits in the COG database (74) and BLAST homology searches (Table S2 in the supplemental material) suggested three different lineage-specific gene expansions likely to have taken place after the divergence of T. maritima from the next closest sequenced organism. A consensus tree based on substrate-binding protein relationships with operon organizations superimposed is shown in Fig. 4. Duplication or acquisition of fully intact Opp/Dpp ABC transport operons (one substrate-binding protein, two permeases, and two ATP-binding subunits) can be inferred, although three solitary substrate-binding proteins are also apparent (Fig. 4 and Table 2). In two instances, these proteins display high levels of homology (>60% identity) to substrate-binding proteins of full transport systems, perhaps suggesting interaction with subunits of other transport systems. Duplication of Opp/Dpp substrate-binding proteins in T. maritima might accomplish expansion of sugar binding capabilities for related substrates, since the peptide specificities of two Opp/Dpp family transporters of Lactococcus lactis IL1403 have been largely attributed to features of substrate-binding proteins (14, 67).



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  		FIG. 4. Representative phylogenetic tree of substrate-binding proteins of peptide family transporters from T. maritima. All operons are shown on one strand to more clearly represent the relative positions of subunits. Black arrows represent substrate-binding proteins of the DppA family (COG0747), white arrows with diagonal stripes represent substrate-binding proteins of the OppA family (COG0747), dark gray arrows represent permease subunits of the DppB/OppB family (COG0601), light gray arrows represent permease subunits of the DppC/OppC family (COG1173), white arrows represent ATP-binding subunits of the DppD/OppD family (COG0444), and dotted white arrows represent ATP-binding subunits of the DppF/OppF family (COG4608). Other non-transport-related genes located between transporter subunits are represented as dotted arrows. Asterisks represent apparent lineage-specific gene expansions which have taken place since the divergence of T. maritima and the next closest fully sequenced organism. Black hairpins represent locations of GC-rich inverted repeats. The tree topology represented here is consistent with trees constructed using protein sequences for ATP-binding and permease subunits and was not altered by using pairwise or complete deletion of missing data or by tree construction method (neighbor-joining, minimum evolution, or maximum parsimony).

Expression of group 1 Opp/Dpp transporters is elevated during growth on ß-linked gluco-oligosaccharide substrates. Three related substrate-binding proteins detected at higher levels during growth with ß-linked sugars can be classified into group 1 of Opp/Dpp family transport operons (Fig. 4). These proteins share considerable similarity with a P. furiosus transporter implicated in the uptake of ß-1,4 linked glucose oligomers, including cellobiose, cellotriose, and laminaribose (29). Sequence similarity patterns suggest that this group likely arose from lateral gene transfer of one or two transport systems from archaea, followed by duplication of the sugar-binding protein and divergence of regulatory strategies and expression specificity (74). We have previously noted the location of a tightly conserved palindromic sequence motif similar to the LacI family consensus upstream of selected genes responsive to growth on carboxymethyl cellulose, barley glucan, glucomannan (11), and cellobiose (C. I. Montero and K. R. Kelly, unpublished observations). The putative regulator binding sites are situated between the –35 and –10 elements of consensus {sigma}A promoter binding sites (Table S2 in the supplemental material). Here, a biological repetition of the barley and glucomannan growth experiments confirmed upregulation of genes encoding cellobiose phosphorylase (TM1848) (58), two endoglucanases (TM1524 and TM1525), the LacI family regulator TM1218, and the Opp/Dpp family ABC transporter subunits encoded by TM1219 to TM1223 (36) (Fig. 5A). In keeping with the designation of the related P. furiosus transporter, we suggest the designation CbtABCDF for the T. maritima transport set. Consistent with observations in P. furiosus, the substrate-binding protein CbtA (TM1223) was more highly upregulated in response to ß-1,4-linked gluco-oligomers than the other transporter subunits (29). We suggest the designation CelR for the LacI family regulator TM1218. A search of the intervening sequence between TM1222 and TM1223 revealed a GC-rich inverted repeat with a spacing of two bases flanked by a {sigma}A-like promoter (Table S2 in the supplemental material). Subsequent searches of other Opp/Dpp family transporter strings revealed five additional cases of GC-rich inverted repeats located between coding sequences of Opp/Dpp family binding proteins and other transporter subunits, with spacing between the inverted repeats varying from n = 2 to n = 5 (Table S2 in the supplemental material and Fig. 4). Transcript levels detected from substrate-binding proteins responded more strongly during growth on the predicted transporter substrate than did other transporter components, raising the intriguing possibility that these inverted repeats might play a role in modulating transcriptional levels of transporter components.






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  		FIG. 5. Expression results for transcripts detected at higher levels on ß-linked polysaccharides. Small hairpin symbols represent locations of GC-rich inverted repeats, while large hairpin symbols represent locations of predicted rho-independent terminators (http://www.tigr.org/software/TransTermResults/btm.html). Predicted {sigma}A promoters are represented by arrows, and an asterisk denotes the position of a putative cellobiose regulator operator. Substrate-binding proteins are outlined in bold and boxed. Spacing between genes is less than 30 bases unless indicated otherwise. (A) Genes within a putative cellobiose transport operon (proposed designation CbtABCDF), including a likely regulator of cellobiose uptake and utilization (proposed designation CelR) and a colocalized mannan-responsive locus (including TM1224 [proposed designation ManR] and TM1226 [proposed designation MbtA]). (B) Genes within a glucomannan and galactomannan responsive locus include the Opp transporter components TM1746 to TM1752 (proposed designation MtpABCDF), Cel5A, and Cel5B and the ß-mannosidase TM1624. (C) Genes within a ß-glucan responsive locus (proposed designation BgtpABCDF), including a putative regulator of ß-glucan uptake (proposed designation BglcR). (D) Predicted pathway for the utilization of ß-glucans and glucomannan by T. maritima. Extracellular enzymes responsible for polysaccharide hydrolysis are shown, as well as periplasmic binding proteins, membrane-embedded permeases, associated ATP-binding subunits, and intracellular hydrolases. References for hydrolases shown in the pathway are listed in Table S1 in the supplemental material.

A second gene string, separated from TM1218 to TM1223 by 132 bases, encodes a XylR family regulatory protein (TM1224), a putative glycosylase (TM1225), a second CbtA homolog (TM1226, 60% identity with TM1223), and ManB (TM1227), a characterized ß-mannanase (55). TM1224 to TM1227 are upregulated on mannose-containing carbon sources (Fig. 5A), a finding consistent with the ability of the carbohydrate-binding domain of TM1227 to accommodate manno-oligosaccharides, galactomannan, and glucomannan degradation products (8). The specificity of the upregulation of TM1224 (here designated ManR) and TM1226 (here designated MbtA) on mannose, glucomannan, and galactomannan is especially striking. It appears likely that TM1226 might interact with the ATP-binding and permease subunits of the cellobiose transporter. In agreement with their close phylogenetic grouping, TM1223 and TM1226 are reciprocal best BLAST homologs; this suggests possible past duplication and specialization of the binding protein for the cellobiose transporter to accommodate mannan oligosaccharides. It also appears likely that expression of TM1226 could be under the transcriptional control of TM1224. Other candidates for regulation by TM1224 include genes previously observed to be upregulated on glucomannan and galactomannan within the TM1745-to-TM1752 gene string and the ß-mannosidase TM1624 (11) (Fig. 5B). Although the OppA-family binding protein TM1746 is more highly upregulated during growth on xylose, other components of the transporter (TM1747 to TM1750), two endoglucanases (Cel5A TM1751 and Cel5B TM1752), and a ß-mannosidase (TM1624) are highest during growth on mannans. We propose to designate the transporter components TM1746 to TM1750 as MtpABCDF (Table 2).

The third substrate-binding protein of group 1 (TM0031) is located within a gene string encoding the laminaribiase BglB/Cel3 (TM0025) (50, 89) and laminarinase TM0024 (7, 88), as well as components of an ABC transport complex homologous to CbtABCDF not examined by Chhabra et al. (11). A XylR family regulator (TM0032) is located upstream of the ABC transporter components. Higher transcript levels for components of this transporter during growth on the ß-1,3-linked glucose polymer laminarin, the mixed ß-1,3-ß-1,4-linkage glucose polysaccharide barley, and the ß-1,6-linked glucose polymer pustulan may suggest a general role in the uptake of ß-linked sugars (Fig. 5C). We suggest the designations BgtpABCDF and BglcR for the transporter and regulator, respectively (Table 2). Similarly to CbtA of the cellobiose transporter, TM0031 (BgtpA) was detected at higher levels in the presence of ß-glucans than other transporter components, and a GC-rich inverted repeat was found in the intervening sequence between BgtpA and TM0030 (BgtpB) (Table S2 in the supplemental material). A proposed pathway for the uptake and utilization of ß-glucan and ß-mannan oligosaccharides is shown in Fig. 5D.

Higher transcript levels of group 2 and 3 Opp/Dpp transporters during growth on xylose and xylose-containing oligosaccharides. Components of two distinct Opp/Dpp family transporters were detected at higher levels in the presence of the simple sugar xylose and the polysaccharide xylan (Table 1). The two sets of transport proteins are located nearby one another, separated by a set of genes predicted to encode enzymes for the catabolism of uronic acids. We have previously noted the similarities in functional composition of this gene cluster (11) to the xylan utilization cluster of Geobacillus stearothermophilus T-6 (68). Both sets of T. maritima transporters are divergently transcribed from family 10 xylanases (xylA/xyl10A, TM0061; xylB/xyl10B, TM0070) (Fig. 6), both reported previously to be active on xylan polysaccharides (13, 43, 79, 81, 82, 87). The similarities in expression profiles and gene content of the two gene sets do not appear to be the result of a recent duplication, as reflected in the consensus phylogenetic tree of Opp/Dpp family transport components (Fig. 4). Comparison with sequences from other sequenced organisms reveals that the TM0071-to-TM0075 gene set clusters with two other T. maritima ABC transporter sets in a grouping which apparently arose from a lateral gene transfer event with archaea (74), likely followed by duplication and divergence within an ancestral lineage (group 2, Fig. 4). In contrast, TM0056 to TM0060 cluster within a group of bacterial transporter proteins (74). The genomic arrangement of the two xylose and xylan-responsive transporter gene sets also differs (Fig. 6).



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  		FIG. 6. ß-Xylan and xylose-responsive operons from groups 2 and 3 of Opp/Dpp family transporters. Small hairpin symbols represent locations of GC-rich inverted repeats found between substrate-binding proteins and other transporter subunits, and large hairpin symbols represent locations of predicted rho-independent terminators (http://www.tigr.org/software/TransTermResults/btm.html). Predicted {sigma}A promoters are represented by arrows, and an asterisk denotes the positions of putative xylan/xylose regulator operator. Substrate-binding proteins are outlined in bold and boxed. Spacing between genes is less than 30 bases unless indicated otherwise. (A) XtpGHJLM, a predicted xylooligosaccharide transport system, is divergently transcribed from xylanase Xyl10A. (B) XtpABCDF, a predicted xylose/xyloside transport system, is divergently transcribed from xylanase Xyl10B.

We propose to designate TM0071 to TM0075 as XtpABCDF in keeping with the names assigned to orthologous proteins found in an unpublished cluster of xylan utilization genes from T. neapolitana (GI:23270356). Transcript levels of TM0071 were slightly higher on xylose than xylan, whereas other members of the transport operon showed various degrees of preference for xylose over xylan (Fig. 6B). In contrast, the substrate-binding protein TM0056 was detected at much higher levels during growth on xylan than xylose (Fig. 6A). Transcripts from the remaining transporter subunits (TM0057 to TM0060) and the {alpha}-glucuronidase AguA (TM0055) (62) were detected at higher levels during growth on xylose and xylan compared to nonxylose sugars. We propose to designate the transport proteins encoded by TM0056 to TM0060 as XtpGHJLM (Table 2). The DppA substrate-binding protein encoded by TM0309 (proposed designation XtpN) is closely related to TM0056 (Table S2) and is found nearby a predicted {alpha}-xylosidase (TM0308). The slight upregulation of both TM0309 (proposed designation XtpN) and TM0310 on xylan may suggest a role for these proteins (and possibly TM0308) in uptake and hydrolysis of an undetermined xylose-containing polysaccharide (Fig. 2).

The variation in expression patterns for the xylanase-associated ABC transporters may relate to differences in the carbohydrate binding specificity for T. maritima Xyl10A and Xyl10B. XylA contains four carbohydrate binding domains absent in XylB: the A1 and A2 domains of XylA have been shown to bind xylan while the C1 and C2 domains bind cellulose and a number of other monosaccharides and polysaccharides (7). The hydrolase content of the two gene strings also differs, suggesting likely specialization of the transporters for differently substituted xylan degradation products. A ß-xylosidase (86) and acetyl xylan esterase colocalize with TM0071 to TM0075, and an {alpha}-glucuronidase colocalizes with TM0056 to TM0060. Although no regulatory proteins are located within either xylanase-transporter gene string, similar inverted repeat sequences found upstream of Xyl10A (TM0061), Xyl10B (TM0070), and a putative {alpha}-xylosidase of glycosyl hydrolase family 31 (TM0308) share similarity with the consensus for a XylR family regulator (Table S2 in the supplemental material). The XylR family regulator (TM0110) is expressed more highly on xylose and laminarin than any other substrate. The observation of similar expression profiles on xylose and laminarin may relate to the co-occurrence of carbohydrate binding domains for binding xylan and mixed linkage glucan carbohydrates by distinct domains in Xyl10A (8) or reflect sequence similarity between the XylR family regulators TM0110 and TM0032 (BglcR).

Higher transcript levels of a group 3 Opp/Dpp transporter during growth on the simple sugar rhamnose. Growth of T. maritima on L-rhamnose (a methyl pentose also known as deoxy-L-mannose) had not been previously demonstrated. Within group 3 of the Opp/Dpp family transporters of T. maritima is a set of ABC transporter components which colocalize with predicted rhamnose catabolic genes (31, 48) (Fig. 7A). Here, the majority of genes that showed higher transcript levels during growth on rhamnose are found in this locus (Fig. 7A). Transcripts of nearly all genes encoding subunits of the transporter (TM1063 to TM1067) were observed at higher levels during growth on rhamnose compared to all other sugars examined here. We suggest the designation RtpABCDF for these transport components (Table 2). Similar to related transport systems, a GC-rich inverted repeat was found in the intervening sequence between RtpA (TM1067) and RtpB (TM1066) (Table S2 in the supplemental material). The presence of an {alpha}-glucuronidase (TM1068, Agu4C) and ß-glucuronidase (TM1062) within this locus suggest that the ABC transporter encoded by TM1063 to TM1067 might also be involved in the uptake of rhamnose-containing disaccharides or oligosaccharides that include glucuronic acid residues. A second candidate rhamnose transporter is encoded by TM1060, which shares sequence similarity with major facilitator superfamily sugar-proton symporters. Although the likely L-rhamnulose aldolase RhaD (TM1072) (53) and predicted rhamnulokinase RhaB (TM1073) are homologous to E. coli K-12 rhamnose catabolic genes, an RhaA rhamnose isomerase homolog is missing. A likely substitute is TM1071, annotated as a putative sugar isomerase, which is homologous to rhamnose isomerase RhaI of Rhizobium leguminosarum bv. trifolii (52) and Bacteroides thetaiotaomicron VPI-5482 (85). Several hypothetical proteins within the rhamnose locus present interesting targets for further work (Table S2 in the supplemental material).



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  		FIG. 7. Rhamnose responsive locus containing Opp/Dpp family transporter from group 3 of Opp/Dpp family transporters. Small hairpin symbols represent locations of GC-rich inverted repeats found between substrate-binding proteins and other transporter subunits. Predicted {sigma}A promoters are represented by arrows. Substrate-binding proteins are outlined in bold and boxed. Spacing between genes is less than 30 bases unless indicated otherwise. (A) A rhamnose-responsive locus contains candidate genes likely to encode enzymes responsible for the transport and hydrolysis of rhamnose-containing di- or oligosaccharides, and the complete catabolism of the simple sugar L-rhamnose. (B) A predicted pathway for the utilization of L-rhamnose by T. maritima. A periplasmic binding protein, membrane-embedded permeases, associated ATP-binding subunits, and rhamnose catabolic enzymes are shown.

Based on this analysis, a predicted pathway for rhamnose utilization in T. maritima is shown in Fig. 7B. Expression data from this locus also suggest a potential mechanism for transcriptional regulation. A DeoR/GlpR family transcriptional regulator (TM1069, COG1349) found within the rhamnose transport and catabolism cluster shares sequence identity with proteins found within rhamnose catabolic clusters of Bacillus halodurans (72) and Oceanobacillus iheyensis (73). Therefore, we propose to designate TM1069 as RhaR.

Opp/Dpp transporters of unknown specificity. Expression data and genomic neighborhood analysis did not reveal specific substrate preferences for several sets of Opp/Dpp family transporter components (Table 2). Further work will be necessary to clarify whether these proteins are involved in uptake of untested sugars or alternative substrates transported by other members of the Opp/Dpp transporter family, such as metal ions (84) or peptides (19, 57).


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DISCUSSION
 
The combination of microarray data with gene neighborhood and sequence analysis represents a powerful high-throughput approach for examining gene regulation and predicting functional roles of genes for microorganisms which lack genetic systems. Here, the genomic contexts and transcriptional responses of T. maritima genes to 14 monosaccharide and polysaccharide substrates were examined to improve upon previous annotations of ABC transporter proteins (48, 59). However, similar approaches could be used to perform substrate-by-substrate analysis of transcriptional responses to additional carbohydrates, peptides, metals, antibiotics, or other elements in microbial species for which microarrays are available. As demonstrated here, a loop experimental design allows efficient collection of large microarray datasets. Mixed model analysis of these datasets then enables comparisons between transcript levels for all pairs of substrates, rather than limiting comparisons to an arbitrary reference condition. In this case, this approach allowed greater flexibility in comparing responses to both changes in carbohydrate composition and branch type.

The transcriptional data presented here support the hypothesis that many members of the Opp/Dpp ABC transporter family of T. maritima are involved in carbohydrate transport, and explain the observation that glycoside hydrolases often colocalize with these genes. Given the differential regulation of related Opp/Dpp transport systems in response to carbohydrates, this strategy has likely allowed the acquisition of new uptake capabilities, perhaps assisting in the adaptation of Thermotoga species to specific environments. Transcriptional information was especially helpful in suggesting candidate substrates for several Opp/Dpp gene sets resulting from apparent lateral gene transfer followed by duplication and divergence (Fig. 4). In two cases, the next closest related transporter gene sets are found in archaea. In total, carbohydrate specificities were proposed for six full or partial operons of Opp/Dpp transporter subunits, and expression results were confirmed for two operons previously examined (11). The results obtained will assist in streamlining biochemical characterizations of substrate-binding protein specificities for T. maritima in progress in our laboratory and others. Although T. maritima does not grow on peptides as a sole carbon source, it is still unclear whether any of its Opp/Dpp transport systems are involved in peptide import. However, transcripts of an Opp/Dpp family transporter operon (TM0500 to TM0503) which lacks a substrate-binding protein are detected at higher levels in high density cocultures of T. maritima and Methanococcus jannaschii (24). This transporter may be involved in export of a small peptide (TM0504) located downstream of the transporter which has been implicated in quorum sensing and biofilm formation (24).

Differential expression information for predicted carbohydrate-responsive transcriptional regulators of T. maritima has now assisted in the prediction of putative functions for previously unannotated members of the LacI (three proteins), XylR (three proteins), and GlpR/DeoR (one protein) families. These include candidates for the control of the uptake of ß-glucans (TM1218 and TM0032) ß-mannans (TM1224), xylose/xylan (TM0110 and TM0949), arabinose (TM0275), and rhamnose (TM1069). Sequences resembling binding sites can be detected upstream of selected carbohydrate-responsive genes (Table S2 in the supplemental material), further supporting the hypothesis that some or all of these proteins are involved in the regulation of carbohydrate import. The specificities of most of these regulators would have been impossible to determine from sequence analysis alone, but transcriptional data now offer insights into plausible substrates for further characterization efforts.

For several Opp/Dpp transporter operons, substrate-binding proteins showed greater transcriptional responses to changes in carbon source than did other transporter subunits. If transcript levels correlate well with protein levels, this might indicate that transporter subunits are present in the absence of substrate. Increased transcription of substrate-binding proteins could allow maximal capture of available carbohydrates to be transported by existing permease and ATPase subunits. A partial explanation for the differential regulation of Opp/Dpp substrate-binding proteins relative to other transporter subunits is suggested by the presence of GC-rich hairpin structures in the intervening sequence between the subunits. The possibility that these hairpin sequences act as partial transcriptional terminators should be explored further.

In contrast to the Opp/Dpp family transporters, most members of known carbohydrate transporter families were not differentially expressed here. A notable exception was the CUT2 transporter which showed transcriptional responses to ribose, arabinose, and xylose. It is possible that other predicted sugar transporters respond to substrates not tested here. For example, maltose and lactose were not examined, but CUT1 transporters of T. maritima do respond to the presence of these sugars (51) (Table 2). The possibility remains that some T. maritima sugar transport operons are transcribed constitutively, perhaps independent of the control of local transcriptional regulators.

The lack of PTS system components in the T. maritima genome argues against mechanisms of global catabolite repression identical to those operating in gram-negative and gram-positive model organisms. Future work using microarrays to examine data from growth experiments with combinations of substrates will be needed to explore alternative mechanisms of preferred substrate utilization T. maritima. Although an alternative mechanism cannot be ruled out, the proximity of regulators and differentially expressed genes involved in sugar utilization provides evidence that local transcriptional regulators play important roles in regulating uptake of individual sugars through inducible ABC transport systems. Inducible and independent transcriptional control of transport systems of varied specificities may assist T. maritima in discriminating between and responding to complex polysaccharides found in its natural environment.


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ACKNOWLEDGMENTS
 
This study was supported in part by grants from the National Science Foundation (grants BES-0317886 and BES-0000487) and the Department of Energy, Energy Biosciences Program (grant DE-FG02-96ER20219).


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FOOTNOTES
 
* Corresponding author. Mailing address: Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905. Phone: (919) 515-6396. Fax: (919) 515-3465. E-mail: rmkelly{at}eos.ncsu.edu. Back

{dagger} Supplemental material for this article may be found at http://jb.asm.org/. Back

{ddagger} Present address: Biosystems Research Department, Sandia National Laboratories, Livermore, CA 94551. Back

§ Present address: Jackson Lab, 600 Main St., Bar Harbor, ME 04609. Back


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Journal of Bacteriology, November 2005, p. 7267-7282, Vol. 187, No. 21
0021-9193/05/$08.00+0     doi:10.1128/JB.187.21.7267-7282.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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