An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
© Wels et al; licensee BioMed Central Ltd. 2008
Received: 29 January 2008
Accepted: 14 July 2008
Published: 14 July 2008
T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism.
Hidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA. This is completely in line with findings reported in literature and with the proposed biological role of the regulatory element. For several species, the functional annotation of a large number of genes encoding proteins involved in amino acid transport could be improved significantly on basis of the amino acid specificity of the identified T-boxes. In addition, these annotations could be extrapolated to a larger number of orthologous systems in other species. Analysis of T-box distribution confirmed that the element is restricted predominantly to species of the phylum Firmicutes. Furthermore, it appeared that the distribution was highly species specific and that in the case of amino acid transport some boxes seemed to "pop-up" only recently.
We have demonstrated that the identification of the molecular specificity of a regulatory element can be of great help in solving notoriously difficult annotation issues, e.g. by defining the substrate specificity of genes encoding amino acid transporters on basis of the amino acid specificity of the regulatory T-box. Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control.
Transcription anti-termination is a regulatory mechanism commonly encountered in all lineages within the bacterial kingdom (see e.g. [1–3]). In transcription anti-termination, the regulation of transcription occurs after the initiation of RNA synthesis, but before transcription of the coding region. The mechanism of anti-termination involves a structural change in the RNA transcript that is dependent on the interaction of the transcript with, for instance, a regulatory protein , a tRNA  or a metabolite . The structural elements that compose these anti-terminators are encoded by conserved sequences on the DNA and can be found by searches for the related sequence motifs in upstream regions of regulated genes .
A well-studied anti-termination element is the so-called T-box. T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of tRNA charged with amino acids [2, 8]. When there is a sufficient supply of charged tRNA in a cell, the T-box folds into a terminator structure, thereby blocking further transcription. Transcription can only proceed upon conversion into an anti-terminator structure, which is induced by binding of a highly conserved 5'-NCCA-3' of the uncharged tRNA with a conserved '5-UGGN-3' sequence in the T-box [9–11]. Although anti-terminator formation involves contacts between many nucleotides, the specificity of the interaction seems largely dependent on the interaction of a tri-nucleotide (anti-anti)-codon in the so-called specifier loop of the T-box with the anti-codon of an amino acid-specific tRNA [12–15]. The structural and kinetic details of this interaction have been well-studied [16–22]. The appropriate assignment of the specifier codon has been used previously to improve the functional annotation of various genes located downstream of the T-box [3, 23–31]. The T-box controlled genes identified thus far encode functionalities that reflect perfectly the pivotal role of uncharged tRNAs in the regulatory mechanism. These functionalities include not only tRNA ligation, but also amino acid biosynthesis and transport [11, 17, 24, 26, 28, 32–34]. The encoded proteins are involved in modulation of the level of uncharged tRNA in the cell, either directly by charging the corresponding tRNA with its cognate amino acid or indirectly by controlling the intracellular concentration of the specific amino acid.
To date, T-boxes have been identified predominantly in the genomes of bacterial species of the phyla Firmicutes (including Mollicutes) and Actinobacteria , although anti-termination systems have been argued to be among the oldest regulatory systems in bacteria because of their independence of regulatory proteins . To investigate this further, we have explored the occurrence of T-boxes in all sequenced prokaryotic genomes. To circumvent potential differences between T-box systems in different bacterial lineages, an iterative HMM-based identification search was performed using the best conserved region of the T-box sequence. Species- and amino acid-specific T-box regulation networks were reconstructed. Most importantly, the acquired knowledge on amino acid specificity could be used to propose an improved functional annotation for many T-box controlled genes and to shed light on the evolution of the regulatory element itself.
Results and discussion
I) A comprehensive collection of T-boxes
The initial search showed prominent variations in the number of T-boxes per genome between different classes of the phylum Firmicutes and between different phyla. Therefore, additional searches with phylum-specific and class-specific T-box HMMs were performed, but generally did not yield novel hits. Only in the case of the Clostridia a limited number of 10 additional T-boxes were identified. Further iterations did not expand the dataset. Visual inspection of the upstream regions of all genes encoding a t-RNA ligase in the Firmicutes indicated that indeed all those regions that contain the distinctive T-box motifs were identified by our algorithm. A comparison of the number of T-boxes identified by us for a representative set of organisms with the number obtained using the Rfam T-box model  proved that our recovery procedure was very efficient (see methods for details).
Identification of the specifier codon and amino acid specificity
Although T-boxes were readily identified, it was more difficult to define their amino acid specificity. To that end, the phylogeny of homologous genes preceded by a T-box from different species was determined and the upstream regions corresponding to each orthologous group were aligned. In all the cases of T-boxes for which the specifier codon had been identified experimentally [3, 5, 9, 11, 12, 14–18, 21, 28, 29, 33], we observed that the specifier codon aligned perfectly within the related orthologous sequences. In fact, this was true for almost all orthologous groups of sequences. Moreover, most of the alignments could easily be clustered by eye into larger groups for which the specifier codon remained directly apparent from the alignment. The resulting alignments and the annotation of the specifier codon can be found at . Nevertheless, there remained a few less clear cases. For some (~5%) a secondary structure prediction could be used to provide the additional information required to define the specifier codon in the specifier loop . Taken together, a specifier codon could be identified directly for over 90% of the identified T-boxes.
Codon usage in the specifier codon
Most amino acids are encoded by multiple codons. Leu for instance, is encoded by six different codons (CUA, CUU, CUG, CUC, UUA and UUG). Remarkably, the T-boxes had a conserved preference for certain codons within as well as between species (Additional file 1). Evaluation of these preferences showed that they complied almost perfectly with the rules observed by Elf et al. for the codon usage by E. coli . In an elegant study these authors analyzed the dependence of the charging of various codon-specific tRNAs on the use of various codons in particular proteins. They concluded that: "when codon reading is part of a control loop that regulates synthesis of missing amino acid, the translation rate of the selected codon should be as sensitive as possible to starvation" . And, in their paper they showed which codons are the most sensitive in E. coli. We found that for all but one of the most predominantly used specifier codons in T-boxes, the corresponding tRNA is among the highest in sensing shortage of that specific amino acid in E. coli as reported by . The only exception was the T-box codon for Ala (GCU). Therefore, assuming the conclusions by Elf et al. are also valid for Gram-positive bacteria, our findings suggest that the codons that are sensitive to depletion are preferentially used in T-box regulation.
Functionalities controlled by a T-box
As expected, the proposed regulatory role of the T-box elements appeared to be perfectly reflected by the genes under their control. The majority of the T-boxes (62%) were found to precede genes encoding tRNA ligases, while most others were found upstream of genes encoding proteins involved in amino acid transport (12%) or amino acid biosynthesis (18%). The remaining T-boxes (8%; 71 genes in total) were found upstream of genes encoding proteins with unknown function (54 genes), or a function that lacks an apparent relation to amino acid metabolism (17 genes). A complete and species-specific subdivision of T-boxes based on function prediction of the proteins encoded downstream and a list of genes with no apparent relation to amino acid metabolism is provided in the supplementary material, in Additional files 1 and 2.
II) The use of regulator specificity to improve annotation of molecular function and biological role
We made two important observations: i) In all cases, the T-boxes identified upstream of the genes encoding a tRNA ligase contained a specifier codon that corresponded with the amino acid specificity of the ligase; and ii) in all other cases where the function of the protein encoded by the gene downstream of the T-box had experimentally been verified, the specifier-codon corresponded to the established functionality of the gene. These observations implied that the employed method for the identification of T-box specificity was reliable and, consequently, that predicted T-box specificities could be extrapolated to the molecular function of the protein encoded by the gene located downstream, as had occasionally been done before. Many of the genes preceded by a T-box had not been specifically annotated to date in the sense that, although the functional category was often evident (e.g. proton symport, ABC transport family, etc.), a specific molecular function had not been attributed. In fact, more than two-third of the non-tRNA ligase genes preceded by a T-box lacked such a specific annotation of molecular function. As importantly, the functional annotation of the genes could be extended to a different level entirely by using the knowledge on T-box (regulator) specificity, as this knowledge discloses (in part) under which conditions the regulated genes will play their biological role (for the distinction between molecular function and biological role see Francke et al. ).
a) T-box regulation of amino acid transport
Overview of T-box regulated transporter genes in different Firmicutes. The type and number (between brackets) of transporters are displayed per species and according to their predicted specificity.
B. anthracis Ames 0581
B. licheniformis ATCC 14580
B. subtilis 168
O. iheyensis HTE813
L. monocytogenes EGD-e
L. plantarum WCFS1
L. acidophilus NCFM
L. johnsonii NCC 533
E. faecalis V583
L. Lactis IL1403
S. pneumoniae R6
C. acetobutylicum ATCC824
C. perfringens ATCC13124
C. tetani E88
Overall, for more than 85% of the T-box regulated transporters the functional annotation (molecular function and/or biological role) could be improved as compared to the entries in the reference database of NCBI. A full list can be found in Additional file 1. We have limited the substrate specificity definition in our annotation to putatively dominant substrates based on the amino acid specificity of the T-box. However, broader substrate specificity is probably more common for transporters. Especially transport systems consisting of only a permease are expected (and have been shown) to display broader substrate specificity (see  and  for examples), whereas systems that require prior substrate-binding (like in ABC transport) will be more specific. We discuss the T-box based functional annotation of some transport systems in more detail in the following paragraphs and in Additional file 3.
The ABC family
The APC family
The LIVCS family
The Bacilli of the Bacillus cereus group, the Lactobacilli and the Clostridia contain several branched-chain amino acid cation symporters of the LIVCS-family , some of which are T-box regulated (Figure 3). Since the three branched-chain amino acids share very similar molecular properties (e.g. size and hydrophobicity) we expect that these transporters are not highly specific despite their proposed amino acid specific control, but merely that expression of the "multi-specific" system has been brought under the control of the individual amino acids. Indeed, the orthologous transporters that have been characterized in L. delbrueckii (BrnQ; ), C. glutamicum (BrnQ; [47, 48]) and P. aeruginosa (BraZ; ) displayed transport of all three branched-chain amino acids.
The NSS family
b) Hypothetical proteins controlled by a T-box
Proposed annotation of the genes regulated by a T-box that were assigned as "hypothetical protein" in the original NCBI annotation file.
Bacillus halodurans C-125
Bacillus subtilis 168
Anti TRAP protein
Enterococcus faecalis V583
Gly related hypothetical
Lactobacillus acidophilus NCFM
Ile related hypothetical
Lactobacillus johnsonii NCC 533
5-methyltetrahydropteroyltriglutamate – homocysteine methyltransferase (Methionine synthase)
Lactobacillus plantarum WCFS1
5-methyltetrahydropteroyltriglutamate – homocysteine methyltransferase (Methionine synthase)
Histidine transport system permease protein hisM
Met related cytosolic hypothetical
Staphylococcus aureus 2
Anthranilate synthase component I
Streptococcus agalactiae 3
Ala-tRNA ligase related hypothetical
Streptococcus pneumoniae 4
Val-tRNA ligase related hypothetical
Ala-tRNA ligase related hypothetical
Gly-tRNA ligase related hypothetical
Thr-tRNA ligase related hypothetical
Trp biosynthesis related hypothetical
Streptococcus thermophilus 5
Val-tRNA ligase related hypothetical
III) Taxonomic variation and T-box evolution
The occurrence of T-boxes in different bacterial phyla. The phyla are taken from the NCBI taxonomy .
Genomes with at least one T-box
Number of T-boxes
To evaluate the phylogenetic distribution of T-boxes in more detail, the correlation between the presence of T-box regulatory elements and the regulated genes was analyzed for the Firmicutes and will be described shortly in the next sections. Furthermore, the scattered appearance of these regulatory boxes as observed for the various transporter families will be discussed.
T-box regulation of genes encoding tRNA ligases in the Firmicutes
It appeared (Figure 4) that regulation by T-boxes is conserved in almost all (at least 29 out of 34) Firmicutes for several tRNA ligases (ileS, a laS, serS and thrS), whereas some tRNA ligases (lysS, asnS and gltX; the latter gene encodes a Glu-tRNA ligase (see also the legend of Figure 4)) appeared to be controlled by a T-box in only a few species. The genes encoding the tRNA ligases for cysteine and asparagine were often found as the second gene in a putative operon that was T-box regulated. In several organisms, multiple copies of amino-acid specific tRNA-ligase encoding genes are found and in more than half of the cases (58%) only one of them is subject to T-box regulation.
A clear phylogenetic effect is observed when the four major orders within the Firmicutes (Bacillales, Clostridia, Lactobacillales and Mollicutes) are compared. This is true for both the number and the type of tRNA-ligase encoding genes regulated by a T-box. Most T-box regulated tRNA-ligase encoding genes are found in the Bacillales and especially in species of the Bacillus cereus group. Within the Lactobacillales, it appears that Streptococci have far less tRNA- ligase encoding genes regulated by T-boxes than Lactobacillus species. The lowest number of tRNA ligases regulated by T-boxes was found for S. thermophilus, S. pneumoniae and some strains of S. pyogenes. The relatively low amount of T-box regulation in these species could be the result of regressive evolution, a process that was suggested to be the underlying mechanism for the large loss of functionally active genes in S. thermophilus .
T-box regulation of genes involved in amino acid biosynthesis in the Firmicutes
The evolution and propagation of T-boxes
An important observation related to T-box evolution was made by Grundy et al. [9, 12]. They showed that a single nucleotide change in the specifier codon of the Tyr T-box of tyrS in B. subtilis was enough to change the amino acid specificity. In addition, while analyzing the distribution of T-boxes over the various transporter families we were struck by the fact that although some of these families are very large, there was only one (or a few) family-member(s) found to be regulated by a T-box and only in a restricted number of species (see Table 1 and e.g. Figure 3). In our opinion, the only likely scenario to explain the phylogenetically limited occurrence of the transporter T-box associations that would not imply massive loss of the T-box regulation was that of acquisition of the regulatory element by the transporter encoding gene in a specific lineage. Moreover, the results of Grundy et al. [9, 12] imply that in principle the T-Box can change specificity easily.
To limit possible obscuring effects of comparing sequences between species, we collected and compared the T-box sequences within species and for clarity restricted the comparison to the T-boxes that accompany transport systems and the related tRNA ligases. For all three analyzed species: B. anthracis, L. acidophilus and L. plantarum. similar phenomena were observed. The multiple sequence alignment of the analyzed T-box sequences and the associated NJ-tree (depicted in Figure 6C for B. anthracis) are strongly suggestive of a close evolutionary relationship between several of the T-boxes. For example in B. anthracis, the Thr T-boxes found in front of BA4970 (transport systems of LIVCS-type) and the Thr-tRNA ligase (BA4820) were highly similar and the same was observed for the Ile T-boxes found in front of another LIVCS homolog and the Ile-tRNA ligase. As the LIVCS homologs appear closely related in time (apparent duplication in the B. cereus group ancestor, see Figure 3), the data imply that the regulatory T-box was not inherited in a similar way but 'acquired' independently. In fact, this explanation fits the observed scattered appearance of the T-boxes for the various transporter families perfectly.
The results presented in Figure 6 are also suggestive of another way in which the T-boxes have evolved. The NJ-tree relates the Phe T-box found in front of one of the NSS family transporters to the Tyr T-box associated with the Tyr-tRNA ligase (Figure 6C). It thus seems that the Tyr T-box of the tRNA ligase was duplicated -as this T-box is present in various Firmicutes species- and has diverged/adapted to control a Phe transporter in the Bacilli of the B. cereus group. In fact, the similarity between the T-box upstream of Tyr-tRNA ligase and the Phe T-box in front of the transporter is higher than between the Tyr T-box and the Tyr T-box preceding BA4353 (NhaC family transporter). This is consistent with the fact that: the Tyr T-box acquisition of the NhaC ortholog should have occurred earlier in history, as the Tyr T-box control of the NhaC ortholog is present in several Firmicutes, and the sequences thus had more time to diverge.
The sequence signature of a T-box is very specific and as a result T-boxes can be readily identified. Using specific T-box HMMs, we identified a large number of the T-boxes and their amino acid specificity in sequenced prokaryote genomes.
An important aspect of this work is that we show that the prediction of the amino acid specificity of the various T-boxes can be used to improve the functional annotation of a large number of genes. In particular, the functional annotation of genes related to amino acid transport and genes with unknown substrate specificity, genes for which it is normally quite difficult to find functional attributes, could be improved significantly. In our opinion, the procedure of improving annotation through knowledge of the regulatory signals can be generalized and should be used on a much broader scale than currently is being done.
Riboswitches have been argued to be among the oldest regulatory systems in bacteria because of their independence of regulatory proteins and widespread biological distribution . One might therefore have expected that T-boxes are abundantly present among all different lineages of bacteria. This clearly can not be concluded from our results and those presented in other studies [52, 55]. In fact, these regulatory elements can only be found in a few bacterial phyla and only abundantly in the phylum Firmicutes. This implies that either Firmicutes developed T-box regulation after their branching off from the other bacteria or that the other bacteria lost the system soon after the branching off of the Firmicutes to evolve more complex regulatory systems. Which of the two scenarios is most likely remains unclear.
Nevertheless our data do allow some extrapolation of the propagation of T-boxes within the phylum Firmicutes. We conclude on basis of our observations that the T-boxes have evolved in four clearly distinct ways: i) by co-evolution with the regulated gene or operon; ii) by co-evolution and divergence with the regulated gene or operon to adopt a new specificity; by iii) duplication and insertion of the regulatory element in front of a gene or operon that encodes functions related to the T-box-specified amino acid; and finally iv) by duplication and divergence toward a new amino acid specificity after duplication. In short, this means that every T-box regulatory element acts as a connected yet independent "functional module". The fact that the isoleucine specific T-box connected to the ile-tRNA ligase encoding gene is the only box present in all T-box containing bacteria suggests this box could very well compose the archetype T-box.
Sequence information and tools
Genome sequences and annotation files of completely sequenced bacterial and archaeal genomes were downloaded from the NCBI repository . In addition, for the analysis of the molecular functions encoded by T-box controlled genes, genomic information was obtained from the ERGO genome analysis and discovery system . Multiple sequence alignments were created with MUSCLE  and bootstrapped Neighbor-Joining trees with CLUSTALX  (corrected for multiple substitutions). HMMs were constructed from a multiple sequence alignment using HMMER 2.3.2 . Conserved nucleotide sequence motifs were recovered via MEME  (settings: maximally 5 motifs, modus ZOOPs, minimal width 10 nt, maximal width 30 nt) and visualized using Weblogo . Hidden Markov Models (HMMs) were constructed on basis of the recovered motifs to perform genome-wide searches. Although HMMsearch  yielded essentially identical results to the search-tool MAST , in our hands the procedure was much faster and the output was easier to interpret (including motif e-values rather than p-values). RNA secondary structure predictions were performed by Mfold  using default settings.
Identification of a general T-box sequence
The T-boxes reported so far in literature were mainly located upstream of tRNA-ligase encoding genes in species of the phylum Firmicutes [7, 26]. We therefore initiated the search for a general T-box sequence motif by collecting the nucleotide sequences (300 nt) preceding all tRNA ligases (n = 910) found in sequenced genomes of the Firmicutes. Five characteristic consecutive motifs were recovered in the nucleotide sequences (displayed in Figure 1). They were part of a generic T-box sequence that spans a length of about 250 nt, as described by . The best-conserved motif (Figure 1, motif 1, E-value = 1.2e-2841), which is located closest to the translation start, had a length of 30 nt and was found in about 61% (n = 553) of the nucleotide sequences. A genome-wide HMMsearch based upon the best-conserved motif yielded 374 new hits. To probe eventual in-homogeneity induced by the fact that only T-boxes associated with tRNA ligases were taken to create the initial T-box HMM, a new HMM based on the non-tRNA ligase associated T-boxes was made and the genomes were searched anew. We found that all t-RNA ligase associated T-boxes were recovered (with an e-value < 1) with this new HMM. This finding implied that the set of recovered T-boxes was relatively homogeneous. The upstream 500 nt of every putative best-conserved T-box motif was then checked for the presence of at least one of the four other conserved T-box specific motifs recovered using MEME. In 40 cases (less than 4% of total) none of the other motifs was detected. Without exception, these were not located in the proximity of a coding sequence and thus unlikely to be related to transcription attenuation. The hits were therefore considered false-positives and were removed. To potentially increase the recovery rate, the remaining 887 T-box sequences were subdivided on basis of the taxonomy of the species and taxonomic class-specific HMMs were built as before. This procedure yielded only 10 additional T-boxes. Finally, the position of all boxes with respect to the start-codon of the proximal gene was determined. It appeared that In 839 cases, motif 1 was found to be located within 300 nucleotides upstream of a predicted gene start. The remaining 48 T-boxes were located 300 to 480 nt upstream of a start-codon. Manual inspection of those T-boxes revealed an overrepresentation of the proximal genes thrZ (11×), trpE (11×), branched amino acid transferase (5×), chorismate mutase (5×) and a sodium symporter (4×). In fact, for both thrZ and trpE it was previously shown that they are preceeded by multiple (2 or 3) adjacently located T-boxes in different bacilli [3, 29].
Functional classification of the genes regulated by T-boxes
The genes downstream of the recovered T-boxes were divided into four different classes on basis of the gene annotation information of the proximal gene: 'tRNA ligation', 'amino acid biosynthesis, 'amino acid transport' and 'other'. In those cases the T-box preceded an operon (45%) it appeared that most of these operons (>75%) contained genes of only one functional class.
Comparison with the Rfam T-box model
The Rfam database  is an excellent reference database to start the identification of specific RNA-motifs. To evaluate the performance of our recovery procedure, we compared our results with predictions based on the Rfam T-box HMM. Unfortunately, a direct comparison with the contents of the database proved not informative as the Rfam database includes all nucleotide sequences present in the TREMBL database, which includes many genome fragments or partially sequenced genomes, whereas our analysis was restricted to completed genomes.
Therefore, we used the Rfam model to search for T-boxes against the same set of complete genome sequences that was used for our analysis. A striking difference between the Rfam-search and our analysis was that the Rfam-search was computationally far more expensive (more than three weeks on an 8 node,16 core, linux cluster compared to 16 hours on a 2 core linux system). For the selected species we predicted 883 T-boxes characterized by the presence of all the characteristic motifs, of which 835 (95%) were within the first 300 nt upstream of a gene start. When using a cut-off of 53.000 bits (described by Rfam as reliable) only 501 (60%) of the 883 T-boxes were predicted using Rfam. In addition to these 501 shared T-boxes Rfam identified 8 additional genuine T-boxes (~0.9 gain) within the first 300 nt. upstream of a gene start. At a lower cutoff-value (25.000 bits), chosen such that ~81% (683) of the boxes identified by us were recovered, the prediction with our HMM and the Rfam results were more alike albeit that Rfam now also yielded a considerable number of false positive identifications: only ~90% of the total number of T-boxes was found within the first 300 nt. upstream of a gene start. Using this cutoff, 6 additional genuine T-boxes were found (~0.7% gain) to be present within the first 300 nt. upstream of a gene start. When applying no cutoff, the Rfam-search retrieved 89% (745) of the T-boxes that were found in our analysis. However, in this case the number of putative false-positives (not located within 300 nt upstream of a gene start) had increased to 65% of the total.
We would like to thank Victor de Jager for his assistance in applying the Rfam calculations, Jos Boekhorst and Richard Notebaart for insightful discussions. Christof Francke gratefully acknowledges the support of NBIC/the Netherlands Genomics Initiative via the Kluyver Centre for Genomics of Industrial Fermentations and the BioRange program. For our work we used the life-science grid, which is part of the Dutch e-Science Grid (BIG GRID) and which is a collaborative effort of Netherlands National Computing Facilities foundation (NCF), the Netherlands Bioinformatics Centre (NBIC) and the National Institute for Nuclear Physics and High Energy Physics (NIKHEF).
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