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Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Canada L8N 3Z5
Correspondence
Radhey S. Gupta
gupta{at}mcmaster.ca
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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The GenBank/EMBL/DDBJ accession numbers for the novel sequences described in this paper are indicated in Figs 1–4
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Full Cox1, CTP synthetase and GluRS alignments and accession numbers of 16S rRNA gene and CTP synthetase gene sequences used are available as supplementary material in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). This lineage is comprised of Gram-positive organisms with a high G+C content (greater than 55 mol%). The phylum encompasses genera covering a wide range of morphology: some species are coccoid (e.g. Micrococcus) or rod–coccoid (e.g. Arthrobacter) in shape, while others display fragmenting hyphal forms (e.g. Nocardia) or permanent and highly differentiated branched mycelium (e.g. Streptomyces) (Atlas, 1997). Previously, organisms producing a mycelium which resembles that of the unrelated fungi were classified as the actinomycetes (Embley & Stackebrandt, 1994; Atlas, 1997). Spore formation is common among the actinobacteria, although not ubiquitous, and spores range from motile zoospores to specialized propagules. They are also physiologically diverse bacteria, as evidenced by their production of numerous extracellular enzymes and by the thousands of metabolic products they synthesize and excrete (Schrempf, 2001), many of which are antibiotics (Lechevalier & Lechevalier, 1967). Actinobacteria, especially members of the Streptomycetaceae, are the major antibiotic producers in the pharmaceutical industry (Davies, 1996; Bentley et al., 2002). However, a few actinobacteria are important human, animal and plant pathogens. For example, Mycobacterium tuberculosis infection results in tuberculosis, Corynebacterium diphtheriae causes diphtheria and Propionibacterium acnes is the causative agent of acne (Leyden, 2001). Actinobacterial species are widely distributed in both terrestrial and aquatic ecosystems, especially in soil (Goodfellow & Williams, 1983; Chun et al., 2000). In nature, actinobacteria play an important role in decomposition and humus formation, which is an integral part of the recycling of biomaterials (Lechevalier & Lechevalier, 1967; Goodfellow & Williams, 1983).
Due to their pharmaceutical, industrial and environmental importance, the taxonomy and phylogeny of the actinobacteria are of great interest (Embley & Stackebrandt, 1994; Stackebrandt et al., 1997; Ahmad et al., 2000; Stach et al., 2003; Richert et al., 2005; Bull et al., 2005). Earlier attempts to determine actinobacterial phylogenies based on morphological and chemotaxonomic traits were found to be unreliable indicators of phylogenetic relationships above the family level (Embley & Stackebrandt, 1994). Hence, our current understanding of the taxonomy and evolutionary relationships of actinobacterial divisions is mainly based on the branching patterns of these species in 16S rRNA trees. Different species have been placed in this group based on 16S rRNA oligonucleotide catalogues and phylogenetic analysis based on full and partial 16S rRNA gene sequences, although some species do not possess a high G+C content (Woese, 1987; Stackebrandt et al., 1997; Labeda & Kroppenstedt, 2000; Ludwig & Klenk, 2001). In 1997, a new taxonomic hierarchical classification for the actinobacteria was proposed by Stackebrandt et al. (1997), which recognized this group as a distinct class, Actinobacteria, within the Gram-positive bacteria. In the latest Bergey's Manual, the actinobacteria have been assigned the rank of a phylum, recognizing that the phylogenetic depth represented in this lineage is equivalent to that of existing phyla and that the group shows clear separation from the Firmicutes (Garrity & Holt, 2001). According to Bergey's Manual (Garrity & Holt, 2001), the phylum Actinobacteria comprises 39 families and 130 genera, making it one of the largest groups within the Bacteria. However, except for their distinct clustering in 16S rRNA trees, no other reliable biochemical or molecular characteristics are presently known which can clearly distinguish species belonging to the phylum Actinobacteria from other bacteria.
Presently, the genomes of at least 14 different actinobacteria (in some cases multiple strains of the same species) have been sequenced: Mycobacterium leprae, Mycobacterium bovis, Mycobacterium tuberculosis, Mycobacterium avium, Corynebacterium diphtheriae, Corynebacterium efficiens, Corynebacterium glutamicum, Tropheryma whipplei, Leifsonia xyli subsp. xyli, Nocardia farcinica, Streptomyces avermitilis, Streptomyces coelicolor, Bifidobacterium longum and Symbiobacterium thermophilum (Smith et al., 1997; Bentley et al., 2002; Schell et al., 2002; Camus et al., 2002; Fleischmann et al., 2002; Garnier et al., 2003; Ikeda et al., 2003; Karlin et al., 2003; Cerdeno-Tarraga et al., 2003; Raoult et al., 2003; Ueda et al., 2004; Bruggemann et al., 2004; Monteiro-Vitorello et al., 2004; Ishikawa et al., 2004). This provides a valuable resource for discovering novel molecular characteristics that are useful for biochemical, taxonomic and phylogenetic purposes (Sutcliffe & Harrington, 2002; Karlin et al., 2003). Our recent work has focused on identifying conserved inserts or deletions (i.e. indels) in widely distributed proteins that are characteristic of the different groups of bacteria and are also helpful in understanding the interrelationships among them (Gupta, 1998, 2001) (see also http://www.bacterialphylogeny.com). We have previously identified a large number of conserved indels (or signature sequences) that provide distinctive molecular markers for the phyla Proteobacteria, Chlamydiae, Cyanobacteria and ‘Deinococcus–Thermus’ (Gupta, 2000, 2004; Gupta et al., 2003; Griffiths & Gupta, 2004a, b) (see also http://www.bacterialphylogeny.com). In the present work, we describe three novel signature indels in three highly conserved and widely distributed proteins [cytochrome-c oxidase subunit 1 (Cox1), glutamyl-tRNA synthetase (GluRS) and CTP synthetase] that are distinctive characteristics of the phylum Actinobacteria and are not found in any other bacteria. Sequence information for these proteins was previously available from only a limited number of actinobacteria, whose genomes have been sequenced. One possible signature for actinobacteria, consisting of a large insert in the 23S rRNA, has previously been described (Roller et al., 1992). However, the validity and specificity of this signature also needs to be further tested using sequence data from additional species. In the present work, we have examined the presence of the newly identified signatures in Cox1, GluRS and CTP synthetase, and also the 23S rRNA signature, from a broad range of actinobacterial species by PCR amplification and sequencing of the corresponding gene fragments. The results of our studies show that the signatures in Cox1, CTP synthetase and 23S rRNA are present in all actinobacterial species, indicating that they are very likely distinctive characteristics of the entire phylum and might be used as molecular markers for this group of species. The signature for GluRS was found to be lacking in two actinobacterial species (Thermobifida fusca and Propionibacterium acnes), which could result from either selective loss or other non-specific mechanisms such as lateral gene transfer.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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. This table also includes information for different actinobacterial species whose genomes have been sequenced and whose sequences were available to us. Together these strains cover a broad range of the diversity represented by this phylum. Various recently described type strains were purchased from the DSMZ (German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) and cultured under the recommended conditions. Chromosomal DNA was purified by the following method. A 100 µl pellet was transferred to a microcentrifuge tube and washed three times with 0·5 ml 10·3 % sucrose. The cell pellet was resuspended in 0·5 ml buffer containing 0·3 M sucrose, 25 mM Tris/HCl, 25 mM EDTA, pH 8·0, and 2 mg lysozyme ml–1 and incubated for 2 h at 37 °C. Next, 50 µl 20 % SDS was added and the cell suspension was incubated at 65 °C for 30 min. The cell lysate was extracted with chloroform twice and the aqueous layer was separated during centrifugation at 14 000 g for 15 min. The DNA was precipitated with 2 vols ethanol and dissolved in sterile water for PCR amplification. Chromosomal DNA of Rhodococcus rhodochrous and Propionibacterium acnes was generously provided to us by Dr L. D. Eltis (University of British Columbia, Canada) (Warren et al., 2004) and Dr Mark Farrar (Leeds University, UK) (Farrar et al., 2000).
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, 2004; Gupta et al., 2003; Griffiths & Gupta, 2004a). To search for actinobacteria-specific signatures, these alignments were inspected visually to identify any indel that was uniquely present in all available actinobacterial homologues and which was flanked by conserved sequences. Indels which were not flanked by conserved regions and/or which were not present in all actinobacterial species were omitted from further consideration. The specificity of potentially useful indels for actinobacteria was further evaluated by carrying out detailed BLAST searches on short sequence segments (usually between 60 and 100 aa) containing the indel and the flanking conserved regions. The purpose of these BLAST searches was to obtain sequence information from all available bacterial homologues to ensure that the identified signatures are only present in the actinobacterial homologues. Sequence information for representative species from different groups for various useful signatures was compiled into signature files such as those shown here. Detailed information for these signatures from all available species is provided as supplementary material in IJSEM Online.
PCR amplification and sequencing.
Degenerate oligonucleotide primers, in opposite orientations, were designed for highly conserved regions that flanked the identified signatures in sequence alignments. The sequences of various PCR primers used in these studies are given in Table 2. The PCR was performed in 30 µl solution and all primer sets were optimized for Mg2+ concentration (in the range of 1·5 to 4 mM) for each strain tested. PCR amplification was carried out in a Techne Progene thermocycler. After an initial denaturation step at 97 °C, the DNA was amplified for 30 cycles (30 s at 97 °C, 30 s at 55 °C, 1 min at 72 °C). The last cycle was followed by a 15 min extension at 72 °C. Because all the genomic actinobacterial DNA we tested contained a high G+C content, the denaturation temperature was set to 97 °C so that the DNA was mostly denatured in a short time with less damage. DNA fragments of the expected size were purified from 0·8 % (w/v) agarose gels and subcloned into the plasmid pDRIVE using a UA cloning kit (Qiagen). After transforming Escherichia coli JM109 cells with the plasmids, inserts from a number of positive clones were sequenced. Sequence information for various actinobacterial species has been deposited in GenBank and accession numbers are given in Figs 1–4.
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). All the fragments were trimmed to the same length as the amplified fragments. Neighbour-joining distance trees showing branch lengths were constructed applying Kimura's correction (Kimura, 1980). The trees were produced by using the TREECON program (Van de Peer & De Wachter, 1994). |
RESULTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). Hence, to determine the actinobacterial specificities of the identified signatures, we have cultured and extracted chromosomal DNA of 23 actinobacterial type strains, covering a large number of orders and suborders (e.g. Rubrobacterineae, Micrococcineae, Corynebacterineae, Micromonosporineae, Propionibacterineae, Pseudonocardineae, Streptomycineae and Streptosporangineae) within this phylum (Table 1). Sequence information for the identified signatures was obtained from many of these species to confirm and validate the specificity of the signatures. A brief description of the newly identified signatures and the work that we have carried out on them is given below.
One of the actinobacteria-specific signatures that we have identified is present in the Cox1 protein. Cytochrome-c oxidase is an intrinsic membrane protein, composed of three subunits, that functions as the terminal enzyme of the respiratory electron transport chain (Michel et al., 1998). In the Cox1 subunit, a 2 aa gap is present in a conserved region (boxed in Fig. 1) that is unique to various actinobacterial species, and is not seen in any other bacteria. Because this sequence gap is absent in Cox1 homologues from all other groups of bacteria, it likely constitutes a deletion in the actinobacterial homologues. By means of PCR amplification, we were successful in obtaining sequence information for the Cox1 gene from 22 additional actinobacterial species belonging to different orders and families. All of these new fragments were also found to contain this 2 aa deletion at the same position. Sequence information for this region from various actinobacterial species (including those sequenced in the present work) and some representatives from other groups of bacteria is presented in Fig. 1. A complete alignment of all available Cox1 homologues in GenBank, which includes 37 sequences from actinobacterial species and 117 sequences from other bacterial groups such as Firmicutes, ‘Deinococcus–Thermus’, Cyanobacteria, Chlamydiae, the Cytophaga–Flavobacterium–Bacteroides–green sulfur bacteria (CFBG), Spirochaetes, Aquifex and Proteobacteria, is provided in Supplementary Fig. S1 available in IJSEM Online. As seen, the observed 2 aa deletion is unique to actinobacteria, and no exceptions were observed. The shared presence of this 2 aa deletion in various actinobacteria strongly indicates that it was introduced only once in a common ancestor of the actinobacteria and passed on to all their descendents. Because of its unique presence in various actinobacteria, this signature provides a good molecular marker for distinguishing actinobacterial species from other bacterial phyla. In the structure of the Cox1 protein from Paracoccus denitrificans, the region where this deletion is present (residues 332–333) is located on the periplasmic surface (Michel et al., 1998), but its functional significance remains to be determined. It should be mentioned that the 2 aa deletion in Cox1 is absent in Symbiobacterium thermophilum, which is presently grouped within the Actinobacteria. However, recent genomic analyses indicate that this species is much more closely related to bacilli and clostridia than to actinobacteria (Ueda et al., 2004) (see Discussion).
Another signature for actinobacteria is present in the enzyme CTP synthetase, which catalyses the conversion of UTP into CTP by transferring an amino group to the 4-oxo group of the uracil ring (Endrizzi et al., 2004). Except for the mycoplasma species, the gene encoding CTP synthetase is present in all other microbial genomes and has only one copy in the genome. A 10 aa insert which is distinctive of various proteobacterial species has previously been identified in this protein (Gupta, 2000). Interestingly, in the same position where this proteobacterial insert is present, a smaller, 4 aa insert is found in all actinobacterial species except Tropheryma whipplei, which contains a 3 aa insert in this position (Fig. 2). This insert is again highly specific for actinobacteria and is not present in the CTP synthetase homologues from any other bacteria whose sequences are available in the databases (see Supplementary Fig. S2). In the present work, we have successfully amplified CTP synthetase gene fragments from 15 additional actinobacterial strains and all of these were found to contain this 4 aa insert in the same position (Fig. 2). We were not able to amplify sequences for other actinobacterial strains, including that for Rubrobacter radiotolerans DSM 5868T, using these primer sets. Based on its shared presence in various actinobacterial species, the identified insert in CTP synthetase was likely introduced in a common ancestor of the phylum Actinobacteria, independently of the insert in the proteobacteria, and it provides a specific and useful molecular marker for the actinobacterial group. The CTP synthetase homologue from Symbiobacterium thermophilum again did not contain the 4 aa insert, supporting the inference from the Cox1 signature and other studies that this species is distinct from other actinobacteria. The enzyme CTP synthetase consists of a single polypeptide containing two domains: the C-terminal glutamine amide transfer (GAT) domain catalyses the hydrolysis of glutamine, whereas the N-terminal synthase domain is responsible for the amination of UTP (Endrizzi et al., 2004). The observed inserts are located in the GAT domain of the enzyme and they are indicated to be present on the outer surface of the protein. However, their functional significance for these groups of bacteria remains to be determined.
In the enzyme glutamyl-tRNA synthetase (GluRS), which plays an essential role in protein synthesis by charging the glutamyl-tRNA with its cognate amino acid (Woese et al., 2000), a 5 aa insert is present in almost all actinobacterial species, with the exception of Thermobifida fusca, Propionibacterium acnes and Rubrobacter xylanophilus, but not found in any other bacterial groups (Fig. 3). Sequence information is presently available from 182 species belonging to other bacterial groups, and they are all found to lack this insert (see Supplementary Fig. S3). We were successful in PCR-amplifying and sequencing GluRS gene fragments from 11 additional actinobacterial strains, and all of them were found to contain this insert (Fig. 3). Sequences for other actinobacterial strains could not be amplified using the primers employed in this work (Table 2). Of the three actinobacterial species that are lacking this insert, Rubrobacter xylanophilus is one of the deepest branching species based on the 16S rRNA tree and other biochemical traits, whereas the other two species belong to the families Nocardiopsaceae (Thermobifida fusca) and Propionibacteriaceae (Propionibacterium acnes) (Embley & Stackebrandt, 1994; Stackebrandt et al., 1997; Bruggemann et al., 2004). Other species belonging to these latter families contain this insert. Hence, the most parsimonious explanation for these results is that the insert in GluRS was introduced after the divergence of Rubrobacter xylanophilus, and that Thermobifida fusca and Propionibacterium acnes have lost this insert as a result of either lateral gene transfer or some other means. The insert in GluRS is also lacking in the homologue from Symbiobacterium thermophilum, supporting the inference from other signatures. In the 3D structure of GluRS, the identified insert is present in a loop between an 
-helix and a 
-sheet (Sekine et al., 2003). Although the flanking conserved regions of this insert are known to be functionally important, the possible consequences of the presence of this insert on GluRS function remain to be determined.
Examination of the actinobacterial specificity of 23S rRNA signature
Roller et al. (1992) have previously described a large insert of about 100 nt in the 23S rRNA that was present in a large number of actinobacterial species, but not found in other groups of bacteria. The original paper describing this signature included 64 high-G+C-content Gram-positive strains from the currently recognized phylum Actinobacteria. However, many of these strains were from the same genus, even the same species, and they represented only 22 genera. To examine the specificity of this signature further, we have successfully amplified and sequenced the 23S rRNA insert region from 13 additional actinobacterial species representing 13 additional genera, covering all of the major groups within this phylum. Sequence information for these sequences as well as various other actinobacterial species and a few other bacterial groups is presented in the partial sequence alignment shown in Fig. 4. As seen, an insert of between 90 and 100 bp is present in all of the actinobacterial species that we sequenced but it is not found in any other bacterial groups (Fig. 1). Sequence information for many other actinobacterial species which has become available in recent years is also included in Fig. 4. Of these species, smaller inserts were present in this position in Tropheryma whipplei (79 bp) and Microbispora bispora (30 bp) and Rubrobacter xylanophilus was found to be lacking the insert entirely. Sequence information for these three strains was available in GenBank. We have also confirmed the absence of this insert in another Rubrobacter species, Rubrobacter radiotolerans, by amplifying and sequencing of the insert from the type strain of this species. Because Rubrobacter represents a deep branch within the phylum Actinobacteria (Stackebrandt et al., 1997; Ludwig & Klenk, 2001), similar to the insert in GluRS, the large insert in 23S rRNA gene was very likely introduced in an actinobacterial ancestor, after the divergence of Rubrobacter.
Phylogenetic analyses of actinobacteria based on 16S rRNA and CTP synthetase sequences
In order to see the inter-relationships among different subgroups within the phylum Actinobacteria, we constructed neighbour-joining trees based on 16S rRNA gene and CTP synthetase protein sequences. Although there are many phylogenetic trees drawn for actinobacteria based on 16S rRNA gene sequences, they generally do not show any bootstrap scores or other measures for the reliability of the branching order (Embley & Stackebrandt, 1994; Stackebrandt et al., 1997; Ludwig & Klenk, 2001). Fig. 5 shows a phylogenetic tree based on 16S rRNA gene sequences from different actinobacterial species for which sequence information is available for different signatures, as well as representative species from other main groups of bacteria. This tree was rooted using the 16S rRNA gene sequence from Archaeoglobus fulgidus. The bootstrap scores for different nodes that were >50 are marked on this tree. As seen, in the 16S rRNA gene tree, most of the actinobacterial species formed a well-defined cluster, branching together in 100 % of the bootstrap replicates. A clade consisting of Rubrobacter radiotolerans and Symbiobacterium thermophilum, which was separated from other actinobacteria by a long branch length, formed the outgroup of the main actinobacterial cluster. A number of subgroups within the Actinobacteria are clearly identified in this tree, including Streptosporangineae, Streptomycineae, the Corynebacterium–Mycobacterium–Nocardia cluster, Propionibacterineae, Pseudonocardineae and Micrococcineae. However, the inter-relationships among these subgroups were not resolved, as seen by the lower (<50) bootstrap scores of the corresponding nodes.
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). The overall topology of the CTP synthetase tree was very similar to that seen in the 16S rRNA gene tree, with the exception of deep branching of Tropheryma whipplei. Phylogenetic studies based on 16S rRNA gene sequences and several other conserved protein sequences indicated that Tropheryma whipplei is closely related to species of the Micrococcaceae. Hence, its deep branching in the CTP synthetase tree is most likely due to its accelerated rate of evolution, which is commonly observed for many genes in intracellular bacteria. No sequence information was available for CTP synthetase from Rubrobacter radiotolerans. However, Symbiobacterium thermophilum was distantly related to the Actinobacteria, as seen in the 16S rRNA gene tree.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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. We have tested the hypothesis that these signatures are distinctive characteristics of actinobacteria by obtaining sequence information from a large number of actinobacterial species, covering a wide range of families and suborders within this phylum, for which no sequence information was available. All of these species were found to contain the indicated signatures, confirming that they are distinctive characteristics of this group.
The placement of a novel bacterial species into the phylum Actinobacteria is at present based solely on the branching pattern in 16S rRNA gene trees. Based on phylogenetic trees, it has proven difficult to circumscribe a given phylum reliably (Ludwig & Klenk, 2001; Gupta & Griffiths, 2002; Oren, 2004). The problems that one faces in these regards are illustrated by the 16S rRNA gene tree shown in Fig. 5. In this tree, most of the actinobacterial species formed a well-defined cluster, branching together in 100 % of the bootstrap replicates. A clade consisting of Rubrobacter radiotolerans and Symbiobacterium thermophilum, which is separated by a large genetic distance from the other actinobacterial species, forms the outgroup of this cluster. As seen by the bootstrap score (<50 %), the two species that form this clade are not specifically related to each other, and the clade itself is only weakly related to other actinobacteria. However, in the current taxonomy based on 16S rRNA trees, both of these species are recognized as part of the phylum Actinobacteria, and the outer boundary of this phylum is placed outside this clade (Ludwig & Klenk, 2001; Maidak et al., 2001). This is despite the fact that analysis of various genes in the Symbiobacterium thermophilum genome indicates that the species is most closely related to members of the Firmicutes rather than the Actinobacteria (Ueda et al., 2004).
In our analyses based on signature sequences, all four signatures (Cox1, CTP synthetase, 23S rRNA and GluRS) that are present in most other actinobacteria were found to be lacking in Symbiobacterium thermophilum, indicating strongly that this species should not be placed in the phylum Actinobacteria despite its high G+C content. For Rubrobacter radiotolerans, the signatures in 23S rRNA as well as the GluRS protein, which are present in most other actinobacteria (two exceptions seen in the case of GluRS), were found to be lacking in this species. Information for Cox1 and CTP synthetase signatures is at present lacking for this species as we were not able to amplify the corresponding gene fragments. However, based on the absence of signatures in the 23S rRNA and GluRS, and the fact that this species is distantly related to other actinobacteria in the 16S rRNA tree (Fig. 5), it is suggested that the species of this genus are not typical actinobacterial species. However, if the future work reveals other reliable characteristics (including shared presence of indels in the Cox1 and CTP synthetase) which are uniquely shared by Rubrobacter species and other actinobacteria, this would validate the placement of this genus in the phylum Actinobacteria.
Based on the distribution of different signatures and phylogenetic studies presented here, it can be inferred that all of these signatures (a 2 aa deletion in Cox1, 4 aa insert in CTP synthetase and a 5 aa insert in GluRS) were introduced in a common ancestor of the typical actinobacteria. There were only two instances in a single protein (absence of the GluRS insert in Thermobifida fusca and Propionibacterium acnes) where these signatures were found to be missing from an actinobacterial species. The other three signatures were present in all of the newly sequenced as well as previously available actinobacterial homologues. These novel molecular signatures should prove helpful in circumscribing the actinobacterial phylum and for the placement of deep branching species within this group.
It is also of much interest to understand the biological and functional significance of these conserved genetic changes in important proteins that are limited to actinobacterial species. Because most of these indels have not been lost from any of the species belonging to this phylum, it is reasonable to assume that they play important biological roles in these organisms. Hence, studies aimed at understanding their functional significance should be of much interest.
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ACKNOWLEDGEMENTS |
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