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Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation.

Hayward D, van Helden PD, Wiid IJ - BMC Evol. Biol. (2009)

Bottom Line: Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not.In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation.Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode.

View Article: PubMed Central - HTML - PubMed

Affiliation: DST/NRF Centre for Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences - Stellenbosch University, South Africa. dh@sun.ac.za

ABSTRACT

Background: Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not.

Results: In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved.

Conclusion: Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria.

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The chromosomal regions of M. leprae and M. ulcerans similar to that of M. tuberculosis containing the glnA3 and glnA4 sequences show that these GS encoding sequences were disrupted by insertions (glnA3, M. ulcerans) or deletions (glnA3, M. leprae; glnA4, M. ulcerans). Similar genes are indicated in the same colour and the percentage amino acid identity to the M. tuberculosis H37Rv reference sequence is indicated between brackets. Open arrows indicate no significant similarity to sequences in the corresponding chromosomal regions.
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Figure 2: The chromosomal regions of M. leprae and M. ulcerans similar to that of M. tuberculosis containing the glnA3 and glnA4 sequences show that these GS encoding sequences were disrupted by insertions (glnA3, M. ulcerans) or deletions (glnA3, M. leprae; glnA4, M. ulcerans). Similar genes are indicated in the same colour and the percentage amino acid identity to the M. tuberculosis H37Rv reference sequence is indicated between brackets. Open arrows indicate no significant similarity to sequences in the corresponding chromosomal regions.

Mentions: The distribution and similarity of GS protein sequences in all the available genomes of organisms defined as members of the phylum Actinobacteria [19] were detected through a BLAST sequence comparison of the M. tuberculosis glnA1, glnA2, glnA3 and glnA4- protein sequences (Table 1). Protein sequence data has been preferred to DNA sequences, since the various Actinobacteria genomes may differ with respect to G/C content that may result in skewing of sequence alignments. Protein sequences of high similarity (>60%) to the M. tuberculosis glnA1 and glnA2 encoded protein sequences could be detected in all the Actinobacteria genomes (Table 1), with Symbiobacterium thermophilum being the only exception, where only a single GS sequence with greater similarity to the glnA1-encoded M. tuberculosis GSIβ (50% similarity) was observed. The genome of S. thermophilum, a high G+C gram positive organism belonging to an as yet undefined taxon situated just outside the phylum Actinobacteria, was included due to its close relationships to the actinobacterial ancestor [19,20]. It was observed that the glnA1 and glnA2 sequences were situated in close proximity to each other in many genomes, but that considerable variance in the distribution and similarity of GS sequences similar to that M. tuberculosis glnA3 and glnA4 sequences was observed. Some Actinobacteria genomes contained an additional glnA protein sequence similar to the M. tuberculosis glnA4 protein sequence. However, this sequence was less conserved than the glnA1 and glnA2 sequences. Only the mycobacteria and some other closely related actinomycetes, such as Frankia and Rhodococcus species, contained sequences similar to the four glnA-encoded GS sequences (summarised in Figure 1). An exception was observed in that sequences similar to glnA3 and glnA4 were absent in the genomes of M. leprae and M. ulcerans, which had glnA sequences similar to glnA1 and glnA2 only. It is well known that M. leprae and M. ulcerans have undergone major reductive evolution [21,22] and as such may have lost these genes. Since the distribution of the glnA sequences (as seen in Figure 1) reflects the evolution of phylum Actinobacteria as defined by 16S phylogenetic analysis [19], it might be argued that there was a sequential acquisition of first glnA4 and later glnA3, rather than a loss of these genes from an actinomycete progenitor. In order to prove that glnA3 and glnA4 were lost in these two mycobacterial species specifically, rather than being separately acquired in different members of the mycobacteria, the chromosomal regions containing the glnA3 and glnA4 genes in M. tuberculosis were compared to the corresponding chromosomal regions of M. leprae and M. ulcerans (Figure 2). It was observed that the chromosomal regions of M. leprae and M. ulcerans contained copies of glnA3 in the form of pseudogenes situated in gene clusters corresponding to that of the M. tuberculosis H37Rv chromosome. In M. ulcerans it was observed that the glnA3 sequence had been disrupted by an insertion element (Figure 2). A copy of glnA4 can be observed in a gene cluster similar to that found on the M. tuberculosis chromosome, suggesting that both sequences have been retained from the mycobacterial ancestor during mycobacterial speciation, but that they have become non-functional through the evolutionary process in some members of the genus Mycobacterium.


Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation.

Hayward D, van Helden PD, Wiid IJ - BMC Evol. Biol. (2009)

The chromosomal regions of M. leprae and M. ulcerans similar to that of M. tuberculosis containing the glnA3 and glnA4 sequences show that these GS encoding sequences were disrupted by insertions (glnA3, M. ulcerans) or deletions (glnA3, M. leprae; glnA4, M. ulcerans). Similar genes are indicated in the same colour and the percentage amino acid identity to the M. tuberculosis H37Rv reference sequence is indicated between brackets. Open arrows indicate no significant similarity to sequences in the corresponding chromosomal regions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667176&req=5

Figure 2: The chromosomal regions of M. leprae and M. ulcerans similar to that of M. tuberculosis containing the glnA3 and glnA4 sequences show that these GS encoding sequences were disrupted by insertions (glnA3, M. ulcerans) or deletions (glnA3, M. leprae; glnA4, M. ulcerans). Similar genes are indicated in the same colour and the percentage amino acid identity to the M. tuberculosis H37Rv reference sequence is indicated between brackets. Open arrows indicate no significant similarity to sequences in the corresponding chromosomal regions.
Mentions: The distribution and similarity of GS protein sequences in all the available genomes of organisms defined as members of the phylum Actinobacteria [19] were detected through a BLAST sequence comparison of the M. tuberculosis glnA1, glnA2, glnA3 and glnA4- protein sequences (Table 1). Protein sequence data has been preferred to DNA sequences, since the various Actinobacteria genomes may differ with respect to G/C content that may result in skewing of sequence alignments. Protein sequences of high similarity (>60%) to the M. tuberculosis glnA1 and glnA2 encoded protein sequences could be detected in all the Actinobacteria genomes (Table 1), with Symbiobacterium thermophilum being the only exception, where only a single GS sequence with greater similarity to the glnA1-encoded M. tuberculosis GSIβ (50% similarity) was observed. The genome of S. thermophilum, a high G+C gram positive organism belonging to an as yet undefined taxon situated just outside the phylum Actinobacteria, was included due to its close relationships to the actinobacterial ancestor [19,20]. It was observed that the glnA1 and glnA2 sequences were situated in close proximity to each other in many genomes, but that considerable variance in the distribution and similarity of GS sequences similar to that M. tuberculosis glnA3 and glnA4 sequences was observed. Some Actinobacteria genomes contained an additional glnA protein sequence similar to the M. tuberculosis glnA4 protein sequence. However, this sequence was less conserved than the glnA1 and glnA2 sequences. Only the mycobacteria and some other closely related actinomycetes, such as Frankia and Rhodococcus species, contained sequences similar to the four glnA-encoded GS sequences (summarised in Figure 1). An exception was observed in that sequences similar to glnA3 and glnA4 were absent in the genomes of M. leprae and M. ulcerans, which had glnA sequences similar to glnA1 and glnA2 only. It is well known that M. leprae and M. ulcerans have undergone major reductive evolution [21,22] and as such may have lost these genes. Since the distribution of the glnA sequences (as seen in Figure 1) reflects the evolution of phylum Actinobacteria as defined by 16S phylogenetic analysis [19], it might be argued that there was a sequential acquisition of first glnA4 and later glnA3, rather than a loss of these genes from an actinomycete progenitor. In order to prove that glnA3 and glnA4 were lost in these two mycobacterial species specifically, rather than being separately acquired in different members of the mycobacteria, the chromosomal regions containing the glnA3 and glnA4 genes in M. tuberculosis were compared to the corresponding chromosomal regions of M. leprae and M. ulcerans (Figure 2). It was observed that the chromosomal regions of M. leprae and M. ulcerans contained copies of glnA3 in the form of pseudogenes situated in gene clusters corresponding to that of the M. tuberculosis H37Rv chromosome. In M. ulcerans it was observed that the glnA3 sequence had been disrupted by an insertion element (Figure 2). A copy of glnA4 can be observed in a gene cluster similar to that found on the M. tuberculosis chromosome, suggesting that both sequences have been retained from the mycobacterial ancestor during mycobacterial speciation, but that they have become non-functional through the evolutionary process in some members of the genus Mycobacterium.

Bottom Line: Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not.In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation.Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode.

View Article: PubMed Central - HTML - PubMed

Affiliation: DST/NRF Centre for Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences - Stellenbosch University, South Africa. dh@sun.ac.za

ABSTRACT

Background: Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not.

Results: In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved.

Conclusion: Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria.

Show MeSH
Related in: MedlinePlus