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Proc Natl Acad Sci U S A. Jun 24, 2003; 100(13): 7877–7882.
Published online Jun 3, 2003. doi:  10.1073/pnas.1130426100
PMCID: PMC164681
Microbiology

The complete genome sequence of Mycobacterium bovis

Abstract

Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette–Guérin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and its comparison with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison with M. leprae reveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host–bacillus interactions or immune evasion. Furthermore, there are no genes unique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis.

In his Nobel Prize address of 1901 Von Behring stated, “As you know, tuberculosis in cattle is one of the most damaging infectious diseases to affect agriculture” (www.nobel.se/medicine/laureates/1901). The past 100 years of research has had little impact on this conclusion in developing countries, whereas in some countries in the developed world with a wildlife reservoir of Mycobacterium bovis there has been an alarming increase in the incidence of bovine tuberculosis. Data for the year 2000 in Great Britain show a national herd incidence of 2.8%, with an exponential increase in cases in the southwest of England over the past 10 years (www.defra.gov.uk/animalh). The current means of tuberculosis control is the “test and slaughter” strategy, whereby animals giving a positive skin reaction to a crude preparation of mycobacterial antigens are identified as infected and slaughtered. The badger (Meles meles) has been suggested to act as a significant source of infection in Great Britain and Ireland, with a large-scale trial currently underway to evaluate the contribution of badger culling to the control of bovine tuberculosis (1). Infection with M. bovis has also been described across a range of animals such as buffalo, kudu, lion, and antelope in the Kruger National Park, having severe implications for the biodiversity of this region (2). In New Zealand, the eradication of bovine tuberculosis is confounded by a continuing problem of wildlife reservoirs of M. bovis, especially in the brushtail possum (Trichosurus vulpecula) (3). The presence of M. bovis infection in white-tailed deer in Michigan poses a serious threat to the control and eradication programs for bovine tuberculosis that are in their final stages in the United States (4). There is a clear need for new control strategies if the worldwide threat from bovine tuberculosis is to be eradicated.

The disease is caused by M. bovis, a Gram-positive bacillus with zoonotic potential that is highly genetically related to Mycobacterium tuberculosis, the causative agent of human tuberculosis (5, 6). Although the human and bovine tubercle bacilli can be differentiated by host range, virulence and physiological features the genetic basis for these differences is unknown. M. bovis was also the progenitor of the only current vaccine against tuberculosis, M. bovis bacillus Calmette–Guérin, a strain that was attenuated by serial passage of M. bovis on potato slices soaked in ox-bile and glycerol over 13 years (7). However, the precise mutations that led to attenuation of bacillus Calmette–Guérin are still unknown, though one key deletion (RD1) appears to have played a role (8).

With the availability of the genome sequence of M. bovis, we are now in a position to address the genetic basis of key phenotypic traits of the bovine tubercle bacillus. Here we use comparative analyses to show that deletion of genetic information has been the dominant force in shaping the genome, with M. bovis not presenting any unique genes per se compared with other members of the M. tuberculosis complex. The analyses we present here suggest that variation of cell wall components and gene expression were key to the evolution of M. bovis.

Methods

For the shotgun phase, a total of 81,146 reads, or ≈7.7 coverage, was generated from pUC18 and M13mp18 small (1–4 kb) insert libraries by using dye-terminator chemistry on ABI377 or ABI3700 automated DNA sequencers (Applied Biosystems). Assembly of the shotgun data were performed by PHRAP (P. Green, unpublished data). The sequence was finished by using GAP4 as described (5), with an extra 13,000 reads from the pUC libraries performed on ABI3700 machines for finishing purposes. Annotation was managed through the ARTEMIS (www.sanger.ac.uk/Software) tool, with comparisons to public and in-house databases performed by using the blast suite and fasta. Comparative genome analysis was achieved by using the Artemis Comparison Tool (ACT; www.sanger.ac.uk/Software) with single-nucleotide polymorphism (SNP) identification performed by using the EMBOSS package (www.hgmp.mrc.ac.uk/Software/EMBOSS). The sequence and annotation have been deposited in the EMBL database under accession no. BX248333.

Results and Discussion

Genome Features. M. bovis AF2122/97 is a fully virulent Great Britain strain isolated in 1997 from a diseased cow suffering caseous lesions in lung and bronchomediastinal lymph nodes. The genome sequence is 4,345,492 bp in length, arranged in a single circular chromosome with an average G + C content of 65.63% (Table 1). The genome contains 3,952 genes encoding proteins, including a prophage and 42 IS elements (Fig. 1). Strikingly, the genome is >99.95% identical at the nucleotide level to that of M. tuberculosis, showing colinearity and no evidence of extensive translocations, duplications or inversions. Before the availability of the M. bovis genome sequence, comparative genomics of the M. tuberculosis complex had been performed by using hybridization-based methods, exploiting this high degree of sequence identity (912). This revealed 11 deletions from the genome of M. bovis, ranging in size from ≈1 to 12.7 kb, and these have been confirmed by the sequence data. Surprisingly, the sequence contains only one locus in M. bovis, termed TbD1 (see below), which is absent from the majority of extant M. tuberculosis strains. Therefore, at a gross level, deletion has been the dominant mechanism in shaping the M. bovis genome.

Fig. 1.
Circular representation of the M. bovis genome. The scale is shown in megabases by the outer black circle. Moving in from the outside, the next two circles show forward and reverse strand CDS, respectively, with colors representing the functional classification. ...
Table 1.
Overview of genome comparison

Comparison with M. tuberculosis: SNPs. There are 2,437 SNPs between M. bovis and M. tuberculosis H37Rv, and 2,423 compared with M. tuberculosis CDC1551 (13) (Table 1). SNPs have previously been shown to be responsible for a number of distinctive characteristics of the bovine bacillus. For example, a point mutation in the pncA gene in M. bovis confers resistance to the key anti-tuberculosis drug pyrazinamide and prevents the accumulation of niacin that is seen in M. tuberculosis (14, 15). Direct comparison of 2,504 coding sequences (CDS) of identical length across the three genomes revealed that 1629 and 1656 M. bovis CDS are identical in M. tuberculosis H37Rv and CDC1551 respectively (Fig. 2). This compares to 2,082 CDS that show no difference between the two M. tuberculosis strains. Across these selected CDS, M. bovis showed 506 synonymous and 769 nonsynonymous SNPs compared with M. tuberculosis H37Rv, with 506 synonymous and 800 nonsynonymous SNPs against M. tuberculosis CDC1551. The two M. tuberculosis strains showed 339 nonsynonymous and 241 synonymous SNPs, respectively. This analysis not only underlines the conservation of gene sequence across members of the M. tuberculosis complex, but also the divergence of M. bovis from M. tuberculosis. The unexpectedly high frequency of nonsynonymous to synonymous changes may be a product of the close evolutionary relationship between these strains.

Fig. 2.
Tripartite comparison of 2,504 CDS of M. bovis, M. tuberculosis H37Rv, and M. tuberculosis CDC1551. The colors represent the M. bovisM. tuberculosis H37Rv comparison (red), M. bovisM. tuberculosis CDC1551 (yellow), and M. tuberculosis ...

Cell Envelope and Antigenic Variation. Cell walls of pathogenic bacteria are known to show variation in protein sequences and macromolecular composition, reflecting selective pressures on these structures. It is therefore notable that the greatest degree of sequence variation between the human and bovine bacilli is found in genes encoding cell wall and secreted proteins (Fig. 3). Variation in genes encoding lipoproteins is seen, with lppO, lpqT, lpqG, and lprM deleted or frameshifted, whereas M. bovis has a duplicated copy of lppA. Similarly, the M. bovis rpfA gene, one of a five-membered family encoding secreted proteins that promote the resuscitation of dormant or nongrowing bacilli (16), shows an in-frame deletion of 240 bp that leads to the synthesis of a shorter protein. Whether this affects the function of the protein, or again reflects antigenic variation, is unclear. There is extensive variation in genes encoding the PE-PGRS and PPE protein families (5). Although initially of unknown function, there is now a considerable body of evidence to suggest that at least some of these proteins are surface exposed and play a role in adhesion and immune modulation (17, 18). Between M. bovis AF2122/97 and M. tuberculosis H37Rv there are blocks of sequence variation in genes encoding 29 different PE-PGRS and 28 PPE proteins resulting from in-frame insertions and deletions, whereas others are frameshifted. Because ≈60% of these proteins differ, this is clearly at odds with the rest of the genome where the majority of genes are identical, and indicates that these gene families can support extensive sequence polymorphism, providing a source of variation for selective pressures to act upon. One of the M. tuberculosis PE-PGRS proteins (Rv1759c) binds fibronectin, and this in turn suggests that alterations to the PE-PGRS repertoire might influence host or tissue tropism (19). The M. bovis orthologue of Rv1759c is a pseudogene.

Fig. 3.
Schematic of the major differences between M. bovis AF2122/97 and M. tuberculosis H37Rv. The blue and red lines represent the cell wall, with blue showing M. tuberculosis and red showing M. bovis. Surface-exposed and transport molecules particular ...

A group of known antigens affected by deletions from M. bovis is the ESAT-6 family. The ESAT-6 protein was originally described as a potent T cell antigen secreted by M. tuberculosis (20), and belongs to a >20-membered family that contains other T cell antigens such as CFP-10 and CFP-7. The demonstration of an interaction between ESAT-6 and CFP-10 suggests that other members of the family may also act in pairs, possibly in a mix-and-match arrangement (21). However, six ESAT-6 proteins, encoded by Rv2346c, Rv2347c, Rv3619c, Rv3620c, Rv3890c (Mb3919c), and Rv3905c (Mb3935c) in M. tuberculosis, are missing or altered in M. bovis (Fig. 3). The consequences of their loss are difficult to predict, though they may impact on antigen load either singly or in combination.

The most striking degree of variation in the secretome is the elevated expression of two serodominant antigens, MPB70 and MPB83, in the bovine bacillus (22). MPB83 is a glycosylated cell wall-associated protein, whereas MPB70 is a secreted protein that can account for 10% of M. bovis culture filtrate proteins (23). Differences are also seen in genes encoding the synthesis (pks) and transport (mmpSL) of polyketides and complex lipids with polyketide moieties (Fig. 3). These lipids are major factors in inducing host pathologies that create more favorable environments for the pathogens (24, 25). The genes pks1, mmpL13, and Mb1695c (a putative macrolide transporter adjacent to the pks10/7/8/17/9/11 cluster) could be translated to functional products in M. bovis, but are disrupted in M. tuberculosis. The opposite is the case (i.e., disrupted in M. bovis) for the linked pks6 and mmpL1 genes and mmpL9. It has been shown functionally that pks1 codes for the biosynthesis of the major phenolic glycolipid of M. bovis and Mycobacterium canettii, whereas in strains where pks1 is disrupted, such as M. tuberculosis, no such lipid is produced (26). It has been suggested that many pks gene products that have never been seen in axenic culture may only be produced by tubercle bacilli in the host (5). Thus, it is curious that one of them, pks6, is disrupted in M. bovis, because inactivation of this gene has been shown to attenuate M. tuberculosis in the mouse model (24).

The TbD1 locus, containing the gene mmpS6 and the 5′ region of mmpL6, is absent from a majority of M. tuberculosis strains (27). Deletion of TbD1 may therefore prevent trafficking of specific lipids to the cell wall of M. tuberculosis. Furthermore, a deletion of 808 bp is proximal to the TbD1 region and truncates the treY gene. As treY encodes a maltooligosyltrehalose synthase, an enzyme in a pathway for trehalose production (two other pathways are intact) (28), its deletion in M. bovis may have an effect on the range of trehalose-based glycolipids that are produced. Deletion analysis has revealed that the treY lesion is not present in all strains of M. bovis, suggesting utility as a marker for deep phylogeny. Disruption of the Rv1373 orthologue (Mb1407/8) accounts for the lack of sulfated-lipids in the envelope, because the encoded enzyme has been shown functionally to be a glycolipid sulfotransferase (29). Overall, these differences could have major effects on phenotype and host interaction.

Global Gene Regulation. The M. bovis and M. tuberculosis genomes are >99.95% identical at the nucleotide level. However, an amplification of difference is achieved when changes are in regulatory genes as perforce each one affects the expression of a wide range of genes. In fact, many differences would appear to inactivate genes encoding regulatory proteins in M. bovis. The M. tuberculosis alkA gene codes for a DNA repair protein with an N-terminal regulatory domain (activated by DNA damage) and a C-terminal DNA glycosylase (30). However the M. bovis alkA contains a frameshift at the start of the CDS, leading to the synthesis of a truncated protein. Based on the Escherichia coli model of AlkA function, it is possible that this lesion impairs the ability of M. bovis to respond to nitrosative stress and induce an effective DNA repair response. An AsnC/Lrp family regulator encoded by Mb2801c (Rv2779c), which has been shown to be up-regulated in response to nutrient starvation in M. tuberculosis (31), shows an 8-aa deletion in the core of the protein that may affect tertiary structure or DNA binding. The pknH gene encoding a serine/threonine protein kinase shows an internal deletion and sequence variation relative to the M. tuberculosis orthologue. Although the putative active sites are conserved, this variation may affect substrate specificity. Another serine/ threonine kinase gene, pknD, is a pseudogene in M. bovis (32), with adjacent gene clusters also showing disruptions, including two pst clusters where the sole pstB orthologue is frameshifted. This would be expected to prevent high affinity phosphate uptake, although the phoT gene, which encodes a protein with similarity to PstB, may complement this activity. In the same region a frameshift leads to fusion of the mntH-encoded manganese transporter with the preceding CDS leading to a 287-aa N-terminal hydrophilic extension, possibly preventing correct positioning of the MntH transporter in the membrane. Inactivation of mntH does not affect the virulence of M. tuberculosis (33). However, because Mn2+ ions are required for regulatory functions such as relaxation of the stringent response (34), lesions in phosphate and manganese transport could affect global gene regulation in M. bovis. It is also probable that the ability to reduce nitrate, one of the characteristic tests that differentiates human and bovine tubercle bacilli, is linked to gene regulation. Classically, M. bovis is described as being nitrate reductase negative (35). However, Bange and colleagues (36) have shown that growth of M. bovis bacillus Calmette–Guérin under oxygen-limiting conditions leads to expression of nitrate reductase activity. Variation in expression networks is undoubtedly central to many phenotypic differences between the tubercle bacilli.

Insights on in Vivo Growth. One of the key in vitro differences between M. bovis and M. tuberculosis is a requirement for pyruvate when glycerol is the sole carbon source (35). This presumably reflects a defect in the metabolism of glycerol by M. bovis. It is therefore intriguing that M. bovis presents multiple lesions in carbohydrate catabolism. The glpK gene of M. bovis AF2122/97, encoding glycerol kinase, is a pseudogene, preventing the phosphorylation of glycerol and therefore its use as a carbon source. Furthermore, ugpA, encoding part of the putative ATP-binding cassette transporter for glycerol-3-phosphate, is also a pseudogene in M. bovis. In addition, a frameshift that fuses the genes encoding the iron–sulfur protein (frdB) and one of the membrane-spanning domains (frdC) of fumarate reductase could affect positioning of this key anaerobic enzyme in the membrane. Strikingly, we have found that M. bovis lacks pyruvate kinase activity, with pykA containing a point mutation that would affect binding of the Mg2+ cofactor. Pyruvate kinase catalyses the final irreversible step in glycolysis, the dephosphorylation of phosphoenolpyruvate to pyruvate. Hence, in M. bovis, glycolytic intermediates are blocked from feeding into oxidative metabolism. Moreover, in another reaction leading to pyruvate the ald gene, encoding alanine dehydrogenase, is a pseudogene, therefore blocking the conversion of alanine to pyruvate.

Our initial analysis has shown that although the frameshift in the glpK of M. bovis AF2122/97 is not universally present in M. bovis strains, other SNPs in genes of carbohydrate catabolism were identical in the M. bovis strains tested. Also, the glpK, ugpA and pykA mutations are not present in the vaccine M. bovis bacillus Calmette–Guérin Pasteur, a strain that does not require pyruvate to be added to glycerinated media and that possesses glycerol kinase and pyruvate kinase activity (unpublished observations). The creation of M. bovis bacillus Calmette–Guérin by the serial passage of a strain of M. bovis for 13 years on glycerol-soaked potato slices must therefore have selected for the correction of key lesions in carbohydrate metabolism (37). It remains to be seen whether alterations in metabolism played a role in the attenuation of M. bovis bacillus Calmette–Guérin. However, it is clear that in vivo M. bovis must rely on amino acids or fatty acids as a carbon source for energy metabolism.

Genome Downsizing. Deletion of information is the dominant trend in the M. bovis genome. This has parallels with the genome of Mycobacterium leprae, which has lost >1.1 Mb and accumulated >1,100 pseudogenes during reductive evolution (38). Indeed, many of the genes either deleted or inactivated are common in the two organisms. For example, genes involved in transport and cell surface structures (pstB, ugpA, mce3A-F, lppO, lpqG, lprM, pks6, mmpL1, mmpL9, Rv1510, Rv1508, Rv1371), fatty acid metabolism (fadE22, echA1), cofactor biosynthesis (moaE, moaC2), detoxification (ephA, ephF, alkA), and intermediary metabolism (epiA, gmdA) are pseudogenes or deleted in both bacilli. Similarly, M. leprae and M. bovis have lost the AtsA system for recycling sulfate (39). AtsA is an arylsulphatase that catalyses the hydrolysis of sulfate esters to release inorganic sulfate. Loss of this function may reflect the lack of sulfated glycolipid in these two mycobacteria. This builds on work that showed that M. bovis bacillus Calmette–Guérin does not need sulfate in vivo as a cysA mutant, inactivated in the sole transporter for sulfate, persisted in vivo as well as the parent strain (40). It also reflects the situation in M. leprae, where cysTWA are pseudogenes. Furthermore, recBCD are deleted in M. leprae, whereas recB is frameshifted in M. bovis. This frameshift removes the C-terminal domain of RecB, which is essential for the nuclease activity of RecBCD (41). However, as M. bovis can support homologous recombination it is likely that polar effects on RecD act to suppress defects in recombination (42).

Conclusions

It has long been thought that human tuberculosis had its origin as a zoonosis, with M. bovis jumping the species barrier and host adapting to humans to become M. tuberculosis at the time of cattle domestication 10,000–15,000 years ago. However, using deletion analysis a new scenario for the evolution of the M. tuberculosis complex has recently been proposed that places M. tuberculosis closer to the common progenitor of the complex than M. bovis (27). The completion of the M. bovis genome sequence has confirmed the predictions of this new scenario, showing that M. bovis has evolved from a progenitor of the M. tuberculosis complex as a clone showing distinct host preference.

The possibility exists that deletion events from the genome of M. bovis represent “black holes,” i.e., the loss of genes that are detrimental to the pathogenic lifestyle in a specific niche (43). However, the analysis we present here suggests that although the adaptation process did not rely on the presence of specific virulence genes per se, alterations in gene expression and exposed components of the cell envelope played leading roles. The genome sequence will therefore have a major impact on our understanding of the evolution, host adaptation and pathobiology of tuberculosis and, in the longer term, on the generation of vaccine candidates and diagnostic reagents to combat disease.

Acknowledgments

This article is dedicated to the memory of Jean-Christophe Camus. We thank Noel Smith, John Maynard Smith, Roland Brosch, Christiane Bouchier, and Rik Myers for advice and discussion. This work was funded by the Department for Environment, Food and Rural Affairs (Great Britain), The Wellcome Trust, the Association Française Raoul Follereau, the Génopole Program, and the Institut Pasteur.

Notes

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: SNP, single-nucleotide polymorphism; CDS, coding sequences.

Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. BX248333).

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