Mycobacterium Tuberculosis Evolutionary Pathogenesis and its Putative Impact on Drug Development

Fabien Le Chevalier; Alessandro Cascioferro; Laleh Majlessi; Jean Louis Herrmann; Roland Brosch

Disclosures

Future Microbiol. 2014;9(8):969-985. 

In This Article

Abstract and Introduction

Abstract

Mycobacterium tuberculosis, the etiological agent of human TB, is the most important mycobacterial pathogen in terms of global patient numbers and gravity of disease. The molecular mechanisms by which M. tuberculosis causes disease are complex and the result of host–pathogen coevolution that might have started already in the time of its Mycobacterium canettii-like progenitors. Despite research progress, M. tuberculosis still holds many secrets of its successful strategy for circumventing host defences, persisting in the host and developing resistance, which makes anti-TB treatment regimens extremely long and often inefficient. Here, we discuss what we have learned from recent studies on the evolution of the pathogen and its putative new drug targets that are essential for mycobacterial growth under in vitro or in vivo conditions.

Introduction

Pathogenic mycobacteria are important causes of human and animal disease. Despite the availability of antibiotics and chemotherapeutic agents that show activity against certain mycobacteria, different drug-resistant forms are on the rise, which requires new efforts in the search for novel active compounds and treatment strategies. Phylogenetically, the genus Mycobacterium is contained within the phylum Actinobacteria, with the genera Corynebacterium and Streptomyces as close relatives. Most of the approximately 130 defined mycobacterial species contain harmless saprophytes,[1] which is most evident for the large group of fast-growing mycobacteria that comprise only very few pathogenic species, such as the Mycobacterium abscessus–Mycobacterium massiliense–Mycobacterium bolletti complex. These latter mycobacteria represent emerging opportunistic pathogens that are more and more often being recognized as causative agents of acute and persistent lung infections in cystic fibrosis patients and are also virulent in animal infection models.[2–5] They pose severe difficulties for treatment in humans due to their extensive level of drug resistance.[6–8]

In contrast to the phylogenetically more diversified fast-growing mycobacteria, the slow-growing mycobacteria form a subcluster in the 16S rRNA-based phylogenetic tree[9] and are well known to harbor major human pathogens, such as Mycobacterium leprae[10] and Mycobacterium tuberculosis,[11,12] and also a series of opportunistic human pathogens, such as Mycobacterium marinum[13] or Mycobacterium kansasii,[14] which are considered to be close relatives of M. tuberculosis. Overall, mycobacteria are considered to be high-GC content, Gram-positive bacteria, but in contrast to other Gram-positive bacteria, such as Staphylococcus or Bacillus species, which have no outer membrane, mycobacteria possess a lipid-rich cell envelope that contains a standard inner membrane and a particular outer membrane, named the mycomembrane, which is specific to mycobacteria and might fulfill a similar barrier function as the outer membrane of Gram-negative bacteria.[15–17] In addition, the mycobacterial cell is also covered by a polysaccharide-based capsule.[18,19] This overall envelope architecture is conserved between nonpathogenic and pathogenic mycobacteria and contributes to the enhanced ability of mycobacteria to resist and persist in different environments. The complex cell envelope necessitates efficient secretion systems that can ensure the transport of a range of biomolecules across this multilayer barrier. Despite the conservation of many core elements in the mycobacterial cell envelope (reviewed in[20]) (Figure 1), over the course of evolution, individual changes in the composition of cell wall components, such as particular lipids or specific secretion and transport systems, have emerged that contribute to the specific lifestyles of pathogenic mycobacterial species. Evolution towards pathogenicity has often been accompanied by a reduction of genome size that is compensated in part by gene acquisition, gene duplications and diversification (Figure 2A).[11,13,14,21–23] When M. tuberculosis is compared with M. marinum, which is characterized by an approximately 6.7-Mb genome and the more distantly related, fast-growing Mycobacterium smegmatis that harbors an approximately 7-Mb genome, a core of 2450 genes that are conserved among the three species can be defined (Figure 2B). This comparison also showed that approximately 600 genes are specific for M. tuberculosis and might contribute to the pathogenicity of M. tuberculosis relative to the other mycobacterial species.[13] When M. tuberculosis is compared within the group of tubercle bacilli (i.e., mycobacteria that cause TB in mammalian species), recent genome comparisons have shown that Mycobacterium canettii strains, which represent rare human isolates with smooth colony morphology from the region of the Horn of Africa, harbor somewhat larger genomes that differ from M. tuberculosis by 16,000–60,000 single-nucleotide polymorphisms and individual accessory genomes of up to 366 genes,[23] which argues for their ancestral status relative to M. tuberculosis. As these M. canettii strains were found to be less virulent and less persistent than M. tuberculosis sensu stricto in laboratory mouse models, their genomes provide very interesting gene repertoires for learning more about the ancestral gene content of the putative progenitor of M. tuberculosis and about possible gene transfers that might have contributed to the virulence gain of M. tuberculosis during evolution. Comparison of several M. canettii strains with M. tuberculosis revealed some 51 genes that were specifically present in M. tuberculosis and absent from M. canettii,[23] such as the gene rv1818 encoding a specific member (PE_PGRS33) of a large mycobacterial protein family named after the Pro–Glu motif in the N-terminus and the presence of polymorphic GC-rich repetitive sequences in the central part or the C-terminus of the proteins.[11] On the other hand, nine genes were found that were specifically absent from M. tuberculosis relative to M. canettii, such as the cobF gene encoding an enzyme in the vitamin ref-12 metabolic pathway.[23,24] The loss of cobF from M. tuberculosis might be compensated by substrates provided by the host, which is presently under investigation. As such, the different genes and their gene products that differ between M. canettii and M. tuberculosis can now be further investigated for their impact on the different phenotypes of the concerned phylogenetically diverging tubercle bacilli.

Figure 1.

Organization of the mycobacterial cell envelope. (A) Model of the cell envelope of Mycobacterium tuberculosis and other tubercle bacilli. (B) Cell envelope of Mycobacterium bovis BCG by cryoelectron microscopy of vitreous sections.
(A) Adapted with permission from [15]; (B) Reproduced with permission from [16].

Figure 2.

Phylogenetic organization and gene content of members of the genus Mycobacterium . (A) Phylogenetic tree based on the consensus of the 230 most parsimonious trees of the 16S rRNA DNA sequences of 80 species of the genus Mycobacterium with the sequence of the species Gordonia aichiensis as the outgroup. Sequenced genomes are highlighted in yellow and underlined species are considered to be pathogens. The division between fast- and slow-growing species is indicated by a dotted line. Genome sizes are indicated according to information from the Gold Genome online database [25]. (B) Venn diagram showing orthologous coding sequences among three mycobacterial species as determined by BLASTClust analysis. Numbers in parentheses include paralogous coding sequences.
Mycobacterium farcinogenesis a slow-growing Mycobacterium.
(A) Adapted with permission from [22]; (B) Adapted with permission from [13].

As mentioned above, genome comparisons between fast-growing mycobacterial saprophytes and slow-growing mycobacterial pathogens show an overall trend of genome size reduction. A possible explanation for the genome downsizing of pathogenic mycobacteria could be that adaptation to a pathogenic lifestyle that includes the exploitation of resources of a host organism might make certain gene functions redundant and subject to gene loss. This feature is most visible in the only 3.2-Mb genome of the obligate intracellular pathogen M. leprae that has undergone a dramatic reductive evolution due to gene decay and gene loss, which is responsible for the fact that M. leprae, despite its discovery by Armauer Hansen more than 140 years ago, can still not be cultured on axenic growth media.[10]

The situation of genome reduction is less pronounced for M. tuberculosis, which harbors a 4.4-Mb genome and has retained the ability to grow on axenic culture media,[11] potentially reflecting the extraordinary faculty of this human pathogen to adapt to numerous intra- and extra-cellular environments encountered during its interplay with the host. The particularity of M. tuberculosis in comparison with many facultative mycobacterial pathogens is that it is an obligatory pathogen whose transmission to new hosts occurs from patients who have developed active disease, implicating lung tissue necrosis, cavity formation and coughing-up of infectious bacilli into the immediate environment as tiny droplets. This infection strategy seems to be highly efficient as it is estimated that approximately a third of the human population is infected with M. tuberculosis, from which 5–10% develop active disease. M. tuberculosis is responsible for 9 million cases of active TB and 1.3 million deaths per year.[26] This situation suggests that by selection, the pathogen has developed a balance for using the human host for its own proliferation and global distribution during a long-lasting coevolution.[23,27,28] This situation poses enormous challenges to scientists in order to unravel the factors that are responsible for the evolutionary success of M. tuberculosis. Knowledge on the molecular features that contribute to pathogenicity, persistence and efficient spreading of M. tuberculosis among humans will provide important input for the development of alternative strategies in TB control.

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