Expert scientists critically review the current and most recent advances in the genomics and molecular biology of mycobacteria. The focus is on the topical and most relevant aspects and the authors aim to give readers an insight into the current understanding of the subject and the future direction of research. Topics covered include strain variation and evolution, hypervirulent strains, electron transport and respiration, lipid biosynthesis, DNA repair, oxygen signaling, sulphur metabolism, protein secretion, the protein kinase family, and much more.
A valuable reference text for all microbiology laboratories and essential reading for all scientists and researchers involved with mycobacteria.
Chapter 1 Strain Variation and Evolution
Sebastien Gagneux
Mycobacterium tuberculosis appears to be more genetically diverse than generally assumed. There is mounting evidence that this genetic diversity translates into significant phenotypic differences between clinical isolates. M. tuberculosis exhibits a biogeographic population structure and different strain lineages are associated with different geographic regions. Phenotypic studies in the laboratory and in clinical settings suggest that this macro-evolutionary strain variation has implications for the development of new diagnostics and vaccines. Micro-evolutionary variation affects the relative fitness and transmission dynamics of antibiotic-resistant strains. In the light of the emerging epidemic of multidrug-resistant and extensively drug-resistant tuberculosis, there is an urgent need to improve our understanding of the evolution and ecological consequences of strain variation in drug-resistant M. tuberculosis.
Chapter 2 Hypervirulent Mycobacterium tuberculosis
Nicola Casali
Tuberculosis outbreaks are often caused by hypervirulent strains of Mycobacterium tuberculosis. In experimental animal infections, these clinical isolates elicit unusual immunopathology and may be either hyper- or hypoinflammatory. Similarly, recombinant hypervirulent M. tuberculosis mutants, which exhibit increased bacterial burden or decreased host survival times in model infections, induce a spectrum of inflammatory responses. The majority of hypervirulent mutants identified have deletions in cell wall modifying enzymes or regulators that respond to environmental stimuli. Studies of these mutants have provided insight into the mechanisms that enable M. tuberculosis to mask its full pathogenic potential, inducing a granuloma that provides a protective niche and enables the bacilli to sustain a long-term persistent infection.
Chapter 3 Electron Transport and Respiration in Mycobacteria
Bavesh D. Kana, Edith E. Machowski, Norman Schechter, Jiah-Shin Teh, Harvey Rubin and Valerie Mizrahi
Bacteria have evolved a modular respiratory system that enables them to optimize energy production in environments that are variable and may be hostile. By adjusting the composition of the system to suit the specific conditions encountered, the organism is able to thrive in a particular environment. The flexibility conferred by a modular respiratory system is critical to the survival of many bacterial pathogens, including Mycobacterium tuberculosis. In this chapter, we firstly review the composition of the respiratory systems of sequenced mycobacterial species as deduced from a comparative analysis of their respiratory gene complements, and from the function of specific system components, as revealed by biochemical and physiological studies. We then review the transcriptional changes of respiratory system components of M. tuberculosis observed in various models of growth and persistence in vitro and in vivo, identify the common themes that have emerged from these studies and relate them to the physiology of this pathogen during infection. These findings are framed in the context of exciting new developments in tuberculosis drug discovery, which are predicated on targeting respiration and electron transport through inhibition of type II NADH dehydrogenase, ATP synthase, and menaquinone biosynthetic enzymes.
Chapter 4 Novel paradigms of complex lipid biosynthetic machinery of Mycobacterium tuberculosis
Arush Chhabra and Rajesh S. Gokhale
Mycobacterium tuberculosis posseses a repertoire of complex lipids. Many of these lipids are crucial to its survival and virulence. Fatty-acyl components of the mycobacterial lipids are synthesised by the concerted action of fatty acid synthases (FASs) and polyketide synthases (PKSs). While the single multifunctional type I FAS carries out de novo biosynthesis from acetyl-CoA, the multicomponent type II FAS generates the very long acyl chains from type I FAS products. Polyketide synthases take over from FAS to complete the biosynthesis of the unusual acyl chains of many exotic lipids like mycolic acids, phthioceroldimycocerosate ester, sulfolipids and mannosyl-beta-1-phophomycoketides. The novel family of fatty acyl-adenylate ligases (FAALs) is crucial to this intricate enzymatic network. FAALs mediate the crosstalk between FAS and PKS by activating long-chain fatty acids to fatty acyl-adenylates which are transacylated onto the PKSs. In this chapter we describe novel components of lipid biosynthetic network, several of which could prove to be promising drug targets.
Chapter 5 DNA Repair: Key to Survival?
Elaine O. Davis and Lorna N. Forse
Sequence comparisons indicate that mycobacteria possess the majority of the key DNA repair pathways identified in other bacterial species, including base excision repair, nucleotide excision repair, recombination repair and non-homologous end-joining. However, there are some notable differences such as the absence of a mismatch repair system, as well as variations in the components of other repair pathways. Currently functional studies of DNA repair within mycobacterial species are limited, but this is an expanding area of research. It has been demonstrated that DNA-damage induced mutagenesis is mediated by a different class of DNA polymerase to that used in Escherichia coli. Although the classical SOS system of gene regulation in response to DNA damage is conserved and functional in mycobacteria, many of the DNA repair genes whose expression increases following DNA damage are controlled by an alternative system or systems that are yet to be characterised. The increase in expression observed for a number of Mycobacterium tuberculosis DNA repair genes in infection models suggests that DNA repair might be particularly important during pathogenesis.
Chapter 6 Oxygen, Nitric Oxide, and Carbon Monoxide Signaling
Martin I. Voskuil, Ryan W. Honaker and Adrie J.C. Steyn
Mycobacterium tuberculosis is an aerobe that can survive extended periods of anaerobiosis. The bacillus responds to inhibition of respiration during hypoxic conditions as well as exposure to NO and CO by the induction of over 60 genes, referred to as the "dormancy regulon". Control of the dormancy regulon by NO and CO, not just hypoxia, is mediated by a three component regulatory system composed of two sensors, DosT and DosS and a transcriptional regulator DosR. The dormancy proteins are part of a programmed strategy employed by the bacilli to survive in the absence of aerobic respiration. In this review we will revisit the role of oxygen in M. tuberculosis physiology, the regulation of the dormancy regulon, the function of regulon proteins, the mechanisms DosT and DosS employ to sense diatomic gases, the role of the dormancy program in animal models of infection and in human latent infection, and will provide an updated comprehensive list of regulon genes.
Chapter 7 Sulphur Metabolism in Mycobacteria
Ryan H. Senaratne and Kathleen Y. Dunphy
Sulphur is a key life-supporting element. The recent combined efforts of genomic analysis and laboratory studies have greatly clarified the mycobacterial sulphur metabolic pathways. Sulphur metabolism contributes to intracellular survival and virulence of Mycobacterium tuberculosis. Several enzymes in the sulphur metabolic pathways are essential for mycobacterial survival.
Chapter 8 The Eukaryotic-like Serine/Threonine Protein Kinase Family in Mycobacteria
Nicole Scherr and Jean Pieters
Mycobacteria have a complex life style comprising different environments and developmental stages. Signal sensing and transduction leading to cellular responses must be tightly regulated to allow survival under variable conditions. Prokaryotes normally regulate their signal transduction processes through two-component systems, however, the genome sequence of Mycobacterium tuberculosis revealed a large number of eukaryotic-like serine/threonine kinases. It is becoming clear that in M. tuberculosis, many of these kinases are involved in the regulation of metabolic processes, transport of metabolites, cell division and virulence. This chapter summarizes the current knowledge on eukaryotic-like serine/threonine protein kinases in mycobacteria. Investigating the biochemistry and physiology of these enzymes may lead to a better understanding of the signalling networks in mycobacteria.
Chapter 9 Specialised Protein Secretion Systems of Mycobacteria
Wilbert Bitter, Edith N.G. Houben and Joen Luirink
Mycobacteria have a highly complex cell wall. Specialised secretion systems are therefore required to transport proteins across this cell wall. However, genome analysis showed that, apart from the omnipresent Sec and Tat systems, all of the known secretion pathways of other bacteria are absent. Mycobacteria do have a second SecA protein (SecA2) that is involved in the extracellular accumulation of a specific protein subset. In addition, a new secretion pathway was recently identified that is responsible for the secretion of various proteins into the culture supernatant. This pathway is present in multiple copies in the mycobacteria and has been named the type VII secretion pathway. Both the SecA2 and the type VII secretion systems are discussed in this chapter.