Biol. Bull. 210: 1-9. (February 2006)
© 2006 Marine Biological Laboratory
Ancient Genes in Contemporary Persistent Microbial Pathogens
Vijayasarathy Srinivasan* and
Harold J. Morowitz
Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, 22030
* To whom correspondence should be addressed. E-mail: vsriniva{at}gmu.edu
 |
Abstract
|
|---|
Autotrophs, the earliest prokaryotes, use CO2 as the sole or the key source in the reductive citric acid cycle for carbon fixation. This pathway, also known as the reductive tricarboxylic acid (rTCA) cycle, has as its center the Krebs cycle running in the reductive direction, using reduced cofactors for energy. During the infection process, persistent pathogenic bacteria like Mycobacterium tuberculosis, Helicobacter pylori, and Salmonella typhi experience diverse and hostile environments both intracellularly (in macrophages) and extracellularly. M. tuberculosis, for example, must adapt to nutrient-deprived, hypoxic conditions in the granuloma. Genomic annotations reveal the presence of the key enzymes of the rTCA cycle—citrate lyase (Enzyme Commission number EC 4.1.3.6) and 2-oxoglutarate synthase (EC 1.2.7.3)—along with the rest of the TCA cycle enzymes. It is possible that there is a metabolic switch to anaerobic respiration in which a complete or a partial TCA cycle may operate in the reductive mode. This switch would both facilitate carbon fixation and restore the balance of oxidative and reductive reactions during environmental transitions, thus enabling the pathogen to survive, grow, and persist. Verification of enzyme function by biochemical investigations and validation of gene essentiality by knockout studies may reveal these enzymes to be rational drug targets for treatment of persistent microbial infections in mechanism-based drug discovery processes.
|
Introduction
|
|---|
For the first 2 billion years of microbial life, the earth’s atmosphere and hydrosphere had a vanishingly small oxygen concentration, so extant life must have been essentially anaerobic. The nature of this early life was unclear until studies beginning in 1966 on the bacterium Chlorobium limicola forma thiosulphatophilum led to the discovery of a metabolic network that has come to be known as the reductive citric acid (rTCA) cycle (Evans et al., 1966). This pathway has also been found in Aquifex (Beh et al., 1993), Hydrogeneobacter (Shiba et al., 1985), and Desulfobacter (Schauder et al., 1987). The chief function of the cycle is to incorporate carbon from carbon dioxide into the cell’s organic compounds. Citrate lyase converts citric acid into acetyl-CoA and oxaloacetic acid. A minor loop goes from acetyl-CoA to pyruvate to oxaloacetate, thus yielding two oxaloacetates from each citrate (Fig. 1A). The two oxaloacetates continue around the cycle and, by yielding two citrates for each original citrate, constitute an autocatalytic network. Energy must be supplied from outside the cycle by environmental oxidation-reduction reactions. The cycle serves as an engine of synthesis instead of one of energy transformation as in most aerobes. In autotrophs, all the anabolic pathways begin in this cycle.
View larger version (21K):
[in this window]
[in a new window]
|
Figure 1. Variants of tricarboxylic acid cycle. (A) Enzymes of the reductive TCA cycle pathway: 4.1.3.6—citrate-oxaloacetate lyase, 4.2.1.3—cis-aconitase, 1.1.1.42—isocitrate dehydrogenase, 1.2.7.3—2-oxoglutarate synthase, 6.2.1.5—succinyl-CoA ligase, 1.3.99.1—fumarate reductase, 4.2.1.2—fumarate hydratase, 1.1.1.37—malate dehydrogenase, 6.2.1.1—acetyl-CoA ligase, 1.2.7.1—pyruvate synthase, 2.7.9.2—phosphoenolpyruvate synthase, 4.1.1.31—phosphoenolpyruvate carboxylase. (B) Enzymes of the oxidative TCA cycle pathway: 2.3.3.1—citrate synthase, 4.2.1.3—cis-aconitase, 1.1.1.42—isocitrate dehydrogenase, 1.2.4.2—2-oxoglutarate dehydrogenase, 6.2.1.5—succinyl Co-A ligase, 1.3.5.1—succinate dehydrogenase, 4.2.1.2—fumarate hydratase, 1.1.1.37—malate dehydrogenase. (C) Enzymes of the reductive acetyl-CoA pathway: 2.3.3.1—citrate synthase, 4.2.1.3—cis-aconitase, 1.1.1.42—isocitrate dehydrogenase, 1.2..7.3—2-oxoglutarate synthase, 6.2.1.5-succinyl Co-A ligase, 1.3.99.1-fumarate reductase, 4.2.1.2—fumarate hydratase, 1.1.1.37—malate dehydrogenase, 6.2.1.1—acetyl Co-A ligase, 1.2.7.1—pyruvate synthase, 2.7.9.2—phosphoenolpyruvate synthase, 4.1.1.31—phosphoenolpyruvate carboxylase.
|
|
"Some two billion years ago, the cyanobacteria that are oxygen-releasing, photosynthetic prokaryotes began the increase in concentration of atmospheric oxygen from far less than one part per thousand to about 200 parts per thousand ..." (Margulis and Schwartz, 1998). After the accumulation of oxygen from this photosynthetic bacterial metabolism (Summons et al., 1999; Brocks et al., 1999), organisms began to use the citric acid cycle in the oxidative direction. This is the familiar Krebs cycle, or tricarboxylic acid (TCA) cycle, that is the core of most contemporary intermediary metabolism. In this role the cycle oxidizes acetate to carbon dioxide and water while yielding reduced NADH (nicotinamide adenine dinucleotide) and FADH2 (flavin adenine dinucleotide) for bioenergetic purposes (Fig. 1B). This cycle still serves as the center of biosynthetic pathways, especially in autotrophs. Since the atmosphere contained very little oxygen for the first 2 billion years after the origin of life, it can be argued that reductive metabolism preceded the oxidative. The simplicity of chemoautotrophy compared to photoautotrophy also suggests that the former preceded the latter. Smith and Morowitz (2004) and Wachtershauser (1990) theorize that the reductive TCA cycle operated in primitive autotrophs. In any case, the same citric acid cycle can be engaged in either a reductive or oxidative direction if the appropriate energy sources are available. Since many of the reactions are reversible, the reductive cycle appears to require two key enzymes not present in the oxidative cycle: citrate lyase and 2-oxoglutarate synthase. The organism Desulfobacter hydrogenophilus can operate as either an oxidative heterotroph, requiring organic substrates, or a reductive autotroph (Moller et al., 1987). In addition, there is the reductive acetyl-CoA pathway (Fig. 1C), which "may be used also in the oxidative direction for the complete oxidation of acetyl-CoA in those heterotrophic anaerobes which do not have the enzymes of a complete oxidative citric acid cycle." (Fuchs, 1989).
The enormous rise in atmospheric oxygen concentration about 2500 million years ago, presumably due to oxygenic photosynthesis, led to a decline of anaerobes, which survived by occupying residual niches with a low concentration of oxygen (Kasting, 2001; Anbar and Knoll, 2002; Catling et al., 2005; Kerr, 2005). Thus, microbes became aerobes, anaerobes, and in-between physiological forms. The horizontal migration of genes allowed for organisms with the potential for living in either environment (Gogarten and Townsend, 2005). These conditions required adjustment in both the energy pathways and the biosynthetic pathways to key building blocks.
Metabolite flux and reversal of TCA cycle
An example of a process that includes both oxidative and reductive steps is anaerobic fermentation by the yeast Saccharomyces cervisiae (Camaresa et al., 2003), such as in wine production. The yeast begin by using glycolysis and the tricarboxylic cycle to provide energy for all the cellular processes. When oxygen gets low, the yeast shift to alcoholic fermentation, going from pyruvate to ethanol and carbon dioxide. Fermentation provides sufficient energy but lacks the intermediates necessary for the citric acid cycle to synthesize cellular components such as succinate. Succinate can be made reductively, if aspartate is the nitrogen source, or oxidatively, when glutamate is the nitrogen source (Fig. 2A). A similar example has been noted by Reed et al. (2003) in a simulation-based metabolic model of Escherichia coli. The model predicts efficient, completely anaerobic growth on 2-oxoglutarate, due to the citrate lyase enzyme. Under progressively oxygen-limiting growth conditions, the reactions that convert 2-oxoglutarate to oxaloacetate are used more heavily by first reversing some of the steps of the TCA cycle to generate citrate, which is split into acetate and oxaloacetate by citrate lyase (Fig. 2B). Indeed, the citric acid cycle in facultative anaerobes such as Escherichia coli is known to be feedback-inhibited by 2-oxoglutarate, specifically through the allosteric deactivation of citrate synthase (Damson et al., 1979). These observations suggest that, depending on the growth conditions, the citric acid cycle—or part of the cycle—may be used oxidatively or reductively to provide the anabolic steps in the survival and growth of the organism.
View larger version (15K):
[in this window]
[in a new window]
|
Figure 2. Partial reversal of tricarboxylic acid cycle. (A) TCA cycle pathways for succinate formation in Saccharomyces cerevisiae. Solid arrows—the TCA pathway operates as a cycle during respiration; dashed arrows—the TCA pathway functions in the oxidative and reductive modes during fermentative metabolism (adapted from Camaresa et al., 2003). (B) During oxygen-limited growth of Escherichia coli on 2-oxoglutarate, the TCA cycle runs in the reductive direction from the 2-oxoglutarate step through isocitrate and citrate. Citrate lyase cleaves citrate to produce oxaloacetate and acetate (adapted from Reed et al., 2003).
|
|
|
Materials and Methods
|
|---|
Information regarding the presence of the rTCA cycle enzymes in the organisms whose genomes have been completely sequenced was obtained by data mining the Kyoto Encyclopedia of Genes and Genomes (KEGG) database—an on-line, public domain, open-source collection of databases that includes metabolic pathways, genome sequences, and analysis (Kanehisa, 1997; Kanehisa and Goto, 2000). The KEGG PATHWAY Database (http://www.genome.jp/kegg/pathway.html) was utilized for retrieval of all information, using the search criteria related to "metabolism," "energy metabolism," "reductive carboxylate cycle (CO2 fixation)," and the entries for each of the enzymes mentioned therein. Numbers in parentheses following enzyme names in the sections that follow are assigned by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology on the basis of the reactions that they catalyze.
|
Results and Discussion
|
|---|
Table 1 lists prokaryotes that are known from sequence studies to contain citrate lyase (EC 4.1.3.6) and 2-oxoglutarate synthase (EC 1.2.7.3). Organisms having both enzymes should be able to drive the entire citric acid cycle reductively; with only one of the two, they might be able to drive part of the reductive cycle. As seen from the yeast case, the ability to drive the cycle both ways might be of value when there is alteration or transient perturbation in the environment. By enabling the organisms to adapt to a changing milieu, this ability could ensure survival and propagation—not only for free-living organisms, but especially for those that have adapted to intracellular residence in suitable hosts. This may be of clinical relevance in dealing with microbial pathogenicity in cases where some of the infectious agents are able to adapt, survive, and persist in privileged physiological niches, well protected from defense mechanisms of the host, for protracted periods.
View this table:
[in this window]
[in a new window]
|
Table 1 Organisms that contain both the key enzymes of the reductive TCA cycle, citrate lyase (EC. 4.1.3.6) and 2-oxoglutarate synthase (EC.1.2.7.3)
|
|
Latent tuberculosis and pathogen survival in granuloma
A case in point is found in Mycobacterium tuberculosis infections. After being inhaled, those invading pathogens that are phagocytosed by alveolar macrophages can survive and even replicate in the phagosomal compartment, assimilating carbon and producing energy. Subsequently, the progressive escalation in the immune response culminates in the formation of granulomas, organized collections of activated macrophages and other immune cells (Stewart et al., 2003). The pathogen persists within these granulomas during this containment phase of the long-term asymptomatic infection, until a compromising change in the immune status of the host results in containment failure. At that point the center of the granuloma undergoes necrotic degradation, or caseation, causing lesions and liberating infectious bacilli, the hallmark of latent tuberculosis (Manabe and Bishai, 2000; Russell, 2001; Cosma et al., 2003). Within the dynamic environment of the lesions, a continuum seems to exist between replication of metabolically active bacteria and phagocytic killing, maintaining a steady-state (Bouley et al., 2001). The implication is that successful persistence requires that the rate of growth and the rate of thermal decay of the bacteria be balanced, and equilibrium can occur only when there is negative feedback (Blaser and Kirchner, 1999). This phenomenon raises a major intriguing question of how the bacteria survive within these lesions, an issue that may be directly related to the mechanisms by which the pathogen adapts to environmental changes—beginning with the invasion, then progressing to intracellular residence in the phagosomal compartments of macrophages and eventually in the interior of the granulomas.
Persistence by adaptation to changing environments
Mycobacterium tuberculosis can alter its mode of metabolism to survive in hostile and austere interior environments that are progressively nutrient-starved, microaerophilic, and oxygen-depleted (Gomez and McKinney, 2004; Voskuil et al., 2004; Wayne and Sohaskey, 2001). An organism that utilizes alternative energy sources must be able to maintain the balance of oxidative and reductive reactions in the metabolic scheme. Reducing equivalents of NADH (reduced nicotinamide adenine dinucleotide), NADPH (reduced nicotinamide adenine dinucleotide phosphate), and FADH2 (reduced flavin adenine dinucleotide) generated under aerobic conditions via glycolysis, the Krebs cycle, and ß-oxidation pathways could be reoxidized efficiently through the electron-transport chain, terminating with oxygen. However, under oxygen-limiting microaerophilic and anaerobic conditions, severe restrictions may be imposed on the reoxidation potential, leading to redox imbalance that results in toxic accumulations of the reducing equivalents. Because the lesions are enriched in CO2 (Haapanen et al., 1959), the reductive TCA cycle, with its remarkable ability to fix carbon solely from CO2, may allow these reducing equivalents to be used efficiently in the anabolic mode. Since this organism has both of the key enzymes for the rTCA cycle (Table 1), a fully functional cycle in the reverse direction may be able to fix carbon in the relatively reductive environment, maintaining replication at a low level that facilitates persistence anaerobically.
This may well be a common theme in the survival strategy among bacteria that cause persistent infections, including Salmonella enterica serovar Typhi and Helicobacter pylori (Monack et al., 2004a). Hosts chronically infected with Salmonella harbor the pathogen within the reticuloendothelial system for long periods of time. The bacteria are inside the classical granulomatous lesions that arise in the spleen, liver, and gall bladder, and in the mesenteric lymph nodes (MLNs) that are the most common site of chronic infection (Vasquez-Torres et al., 1999; Monack et al., 2004b). In low numbers, the persistent bacteria colonize the interior of macrophages residing in the MLNs (Monack et al., 2004b). H. pylori, a gram-negative, microaerophilic bacteria, colonizes the upper gastrointestinal tract of humans and plays a causative role in the development of chronic gastritis, gastric and duodenal ulcers, and gastric adenocarcinoma. The bacterium proliferates in the mucous layer of the stomach, and its invasion of the gastric epithelium results in the recruitment of macrophages, polymorphonuclear phagocytes, and lymphocytes to the gastric mucosa. In spite of this host response, the pathogen can persist for decades (Blaser and Atherton, 2004). Again, like the Mycobacteria and Salmonella, H. pylori cells ingested by macrophages manage to survive and replicate intracellularly, excluded from immune surveillance, and to persist and distribute themselves in multiple locales in the gastric ecosystem throughout the life of the host (Allen et al., 2000).
Carbon fixation and restoration of redox balance by rTCA cycle
The ability of these persistent pathogens to survive and proliferate through extracellular and intracellular phases in varying hostile environments of the host requires novel metabolic strategies for carbon fixation. The reductive TCA cycle may provide such a strategy, facilitating anaerobic carbon fixation and restoring redox balance. Most enzymes of the cycle are shared in both the oxidative and reductive directions, with citrate lyase (EC 4.1.3.6) and 2-oxoglutarate synthase (EC 1.2.7.3) being the key enzymes for the complete reductive mode. Examination of the genomes of Mycobacteria has revealed the presence of both the above-mentioned enzymes of the rTCA cycle in M. tuberculosis and M. bovis, while Salmonella typhi and H. pylori have, respectively, citrate lyase and 2-oxoglutarate synthase, along with the rest of the enzymes (Tables 1 and 2). Similarly, a number of other pathogenic bacteria also seem to possess one of the two marker enzymes of the reductive TCA cycle (Table 2).
View this table:
[in this window]
[in a new window]
|
Table 2 Organisms that contain either of the two key enzymes of the reductive TCA cycle, citrate lyase (EC. 4.1.3.6) or 2-oxoglutarate synthase (EC.1.2.7.3)
|
|
Key enzymes of rTCA cycle as drug targets
As we have seen, the bacteria responsible for many persistent microbial infections must sustain the stress of encountering varied and unfavorable conditions in the host, respond with alternate metabolic strategies, and adapt to the environmental transitions and alterations. Under nutritional stress and microaerophilic and anaerobic conditions, a partial or fully functional reductive TCA cycle could depending on the metabolite balance, permit carbon acquisition, ensuring survival and proliferation of the microbe. It is possible that such a mechanism functions in these persistent bacterial infections. Biochemical investigations with bacteria grown under the appropriate microaerophilic or anaerobic conditions should establish whether the rTCA cycle is operative in these organisms. If it is, the rTCA cycle would be a point of vulnerability that could be exploited for therapeutic intervention. The key enzymes citrate lyase and 2-oxoglutarate synthase would qualify as candidates to be targeted in a mechanism-based search for new therapeutic agents. The absence of these two enzymes in the host and closely related organisms further enhances their suitability as drug targets; gene disruption or knockout studies could be used to reveal their functional significance and essentiality in persistent microbial pathogenesis.
Acquisition of ancient genes by horizontal gene transfer
It is intriguing that rTCA cycle genes that are central to the metabolism of the most ancient organisms—the chemolithoautotrophs of the reductive world, which are placed at the deep end of the root of the phylogenetic tree (Burggraf et al., 1992)—are revealed to be present in evolutionarily very distant organisms (see Tables 1 and 2). Besides their predominant distribution in actinobacteria and proteobacteria, the genes of the rTCA cycle (including one or both of the key enzymes) are found in a number of organisms of the archaeal kingdom. The major forces that shape the prokaryotic genomes and influence the gene content are gene genesis, gene loss, and horizontal gene transfer (HGT)—a process by which genomes acquire sequences from organisms that may be distantly related (Boucher et al., 2003). HGT is also believed to contribute a major source of genetic diversity in bacteria (Woese, 2002). In light of the wide diversity and distribution of both archaea and bacteria, it is possible that these bacteria have acquired these ancient genes through HGT. Thus the genomes of archaea may serve as a source of genes essential to the metabolic flexibility of bacteria, including the persistent pathogens. Incorporation of such metabolic capabilities into their gene pool may confer innovative adaptational strategies for survival in diverse environments and make it possible to select even hostile host niches by breaching host barriers that exclude other organisms. Thus archaea, which by themselves are nonpathogenic, might have indirectly contributed to bacterial pathogenicity.
It seems strange indeed that enzymes thought to be associated with very early organisms near the root of the taxonomic tree turn up in vertebrate pathogens as possible elements of persistent infection. It is an example of the inter-relatedness of all biology—an association that is further reified by horizontal gene transfer.
|
Acknowledgments
|
|---|
We are indebted to the Sir John Templeton Foundation for support.
|
Footnotes
|
|---|
Received 23 May 2005; accepted 17 October 2005.
|
Literature Cited
|
|---|
Allen, L. A., L. S. Schlesinger, and B. Kang. 2000. Virulent strains of Helicobacter pylori demonstrate delayed phagocytosis and stimulate homotypic phagosome fusion in macrophages. J. Exp. Med.191:115–127.[Abstract/Free Full Text]
Anbar, A. D., and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioorganic bridge? Science297:1137–1142.[Web of Science][Medline]
Beh, M., G. Strauss, R. Huber, K.O. Stetter, and G. Fuchs. 1993. Enzymes of the reductive citric acid cycle in the autotrophic bacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus TK-6. Arch. Microbiol.160:306–311.[Web of Science]
Blaser, M. J., and J. C. Atherton. 2004. Helicobacter pylori persistence: biology and disease. J. Clin. Investig.113:321–333.
Blaser, M. J., and D. Kirchner. 1999. Dynamics of Helicobacter pylori colonization in relation to the host response. Proc. Natl. Acad. Sci. USA96:8359–8364.[Abstract/Free Full Text]
Boucher, Y., C. J. Douady, T. Papke, D. A. Walsh, M. E. R. Boudreau, C. L. Nesbo, R. J. Case, and W. F. Doolittle. 2003. Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet.37:283–328.[Web of Science][Medline]
Bouley, D. M., N. Ghori, K. L. Mercer, S. Falkow, and L. Ramakrishnan. 2001. Dynamic nature of host-pathogen interactions in Mycobacterium tuberculosis granulomas. Infect. Immun.69:7820–7831.[Abstract/Free Full Text]
Brocks, J. J., G. A. Logan, R. Buick, and R. E. Summons. 1999. Archean molecular fossils and the early rise of eukaryotes. Science285:1033–1036.[Web of Science][Medline]
Burggraf, S., G. J. Olsen, K. O. Stetter, and C. R. Woese. 1992. A phylogenetic analysis of Aquifex pyrophilus. Syst. Appl. Microbiol. 15:352–356.
Camarasa, C., J. P. Grivet, and S. Dequin. 2003. Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation. Microbiology149:2669–2768.[Abstract/Free Full Text]
Catling, D. C., C. R. Glein, K. J. Zahnie, and C. P. McKay. 2005. Why O2 is required by complex life on habitable planets and the concept of planetary "oxygenation time." Astrobiology 5:415–438.
Cosma, C. L., D. R. Sherman, and L. Ramakrishnan. 2003. The secret lives of the pathogenic Mycobacteria. Annu. Rev. Microbiol. 57:641–676.
Danson, M. J., S. Harford, and P. D. J. Weitzman. 1979. Studies of a mutant form of Escherichia coli citrate synthase desensitized to allosteric effectors. Eur. J. Biochem.101:515–521.[Medline]
Evans, M. C., B. B. Buchanan, and D. I. Arnon. 1966. A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc. Natl. Acad. Sci. USA55:928–934.[Free Full Text]
Fuchs, G. 1989. Alternate pathways of autotrophic CO2 fixation. Pp. 365–382 in Autotrophic Bacteria, H. G. Schlegel and B. Bowien, eds. Science and Technology Press, Madison, WI.
Gogarten, P. J., and J. P. Townsend. 2005. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol.3:679–687.[Web of Science][Medline]
Gomez, J.E., and J. D. McKinney. 2004 M. tuberculosis persistence, latency and drug tolerance. Tuberculosis84:29–44.[Medline]
Haapanen, J. H., I. Kass, G. Gensini, and G. Middlebrook. 1959. Studies on the gaseous content of tuberculous cavities. Am. Rev. Respir. Dis.80:1–5.[Web of Science][Medline]
Kanehisa, M. 1997. A database for post-genome analysis. Trends Genet.13:375–376.[Web of Science][Medline]
Kanehisa, M., and S. Goto. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res.28:27–30.[Abstract/Free Full Text]
Kasting, J. F. 2001. The rise of atmospheric oxygen. Science293:819–820.[Web of Science]
KEGG Pathway Database, Kyoto Encyclopedia of Genes and Genomes. [Online] Available: http://www.genome.jp/kegg/pathway.html [accessed October 2005].
Kerr, R. A. 2005. The story of O2. Science308:1730–1732.[Abstract/Free Full Text]
Manabe, Y. C., and W. R. Bishai. 2000. Latent Mycobacterium tuberculosis—persistence, patience and winning by waiting. Nat. Med.6:1327–1329.[Web of Science][Medline]
Margulis, L., and K. V. Schwartz. 1998. P. 51 in Five Kingdoms—An Illustrated Guide to the Phyla of Life on Earth. 3rd edition. W. H. Freeman, New York.
Moller, D., R. Schauder, G. Fuchs, and R. K. Thauer. 1987. Acetate oxidation to CO2 via citric acid cycle involving an ATP-citrate lyase: mechanism for the synthesis of ATP via substrate level phosphorylation in Desulfobacter hydrogenophilus growing on acetate and sulfate. Arch. Microbiol.148:202–207.
Monack, D. M., A. Mueller, and S. Falkow. 2004a. Persistent bacterial infections: the interface of the pathogen and the host immune system. Nat. Rev. Microbiol. 2:747–765.
Monack, D. M., D. M. Bouley, and S. Falkow. 2004b. Salmonella typhimurium persists within macrophages in the mesenteric lymph nodes of chronically infected Nramp1+/+ mice and can be reactivated by IFN
neutralization. J. Exp. Med.199:231–241.[Abstract/Free Full Text]
Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol.4:R54.1–54.12.[Medline]
Russell, D. G. 2001. Mycobacterium tuberculosis: here today, and here tomorrow. Nat. Rev. Mol. Cell Biol.2:1–9.
Schauder, R., F. Widdel, and G. Fuchs. 1987. Carbon assimilation pathways in sulfate reducing bacteria. II. Enzymes of the reductive citric acid cycle in the autotrophic Desulfobacter hydrogenophilus. Arch. Microbiol. 148:218–225.
Shiba, H., T. Kawasumi,Y. Igarashi, T. Kodama, and Y. Minoda. 1985. The CO2 assimilation via the reductive tricarboxylic acid cycle in an autotrophic, aerobic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus. Arch Microbiol. 141:198–203.
Smith, E., and H. J. Morowitz. 2004. Universality in intermediary metabolism. Proc. Natl. Acad. Sci. USA 101:13168–13173.
Stewart, G. R., B. D. Robertson, and D. B. Young. 2003. Tuberculosis: a problem with persistence. Nat. Rev. Microbiol.1:97–106.[Web of Science][Medline]
Summons, R. E., L. L. Jahnke, J. M. Hope, and G. A. Logan. 1999. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature400:554–557.[Medline]
Vasquez-Torres, A., J. Jones-Carson, A. J. Baumler, S. Falkow, R. Valdivia, W. Brown, M. Le, R. Berggren, W. T. Parks, and F. Fang. 1999. Extraintestinal dissemination of Salmonella via CD18-expressing phagocytes. Nature401:804–808.[Medline]
Voskuil, M. I., K. C. Visconti, and G. K. Schoolnik. 2004. Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis84:218–227.
Wachtershauser, G. 1990. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA87:200–204.[Abstract/Free Full Text]
Wayne, L. G., and C. D. Sohaskey. 2001. Non-replicating persistence of Mycobacterium tuberculosis. Annu. Rev. Microbiol. 55:139–163.
Woese, C. R. 2002. On the evolution of cells. Proc. Natl. Acad. Sci. USA99:8742–8747.[Abstract/Free Full Text]
This article has been cited by other articles:
|
|
|
|
 
B. J. M. Vlaminckx, F. H. J. Schuren, R. C. Montijn, M. P. M. Caspers, A. C. Fluit, W. J. B. Wannet, L. M. Schouls, J. Verhoef, and W. T. M. Jansen
Determination of the Relationship between Group A Streptococcal Genome Content, M Type, and Toxic Shock Syndrome by a Mixed Genome Microarray
Infect. Immun.,
May 1, 2007;
75(5):
2603 - 2611.
[Abstract]
[Full Text]
[PDF]
|
|
|
TOP
Abstract
Introduction
