Sterol Biosynthesis Is Required for Heat Resistance but Not Extracellular Survival in Leishmania

Sterol biosynthesis is a crucial pathway in eukaryotes leading to the production of cholesterol in animals and various C24-alkyl sterols (ergostane-based sterols) in fungi, plants, and trypanosomatid protozoa. Sterols are important membrane components and precursors for the synthesis of powerful bioactive molecules, including steroid hormones in mammals. Their functions in pathogenic protozoa are not well characterized, which limits the development of sterol synthesis inhibitors as drugs. Here we investigated the role of sterol C14α-demethylase (C14DM) in Leishmania parasites. C14DM is a cytochrome P450 enzyme and the primary target of azole drugs. In Leishmania, genetic or chemical inactivation of C14DM led to a complete loss of ergostane-based sterols and accumulation of 14-methylated sterols. Despite the drastic change in lipid composition, C14DM-null mutants (c14dm ⁻) were surprisingly viable and replicative in culture. They did exhibit remarkable defects including increased membrane fluidity, failure to maintain detergent resistant membrane fraction, and hypersensitivity to heat stress. These c14dm ⁻ mutants showed severely reduced virulence in mice but were highly resistant to itraconazole and amphotericin B, two drugs targeting sterol synthesis. Our findings suggest that the accumulation of toxic sterol intermediates in c14dm ⁻ causes strong membrane perturbation and significant vulnerability to stress. The new knowledge may help improve the efficacy of current drugs against pathogenic protozoa by exploiting the fitness loss associated with drug resistance.     

Characterization of the Major Superoxide Dismutase of Staphylococcus aureus and Its Role in Starvation Survival, Stress Resistance, and Pathogenicity

A Staphylococcus aureus mutant (SPW1) which is unable to survive long-term starvation was shown to have a transposon insertion within a gene homologous to the sodA family of manganese-dependent superoxide dismutases (SOD). Whole-cell lysates of the parental 8325-4 strain demonstrated three zones of SOD activity by nondenaturing gel electrophoresis. The activities of two of these zones were dependent on manganese for activity and were absent in SPW1. The levels of SOD activity and sodA expression were growth-phase dependent, occurring most during postexponential phase. This response was also dependent on the level of aeration of the culture, with highest activity and expression occurring only under high aeration. Expression of sodA and, consequently, SOD activity could be induced by methyl viologen but only during the transition from exponential- to postexponential-phase growth. SPW1 was less able to survive amino acid limitation and acid stress but showed no alteration in pathogenicity in a mouse abscess model of infection compared to the parental strain 8325-4.     

A Staphylococcus aureus Small RNA Is Required for Bacterial Virulence and Regulates the Expression of an Immune-Evasion Molecule

Staphylococcus aureus, a pathogen responsible for hospital and community-acquired infections, expresses many virulence factors under the control of numerous regulatory systems. Here we show that one of the small pathogenicity island RNAs, named SprD, contributes significantly to causing disease in an animal model of infection. We have identified one of the targets of SprD and our in vivo data demonstrate that SprD negatively regulates the expression of the Sbi immune-evasion molecule, impairing both the adaptive and innate host immune responses. SprD interacts with the 5′ part of the sbi mRNA and structural mapping of SprD, its mRNA target, and the ‘SprD-mRNA’ duplex, in combination with mutational analysis, reveals the molecular details of the regulation. It demonstrates that the accessible SprD central region interacts with the sbi mRNA translational start site. We show by toeprint experiments that SprD prevents translation initiation of sbi mRNA by an antisense mechanism. SprD is a small regulatory RNA required for S. aureus pathogenicity with an identified function, although the mechanism of virulence control by the RNA is yet to be elucidated.     

GUN4 Is Required for Posttranslational Control of Plant Tetrapyrrole Biosynthesis

In aerobic photosynthetic organisms, GUN4 binds the chlorophyll intermediates protoporphyrin and Mg protoporphyrin, stimulates Mg chelatase activity, and is implicated in plastidic retrograde signaling. GUN4 expression is most abundant in young and greening tissues and parallels the activity of 5-aminolevulinic acid （ALA） ALA and Mg porphyrin biosynthesis during photoperiodic growth. We explored function and mode of action of GUN4 using GUN4- deficient and overexpressing plants. GUN4 overexpression leads to a general activation of the enzymes of chlorophyll biosynthesis. During photoperiodic growth GUN4 deficiency prevents ALA synthesis and chlorophyll accumulation. All these metabolic changes do not correlate with altered gene expression or changes of protein abundance in tetrapyrrole biosynthesis. While ALA feeding fails to compensate GUN4 deficiency during light-dark growth, this approach results in chlorophyll accumulation under continuous dim light. A new model defines the involvement of GUN4 in posttranslational regulation of ALA and Mg porphyrin synthesis, to sustain chlorophyll synthesis, namely under varying environmental conditions.     

Biosynthesis of cardiolipin from phosphatidylglycerol in Staphylococcus aureus

Cardiolipin (CL) synthetase from Staphylococcus aureus catalyzes the complete conversion of two molecules of phosphatidylglycerol (PG) to one molecule of CL and one molecule of glycerol. The fatty acids and phosphates of the two PG molecules can be quantitatively recovered in the CL. The enzyme is membrane-bound, shows a linear relationship with the product formed between 10 and 125 mug of membrane protein, has a pH optimum at 4.4, a temperature optimum between 37 and 45 C, a K(m) for PG of 2.1 x 10(-4)m, a V(max) of 200 nmoles of CL per min per mg of membrane protein, and does not require monovalent or divalent metals for activity. The enzyme has no nucleotide requirement and is not affected by prolonged dialysis, and treatment of the enzyme with charcoal has no effect on its activity. The enzyme has no phosphomonoesterase or phosphodiesterase activity, does not act on CL, is specific for PG, and CL and glycerol are the sole products of its activity. Other lipids do not stimulate or inhibit its activity. The enzyme is inhibited by organic solvents and some detergents. There is sufficient CL synthetase activity to account for CL synthesis during exponential growth. Inhibition of CL hydrolysis during growth results in an increase in CL that is balanced by a loss of PG. The activity of CL synthetase is not affected by cytidine diphosphate diglyceride but is inhibited competitively by the product, CL.     

Both GtfA and GtfB are Required for SraP Glycosylation in Staphylococcus aureus

Staphylococcus aureus has been shown to bind to human platelets through a variety of surface molecules, including serine-rich adhesin for platelets (SraP). The SraP mutant strain of S. aureus is significantly impaired in its ability to initiate infection compared with the wild strain. SraP is a cell wall-anchored, glycosylated protein. A previous study revealed that SecY2, Asp1, Asp2, Asp3, and SecA2 in the SraP operon were required for the efficient transport of glycosylated SraP from the cytoplasm to the bacterial cell surface. However, no glycosyltransferase (Gtf) was found to be involved in the glycosylation of SraP. In this study, SraP was found in all of the 55 clinical isolates of S. aureus using a real-time polymerase chain reaction assay. Sequence and phylogenetic analysis showed that GtfA and GtfB in the SraP operon were highly conserved in most of these clinical isolates. Conserved domains analysis revealed that both GtfA and GtfB contained a GT1_GtfA-like domain. Structural homology analysis inferred that they are both Gtfs. We then constructed an in vivo glycosylation system in Escherichia coli using SraP_1–743 as the substrate and GtfA and GtfB as the Gtfs. Using this system, we found that GtfA and GtfB were the Gtfs that transferred the N-acetylglucosamine-containing oligosaccharides to the recombinant SraP_1–743. Deletion of either one or both of the Gtfs abolished the glycosylation of SraP. In summary, GtfA and GtfB in the SraP operon are highly conserved in most clinical isolates of S. aureus, and both GtfA and GtfB are required for SraP glycosylation.     

A DNA Damage-Regulated BRCT-Containing Protein, TopBP1, Is Required for Cell Survival

BRCA1 carboxyl-terminal (BRCT) motifs are present in a number of proteins involved in DNA repair and/or DNA damage-signaling pathways. Human DNA topoisomerase II binding protein 1 (TopBP1) contains eight BRCT motifs and shares sequence similarity with the fission yeast Rad4/Cut5 protein and the budding yeast DPB11 protein, both of which are required for DNA damage and/or replication checkpoint controls. We report here that TopBP1 is phosphorylated in response to DNA double-strand breaks and replication blocks. TopBP1 forms nuclear foci and localizes to the sites of DNA damage or the arrested replication forks. In response to DNA strand breaks, TopBP1 phosphorylation depends on the ataxia telangiectasia mutated protein (ATM) in vivo. However, ATM-dependent phosphorylation of TopBP1 does not appear to be required for focus formation following DNA damage. Instead, focus formation relies on one of the BRCT motifs, BRCT5, in TopBP1. Antisense Morpholino oligomers against TopBP1 greatly reduced TopBP1 expression in vivo. Similar to that of ataxia telangiectasia-related protein (ATR), Chk1, or Hus1, downregulation of TopBP1 leads to reduced cell survival, probably due to increased apoptosis. Taken together, the data presented here suggest that, like its putative counterparts in yeast species, TopBP1 may be involved in DNA damage and replication checkpoint controls.     

Aflatoxin Biosynthesis Cluster Gene cypA Is Required for G Aflatoxin Formation

Aspergillus flavus isolates produce only aflatoxins B1 and B2, while Aspergillus parasiticus and Aspergillus nomius produce aflatoxins B1, B2, G1, and G2. Sequence comparison of the aflatoxin biosynthesis pathway gene cluster upstream from the polyketide synthase gene, pksA, revealed that A. flavus isolates are missing portions of genes (cypA and norB) predicted to encode, respectively, a cytochrome P450 monooxygenase and an aryl alcohol dehydrogenase. Insertional disruption of cypA in A. parasiticus yielded transformants that lack the ability to produce G aflatoxins but not B aflatoxins. The enzyme encoded by cypA has highest amino acid identity to Gibberella zeae Tri4 (38%), a P450 monooxygenase previously shown to be involved in trichodiene epoxidation. The substrate for CypA may be an intermediate formed by oxidative cleavage of the A ring of O-methylsterigmatocystin by OrdA, the P450 monooxygenase required for formation of aflatoxins B1 and B2.     

Maturation by LctT Is Required for Biosynthesis of Full-Length Lantibiotic Lacticin 481

In lantibiotic lacticin 481 biosynthesis, LctT cleaves the precursor peptide and exports mature lantibiotic. Matrix-assisted laser desorption ionization-time of flight mass spectrometry revealed that a truncated form of lacticin 481 is produced in the absence of LctT or after cleavage site inactivation. Production of truncated lacticin 481 is 4-fold less efficient, and its specific activity is about 10-fold lower.     

The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome bd Oxidase Complex and Is Required for Cytochrome bd Oxidase Activity

Cytochrome bd oxidase operons from more than 50 species of bacteria contain a short gene encoding a small protein that ranges from ∼30 to 50 amino acids and is predicted to localize to the cell membrane. Although cytochrome bd oxidases have been studied for more than 70 years, little is known about the role of this small protein, denoted CydX, in oxidase activity. Here we report that Escherichia coli mutants lacking CydX exhibit phenotypes associated with reduced oxidase activity. In addition, cell membrane extracts from ΔcydX mutant strains have reduced oxidase activity in vitro. Consistent with data showing that CydX is required for cytochrome bd oxidase activity, copurification experiments indicate that CydX interacts with the CydAB cytochrome bd oxidase complex. Together, these data support the hypothesis that CydX is a subunit of the CydAB cytochrome bd oxidase complex that is required for complex activity. The results of mutation analysis of CydX suggest that few individual amino acids in the small protein are essential for function, at least in the context of protein overexpression. In addition, the results of analysis of the paralogous small transmembrane protein AppX show that the two proteins could have some overlapping functionality in the cell and that both have the potential to interact with the CydAB complex.     

Tam41 Is a CDP-Diacylglycerol Synthase Required for Cardiolipin Biosynthesis in Mitochondria

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Proline Biosynthesis Is Required for Endoplasmic Reticulum Stress Tolerance in Saccharomyces cerevisiae

The amino acid proline is uniquely involved in cellular processes that underlie stress response in a variety of organisms. Proline is known to minimize protein aggregation, but a detailed study of how proline impacts cell survival during accumulation of misfolded proteins in the endoplasmic reticulum (ER) has not been performed. To address this we examined in Saccharomyces cerevisiae the effect of knocking out the PRO1, PRO2, and PRO3 genes responsible for proline biosynthesis. The null mutants pro1, pro2, and pro3 were shown to have increased sensitivity to ER stress relative to wild-type cells, which could be restored by proline or the corresponding genetic complementation. Of these mutants, pro3 was the most sensitive to tunicamycin and was rescued by anaerobic growth conditions or reduced thiol reagents. The pro3 mutant cells have higher intracellular reactive oxygen species, total glutathione, and a NADP⁺/NADPH ratio than wild-type cells under limiting proline conditions. Depletion of proline biosynthesis also inhibits the unfolded protein response (UPR) indicating proline protection involves the UPR. To more broadly test the role of proline in ER stress, increased proline biosynthesis was shown to partially rescue the ER stress sensitivity of a hog1 null mutant in which the high osmolality pathway is disrupted.     

Osmotic Regulation Is Required for Cancer Cell Survival under Solid Stress

For a solid tumor to grow, it must be able to support the compressive stress that is generated as it presses against the surrounding tissue. Although the literature suggests a role for the cytoskeleton in counteracting these stresses, there has been no systematic evaluation of which filaments are responsible or to what degree. Here, using a three-dimensional spheroid model, we show that cytoskeletal filaments do not actively support compressive loads in breast, ovarian, and prostate cancer. However, modulation of tonicity can induce alterations in spheroid size. We find that under compression, tumor cells actively efflux sodium to decrease their intracellular tonicity, and that this is reversible by blockade of sodium channel NHE1. Moreover, although polymerized actin does not actively support the compressive load, it is required for sodium efflux. Compression-induced cell death is increased by both sodium blockade and actin depolymerization, whereas increased actin polymerization offers protective effects and increases sodium efflux. Taken together, these results demonstrate that cancer cells modulate their tonicity to survive under compressive solid stress.     

Penicillin-Binding Protein 1 of Staphylococcus aureus Is Essential for Growth

pbpA, a gene encoding penicillin-binding protein (PBP) 1 of Staphylococcus aureus, was cloned in an Escherichia coli MC1061 transformant which grew on a plate containing 512 μg of vancomycin per ml. This gene encodes a 744-amino-acid sequence which conserves three motifs of PBPs, SXXK, SXN, and KTG. The chromosomal copy of pbpA could be disrupted only when RN4220, a methicillin-sensitive S. aureus strain, had additional copies of pbpA in its episome. Furthermore, these episomal copies of pbpA could not be eliminated by an incompatible plasmid when the chromosomal copy of pbpA was disrupted beforehand. Based on these observations, we concluded that pbpA is essential for the growth of methicillin-sensitive S. aureus.     

Survival of Staphylococcus aureus inside neutrophils contributes to infection

Neutrophils have long been regarded as essential for host defense against Staphylococcus aureus infection. However, survival of the pathogen inside various cells, including phagocytes, has been proposed as a mechanism for persistence of this microorganism in certain infections. Therefore, we investigated whether survival of the pathogen inside polymorphonuclear neutrophils (PMN) contributes to the pathogenesis of S. aureus infection. Our data demonstrate that PMN isolated from the site of infection contain viable intracellular organisms and that these infected PMN are sufficient to establish infection in a naive animal. In addition, we show that limiting, but not ablating, PMN migration into the site of infection enhances host defense and that repletion of PMN, as well as promoting PMN influx by CXC chemokine administration, leads to decreased survival of the mice and an increased bacterial burden. Moreover, a global regulator mutant of S. aureus (sar-) that lacks the expression of several virulence factors is less able to survive and/or avoid clearance in the presence of PMN. These data suggest that the ability of S. aureus to exploit the inflammatory response of the host by surviving inside PMN is a virulence mechanism for this pathogen and that modulation of the inflammatory response is sufficient to significantly alter morbidity and mortality induced by S. aureus infection.     

NDRG4 Is Required for Cell Cycle Progression and Survival in Glioblastoma Cells

NDRG4 is a largely unstudied member of the predominantly tumor suppressive N-Myc downstream-regulated gene (NDRG) family. Unlike its family members NDRG1–3, which are ubiquitously expressed, NDRG4 is expressed almost exclusively in the heart and brain. Given this tissue-specific expression pattern and the established tumor suppressive roles of the NDRG family in regulating cellular proliferation, we investigated the cellular and biochemical functions of NDRG4 in the context of astrocytes and glioblastoma multiforme (GBM) cells. We show that, in contrast to NDRG2, NDRG4 expression is elevated in GBM and NDRG4 is required for the viability of primary astrocytes, established GBM cell lines, and both CD133⁺ (cancer stem cell (CSC)-enriched) and CD133⁻ primary GBM xenograft cells. While NDRG4 overexpression has no effect on cell viability, NDRG4 knockdown causes G₁ cell cycle arrest followed by apoptosis. The initial G₁ arrest is associated with a decrease in cyclin D1 expression and an increase in p27^Kip1 expression, and the subsequent apoptosis is associated with a decrease in the expression of XIAP and survivin. As a result of these effects on cell cycle progression and survival, NDRG4 knockdown decreases the tumorigenic capacity of established GBM cell lines and GBM CSC-enriched cells that have been implanted intracranially into immunocompromised mice. Collectively, these data indicate that NDRG4 is required for cell cycle progression and survival, thereby diverging in function from its tumor suppressive family member NDRG2 in astrocytes and GBM cells.The N-Myc downstream-regulated gene (NDRG)⁵ family consists of four genes (NDRG1–4) that can be divided into two subfamilies based on sequence homology: NDRG1 and NDRG3 are in the first subfamily, and NDRG2 and NDRG4 make up the second subfamily. Although the four NDRG family members show distinct spatiotemporal expression patterns during embryonic development and in adult tissues (1–10), all four are highly expressed in the brain (4). To date, however, NDRG2 is the only NDRG family member that has been studied in the context of GBM cells and astrocytes. NDRG2 mRNA and protein levels are lower in GBM than in normal brain tissue, normal glial cells, and low grade astrocytomas (11–14), suggesting a tumor suppressive function. Data from experimental and clinical studies support this hypothesis: NDRG2 overexpression inhibits GBM cell proliferation (15), and decreased NDRG2 expression correlates with decreased GBM patient survival (13).In contrast to its subfamily member NDRG2, NDRG4 has not been studied in GBM cells or astrocytes. Nevertheless, available evidence supports the hypothesis that NDRG4 has an important role in this context that is similar to the role of NDRG2. First, unlike the relatively ubiquitous expression patterns of NDRG1–3, NDRG4 expression is restricted to a small number of tissues including the brain, where it is expressed at particularly high levels (7, 10). This restricted expression pattern suggests that NDRG4 plays an important role within the central nervous system. Second, NDRG4 is more than 60% identical in amino acid sequence to NDRG2. This sequence similarity is likely behind the overlapping functions of these two proteins in certain cell types within the brain. For example, in PC12 neuronal cells, both NDRG4 and NDRG2 promote neurite extension (16–18). In combination with the brain-specific expression pattern of NDRG4, these functional and sequence similarities suggest that NDRG4 may recapitulate the tumor suppressive function of NDRG2 in primary brain neoplasms.To determine if the similarities between NDRG2 and NDRG4 extend to the context of GBM, we investigated the role of NDRG4 in GBM cell lines and primary human astrocytes. In contrast to the established roles of NDRG2 and other NDRG family members, we found that the role of NDRG4 in GBM is not tumor suppressive. On the contrary, both astrocytes and GBM cells require the presence of NDRG4 for cell cycle progression and survival.     

Evidence that Ubiquinone Is a Required Intermediate for Rhodoquinone Biosynthesis in Rhodospirillum rubrum

Rhodoquinone (RQ) is an important cofactor used in the anaerobic energy metabolism of Rhodospirillum rubrum. RQ is structurally similar to ubiquinone (coenzyme Q or Q), a polyprenylated benzoquinone used in the aerobic respiratory chain. RQ is also found in several eukaryotic species that utilize a fumarate reductase pathway for anaerobic respiration, an important example being the parasitic helminths. RQ is not found in humans or other mammals, and therefore inhibition of its biosynthesis may provide a parasite-specific drug target. In this report, we describe several in vivo feeding experiments with R. rubrum used for the identification of RQ biosynthetic intermediates. Cultures of R. rubrum were grown in the presence of synthetic analogs of ubiquinone and the known Q biosynthetic precursors demethylubiquinone, demethoxyubiquinone, and demethyldemethoxyubiquinone, and assays were monitored for the formation of RQ₃. Data from time course experiments and S-adenosyl-l-methionine-dependent O-methyltransferase inhibition studies are discussed. Based on the results presented, we have demonstrated that Q is a required intermediate for the biosynthesis of RQ in R. rubrum.Rhodospirillum rubrum is a well-characterized and metabolically diverse member of the family of purple nonsulfur bacteria (29, 61). R. rubrum is typically found in aquatic environments and can adapt to a variety of growth conditions by using photosynthesis, respiration, or fermentation pathways (28, 70). In the light, R. rubrum exhibits photoheterotrophic growth using organic substrates or photoautotrophic growth using CO₂ and H₂ (15, 70). In the dark, R. rubrum can utilize either aerobic respiration (70, 73) or anaerobic respiration with a fumarate reduction pathway or with nonfermentable substrates in the presence of oxidants such as dimethyl sulfoxide (DMSO) or trimethylamine oxide (15, 58, 73). R. rubrum can also grow anaerobically in the dark by fermentation of sugars in the presence of bicarbonate (58). The focus of this work was the biosynthesis of quinones used by R. rubrum for aerobic and anaerobic respiration.Rhodoquinone (RQ; compound 1 in Fig. ​Fig.1)1) is an aminoquinone structurally similar to ubiquinone (coenzyme Q or Q [compound 2]) (44); however, the two differ considerably in redox potential (that of RQ is −63 mV, and that of Q is +100 mV) (2). Both RQ and Q have a fully substituted benzoquinone ring and a polyisoprenoid side chain that varies in length (depending on the species; see Fig. ​Fig.11 for examples). The only difference between the structures is that RQ has an amino substituent (NH₂) instead of a methoxy substituent (OCH₃) on the quinone ring. While Q is a ubiquitous lipid component involved in aerobic respiratory electron transport (9, 36, 60), RQ functions in anaerobic respiration in R. rubrum (19) and in several other phototrophic purple bacteria (21, 22, 41) and is also present in a few aerobic chemotrophic bacteria, including Brachymonas denitrificans and Zoogloea ramigera (23). In these varied species of bacteria, RQ has been proposed to function in fumarate reduction to maintain NAD⁺/NADH redox balance, either during photosynthetic anaerobic metabolism (12, 15-18, 64) or in chemotrophic metabolism when the availability of oxygen as a terminal oxidant is limiting (23). Another recent finding is that RQH₂ is capable of inducing Q-cycle bypass reactions in the cytochrome bc₁ complex in Saccharomyces cerevisiae, resulting in superoxide formation (7). If RQ/RQH₂ coexists in the cytoplasmic membrane with Q/QH₂ in R. rubrum, it might serve as both a substrate for and an inhibitor of the bc₁ complex (47).Open in a separate windowFIG. 1.Proposed pathways for RQ biosynthesis. The number of isoprene units (n) varies by species (in S. cerevisiae, n = 6; in E. coli, n = 8; in C. elegans, n = 9; in helminth parasites, n = 9 or 10; in R. rubrum, n = 10; in humans, n = 10). RQ is not found in S. cerevisiae, E. coli, or humans. Known Coq (from S. cerevisiae) and Ubi (from E. coli) gene products required for the biosynthesis of ubiquinone (Q, compound 2) are labeled. A polyisoprenyl diphosphate (compound 5) is assembled from dimethylallyl disphosphate (compound 3) and isopentyl diphosphate (compound 4). Coupling of compound 5 with p-hydroxybenzoic acid (compound 6) yields 3-polyprenyl-4-hydroxybenzoic acid (compound 7). The next three steps differ between S. cerevisiae and E. coli. However, they merge at the common intermediate (compound 8), which is oxidized to demethyldemethoxyubiquinone (DDMQ_n, compound 9). RQ (compound 1) has been proposed to arise from compound 9, demethoxyubiquinone (DMQ_n; compound 10), demethylubiquinone (DMeQ_n; compound 11), or compound 2 (by pathway A, B, C, or D). Results presented in this work support pathway D as the favored route for RQ biosynthesis in R. rubrum.RQ is also found in the mitochondrial membrane of eukaryotic species capable of fumarate reduction, such as the flagellate Euglena gracilis (25, 53), the free-living nematode Caenorhabditis elegans (62), and the parasitic helminths (65, 66, 68, 72). Similar to R. rubrum, these species can adapt their metabolism to both aerobic and anaerobic conditions throughout their life cycle. For example, most adult parasitic species (e.g., Ascaris suum, Fasciola hepatica, and Haemonchus contortus) rely heavily on fumarate reduction for their energy generation while inside a host organism, where the oxygen tension is very low (30, 65, 72). Under these conditions, the biosynthesis of RQ is upregulated; however, during free-living stages of their life cycle, the helminth parasites use primarily aerobic respiration, which requires Q (30, 65, 72). The anaerobic energy metabolism of the helminthes has been reviewed (63, 67). Humans and other mammalian hosts use Q for aerobic energy metabolism but do not produce or require RQ; therefore, selective inhibition of RQ biosynthesis may lead to highly specific antihelminthic drugs that do not have a toxic effect on the host (35, 48).R. rubrum is an excellent facultative model system for the study of RQ biosynthesis. The complete genome of R. rubrum has recently been sequenced by the Department of Energy Joint Genome Institute, finished by the Los Alamos Finishing Group, and further validated by optical mapping (57). The 16S rRNA sequence of R. rubrum is highly homologous to cognate eukaryotic mitochondrial sequences (46). Due to the similarities in structure, the biosynthetic pathways of RQ and Q have been proposed to diverge from a common precursor (67). Proposed pathways for RQ biosynthesis (A to D), in conjunction with the known steps in Q biosynthesis, are outlined in Fig. ​Fig.11 (31, 34, 60). Parson and Rudney previously showed that when R. rubrum was grown anaerobically in the light in the presence of [U-¹⁴C]p-hydroxybenzoate, ¹⁴C was incorporated into both Q₁₀ and RQ₁₀ (50). In their growth experiments, the specific activity of Q₁₀ was measured at its maximal value 15 h after inoculation and then began to decrease. However, the specific activity of RQ₁₀ continued to increase for 40 h before declining. These results suggested that Q₁₀ was a biosynthetic precursor of RQ₁₀, although this was not directly demonstrated using radiolabeled Q₁₀; hence, the possibility remained that the labeled RQ₁₀ was derived from another radiolabeled lipid species. We have done this feeding experiment with a synthetic analog of Q where n = 3 (Q₃) and monitored for the production of RQ₃. The synthesis and use of farnesylated quinone and aromatic intermediates for characterization of the Q biosynthetic pathway in S. cerevisiae and Escherichia coli has been well documented (4, 5, 38, 52, 59). The other proposed precursors of RQ shown in Fig. ​Fig.11 were also fed to R. rubrum, and the lipid extracts from these assays were analyzed for the presence of RQ₃, i.e., demethyldemethoxyubiquinone-3 (DDMQ₃; compound 9), demethoxyubiquinone-3 (DMQ₃; compound 10), and demethylubiquinone-3 (DMeQ₃; compound 11).In S. cerevisiae and E. coli, the last O-methylation step in Q biosynthesis is catalyzed by the S-adenosyl-l-methionine (SAM)-dependent methyltransferases Coq3 and UbiG, respectively (26, 52); this final methylation step converts DMeQ to Q. Using the NCBI Basic Local Alignment Search Tool, an O-methyltransferase (GeneID no. 3834724 Rru_A0742) that had 41% and 59% sequence identity with Coq3 and UbiG, respectively, was identified in R. rubrum. S-Adenosyl-l-homocysteine (SAH) is a well-known inhibitor of SAM-dependent methyltransferases (13, 24). Because SAH is the transmethylation by-product of SAM-dependent methyltransferases, it is not readily taken up by cells and must be generated in vivo (24). SAH can be produced in vivo from S-adenosine and l-homocysteine thiolactone by endogenous SAH hydrolase (SAHH) (37, 71). A search of the R. rubrum genome also confirmed the presence of a gene encoding SAHH (GeneID no. 3836896 Rru_A3444). It was proposed that if DMeQ is the immediate precursor of RQ, then SAH inhibition of the methyltransferase required for Q biosynthesis should have little effect on RQ production. Conversely, if Q is required for RQ synthesis, then inhibition of Q biosynthesis should have a significant effect on RQ production. Assays were designed to quantify the levels of RQ₃ produced from DMeQ₃ and Q₃ in R. rubrum cultures at various concentrations of SAH.