Matthew Wipperman | Memorial Sloan-Kettering Cancer Center (original) (raw)
Papers by Matthew Wipperman
mBio
The assembly of microbial communities that populate all mucosal surfaces of the human body begins... more The assembly of microbial communities that populate all mucosal surfaces of the human body begins right after birth. This process is prone to disruption as newborns and young infants are increasingly exposed to antibiotics, both deliberately for therapeutic purposes, and as a consequence of transmaternal exposure.
Antibiotic therapy cures infection predominantly by killing the infecting pathogen, but for infec... more Antibiotic therapy cures infection predominantly by killing the infecting pathogen, but for infections such as tuberculosis (TB), which are accompanied by chronic inflammation, the salutary effects of antibiotic therapy may reflect a combination of pathogen killing and microbiome alteration. This question has not been examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic induced pathogen clearance and microbiome alteration. We analyzed sputum TB bacterial load, microbiome composition, and peripheral blood transcriptomics from a clinical trial (NCT02684240) comparing two antimicrobial therapies for tuberculosis, only one of which was clinically effective. We confirm that standard TB therapy (HRZE) rapidly depletes Clostridia from the intestinal microbiota. The antiparasitic drug nitazoxanide (NTZ), although ineffective in reducing Mycobacterium tuberculosis (Mtb) bacterial load in the sputum, caused profound alterations to host microbiome comp...
Scientific Reports
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's popu... more Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world's most common infection on human ecology. Each year, up to 3-4% of all deaths worldwide from any cause are attributable to infection with the bacterial pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis (TB) disease, which amounts to almost 5,000 TB-related deaths each day 1. This colossal disease burden necessitates a thorough understanding of both the pathogenic strategies Mtb uses to cause disease, as well as the host susceptibilities Mtb has evolved to exploit. Individuals can be Mtb uninfected, infected with latent Mtb, have active TB disease, or be cured through antibiotic therapy. Many factors can influence the probability that some individuals transition from one of these stages to another, but most defined risk factors compromise immune function 2. For example, untreated HIV infection, which depletes CD4+ T cells, is associated with elevated risk of TB disease. Overall, immune status is also affected by age-the elderly and young infants are at a disproportionately high risk of Mtb infection and subsequent TB disease. Furthermore, individuals with germline mutations in pathways involved in controlling mycobacterial infection, such as IFNγ and TNFα, have an increased risk of active TB disease 3. Despite these examples, known immune deficiencies are not sufficient to explain why the incidence of new active TB cases hovers over 10 million people each year, with a mortality rate between 1.5-2 million people 1. Furthermore, it is
Scientific Reports
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's popu... more Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world's most common infection on human ecology. Each year, up to 3-4% of all deaths worldwide from any cause are attributable to infection with the bacterial pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis (TB) disease, which amounts to almost 5,000 TB-related deaths each day 1. This colossal disease burden necessitates a thorough understanding of both the pathogenic strategies Mtb uses to cause disease, as well as the host susceptibilities Mtb has evolved to exploit. Individuals can be Mtb uninfected, infected with latent Mtb, have active TB disease, or be cured through antibiotic therapy. Many factors can influence the probability that some individuals transition from one of these stages to another, but most defined risk factors compromise immune function 2. For example, untreated HIV infection, which depletes CD4+ T cells, is associated with elevated risk of TB disease. Overall, immune status is also affected by age-the elderly and young infants are at a disproportionately high risk of Mtb infection and subsequent TB disease. Furthermore, individuals with germline mutations in pathways involved in controlling mycobacterial infection, such as IFNγ and TNFα, have an increased risk of active TB disease 3. Despite these examples, known immune deficiencies are not sufficient to explain why the incidence of new active TB cases hovers over 10 million people each year, with a mortality rate between 1.5-2 million people 1. Furthermore, it is
Microbiome, Jul 7, 2017
Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of d... more Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations. While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among t...
Microbiome, Jul 7, 2017
Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of d... more Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations. While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among t...
mBio, Jan 18, 2018
Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied bo... more Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. During the past two decades, it has become clear that the microbiota-the trillion organisms that reside at mucosal surfaces within and on the body-can exert a major influence on disease outcome through its effects on host innate and adaptive immune function and metabolism. This new recognition of the potentially pleiotropic participation of the microbiome in immune responses has raised the possibility that the microbiota may influence infection and/or disease. Similarly, treatment of TB may alter the healthy steady-state composition and function of the microbiome, possibly affecting treatment outcome in addition to other host phy...
Biochemistry
Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturall... more Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturally distinct subfamily of acyl coenzyme A dehydrogenases (ACADs) for steroid catabolism. These ACADs are α 2 β 2 heterotetramers that are usually encoded by adjacent fadE-like genes. In mycobacteria, ipdE1 and ipdE2 (formerly fadE30 and fadE33) occur in divergently transcribed operons associated with the catabolism of 3aα-H-4α(3′-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), a steroid metabolite. In Mycobacterium smegmatis, ΔipdE1 and ΔipdE2 mutants had similar phenotypes, showing impaired growth on cholesterol and accumulating 5-OH HIP in the culture supernatant. Bioinformatic analyses revealed that IpdE1 and IpdE2 share many of the features of the αand β-subunits, respectively, of heterotetrameric ACADs that are encoded by adjacent genes in many steroid-degrading proteobacteria. When coproduced in a rhodococcal strain, IpdE1 and IpdE2 of Mtb formed a complex that catalyzed the dehydrogenation of 5OH-HIP coenzyme A (5OH-HIP-CoA) to 5OH-3aα-H-4α(3′-prop-1-enoate)-7aβ-methylhexahydro-1,5-indanedione coenzyme A ((E)-5OH-HIPE-CoA). This corresponds to the initial step in the pathway that leads to degradation of steroid C and D rings via β-oxidation. Small-angle X-ray scattering revealed that the IpdE1-IpdE2 complex was an α 2 β 2 heterotetramer typical of other ACADs involved in steroid catabolism. These results provide insight into an important class of steroid catabolic enzymes and a potential virulence determinant in Mtb.
ACS Infectious Diseases, 2015
The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for... more The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for both its virulence and pathogenesis, although how and why cholesterol metabolism is required is not fully understood. Mtb uses a unique set of catabolic enzymes that are homologous to those required for classical β-oxidation of fatty acids but are specific for steroid-derived substrates. Here, we identify and assign the substrate specificities of two of these enzymes, ChsE4-ChsE5 (Rv3504-Rv3505) and ChsE3 (Rv3573c), that carry out cholesterol side chain oxidation in Mtb. Steady-state assays demonstrate that ChsE4-ChsE5 preferentially catalyzes the oxidation of 3-oxo-cholest-4-en-26-oyl CoA in the first cycle of cholesterol side chain β-oxidation that ultimately yields propionyl-CoA, whereas ChsE3 specifically catalyzes the oxidation of 3-oxo-chol-4-en-24-oyl CoA in the second cycle of βoxidation that generates acetyl-CoA. However, ChsE4-ChsE5 can catalyze the oxidation of 3-oxo-chol-4-en-24-oyl CoA as well as 3-oxo-4-pregnene-20-carboxyl-CoA. The functional redundancy of ChsE4-ChsE5 explains the in vivo phenotype of the igr knockout strain of Mycobacterium tuberculosis; the loss of ChsE1-ChsE2 can be compensated for by ChsE4-ChsE5 during the chronic phase of infection. The X-ray crystallographic structure of ChsE4-ChsE5 was determined to a resolution of 2.0 Å and represents the first high-resolution structure of a heterotetrameric acyl-CoA dehydrogenase (ACAD). Unlike typical homotetrameric ACADs that bind four flavin adenine dinucleotide (FAD) cofactors, ChsE4-ChsE5 binds one FAD at each dimer interface, resulting in only two substrate-binding sites rather than the classical four active sites. A comparison of the ChsE4-ChsE5 substrate-binding site to those of known mammalian ACADs reveals an enlarged binding cavity that accommodates steroid substrates and highlights novel prospects for designing inhibitors against the committed β-oxidation step in the first cycle of cholesterol side chain degradation by Mtb.
Journal of Bacteriology, 2013
The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol an... more The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol and the roles that these compounds play in the virulence and pathogenesis of this organism are increasingly evident. Here, we demonstrate through experiments and bioinformatic analysis the existence of an architecturally distinct subfamily of acyl coenzyme A (acyl-CoA) dehydrogenase (ACAD) enzymes that are ␣ 2  2 heterotetramers with two active sites. These enzymes are encoded by two adjacent ACAD (fadE) genes that are regulated by cholesterol. FadE26-FadE27 catalyzes the dehydrogenation of 3-hydroxy-chol-5-en-24-oyl-CoA, an analog of the 5-carbon side chain cholesterol degradation intermediate. Genes encoding the ␣ 2  2 heterotetrameric ACAD structures are present in multiple regions of the M. tuberculosis genome, and subsets of these genes are regulated by four different transcriptional repressors or activators: KstR1 (also known as KstR), KstR2, Mce3R, and SigE. Homologous ACAD gene pairs are found in other Actinobacteria, as well as Proteobacteria. Their structures and genomic locations suggest that the ␣ 2  2 heterotetrameric structural motif has evolved to enable catalysis of dehydrogenation of steroid-or polycyclic-CoA substrates and that they function in four subpathways of cholesterol metabolism. Gene transcription induced by cholesterol Gene transcription repressed by cholesterol Not transcriptionally regulated by cholesterol FIG 2 Operonic organization of M. tuberculosis fadE genes studied in this work. In the M. tuberculosis genome, there are six operons containing multiple genes annotated as fadE genes, all of which are regulated by cholesterol (6) except in the operon containing fadE12 and fadE13. Wipperman et al. 4332 jb.asm.org Journal of Bacteriology
The Journal of organic chemistry, Jan 6, 2012
cis,anti,cis-Tricyclo[7.4.0.0(2,8)]tridec-10-ene (13TCT) undergoes [1,3] sigmatropic rearrangemen... more cis,anti,cis-Tricyclo[7.4.0.0(2,8)]tridec-10-ene (13TCT) undergoes [1,3] sigmatropic rearrangements at 315 °C in the gas phase to the si product 1 and to the sr product 2 with si/sr = 2.1. The dominant thermal isomerization process, however, is epimerization at C8 to afford product 3. That stereomutation at C8 occurs 50% faster than the si and sr shifts combined.
Organic & Biomolecular Chemistry, 2013
Bicyclo[3.2.0]hept-2-enes undergo thermal rearrangement to norbornenes via diradical transition s... more Bicyclo[3.2.0]hept-2-enes undergo thermal rearrangement to norbornenes via diradical transition structures. The synthesis of exo-7-cyclopropylbicyclo[3.2.0]hept-2-ene has been achieved by cycloaddition of cyclopentadiene and cyclopropylketene, generated by treatment of cyclopropylacetyl chloride with triethylamine. A comparison of the cyclopropyl substituent effect with that of other C7 substituents provides experimental evidence of an electron-donating conjugative effect on the transient diradical transition structure in the thermal reaction of exo-7-cyclopropylbicyclo[3.2.0]hept-2-ene.
The ability of science and medicine to control the pathogen Mycobacterium tuberculosis (Mtb) requ... more The ability of science and medicine to control the pathogen Mycobacterium tuberculosis (Mtb) requires an understanding of the complex host environment within which it resides. Pathological and biological evidence overwhelmingly demonstrate how the mammalian steroid cholesterol is present throughout the course of infection. Better understanding Mtb requires a more complete understanding of how it utilizes molecules like cholesterol in this environment to sustain the infection of the host. Cholesterol uptake, catabolism and broader utilization are important for maintenance of the pathogen in the host and it has been experimentally validated to contribute to virulence and pathogenesis. Cholesterol is catabolized by at least three distinct sub-pathways, two for the ring system and one for the side chain, yielding dozens of steroid intermediates with varying biochemical properties. Our ability to control this worldwide infectious agent requires a greater knowledge of how Mtb uses cholesterol to its advantage throughout the course of infection. Herein, the current state of knowledge of cholesterol metabolism by Mtb is reviewed from a biochemical perspective with a focus on the metabolic genes and pathways responsible for cholesterol steroid catabolism.
mBio
The assembly of microbial communities that populate all mucosal surfaces of the human body begins... more The assembly of microbial communities that populate all mucosal surfaces of the human body begins right after birth. This process is prone to disruption as newborns and young infants are increasingly exposed to antibiotics, both deliberately for therapeutic purposes, and as a consequence of transmaternal exposure.
Antibiotic therapy cures infection predominantly by killing the infecting pathogen, but for infec... more Antibiotic therapy cures infection predominantly by killing the infecting pathogen, but for infections such as tuberculosis (TB), which are accompanied by chronic inflammation, the salutary effects of antibiotic therapy may reflect a combination of pathogen killing and microbiome alteration. This question has not been examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic induced pathogen clearance and microbiome alteration. We analyzed sputum TB bacterial load, microbiome composition, and peripheral blood transcriptomics from a clinical trial (NCT02684240) comparing two antimicrobial therapies for tuberculosis, only one of which was clinically effective. We confirm that standard TB therapy (HRZE) rapidly depletes Clostridia from the intestinal microbiota. The antiparasitic drug nitazoxanide (NTZ), although ineffective in reducing Mycobacterium tuberculosis (Mtb) bacterial load in the sputum, caused profound alterations to host microbiome comp...
Scientific Reports
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's popu... more Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world's most common infection on human ecology. Each year, up to 3-4% of all deaths worldwide from any cause are attributable to infection with the bacterial pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis (TB) disease, which amounts to almost 5,000 TB-related deaths each day 1. This colossal disease burden necessitates a thorough understanding of both the pathogenic strategies Mtb uses to cause disease, as well as the host susceptibilities Mtb has evolved to exploit. Individuals can be Mtb uninfected, infected with latent Mtb, have active TB disease, or be cured through antibiotic therapy. Many factors can influence the probability that some individuals transition from one of these stages to another, but most defined risk factors compromise immune function 2. For example, untreated HIV infection, which depletes CD4+ T cells, is associated with elevated risk of TB disease. Overall, immune status is also affected by age-the elderly and young infants are at a disproportionately high risk of Mtb infection and subsequent TB disease. Furthermore, individuals with germline mutations in pathways involved in controlling mycobacterial infection, such as IFNγ and TNFα, have an increased risk of active TB disease 3. Despite these examples, known immune deficiencies are not sufficient to explain why the incidence of new active TB cases hovers over 10 million people each year, with a mortality rate between 1.5-2 million people 1. Furthermore, it is
Scientific Reports
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's popu... more Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world's most common infection on human ecology. Each year, up to 3-4% of all deaths worldwide from any cause are attributable to infection with the bacterial pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis (TB) disease, which amounts to almost 5,000 TB-related deaths each day 1. This colossal disease burden necessitates a thorough understanding of both the pathogenic strategies Mtb uses to cause disease, as well as the host susceptibilities Mtb has evolved to exploit. Individuals can be Mtb uninfected, infected with latent Mtb, have active TB disease, or be cured through antibiotic therapy. Many factors can influence the probability that some individuals transition from one of these stages to another, but most defined risk factors compromise immune function 2. For example, untreated HIV infection, which depletes CD4+ T cells, is associated with elevated risk of TB disease. Overall, immune status is also affected by age-the elderly and young infants are at a disproportionately high risk of Mtb infection and subsequent TB disease. Furthermore, individuals with germline mutations in pathways involved in controlling mycobacterial infection, such as IFNγ and TNFα, have an increased risk of active TB disease 3. Despite these examples, known immune deficiencies are not sufficient to explain why the incidence of new active TB cases hovers over 10 million people each year, with a mortality rate between 1.5-2 million people 1. Furthermore, it is
Microbiome, Jul 7, 2017
Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of d... more Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations. While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among t...
Microbiome, Jul 7, 2017
Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of d... more Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations. While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among t...
mBio, Jan 18, 2018
Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied bo... more Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. During the past two decades, it has become clear that the microbiota-the trillion organisms that reside at mucosal surfaces within and on the body-can exert a major influence on disease outcome through its effects on host innate and adaptive immune function and metabolism. This new recognition of the potentially pleiotropic participation of the microbiome in immune responses has raised the possibility that the microbiota may influence infection and/or disease. Similarly, treatment of TB may alter the healthy steady-state composition and function of the microbiome, possibly affecting treatment outcome in addition to other host phy...
Biochemistry
Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturall... more Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturally distinct subfamily of acyl coenzyme A dehydrogenases (ACADs) for steroid catabolism. These ACADs are α 2 β 2 heterotetramers that are usually encoded by adjacent fadE-like genes. In mycobacteria, ipdE1 and ipdE2 (formerly fadE30 and fadE33) occur in divergently transcribed operons associated with the catabolism of 3aα-H-4α(3′-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), a steroid metabolite. In Mycobacterium smegmatis, ΔipdE1 and ΔipdE2 mutants had similar phenotypes, showing impaired growth on cholesterol and accumulating 5-OH HIP in the culture supernatant. Bioinformatic analyses revealed that IpdE1 and IpdE2 share many of the features of the αand β-subunits, respectively, of heterotetrameric ACADs that are encoded by adjacent genes in many steroid-degrading proteobacteria. When coproduced in a rhodococcal strain, IpdE1 and IpdE2 of Mtb formed a complex that catalyzed the dehydrogenation of 5OH-HIP coenzyme A (5OH-HIP-CoA) to 5OH-3aα-H-4α(3′-prop-1-enoate)-7aβ-methylhexahydro-1,5-indanedione coenzyme A ((E)-5OH-HIPE-CoA). This corresponds to the initial step in the pathway that leads to degradation of steroid C and D rings via β-oxidation. Small-angle X-ray scattering revealed that the IpdE1-IpdE2 complex was an α 2 β 2 heterotetramer typical of other ACADs involved in steroid catabolism. These results provide insight into an important class of steroid catabolic enzymes and a potential virulence determinant in Mtb.
ACS Infectious Diseases, 2015
The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for... more The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for both its virulence and pathogenesis, although how and why cholesterol metabolism is required is not fully understood. Mtb uses a unique set of catabolic enzymes that are homologous to those required for classical β-oxidation of fatty acids but are specific for steroid-derived substrates. Here, we identify and assign the substrate specificities of two of these enzymes, ChsE4-ChsE5 (Rv3504-Rv3505) and ChsE3 (Rv3573c), that carry out cholesterol side chain oxidation in Mtb. Steady-state assays demonstrate that ChsE4-ChsE5 preferentially catalyzes the oxidation of 3-oxo-cholest-4-en-26-oyl CoA in the first cycle of cholesterol side chain β-oxidation that ultimately yields propionyl-CoA, whereas ChsE3 specifically catalyzes the oxidation of 3-oxo-chol-4-en-24-oyl CoA in the second cycle of βoxidation that generates acetyl-CoA. However, ChsE4-ChsE5 can catalyze the oxidation of 3-oxo-chol-4-en-24-oyl CoA as well as 3-oxo-4-pregnene-20-carboxyl-CoA. The functional redundancy of ChsE4-ChsE5 explains the in vivo phenotype of the igr knockout strain of Mycobacterium tuberculosis; the loss of ChsE1-ChsE2 can be compensated for by ChsE4-ChsE5 during the chronic phase of infection. The X-ray crystallographic structure of ChsE4-ChsE5 was determined to a resolution of 2.0 Å and represents the first high-resolution structure of a heterotetrameric acyl-CoA dehydrogenase (ACAD). Unlike typical homotetrameric ACADs that bind four flavin adenine dinucleotide (FAD) cofactors, ChsE4-ChsE5 binds one FAD at each dimer interface, resulting in only two substrate-binding sites rather than the classical four active sites. A comparison of the ChsE4-ChsE5 substrate-binding site to those of known mammalian ACADs reveals an enlarged binding cavity that accommodates steroid substrates and highlights novel prospects for designing inhibitors against the committed β-oxidation step in the first cycle of cholesterol side chain degradation by Mtb.
Journal of Bacteriology, 2013
The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol an... more The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol and the roles that these compounds play in the virulence and pathogenesis of this organism are increasingly evident. Here, we demonstrate through experiments and bioinformatic analysis the existence of an architecturally distinct subfamily of acyl coenzyme A (acyl-CoA) dehydrogenase (ACAD) enzymes that are ␣ 2  2 heterotetramers with two active sites. These enzymes are encoded by two adjacent ACAD (fadE) genes that are regulated by cholesterol. FadE26-FadE27 catalyzes the dehydrogenation of 3-hydroxy-chol-5-en-24-oyl-CoA, an analog of the 5-carbon side chain cholesterol degradation intermediate. Genes encoding the ␣ 2  2 heterotetrameric ACAD structures are present in multiple regions of the M. tuberculosis genome, and subsets of these genes are regulated by four different transcriptional repressors or activators: KstR1 (also known as KstR), KstR2, Mce3R, and SigE. Homologous ACAD gene pairs are found in other Actinobacteria, as well as Proteobacteria. Their structures and genomic locations suggest that the ␣ 2  2 heterotetrameric structural motif has evolved to enable catalysis of dehydrogenation of steroid-or polycyclic-CoA substrates and that they function in four subpathways of cholesterol metabolism. Gene transcription induced by cholesterol Gene transcription repressed by cholesterol Not transcriptionally regulated by cholesterol FIG 2 Operonic organization of M. tuberculosis fadE genes studied in this work. In the M. tuberculosis genome, there are six operons containing multiple genes annotated as fadE genes, all of which are regulated by cholesterol (6) except in the operon containing fadE12 and fadE13. Wipperman et al. 4332 jb.asm.org Journal of Bacteriology
The Journal of organic chemistry, Jan 6, 2012
cis,anti,cis-Tricyclo[7.4.0.0(2,8)]tridec-10-ene (13TCT) undergoes [1,3] sigmatropic rearrangemen... more cis,anti,cis-Tricyclo[7.4.0.0(2,8)]tridec-10-ene (13TCT) undergoes [1,3] sigmatropic rearrangements at 315 °C in the gas phase to the si product 1 and to the sr product 2 with si/sr = 2.1. The dominant thermal isomerization process, however, is epimerization at C8 to afford product 3. That stereomutation at C8 occurs 50% faster than the si and sr shifts combined.
Organic & Biomolecular Chemistry, 2013
Bicyclo[3.2.0]hept-2-enes undergo thermal rearrangement to norbornenes via diradical transition s... more Bicyclo[3.2.0]hept-2-enes undergo thermal rearrangement to norbornenes via diradical transition structures. The synthesis of exo-7-cyclopropylbicyclo[3.2.0]hept-2-ene has been achieved by cycloaddition of cyclopentadiene and cyclopropylketene, generated by treatment of cyclopropylacetyl chloride with triethylamine. A comparison of the cyclopropyl substituent effect with that of other C7 substituents provides experimental evidence of an electron-donating conjugative effect on the transient diradical transition structure in the thermal reaction of exo-7-cyclopropylbicyclo[3.2.0]hept-2-ene.
The ability of science and medicine to control the pathogen Mycobacterium tuberculosis (Mtb) requ... more The ability of science and medicine to control the pathogen Mycobacterium tuberculosis (Mtb) requires an understanding of the complex host environment within which it resides. Pathological and biological evidence overwhelmingly demonstrate how the mammalian steroid cholesterol is present throughout the course of infection. Better understanding Mtb requires a more complete understanding of how it utilizes molecules like cholesterol in this environment to sustain the infection of the host. Cholesterol uptake, catabolism and broader utilization are important for maintenance of the pathogen in the host and it has been experimentally validated to contribute to virulence and pathogenesis. Cholesterol is catabolized by at least three distinct sub-pathways, two for the ring system and one for the side chain, yielding dozens of steroid intermediates with varying biochemical properties. Our ability to control this worldwide infectious agent requires a greater knowledge of how Mtb uses cholesterol to its advantage throughout the course of infection. Herein, the current state of knowledge of cholesterol metabolism by Mtb is reviewed from a biochemical perspective with a focus on the metabolic genes and pathways responsible for cholesterol steroid catabolism.