Protein-Protein Interactions in the Mammalian Heme Degradation Pathway: Heme Oxygenase-2, Cytochrome P450 Reductase and Biliverdin Reductase.

Heme oxygenase (HO) catalyzes the rate-limiting step in the degradation of heme to biliverdin, CO and Fe, and requires electrons delivered from NADPH via cytochrome P450 reductase (CPR). Biliverdin reductase (BVR) then catalyzes conversion of biliverdin to bilirubin. The HO pathway is important for many cellular processes, including the maintenance of heme levels below toxic concentrations, iron homeostasis, carbon monoxide production, and antioxidant protection. Understanding protein-protein interactions of the heme degradation pathway will provide insight into potential regulatory mechanisms for the pathway. While the more well-studied HO isoform, HO-1, is reported to form complexes with CPR and BVR, little is known regarding the ability of HO-2 to bind either protein. In this thesis I describe various in vitro studies aimed at evaluating interactions of soluble HO-2 with CPR and BVR. The 1H-15N TROSY NMR spectrum of HO-2 reveals specific residues, including L201, near the heme face of HO-2 that are affected by the addition of CPR, implicating this residue at the HO/CPR interface. Alanine substitutions at HO-2 residues L201 and K169 cause a respective 3- and 22-fold increase in Km for CPR, consistent with a role for these residues in CPR binding. Sedimentation velocity experiments confirm the transient nature of the HO-2/CPR complex (Kd = 15.1 μM). Our results also indicate that HO-2 and BVR form a very weak complex that is only observed by cross-linking. Fluorescence quenching experiments suggest that the previously reported high affinity of BVR for HO is artifactual, resulting from the effects of free heme (dissociated from HO) on BVR fluorescence. Studies were also performed to evaluate the role of cysteine residues in catalytic activity and substrate inhibition for human BVR. Alanine substitution of C74 reduced catalytic activity by ~80% and this variant is less sensitive to substrate inhibition. Alanine substitution of C281, C292, C293 or C292/C293 had little effect on either catalytic activity or substrate inhibition. The studies described herein elucidate mechanisms which may be important features of regulation for the HO system in the cell, and thus have implications for regulating the cellular processes affected by HO and BVR.PHDCellular and Molecular BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/110320/1/almor_1.pd

Protein/Protein Interactions in the Mammalian Heme Degradation Pathway: Heme Oxygenase-2, Cytochrome P450 Reductase, and Biliverdin Reductase

Heme oxygenase (HO) catalyzes the rate-limiting step in the O2- dependent degradation of heme to biliverdin, CO, and iron with electrons delivered from NADPH via cytochrome P450 reductase (CPR). Biliverdin reductase (BVR) then catalyzes conversion of bili­verdin to bilirubin. We describe mutagenesis combined with kinetic, spectroscopic (fluorescence and NMR), surface plasmon resonance, cross-linking, gel filtration, and analytical ultracentrifugation studies aimed at evaluating interactions of HO-2 with CPR and BVR. Based on these results, we propose a model in which HO-2 and CPR form a dynamic ensemble of complex(es) that precede formation of the productive electron transfer complex. The 1H-15N TROSY NMR spectrum of HO-2 reveals specific residues, including Leu-201, near the heme face of HO-2 that are affected by the addition of CPR, im­plicating these residues at the HO/CPR interface. Alanine substitu­tions at HO-2 residues Leu-201 and Lys-169 cause a respective 3- and 22-fold increase in Km values for CPR, consistent with a role for these residues in CPR binding. Sedimentation velocity experiments confirm the transient nature of the HO-2·CPR complex (Kd = 15.1 μm). Our results also indicate that HO-2 and BVR form a very weak complex that is only captured by cross-linking. For example, under conditions where CPR affects the 1H-15N TROSY NMR spectrum of HO-2, BVR has no effect. Fluorescence quenching experiments also suggest that BVR binds HO-2 weakly, if at all, and that the previously reported high affinity of BVR for HO is artifactual, resulting from the effects of free heme (dissociated from HO) on BVR fluorescenc

Protein/Protein Interactions in the Mammalian Heme Degradation Pathway: Heme Oxygenase-2, Cytochrome P450 Reductase, and Biliverdin Reductase

Heme oxygenase (HO) catalyzes the rate-limiting step in the O2- dependent degradation of heme to biliverdin, CO, and iron with electrons delivered from NADPH via cytochrome P450 reductase (CPR). Biliverdin reductase (BVR) then catalyzes conversion of bili­verdin to bilirubin. We describe mutagenesis combined with kinetic, spectroscopic (fluorescence and NMR), surface plasmon resonance, cross-linking, gel filtration, and analytical ultracentrifugation studies aimed at evaluating interactions of HO-2 with CPR and BVR. Based on these results, we propose a model in which HO-2 and CPR form a dynamic ensemble of complex(es) that precede formation of the productive electron transfer complex. The 1H-15N TROSY NMR spectrum of HO-2 reveals specific residues, including Leu-201, near the heme face of HO-2 that are affected by the addition of CPR, im­plicating these residues at the HO/CPR interface. Alanine substitu­tions at HO-2 residues Leu-201 and Lys-169 cause a respective 3- and 22-fold increase in Km values for CPR, consistent with a role for these residues in CPR binding. Sedimentation velocity experiments confirm the transient nature of the HO-2·CPR complex (Kd = 15.1 μm). Our results also indicate that HO-2 and BVR form a very weak complex that is only captured by cross-linking. For example, under conditions where CPR affects the 1H-15N TROSY NMR spectrum of HO-2, BVR has no effect. Fluorescence quenching experiments also suggest that BVR binds HO-2 weakly, if at all, and that the previously reported high affinity of BVR for HO is artifactual, resulting from the effects of free heme (dissociated from HO) on BVR fluorescenc

Modelling Immunological Systems using PEPA: a preliminary report

We present preliminary work on modelling aspects of the immune system using process algebra. The problem addressed is how T-helper cell populations respond to co-infections with parasites making conflicting immunological demands. Our goal is to build PEPA models of alternative hypotheses around T-helper cell behaviour and to evaluate those with respect to experimental data

An EPR Investigation of defect structure and electron transfer mechanism in mixed-conductive LiBO2-V2O5 glasses

Continuous Wave (CW) Electron Paramagnetic Resonance (EPR) spectroscopy was used to study the defect structure and electron transfer mechanism in a series of LiBO2-V2O5 mixed conductive glasses of varying V2O5 content. These glassy materials are attracting growing interest for energy storage devices. At low V2O5 content (VLB1), an isolated S = ½ vanadium defect centre is found at a network modifying position within the LiBO2 matrix. The observed spin Hamiltonian parameters are consistent with a V4+ centre possessing a distorted octahedral configuration and dxy orbital ground state. At high V2O5 content (VLB3), the vanadium hyperfine structure is absent indicative of a distinct exchange-narrowed signal. A model was developed to analyse the linewidth and g-tensor component of the EPR signals, revealing a marked temperature dependent behaviour, consistent with a polaron hopping mechanism of electron transfer and inter-electronic exchange along the g3 direction, coincident with the electron transfer axis. The activation energy (Ea) was estimated to be 0.0805 eV, consistent with other conducting glasses. A relaxation-dominated line broadening mechanism was further supported by multi-frequency EPR measurements, which also identified unresolved features at high frequencies due to unaccounted for anisotropic exchange / speciation within the disordered network. This analysis provides a straight-forward method for the use of EPR to investigate solid-state glassy materials

Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios

Female members of many cephalopod species house a bacterial consortium that is part of their reproductive system, the accessory nidamental gland (ANG). These bacteria are deposited into eggs that are then laid in the environment where they must develop unprotected from predation, pathogens and fouling. In this study, we characterized the genome and secondary metabolite production of Leisingera sp. JC1, a member of the roseobacter clade (Rhodobacteraceae) of Alphaproteobacteria isolated from the jelly coat of eggs from the Hawaiian bobtail squid, Euprymna scolopes. Whole genome sequencing and MLSA analysis revealed that Leisingera sp. JC1 falls within a group of roseobacters associated with squid ANGs. Genome and biochemical analyses revealed the potential for and production of a number of secondary metabolites, including siderophores and acyl-homoserine lactones involved with quorum sensing. The complete biosynthetic gene cluster for the pigment indigoidine was detected in the genome and mass spectrometry confirmed the production of this compound. Furthermore, we investigated the production of indigoidine under co-culture conditions with Vibrio fischeri, the light organ symbiont of E. scolopes, and with other vibrios. Finally, both Leisingera sp. JC1 and secondary metabolite extracts of this strain had differential antimicrobial activity against a number of marine vibrios, suggesting that Leisingera sp. JC1 may play a role in host defense against other marine bacteria either in the eggs and/or ANG. These data also suggest that indigoidine may be partially, but not wholly, responsible for the antimicrobial activity of this squid-associated bacterium.

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin (Hb) function in high-altitude Andean house wrens (Troglodytes aedon). Results of experiments on native Hb variants and engineered, recombinant Hb mutants demonstrate that a nonsynonymous mutation at a CpG dinucleotide in the βA-globin gene is responsible for an evolved difference in Hb–O2 affinity between high- and low-altitude house wren populations. Moreover, patterns of genomic differentiation between high- and low-altitude populations suggest that altitudinal differentiation in allele frequencies at the causal amino acid polymorphism reflects a history of spatially varying selection. The experimental results highlight the influence of mutation rate on the genetic basis of phenotypic evolution by demonstrating that a large-effect allele at a highly mutable CpG site has promoted physiological differentiation in blood O2 transport capacity between house wren populations that are native to different elevations

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control

Global, regional, and national incidence, prevalence, andyears lived with disability for 354 diseases and injuries for195 countries and territories, 1990–2017: a systematicanalysis for the Global Burden of Disease Study 2017

The Global Burden of Diseases, Injuries, and Risk Factors Study 2017 (GBD 2017) includes a comprehensive assessment of incidence, prevalence, and years lived with disability (YLDs) for 354 causes in 195 countries and territories from 1990 to 2017. Previous GBD studies have shown how the decline of mortality rates from 1990 to 2016 has led to an increase in life expectancy, an ageing global population, and an expansion of the non-fatal burden of disease and injury. These studies have also shown how a substantial portion of the world’s population experiences non-fatal health loss with considerable heterogeneity among different causes, locations, ages, and sexes. Ongoing objectives of the GBD study include increasing the level of estimation detail, improving analytical strategies, and increasing the amount of high-quality data.Research reported in this publication was supported by the Bill & Melinda Gates Foundation, the University of Melbourne, Public Health England, the Norwegian Institute of Public Health, St Jude Children’s Research Hospital, the National Institute on Ageing of the National Institutes of Health (award P30AG047845), and the National Institute of Mental Health of the National Institutes of Health (award R01MH110163)