Human Fumarase Research Articles

Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition

Schistosomiasis is a neglected tropical disease that affects more than 250 million people worldwide. The only drug available for its treatment undergoes first-pass hepatic metabolism and is not capable of preventing reinfection, which makes the search of new therapies urgently needed. Due to the essential role of fumarases in metabolism, these enzymes represent potential targets for developing novel schistosomiasis treatments. Here, we evaluate the expression profiles for class I and class II fumarases from Schistosoma mansoni (SmFHI and SmFHII, respectively), and report the complete characterization of SmFHII. The first SmFHII structure in complex with L-malate was determined at 1.85 Å resolution. The significant thermoshift observed for SmFHII in the presence of identified ligands makes the differential scanning fluorimetry an adequate technique for ligand screening. A complete kinetic characterization of SmFHII was performed, and comparison with the human fumarase (HsFH) revealed differences regarding the turnover number (kcat). Structural characterization allowed us to identify differences between SmFHII and HsFH that could be explored to design new selective inhibitors. This work represents the very first step towards validate the fumarases as drug targets to treat schistosomiasis. Our results provide the structural basis to rational search for selective ligands.

Changing the Rules of TB-Drug Discovery.

The discovery of new drugs with novel targets is paramount to the continued success of tuberculosis (TB) treatment due to the increasing prevalence of antibiotic resistant infections in the TB population. Mycobacterium tuberculosis (Mtb) fumarate hydratase (fumarase) is a highly conserved essential protein that shares an active site with human fumarase, making active site inhibition equally cytotoxic for both bacteria and humans. The recent discovery of a set of new Mtb inhibitory compounds that target Mtb-fumarase by binding to a nonconserved allosteric site is a major advancement, providing further evidence to dispel the antibiotic discovery dogma that conserved proteins do not make good antibiotic targets.

Alterations within fumarase C reveal newly observed SS Loop conformations

Fumarase belongs to a larger superfamily of enzymes including aspartase, adenylosuccinate lyase, arginosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme. Each enzyme member shares a common quaternary structure and harbors a flexible active site loop, termed the SS Loop. The SS Loop lies within the fumarase superfamily signature sequence 317GS318SxMxK324xN326xxPxE331 and plays a fundamental role during catalysis. Recently, human fumarase deficiencies have been linked to renal cell carcinoma and benign uterine tumor formation. In this study we site-selectively altered SS Loop residues serine 318, lysine 324, asparagine 326 and glutamic acid 331 to alanine. The fumarase C SS Loop variants were characterized functionally and structurally. Functionally, steady-state kinetic experiments were conducted in the classic Krebs Cycle sense (fumarate to S-malate) and in the reductive biosynthetic direction (S-malate to fumarate). Structurally, the single-site SS Loop variants were analyzed via circular dichroism and x-ray crystallography. The steady-state kinetic results report minimal effect on the S-malate and fumarate Km values, while reducing kcat significantly. We have placed the kcat reduction into two categories: (1) diminished charge-relay influence and (2) SS Loop immobility. Structurally, the SS Loop single-site alanine variants have similar thermal and chemical denaturation profiles. Thus, we suggest the overall homotetrameric quaternary structure, a requisite for a functional multi-subunit active site, is intact. X-ray crystallographic results for both the serine 318 to alanine (S318A) and lysine 324 to alanine (K324A) variants report a newly discovered fumarase C active site architecture. The SS Loop in both the S318A and K324A active sites undertakes two disparate conformations leading to two unique active sites. These two active sites are non-crystallographically related and undertake ordered-open and ordered-closed conformations. Thus, alteration of serine 318 and lysine 324 has facilitated crystallographic order within the SS Loop region. Ordering and closure of the S318A SS Loop has created an electrostatic gate between the multi-subunit active site and an auxiliary single-subunit citrate binding site. Adaptation within the K324A crystal structure includes additionally ordered active site water molecules. Effectively, the newly observed water molecules re-establish electrostatic interactions between serine 98, threonine 100, asparagine 141, histidine 188 and the previously observed active site water. Our structural and functional results further establish the importance of SS Loop conformational mobility within the fumarase superfamily. S318A SS Loop and domain 3 movement lead to closure of the fumarase C active site. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Biochemical Characterization of Two Clinically-Relevant Human Fumarase Variants Defective for Oligomerization.

Background:Fumarase, a significant enzyme of energy metabolism, catalyzes the reversible hydration of fumarate to L-malate. Mutations in the FH gene, encoding human fumarase, are associated with fumarate hydratase deficiency (FHD) and hereditary leiomyomatosis and renal cell cancer (HLRCC). Fumarase assembles into a homotetramer, with four active sites. Interestingly, residues from three of the four subunits within the homotetramer comprise each active site. Hence, any mutation affecting oligomerization is predicted to disrupt enzyme activity.Methods:We constructed two variants of hexahistidine-tagged human recombinant fumarase, A308T and H318Y, associated with FHD and HLRCC, respectively. Both Ala308 and His318 lie within the fumarase intersubunit interface. We purified unmodified human fumarase and the two variants, and analyzed their enzymatic activities and oligomerization states in vitro.Results:Both variants showed severely diminished fumarase activity. Steady-state kinetic analysis demonstrated that the variants were largely defective due to decreased turnover rate, while displaying Km values for L-malate similar to unmodified human recombinant fumarase. Blue native polyacrylamide gel electrophoresis and gel filtration experiments revealed that each variant had an altered oligomerization state, largely forming homodimers rather than homotetramers.Conclusion:We conclude that A308T and H318Y render human fumarase enzymatically inactive via defective oligomerization. Therefore, some forms of FHD and HLRCC can be linked to improperly folded quaternary structure.

Characterisation of the fumarate hydratase repertoire in Trypanosoma cruzi

Nifurtimox and benznidazole represent the only treatments options available targeting Chagas disease, the most important parasitic infection in the Americas. However, use of these is problematic as they are toxic and ineffective against the more severe stages of the disease. In this work, we used a multidisciplinary approach to characterise the fumarases from Trypanosoma cruzi, the causative agent of Chagas Disease. We showed this trypanosome expresses cytosolic and mitochondrial fumarases that via an iron-sulfur cluster mediate the reversible conversion of fumarate to S-malate. Based on sequence, biochemical properties and co-factor binding, both T. cruzi proteins share characteristics with class I fumarases, enzymes found in bacteria and some other protozoa but absent from humans, that possess class II isoforms instead. Gene disruption suggested that although the cytosolic or mitochondrial fumarase activities are individually dispensable their combined activity is essential for parasite viability. Finally, based on the mechanistic differences with the human (host) fumarase, we designed and validated a selective inhibitor targeting the parasite enzyme. This study showed that T. cruzi fumarases should be exploited as targets for the development of new chemotherapeutic interventions against Chagas disease.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of recombinant human fumarase.

Human fumarase (HsFH) is a well-known citric acid cycle enzyme and is therefore a key component in energy metabolism. Genetic studies on human patients have shown that polymorphisms in the fumarase gene are responsible for diseases such as hereditary leiomyomatosis and renal cell cancer. As a first step in unravelling the molecular basis of the mechanism of fumarase deficiency in genetic disorders, the HsFH gene was cloned in pET-28a, heterologously expressed in Escherichia coli, purified by nickel-affinity chromatography and crystallized using the vapour-diffusion technique. X-ray diffraction experiments were performed at a synchrotron source and the structure was solved at 2.1 Å resolution by molecular replacement.

Relative Enzymatic Activity Levels from In Silico Mutagenesis.

We propose a new computational approach for predicting the impact of point mutations on residual enzymatic activities. We build on the general linear trends existing between free energy and enthalpy of transfer of substrates from cytosol to enzyme active sites (protein–ligand binding), therefore linking the docking energies to the binding free energies. In this very first step, we rationalize these trends in terms of a compensation effect decomposed into explicit thermodynamics contributions. In a second step, we combine the latter with the assumption that free energies of transfer, estimated from docking, and free energies of activation are linearly related through a Brönsted–Evans–Polanyi (BEP) relationship, allowing us in fine to predict enzyme activity. As a result, we propose generic Langmuir–Hinshelwood kinetic equations “trained” on the wild type, which provide excellent predictions of rates of catalytic transformations for mutated enzymes from the combination of in silico docking energies to a set of system-specific experimental data. This generalized approach is validated against clinical data on the particular case of human fumarase with major implications for the understanding of hereditary fumarase deficiency.

Subcellular localization of fumarase in mammalian cells and tissues

Fumarase, a mitochondrial matrix protein, is previously indicated to be present in substantial amounts in the cytosol as well. However, recent studies show that newly synthesized human fumarase is efficiently imported into mitochondria with no detectable amount in the cytosol. To clarify its subcellular localization, the subcellular distribution of fumarase in mammalian cells/tissues was examined by a number of different methods. Cell fractionation using either a mitochondria fraction kit or extraction with low concentrations of digitonin, detected no fumarase in a 100,000 g supernatant fraction. Immunofluorescence labeling with an affinity-purified antibody to fumarase and an antibody to the mitochondrial Hsp60 protein showed identical labeling pattern with labeling seen mainly in mitochondria. Detailed studies were performed using high-resolution immunogold electron microscopy to determine the subcellular localization of fumarase in rat tissues, embedded in LR White resin. In thin sections from kidney, liver, heart, adrenal gland and anterior pituitary, strong and specific labeling due to fumarase antibody was only detected in mitochondria. However, in the pancreatic acinar cells, in addition to mitochondria, highly significant labeling was also observed in the zymogen granules and endoplasmic reticulum. The observed labeling in all cases was completely abolished upon omission of the primary antibody indicating that it was specific. In a western blot of purified zymogen granules, a fumarase-antibody cross-reactive protein of the same molecular mass as seen in the mitochondria was present. These results provide evidence that fumarase in mammalian cells/tissues is mainly localized in mitochondria and significant amounts of this protein are not present in the cytosol. However, these studies also reveal that in certain tissues, in addition to mitochondria, this protein is also present at specific extramitochondrial sites. Although the cellular function of fumarase at these extramitochondrial locations is not known, the appearance/localization of fumarase outside mitochondria may help explain how mutations in this mitochondrial protein can give rise to a number of different types of cancers.

Mitochondrial import of human and yeast fumarase in live mammalian cells: Retrograde translocation of the yeast enzyme is mainly caused by its poor targeting sequence

Studies on yeast fumarase provide the main evidence for dual localization of a protein in mitochondria and cytosol by means of retrograde translocation. We have examined the subcellular targeting of yeast and human fumarase in live cells to identify factors responsible for this. The cDNAs for mature yeast or human fumarase were fused to the gene for enhanced green fluorescent protein (eGFP) and they contained, at their N-terminus, a mitochondrial targeting sequence (MTS) derived from either yeast fumarase, human fumarase, or cytochrome c oxidase subunit VIII (COX) protein. Two nuclear localization sequences (2× NLS) were also added to these constructs to facilitate detection of any cytosolic protein by its targeting to nucleus. In Cos-1 cells transfected with these constructs, human fumarase with either the native or COX MTSs was detected exclusively in mitochondria in >98% of the cells, while the remainder 1–2% of the cells showed varying amounts of nuclear labeling. In contrast, when human fumarase was fused to the yeast MTS, >50% of the cells showed nuclear labeling. Similar studies with yeast fumarase showed that with its native MTS, nuclear labeling was seen in 80–85% of the cells, but upon fusion to either human or COX MTS, nuclear labeling was observed in only 10–15% of the cells. These results provide evidence that extramitochondrial presence of yeast fumarase is mainly caused by the poor mitochondrial targeting characteristics of its MTS (but also affected by its primary sequence), and that the retrograde translocation mechanism does not play a significant role in the extramitochondrial presence of mammalian fumarase.

X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation.

Fumarase catalyzes the reversible conversion of fumarate to S- malate during the operation of the ubiquitous Kreb's cycle. Previous studies have shown that the active site includes side chains from three of the four subunits within the tetrameric enzyme. We used a clinically observed human mutation to narrow our search for potential catalytic groups within the fumarase active site. Offspring homozygous for the missense mutation, a G-955-C transversion in the fumarase gene, results in the substitution of a glutamine at amino acid 319 for the normal glutamic acid. To more fully understand the implications of this mutation, a single-step site-directed mutagenesis method was used to generate the homologous substitution at position 315 within fumarase C from Escherichia coli. Subsequent kinetic and X-ray crystal structure analyses show changes in the turnover number and the cocrystal structure with bound citrate.

Molecular Analysis and Prenatal Diagnosis of Human Fumarase Deficiency

Fumarase deficiency is a rare autosomal recessive disorder of the citric acid cycle causing severe neurological impairment. The cDNA for both the rat and human enzymes has been cloned previously and shown to encode a coding region of 1.46 kb. To scan for mutations in fumarase-deficient patients we amplified the coding region of fumarase from fibroblast/lymphoblast cDNA employing the oligonucleotide primers designed from the published human and rat cDNA sequence. We then directly sequenced the polymerase chain reaction product. In seven unrelated patients, we detected four missense mutations (A265T, D383V, F269C, K187R), a nonsense mutation (W458X), a 3-bp AAA insertion that introduces an additional lysine residue at codon 435, and a spontaneous new mutation resulting in a 74-bp deletion (66del74). Seven at-risk pregnancies were monitored with one prenatal diagnosis of fumarase deficiency by molecular analysis and favorable outcome of the other pregnancies as predicted by enzyme assay of cultured fetal cells or molecular analysis.

Further characterization of the human fumarase variant, FH 2--1.

1. Further investigation of fumarase using lymphoblastoid cells derived from an individual of the FH 2--1 phenotype has confirmed that the mitochondrial (FHM) and soluble (FHS) forms of fumarase are determined at the same structural locus. 2. The FH 2--1 variant is associated with enzyme deficiency: c. 70% of normal in lymphoblastoid cells and c. 20% of normal in red cells. 3. The pH optimum and apparent Michaelis constant of the variant fumarase were normal but heat-inactivation studies suggest that the isozymes containing polypeptides determined by the variant allele are unstable.