Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489)

Folate-mediated one-carbon metabolism as a potential antifungal target for the sustainable cultivation of microalga Haematococcus pluvialis

BACKGROUND

Microalgae are widely considered as multifunctional cell factories that are able to transform the photo-synthetically fixed CO₂ to numerous high-value compounds, including lipids, carbohydrates, proteins and pigments. However, contamination of the algal mass culture with fungal parasites continues to threaten the production of algal biomass, which dramatically highlights the importance of developing effective measures to control the fungal infection. One viable solution is to identify potential metabolic pathways that are essential for fungal pathogenicity but are not obligate for algal growth, and to use inhibitors targeting such pathways to restrain the infection. However, such targets remain largely unknown, making it challenging to develop effective measures to mitigate the infection in algal mass culture.

RESULTS

In the present study, we conducted RNA-Seq analysis for the fungus Paraphysoderma sedebokerense, which can infect the astaxanthin-producing microalga Haematococcus pluvialis. It was found that many differentially expressed genes (DEGs) related to folate-mediated one-carbon metabolism (FOCM) were enriched in P. sedebokerense, which was assumed to produce metabolites required for the fungal parasitism. To verify this hypothesis, antifolate that hampered FOCM was applied to the culture systems. Results showed that when 20 ppm of the antifolate co-trimoxazole were added, the infection ratio decreased to ~ 10% after 9 days inoculation (for the control, the infection ratio was 100% after 5 days inoculation). Moreover, application of co-trimoxazole to H. pluvialis mono-culture showed no obvious differences in the biomass and pigment accumulation compared with the control, suggesting that this is a potentially algae-safe, fungi-targeted treatment.

CONCLUSIONS

This study demonstrated that applying antifolate to H. pluvialis culturing systems can abolish the infection of the fungus P. sedebokerense and the treatment shows no obvious disturbance to the algal culture, suggesting FOCM is a potential target for antifungal drug design in the microalgal mass culture industry.

Functional prediction, characterization, and categorization of operome from Acetoanaerobium sticklandii DSM 519

Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia producing anaerobic bacterium that can be able utilizes amino acids as sole carbon and energy sources for its growth and energetic metabolism. A lack of knowledge on its molecular machinery and 30.5% conserved hypothetical proteins (HPs; operome) hinders the successful utility in biofuel applications. In this study, we have predicted, characterized and categorized its operome whose functions are still not determined accurately using a combined bioinformatics approach. The functions of 64 of the 359 predicted HPs are involved in diverse metabolic subsystems. A. sticklandii operome has consisted of 16% Rossmann fold and 46% miscellaneous folds. Subsystems-based technology has classified 51 HPs contributing to the small-molecular reactions, 26 in macromolecular reactions and 12 in the biosynthesis of cofactors, prosthetic groups and electron carriers. A generality of functions predicted from its operome contributed to the cell cycle, amino acid metabolism, membrane transport, and regulatory processes. Many of them have duplicated functions as paralogs in this genome. A. sticklandii has the ability to compete with invading microorganisms and tolerate abiotic stresses, which can be overwhelmed by the predicted functions of its operome. Results of this study revealed that it has specialized systems for amino acid catabolism-directed solventogenesis and acidogenesis but the level of gene expression may determine the metabolic function in amino acid fermenting niches in the rumina of cattle. As shown by our analysis, the predicted functions of its operome allow us for a better understanding of the growth and physiology at systems-scale.

Investigations of Amino Acids in the 5-Formyltetrahydrofolate Binding Site of 5,10-Methenyltetrahydrofolate Synthetase from Mycoplasma pneumonia

5,10-Methenyltetrahydrofolate synthetase plays a significant role in folate metabolism by catalyzing the conversion of 5-formyltetrahydrofolate into 5,10-methenyltetrahydrofolate. The enzyme is important in some forms of chemotherapy, and it has been implicated in resistance to antifolate antibiotics. A co-crystal structure of the enzyme (1U3G) and primary sequence analysis were used to select highly conserved amino acids in close proximity to bound 5-formyltetrahydrofolate. The amino acids were then investigated using site directed mutagenesis and kinetics. Y123, E55, and F118 were concluded to be important for binding 5-formyltetrahydrofolate in the active site and/or for substrate turnover of the enzyme. Replacement of E55 or Y123 with alanine resulted in no detectable activity. The more subtle replacement of E55 with glutamine was also inactive suggesting an ionic interaction with 5-formyltetrahydrofolate. Mutations to F118 resulted in substantial increases in apparent K_m for both 5-formyltetrahydrofolate and ATP, but did not substantially affect catalytic turnover. Outside the active site, the replacement of Q144 with alanine yielded an enzyme that bound the substrates of ATP and 5-formyltetrahydrofolate with higher apparent K_m values than the wild-type enzyme, but demonstrated a 3.1 fold increase in k_cat.

Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW

A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively. XJLW has a chromosome DNA and a mega-plasmid DNA. Ten percent of genes on chromosome DNA are strain-specific in genus Methylobacterium. Transcriptome analysis results showed that 623 genes were significantly up-regulated and that 207 genes were significantly down-regulated for growth in methanol. Among the up-regulated genes, 90 genes belong to strain-specific regions and are densely distributed in three areas. A specific gene (A3862_27225) annotated as methyltransferase was found ranking in the top 4 of up-regulated genes. This methyltransferase may play a role in the specific C1 metabolism of XJLW. Methylobacterium sp. XJLW should contain a potential methyl transport pathway via the novel methyltransferase, which is different from known pathways. These findings provide the basis for additional possibilities, which improve the formaldehyde-degrading ability of Methylobacterium sp. XJLW.

Metabolic Regulation: A Master Role for Ribulose-1,5-Bisphosphate in One-Carbon Assimilation

Engineering organisms for biotechnology applications requires knowledge of their essential genes and associated regulatory networks. A new study of methylotrophic metabolism in Methylobacterium reveals essentiality of the unregulated, off-pathway phosphoribulokinase gene and an unexpected key regulatory role for its product ribulose-1,5-bisphosphate.

Transposon Sequencing Uncovers an Essential Regulatory Function of Phosphoribulokinase for Methylotrophy

Methylotrophy is the ability of organisms to grow at the expense of reduced one-carbon compounds, such as methanol or methane. Here, we used transposon sequencing combining hyper-saturated transposon mutagenesis with high-throughput sequencing to define the essential methylotrophy genome of Methylobacterium extorquens PA1, a model methylotroph. To distinguish genomic regions required for growth only on methanol from general required genes, we contrasted growth on methanol with growth on succinate, a non-methylotrophic reference substrate. About 500,000 insertions were mapped for each condition, resulting in a median insertion distance of five base pairs. We identified 147 genes and 76 genes as specific for growth on methanol and succinate, respectively, and a set of 590 genes as required under both growth conditions. For the integration of metabolic functions, we reconstructed a genome-scale metabolic model and performed in silico essentiality analysis. In total, the approach uncovered 95 genes not previously described as crucial for methylotrophy, including genes involved in respiration, carbon metabolism, transport, and regulation. Strikingly, regardless of the absence of the Calvin cycle in the methylotroph, the screen led to the identification of the gene for phosphoribulokinase as essential during growth on methanol, but not during growth on succinate. Genetic experiments in addition to metabolomics and proteomics revealed that phosphoribulokinase serves a key regulatory function. Our data support a model according to which ribulose-1,5-bisphosphate is an essential metabolite that induces a transcriptional regulator driving one-carbon assimilation.

Dissemination of 6S RNA among bacteria

6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.

Investigations of amino acids in the ATP binding site of 5,10-methenyltetrahydrofolate synthetase

5-Formyltetrahydrofolate is a compound that is administered as a rescue agent in methotrexate chemotherapy and in 5-fluorouracil chemotherapy for synergistic effects. It has also recently been suggested to play a role in bacterial resistance to antifolate therapy. 5,10-methenyltetrahydrofolate synthetase (MTHFS) is the only enzyme known to catalyze the conversion of this compound to 5,10-methenyltetrahydrofolate along with the hydrolysis of ATP to ADP. To better understand the roles of specific amino acids in the ATP binding pocket of this enzyme, we used site-directed mutagenesis to create 10 modified forms of the Mycoplasma pneumoniae ortholog. The Michaelis constant (K(m)) for each substrate and the turnover number (k(cat)) was determined for each mutant to help elucidate the role of individual amino acids. Data were compared to crystal structures of human and M. pneumoniae orthologs of MTHFS. Results were largely consistent with a simple coulombic and proximity model; the larger the predicted charges of an interaction and the closer those interactions were to the phosphate transferred between the substrates, the greater the reduction in ATP binding and catalytic activity of the enzyme.

Structural basis for the inhibition of human 5,10-methenyltetrahydrofolate synthetase by N10-substituted folate analogues

5,10-Methenyltetrahydrofolate synthetase (MTHFS) regulates the flow of carbon through the one-carbon metabolic network, which supplies essential components for the growth and proliferation of cells. Inhibition of MTHFS in human MCF-7 breast cancer cells has been shown to arrest the growth of cells. Absence of the three-dimensional structure of human MTHFS (hMTHFS) has hampered the rational design and optimization of drug candidates. Here, we report the structures of native hMTHFS, a binary complex of hMTHFS with ADP, hMTHFS bound with the N5-iminium phosphate reaction intermediate, and an enzyme-product complex of hMTHFS. The N5-iminium phosphate captured for the first time in our crystal structure unravels a unique strategy used by hMTHFS for recognition of the substrate and provides structural basis for the regulation of enzyme activity. Binding of N10-substituted folate analogues places Y152 in the middle of the channel connecting ATP binding site with the substrate binding pocket, precluding the positioning of gamma-phosphate for a nucleophilic attack. Using the structures of hMTHFS as a guide, we have probed the role of residues surrounding the active site in catalysis by mutagenesis. The ensemble of hMTHFS structures and the mutagenesis data yield a coherent picture of the MTHFS active site, determinants of substrate specificity, and new insights into the mechanism of inhibition of hMTHFS.

Investigations of the roles of arginine 115 and lysine 120 in the active site of 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae

5,10-Methenyltetrahydrofolate synthetase (MTHFS) catalyzes the conversion of 5-formyltetrahydrofolate to 5,10-methenyltetrahydrofolate coupled to the hydrolysis of ATP. A co-crystal structure of MTHFS bound to its substrates has been published (Chen et al., Proteins 56:839-843, 2005) that provides insights into the mechanism of this reaction. To further investigate this mechanism, we have replaced the arginine at position 115 and the lysine at position 120 with alanine (R115A and K120A, respectively). Circular dichroism spectra for both mutants are consistent with folded proteins. R115A shows no activity, suggesting that R115 plays a critical role in the activity of the enzyme. The K120A mutation increases the Michaelis constant (K(m)) for ATP from 76 to 1,200 microM and the K(m) for 5-formylTHF from 2.5 to 7.1 microM. The weaker binding of substrates by K120A may be due to movement of a loop consisting of residues 117 though 120, which makes several hydrogen bonds to ATP and may be held in position by K120.