Purification and some properties of hydroxypyruvate isomerase of Bacillus fastidiosus

Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal

In the chemoautotrophic theory for the origin of life, offered as an alternative to broth theory, the archaic reductive citric acid cycle operating without enzymes is in the center. The non-enzymatic (methyl)glyoxalase pathway has been suggested to be the anaplerotic route for the reductive citric acid cycle. In the recent years, much has been learned about methylglyoxal, but its importance in the metabolic machinery is still uncovered. If methylglyoxal had been essential participant of the early stage of evolution, then it is a legitimate question whether it might have played a role in the early oxido-reduction network, too. Therefore, an oxido-reduction network of methylglyoxal that might have functioned under ancient circumstances without enzymes was constructed and analyzed by virtue of group contribution method. Taking methylglyoxal as input material, it turned out that the evolutionary value of reactions and biomolecules were not similar. Glycerol, glycerate, and tartonate, the output components, were conserved to different degrees. Although the tartonate route was similarly favorable from energetic point of view, its intermediates are almost not present in extant biochemistry. The presence of two carboxyl or aldehyde groups, or their combination in tricarbons of the constructed network seemed disadvantageous for selection, and the inductive effect, resulting in an asymmetry in electron cloud of chemicals, might have been important. The evolutionary role for cysteine, H₂S, and formaldehyde in the emergence of high-energy bonds in the form of thioesters and in Fe-S cluster formation as well as in imidazole synthesis was shown to bridge the gap between prebiotic chemistry and contemporary biochemistry. Overall, the ideas developed here represent an approach fitting to chemoautotrophic origin of life and implying to the role of methylglyoxal in triose formation. The proposed network is expected to have an impact upon how one may think of prebiological chemical processes on methylglyoxal, too. Finally, along the evolutionary time line, the network functioning without enzymes is situated between the formation of simple organic compounds and primeval cells, being closer to the former and well preceding the last common metabolic ancestor developed after primitive cells emerged.

Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae

Haemophilus influenzae, a Gram-negative bacterium and a member of the family Pasteurellaceae, causes chronic bronchitis, bacteremia, meningitis, etc. The H. influenzae is the first organism whose genome was completely sequenced and annotated. Here, we have extensively analyzed the genome of H. influenzae using available proteins structure and function analysis tools. The objective of this analysis is to assign a precise function to hypothetical proteins (HPs) whose functions are not determined so far. Function prediction of these proteins is helpful in precise understanding of mechanisms of pathogenesis and biochemical pathways important for selecting novel therapeutic target. After an extensive analysis of H. Influenzae genome we have found 13 HPs showing high level of sequence and structural similarity to the enzyme isomerase. Consequently, the structures of HPs have been modeled and analyzed to determine their precise functions. We found these HPs are alanine racemase, lysine 2, 3-aminomutase, topoisomerase DNA-binding C4 zinc finger, pseudouridine synthase B, C and E (Rlu B, C and E), hydroxypyruvate isomerase, nucleoside-diphosphate-sugar epimerase, amidophosphoribosyltransferase, aldose-1-epimerase, tautomerase/MIF, Xylose isomerase-like, have TIM barrel domain and sedoheptulose-7-phosphate isomerase like activity, signifying their corresponding functions in the H. influenzae. This work provides a better understanding of the role HPs with isomerase activities in the survival and pathogenesis of H. influenzae.

AllR Controls the Expression of Streptomyces coelicolor Allantoin Pathway Genes

Streptomyces species are native inhabitants of soil, a natural environment where nutrients can be scarce and competition fierce. They have evolved ways to metabolize unusual nutrients, such as purines and its derivatives, which are highly abundant in soil. Catabolism of these uncommon carbon and nitrogen sources needs to be tightly regulated in response to nutrient availability and environmental stimulus. Recently, the allantoin degradation pathway was characterized in Streptomyces coelicolor. However, there are questions that remained unanswered, particularly regarding pathway regulation. Here, using a combination of proteomics and genetic approaches, we identified the negative regulator of the allantoin pathway, AllR. In vitro studies confirmed that AllR binds to the promoter regions of allantoin catabolic genes and determined the AllR DNA binding motif. In addition, effector studies showed that allantoic acid, and glyoxylate, to a lesser extent, inhibit the binding of AllR to the DNA. Inactivation of AllR repressor leads to the constitutive expression of the AllR regulated genes and intriguingly impairs actinorhodin and undecylprodigiosin production. Genetics and proteomics analysis revealed that among all genes from the allantoin pathway that are upregulated in the allR mutant, the hyi gene encoding a hydroxypyruvate isomerase (Hyi) is responsible of the impairment of antibiotic production.

Comparative analysis of proteome maps of silkworm hemolymph during different developmental stages

Background

The silkworm Bombyx mori is a lepidopteran insect with four developmental stages: egg, larva (caterpillar), pupa, and adult. The hemolymph of the silkworm is in an open system that circulates among all organs, and functions in nutrient and hormone transport, injury, and immunity. To understand the intricate developmental mechanisms of metamorphosis, silkworm hemolymph from different developmental stages, including the 3^rd day of fifth instar, the 6^th day of fifth instar, the 3^rd day of pupation, the 8^th day of pupal stage and the first day of the moth stage, was investigated by two-dimensional electrophoresis and mass spectrometry.

Results

Two-dimensional polyacrylamide gel electrophoresis showed that from the larval to moth stages, silkworm hemolymph proteins changed markedly. Not only did major proteins such as SP1, SP2, and the 30 K lipoprotein change, but other proteins varied greatly at different stages. To understand the functions of these proteins in silkworm development, 56 spots were excised from gels for analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). We identified 34 proteins involved in metamorphosis, programmed cell death, food digestion, metabolism, and nutrient storage and transport. Most proteins showed different expression at different stages, suggesting functions in development and metamorphosis. An abundance of proteins related to immunity were found, including hemolin, prophenoloxidase, serine proteinase-like protein, paralytic peptide-binding protein, and protease inhibitor.

Conclusions

Proteomics research not only provides the opportunity for direct investigation of protein expression patterns, but also identifies many attractive candidates for further study. Two-dimensional maps of hemolymph proteins expressed during the growth and metamorphosis of the silkworm offer important insights into hemolymph function and insect metamorphosis.

Biochemical evidence that Escherichia coli hyi (orf b0508, gip) gene encodes hydroxypyruvate isomerase

We found a significant activity of hydroxypyruvate isomerase in Escherichia coli clone cells harboring an E. coli gene (called orf b0508 or gip), which is located downstream of the glyoxylate carboligase gene. We newly designated the gene hyi. The enzyme was purified from cell extracts of the E. coli clone. The enzyme had a molecular mass of 58 kDa and was composed of two identical subunits. The optimum pH for the isomerization of hydroxypyruvate was 6.8-7.2. The enzyme required no cofactor. It exclusively catalyzed the isomerization between hydroxypyruvate and tartronate semialdehyde. The apparent K(m) value for hydroxypyruvate was 12.5 mM. The amino acid sequence of E. coli hydroxypyruvate isomerase is highly similar to those of glyoxylate-induced proteins, Gip, found widely from prokaryotes to eukaryotes.

The level of enzymes involved in the allantoin metabolism of Bacillus fastidiosus grown under different conditions

Bacillus fastidiosus was cultivated in batch and continuous culture on various carbon and nitrogen sources. The enzymes involved in allantoin degradation (allantoinase, urease, carboligase) of B. fastidiosus were hardly affected by either carbon or nitrogen source. In contrast, the enzymes involved in glycerol utilization (glycerol kinase, glycerol 3-phosphate dehydrogenase) were induced during growth on glycerol, but were not affected by the amount of allantoin present.

Glyoxylate conversion by Hyphomicrobium species grown on allantoin as nitrogen source

Glyoxylate, formed as a result of allantoin degradation, is converted by Hyphomicrobium species to glycerate via tartronate semialdehyde. Glyoxylate carboligase and tartronate semialdehyde reductase, the two enzymes involved, are present only in cells grown on allantoin as nitrogen source.