In silico Characterization and Homology Modeling of Cyanobacterial Phosphoenolpyruvate Carboxylase Enzymes with Computational Tools and Bioinformatics Servers

Computational Analysis of the Hypothetical Protein P9303_05031 from Marine Cyanobacterium Prochlorococcus Marinus MIT 9303

Prochlorococcus marinus MIT 9303 is a marine cyanobacterium found in sea waters. It was first isolated from a depth of 100 m in the Sargasso Sea in the year 1992. This cyanobacterium serves as a good model system for scientific research due to the presence of many desirable characteristics like smaller in size, ability to perform photosynthesis and the ease of culture maintenance. The genome of this cyanobacterium encodes for about 3022 proteins. Out of these 3022 proteins, few proteins were annotated as hypothetical proteins. We performed a computational study to characterize one of the hypothetical proteins "P9303_05031" to deduce its functional role in the cell using various bioinformatics techniques. After in-depth analysis, this hypothetical protein showed the conserved domain as of Hsp10 of molecular chaperonins of GroES. In this work, we have predicted the bidirectional best hits for the hypothetical protein P9303_05031 followed by the prediction of protein properties such as primary, secondary and tertiary structures. The existence of the Hsp10 domain indicates its role is essential for the folding of proteins during heat shock. This work represents the first structural and physicochemical study of the hypothetical protein P9303_05031 in Prochlorococcus marinus MIT 9303.

Oligomerization and characteristics of phosphoenolpyruvate carboxylase in Synechococcus PCC 7002

Phosphoenolpyruvate carboxylase (PEPc) is an essential enzyme in plants. A photosynthetic form is present both as dimer and tetramer in C4 and CAM metabolism. Additionally, non-photosynthetic PEPcs are also present. The single, non-photosynthetic PEPc of the unicellular cyanobacterium Synechococcus PCC 7002 (Synechococcus), involved in the TCA cycle, was examined. Using size exclusion chromatography (SEC) and small angle X-ray scattering (SAXS), we observed that PEPc in Synechococcus exists as both a dimer and a tetramer. This is the first demonstration of two different oligomerization states of a non-photosynthetic PEPc. High concentration of Mg2+, the substrate PEP and a combination of low concentration of Mg2+ and HCO3- induced the tetramer form of the carboxylase. Using SEC-SAXS analysis, we showed that the oligomerization state of the carboxylase is concentration dependent and that, among the available crystal structures of PEPc, the scattering profile of PEPc of Synechococcus agrees best with the structure of PEPc from Escherichia coli. In addition, the kinetics of the tetramer purified in presence of Mg2+ using SEC, and of the mixed population purified in presence of Mg2+ using a Strep-tagged column were examined. Moreover, the enzyme showed interesting allosteric regulation, being activated by succinate and inhibited by glutamine, and not affected by either malate, 2-oxoglutarate, aspartic acid or citric acid.

Allosteric Inhibition of Phosphoenolpyruvate Carboxylases is Determined by a Single Amino Acid Residue in Cyanobacteria

Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme for CO₂ fixation and primary metabolism in photosynthetic organisms including cyanobacteria. The kinetics and allosteric regulation of PEPCs have been studied in many organisms, but the biochemical properties of PEPC in the unicellular, non-nitrogen-fixing cyanobacterium Synechocystis sp. PCC 6803 have not been clarified. In this study, biochemical analysis revealed that the optimum pH and temperature of Synechocystis 6803 PEPC proteins were 7.3 and 30 °C, respectively. Synechocystis 6803 PEPC was found to be tolerant to allosteric inhibition by several metabolic effectors such as malate, aspartate, and fumarate compared with other cyanobacterial PEPCs. Comparative sequence and biochemical analysis showed that substitution of the glutamate residue at position 954 with lysine altered the enzyme so that it was inhibited by malate, aspartate, and fumarate. PEPC of the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 was purified, and its activity was inhibited in the presence of malate. Substitution of the lysine at position 946 (equivalent to position 954 in Synechocystis 6803) with glutamate made Anabaena 7120 PEPC tolerant to malate. These results demonstrate that the allosteric regulation of PEPC in cyanobacteria is determined by a single amino acid residue, a characteristic that is conserved in different orders.