Saturday, March 26, 2011

All About RuBisCo

“Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evollution and structure/function relationships”
Tabita et. al. in Journal of Experimental Botany, Vol. 59, No. 7, pp. 1515-1524, 2008

Rubisco is the most abundant protein in nature. It catalyzes the carbon-fixing reaction in which a molecule of CO2 is added to the enediol form of ribulose-1,5-bisphosphate (RuBP). The active site is located between two large subunits, and it involves residues from the amino terminus of one subunit and the carboxy terminus of the other. This site accepts both CO2 and O2, and its ability to distinguish between the two is limited. Tabita et. al. provide this figure to illustrate the competing reactions. Rubisco is found in four forms, and form I (consisting of eight large catalytic subunits and eight smaller subunits, annotated L8S8) is the most common, being found in eukaryotes and bacteria. However, the three other forms are not insignificant, and Rubisco-like protein shows a great deal of homology to the Rubisco proteins, and yet is not able to catalyze either carboxylation or oxygenation. The paper goes on to explore the evolutionary relationships between these protein forms and concludes that they are related by divergent evolution. Each form of Rubisco is optimized to suit the specific temperature and CO2/O2 ratio of the organism. 

“Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized”
Tcherkez et. al. in PNAS, Vol. 103, No. 19, pp. 7246-7251, May 9, 2006

Each cell invests large amounts of nitrogen into producing many Rubisco complexes; however, these complexes are both slow and nonspecific (unable to discriminate between CO2 and O2). Although some research groups have tried to improve upon Rubisco, they have only met with modest success. This paper shows that in fact, the slow catalysis is the enzyme’s way of discriminating between the two featureless gases. By making the transition state very similar to the products rather than the reactants, the enzyme can tell the difference between CO2 and O2; however, a product-like transition state is more ordered and makes the product bind tightly such that it decreases the catalytic rate. Thus, the enzyme must strike a balance between specificity and speed, and each individual Rubisco is optimized for the CO2/O2 ratio in which it is found: enzymes present in environments with lower CO2/O2 ratios have higher specificity and slower rates, while enzymes in environments with higher ratios may be more promiscuous and have faster rates. Thus, Rubisco cannot be dramatically improved because it is already nearly perfect.

“Highly Conserved Small Subunit Residues Influence Rubisco Large Subunit Catalysis”
Genkov and Spreitzer in the Journal of Biological Chemistry, Vol. 284, No. 44, pp. 30105-30112, October 30, 2009

Although the active site of Rubisco is found between the carboxyl-terminal α/β-barrel of one large subunit and the amino terminus of its neighboring large subunit, extensive studies of the large subunit have not yielded any significant increases in the protein’s catalytic rate or its specificity for CO2 over O2. Although the CO2/O2 specificity (termed Ω) differs between prokaryotes and eukaryotes, the large subunit is highly conserved; instead, the small subunit displays the most variation. These authors hypothesize that the small subunit may be more responsible for modulating Ω and set out to study the regulatory role of the small subunit. They replaced each of the ten residues which are highly conserved among all small subunits with alanine and monitored the effect on catalysis and specificity. None of the tested residues are essential for the Rubisco structural integrity or function. Three of the mutations showed no changes at all; one decreased the stability of the enzyme complex; two decreased the specificity of the enzyme; and four affected catalysis with differing changes in enzyme stability. Because the residues tested were conserved across all L8S8 Rubisco enzymes, these differences can only be used to explain the differences between L8S8 and L2 enzymes, but not the differences within the L8S8 subset.

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