Cummins Peter L, Kannappan Babu, Gready Jill E
Gready Group, Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.
Front Plant Sci. 2018 Mar 1;9:183. doi: 10.3389/fpls.2018.00183. eCollection 2018.
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
普遍存在的酶核酮糖-1,5-二磷酸羧化酶/加氧酶（RuBisCO）在卡尔文-本森循环中固定大气中的二氧化碳，大多数光合生物都利用该循环。尽管RuBisCO具有这一核心作用，但其效率却令人惊讶地不尽人意，其转化为产物的速率非常缓慢，底物特异性也受损，长期以来这些特性一直是个谜，因为人们认为其效率受到强大的进化压力。RuBisCO的底物特异性受到损害，因为它催化与大气氧气的副固定反应；实验动力学结果表明，在相对特异性和低催化周转率之间存在权衡趋势。尽管主流假设是活性位点化学限制了该酶的进化，但最近一项关于RuBisCO稳定性和适应性的研究表明存在相互竞争的选择压力。阐明这些限制对于指导未来提高光合作用的研究至关重要，因为目前的文献对定点诱变提高RuBisCO效率的潜在有效性提出了质疑。在这里，我们使用回归分析来量化从跨越RuBisCO广泛进化范围的实验数据集获得的动力学参数之间的关系。最显著的是，我们发现二氧化碳从酶复合物中解离的速率常数远高于先前的估计，并且与相应的催化速率常数相当。相对特异性和周转率之间观察到的趋势可以表示为负相关因子和正相关因子的乘积。这从简单的动力学角度解释了相对特异性的自然变化以及通过报道的定点诱变结果获得的变化。我们证明，动力学行为表明RuBisCO的限制较小而非较大，这与相对特异性更高变异性的越来越多的实验证据一致。总之，我们的分析支持了一种解释，即特异性和周转率之间权衡的起源是由于蛋白质稳定性和活性之间的竞争，而不是基础化学所施加的速率常数之间的限制。我们的分析表明，同时提高RuBisCO的特异性和周转率是可能的。
