RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective

Abstract

RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.

RubisCO and the Search for Biomolecular Culprits of Planetary Change

“…The recent proposal that d ‐ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RubisCO), Earth's major carbon‐fixing enzyme, arose ≈2.9 billion years (Ga)‐ago as a side product of oxygenation prior to the rise of planetary oxygen opens new ideas on how to explore the history of biochemistry and its terraforming and sculpting roles. Here, in reference to a paper published by Ślezak et al in this issue, I discuss the possible emergence of the catalytic domain of RubisCO ≈1.5 Ga‐ago by recruitment of an ancient glycine‐rich structural protein loop with RubisCO's main functionalities that appeared ≈3.5 Ga‐ago in a first wave of metabolic innovation.…”

“…It is expected that some few had profound planetary influence, including innovations that led to Earth's oxygenation, while perhaps some other are still forthcoming. In their “hypothesis” paper, Ślezak et al review the kinetics of extant and resurrected forms of RubisCO (Enzyme Commission no. 4.1.1.39), the fundamental CO 2 ‐reducing enzyme of the Calvin‐Benson‐Bassham (CBB) reductive pentose phosphate cycle that is largely responsible for Earth's biomass accumulation.…”

“…The main hypothesis of Ślezak et al is that RubisCO's side reaction, the apparently “wasteful” oxygenation of the main RuBP substrate that produces phosphoglycolate and 3‐phosphoglycerate (Figure A), unfolded together with carboxylation in microoxic environments of early Earth − ≈3.5 billion years (Ga)‐ago according to, at a time when oxygen levels had not increased significantly in our planet. Support for the hypothesis comes from the coexistence of carboxylation/oxygenation in all forms of the enzyme (including form III that is present in Archaea) and the possible relation between oxygenic activity and intrinsic antioxidant systems in anaerobic microbes.…”

“…Catalytic efficiency appears conserved relative to that of resurrected forms IA, IB, and IAB enzymes that represent ≈1.5 Ga‐old enzymatic ancestors of modern proteins . This conservation occurs throughout all enzymatic forms and for both carboxylation and oxygenation . Thus, it is surmised that RubisCO's enzymatic activities are very old and that oxygen or some related substrate was already present in microquantities at that time of early Earth, contributing to the oxygenase properties of the enzyme.…”

“…The evolution of different forms of RubisCO can be inferred from amino acid sequence alignments and ancestral sequences can be reconstructed and resurrected . However, the deep evolutionary signal that is present in the alignments depends on some few amino acid sites that are evolutionarily highly conserved .…”