Structural plasticity enables evolution and innovation of RuBisCO assemblies

Abstract

Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.

The role of oligomerization in the optimization of cyclohexadienyl dehydratase conformational dynamics and catalytic activity

“…For example, as few as two mutations were required to switch between dimeric and tetrameric states during the evolution of vertebrate hemoglobin. 8 Additionally, quaternary structure plasticity has been attributed to functional diversification in other protein families, including RuBisCO 6 and MAT. 20 …”

“…A large proportion of proteins self‐associate to form homo‐oligomers comprising two or more identical subunits. 1 , 2 , 3 , 4 Among other things, homo‐oligomerization has been shown to play an important role in conferring gain of function, 5 , 6 protection from degradation, 7 cooperative binding properties, 8 allosteric regulation of enzyme activity, 9 and enhanced thermostability of proteins. 10 , 11 On the other hand, Lynch and others have demonstrated that oligomers can also arise and become entrenched even when there is no apparent adaptive advantage associated with the initial formation of the complex.…”

“… 8 Similarly, ASR revealed the role of quaternary structure plasticity during the evolution and diversification of Ribulose‐1,5‐bisphosphate carboxylase‐oxygenase (RuBisCO) function. 6 Shifts in oligomeric states have also been linked to enhanced thermostability during the laboratory‐directed evolution of an αE7 carboxylesterase 10 and the tailoring of activity and structural stability amongst bacterial methionine S‐adenosyltransferase (MAT) homologs. 20 On the other hand, a dimerization event that occurred during the evolution of steroid hormone receptors provided no immediate selective advantage.…”

The role of evolutionarily metastable oligomeric states in the optimization of catalytic activity

“…For example, as few as two mutations were required to switch between dimeric into a tetrameric states during the evolution of vertebrate haemoglobin 8 . Additionally, quaternary structure plasticity has been attributed to functional diversification in other protein families, including RuBisCO 6 and methionine S-adenosyltransferase 20 .…”

“…A large proportion of proteins self-associate to form homo-oligomers comprising two or more identical subunits. 1–4 Among other things, homo-oligomerization has been shown to play an important role in conferring gain of function 5,6 , protection from degradation 7 , cooperative binding properties 8 , allosteric regulation of enzyme activity 9 , and enhanced thermostability of proteins 10,11 . On the other hand, Lynch and others have demonstrated that oligomers can also arise and become entrenched even when there is no apparent adaptive advantage associated with the initial formation of the complex.…”