Diversity-driven biochemical survey reveals dimeric structural origin of rubisco

Area of Science:

• Biochemistry and Molecular Biology
• Microbial Ecology
• Evolutionary Biology

Background:

• Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a crucial enzyme for carbon fixation, present across all life domains.
• Biochemical studies have historically focused on a limited range of Rubisco types, despite advances in metagenomics revealing vast microbial diversity.
• The rapid growth of sequence data outpaces biochemical characterization, leaving significant gaps in understanding Rubisco's functional and structural diversity.

Purpose of the Study:

• To systematically survey the functional and structural diversity of the Rubisco enzyme superfamily.
• To characterize previously underrepresented and deep-branching Rubisco clades.
• To integrate phylogenetic and biochemical data for a revised Rubisco nomenclature.

Main Methods:

• Systematic sampling and synthesis of a diverse library of Rubisco sequences, emphasizing understudied clades.
• Updated phylogenetic analysis to reconstruct evolutionary relationships within the Rubisco superfamily.
• Biochemical and structural characterization of novel Rubisco enzymes, including the largest identified to date.

Main Results:

• Phylogenetic analysis indicates that many deep-branching Rubiscos form dimers, supporting a dimeric origin for the enzyme superfamily.
• Discovery and structural characterization of the largest Rubisco enzyme yet described, from a cryptic, early-branching subclade.
• Identification of novel structural folds within this large Rubisco, previously unobserved in the superfamily.

Conclusions:

• The Rubisco superfamily likely originated from dimeric forms, contrasting with the currently dominant hexadecameric Form I.
• The discovery of novel structures and large enzymes expands the known diversity of Rubisco.
• A revised nomenclature is proposed to better reflect current evolutionary and structural insights and accommodate future discoveries.