Functional discovery and promiscuity in the RuBisCO superfamily

To keep pace with large scale sequencing projects that are filling sequence databases with misannotated sequences, a new method of functional annotation is necessary. The new method is called “genomic enzymology” and utilizes bioinformatics, molecular docking, microbiology, and enzymology. For a superfamily to benefit from this new strategy there must exist a set of solved functions and crystal structures. D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the carboxylation of D-ribulose 1,5-bisphosphate to yield two molecules of 3-phosphoglycerate. Currently, there are four forms of RuBisCO, three of which catalyze the canonical carboxylation reaction. Form IV RuBisCOs (also known as RuBisCO-like proteins (RLPs)) do not catalyze the carboxylation reaction and are of interest because they can provide a wealth of information on structure/function relationships of the superfamily. The work here focuses on identification of novel functions as well as determination of promiscuity in the (RuBisCO) superfamily. To identify novel functions, novel sequences were targeted for cloning, purification, and assaying. This approach was used on sequences in the family homologous to R. rubrum RLP that has a published function of 5-methylthio-D-ribulose 1-phosphate 1,3-isomerase. Efforts to isolate usable RLP failed, but collaborators at AECOM were able to purify functional enzyme of a downstream cupin that was then mechanistically characterized. The function of the cupin also provided evidence for the physiological context of the R. rubrum RLP. The investigation of promiscuity in the RuBisCO superfamily stems from previous research showing that an authentic RuBisCO can complement an RLP knockout. If an authentic RuBisCO were able to catalyze RLPs reactions, this would be an important element for determining the origin of RuBisCO and for determining the structure/function relationship. Both in vitro and in vivo analysis, showed no promiscuity in the authentic RuBisCO for RLP reactions.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2013

Author dc:creator

• Warlick, Benjamin

Contributors dc:contributor

• Gerlt, John A.
• Cronan, John E.
• Nair, Satish K.
• Mitchell, Douglas A.

• RuBisCO-like proteins (RLPs)
• D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO)

Statement dc:rights

• Copyright 2013 Benjamin Warlick

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/45444

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/45444