Genetic Dissection of Rubisco Structure and Function

Spreitzer, Robert J.

doi:10.1146/annurev.pp.44.060193.002211

Cited by 134 publications

(111 citation statements)

References 52 publications

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“…Thus, the wild type, despite encoding a highly robust protein that retains function after most mutations, will appear mutationally fragile over evolutionary time. A striking example of this robust-molecule͞fragile-gene behavior may be found in ribulose-1,5-bisphosphate carboxylase͞oxygenase (Rubisco), perhaps the most abundant protein on Earth and a rigidly conserved, generally essential enzyme for which genetic studies have nonetheless been hampered by the difficulty of finding inactivating missense mutations (48).…”

Section: Discussionmentioning

confidence: 99%

Why highly expressed proteins evolve slowly

Drummond

Bloom

Adami

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

755

758

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Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons that have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors. Pressure for translational robustness increases with expression level and constrains sequence evolution. Using several sequenced yeast genomes, global expression and protein abundance data, and sets of paralogs traceable to an ancient whole-genome duplication in yeast, we rule out several confounding effects and show that expression level explains roughly half the variation in Saccharomyces cerevisiae protein evolutionary rates. We examine causes for expression's dominant role and find that genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency. Our results suggest that proteins evolve at rates largely unrelated to their functions and can explain why highly expressed proteins evolve slowly across the tree of life.evolutionary rate ͉ protein misfolding ͉ yeast ͉ translation errors ͉ gene duplication A central problem in molecular evolution is why proteins evolve at different rates. Protein evolutionary rates, quantified by the number of nonsynonymous nucleotide changes per site (dN) in the encoding genes, are routinely used to build phylogenetic trees, detect selection, find orthologous proteins among related species (1), and evaluate the functional importance of genes (2), yet we possess only hints of the biophysical cause of rate differences. Thirty years ago, Zuckerkandl (3) proposed that a protein's sequence will evolve at a rate primarily determined by the proportion of its sites involved in specific functions (or ''functional density''). Although this proposal has gained wide acceptance (2), measurement of functional density remains problematic because residues may contribute to protein function in unpredictable ways, and arduous sequence-wide saturation mutagenesis and mutant characterization studies are required to ascertain these effects.Instead, many recent studies have focused on other, more readily obtained, measures that may approximate functional density. For example, protein-protein interactions presumably constrain interfacial residues, and some reports indicate that highly interactive proteins evolve slowly (4). The intuition that a protein's overall functional importance should amplify the fitness costs of mutations at sites that make subtle functional contributions has been captured in analyses of how a gene's functional category (5, 6), its essentiality for organism survival (6-8), or the fitness effect of its deletion (or ''dispensability'') (9, 10) correlate with evolutionary rate. In all cases, the effects under consideration explain only a small fraction (Ϸ5% or less) of the observed variation in evolutionary...

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Section: Discussionmentioning

confidence: 99%

Why highly expressed proteins evolve slowly

Drummond

Bloom

Adami

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

755

758

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“…In land plants and green algae, Rubisco exists as a holoenzyme composed of eight large subunits (LSUs; 55 kD) encoded by the chloroplast large subunit of Rubisco (rbcL) gene, and eight small subunits (SSU; 15-18 kD) produced by a nuclear family of small subunit of Rubisco (rbcS) genes (Spreitzer, 1993). This L8S8 form of the complex is denoted form I (Spreitzer, 1999).…”

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confidence: 99%

A Conserved Mechanism Controls Translation of Rubisco Large Subunit in Different Photosynthetic Organisms

2006

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We previously proposed a mechanism for control of Rubisco expression and assembly during oxidative stress in Chlamydomonas reinhardtii. The N terminus of the large subunit (LSU) comprises an RNA recognition motif (RRM) that is normally buried in the protein, but becomes exposed under oxidizing conditions when the glutathione pool shifts toward its oxidized form. Thus, de novo translation and assembly of Rubisco LSU stop with similar kinetics and the unpaired small subunit (SSU) is rapidly degraded. Here we show that the structure of the N-terminal domain is highly conserved throughout evolution, despite its relatively low sequence similarity. Furthermore, Rubisco from a broad evolutionary range of photosynthetic organisms binds RNA under oxidizing conditions, with dissociation constant values in the nanomolar range. In line with these observations, oxidative stress indeed causes a translational arrest in land plants as well as in Rhodospirillum rubrum, a purple bacterium that lacks the SSU. We highlight an evolutionary conserved element located within a-helix B, which is located in the center of the RRM and is also involved in the intramolecular interactions between two LSU chains. Thus, assembly masks the N terminus of the LSU hiding the RRM. When assembly is interrupted due to structural changes that occur under oxidizing conditions or in the absence of a dedicated chaperone, the N-terminal domain can become exposed, leading to the translational arrest of Rubisco LSU. Taken together, these results support a model by which LSU translation is governed by its dimerization. In the case that regulation of type I and type II Rubisco is conserved, the SSU does not appear to be directly involved in LSU translation.

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“…1). The enzyme initiates photosynthetic CO 2 ®xation or the wasteful process of photorespiration (reviewed by Spreitzer, 1993). The mutual competition between CO 2 and O 2 at the active site is the rate-limiting step for catalyis (reviewed by Hartman & Harpel, 1994).…”

Section: Introductionmentioning

confidence: 99%

“…A number of crystal structures for two types of Rubisco holoenzyme are known: L 2 (large subunit dimers) for some photosynthetic bacteria (Lundqvist & Schneider, 1991), and L 8 S 8 (eight large and eight small subunits) for cyanobacteria and plants (Newman & Gutteridge, 1993;Schreuder et al, 1993;Andersson, 1996). The function of the small subunit is not yet known (reviewed by Spreitzer, 1993). The active site is highly conserved between L 2 and L 8 S 8 Rubisco.…”

Section: Introductionmentioning

confidence: 99%

“…2) may serve as a¯exible¯ap that covers the active site upon substrate binding (Schreuder et al, 1993). In contrast to higher plants and photosynthetic prokaryotes, the green alga C. reinhardtii has allowed the application of chloroplast genetic methods for the recovery of Rubisco largesubunit mutants (Spreitzer, 1993). The C. reinhardtti large subunit has high sequence identity ($90%) with higher plant large subunits, whereas there is low sequence identity ($30%) with the L 2 holoenzyme.…”

Section: Introductionmentioning

confidence: 99%

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Preliminary X-ray crystallographic study of wild-type and mutant ribulose-1,5-bisphosphate carboxylase/oxygenase fromChlamydomonas reinhardtii

et al. 1998

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Ribulose-1,5-bisphosphate carboxylase/oxygenase is the key enzyme for photosynthesis. The wild-type and mutant (aminoacid substitutions in the catalytically important loop 6 region) enzymes from Chlamydomonas reinhardtii, a unicellular green alga, were crystallized. Wild-type, single-mutant (V331A) and two double-mutant (V331A/T342I and V331A/G344S) proteins were activated with cofactors CO 2 and Mg 2+ , complexed with the substrate analog 2 H -carboxyarabinitol-1,5-bisphosphate, and crystallized in apparently isomorphous forms. Unit-cell determinations have been completed for three of the enzymes.

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Genetic Dissection of Rubisco Structure and Function

Cited by 134 publications

References 52 publications

Why highly expressed proteins evolve slowly

Why highly expressed proteins evolve slowly

A Conserved Mechanism Controls Translation of Rubisco Large Subunit in Different Photosynthetic Organisms

Preliminary X-ray crystallographic study of wild-type and mutant ribulose-1,5-bisphosphate carboxylase/oxygenase fromChlamydomonas reinhardtii

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