Evolutionary Rates and Expression Level in Chlamydomonas

Popescu, Cristina; Borza, Tudor; Bielawski, Joseph P.; Lee, William R.

doi:10.1534/genetics.105.047399

Cited by 39 publications

(34 citation statements)

References 75 publications

(93 reference statements)

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“…Genes with high mRNA expression levels encode slow-evolving proteins, from bacteria [6,36], yeast [17,22], and algae [37] to nematodes [24], plants [20,38], fruit flies [15], mice, and humans [18]. Whereas most variables have little, if any, explanatory power, expression levels account for a significant proportion of the variance in the evolutionary rates of proteins.…”

Section: What the Functional Hypothesis Cannot Explainmentioning

confidence: 99%

“…Whereas most variables have little, if any, explanatory power, expression levels account for a significant proportion of the variance in the evolutionary rates of proteins. Expression, measured indirectly using codon usage bias, accounts for $30% of all variance in protein substitution rates in bacteria [36], $36% in yeast [17], $32% in Chlamydomonas [37] and $25% in Drosophila [39] (for review, see [35]). Other proxies of expression levels lead to qualitatively similar results.…”

Section: What the Functional Hypothesis Cannot Explainmentioning

confidence: 99%

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RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Park

Choi

2009

FEBS Letters

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Edited by Takashi Gojobori Keywords:Protein evolutionary rate Functional hypothesis Mistranslation-induced protein misfolding hypothesis Translational robustness Expression abundance a b s t r a c t Protein evolutionary rates have been presumed to be mostly determined by the density of functionally important amino acids in a given protein. They have been shown to correlate with variables intuitively related to functional importance of proteins, such as protein dispensability and protein-protein interactions. Surprisingly, the best correlate of the evolutionary rates has turned out to be not the functional importance of a protein, but the expression level of the protein. Drummond and Wilke suggest that the dominant role of expression levels in slowing the rate of protein evolution stems from a selection pressure against mistranslation-induced protein misfolding. We will review current evidence for and against different hypotheses on determining evolutionary rates.

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Section: What the Functional Hypothesis Cannot Explainmentioning

confidence: 99%

Section: What the Functional Hypothesis Cannot Explainmentioning

confidence: 99%

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Park

Choi

2009

FEBS Letters

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“…The portion of the C. incerta nuclear LSU rRNA gene encoding 28S rRNA was obtained by sequencing both strands of several overlapping PCR products. Moreover, authentication of the C. incerta rDNA sequences was based on comparisons with the EST sequences retrieved from our C. incerta cDNA libraries (Popescu et al 2006) that correspond to the nuclear SSU and LSU rRNA-coding regions. The nuclear SSU and LSU (28S) rRNA-coding regions of C. reinhardtii were accessed from GenBank (M32703) and ChlamyDB at http:/ /www.chlamy.…”

Section: Methodsmentioning

confidence: 99%

“…In this study, we have undertaken the sequencing of the Chlamydomonas incerta mtDNA to estimate rates of nucleotide substitution between C. reinhardtii and C. incerta mitochondrial protein-coding genes and to compare these rates with those recently reported for the nuclear genes from the same taxa (Popescu et al 2006). This work also measures the rates of substitution in the mitochondrial-and nuclear-encoded SSU and LSU rRNA-coding regions between the two taxa.…”

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confidence: 99%

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Popescu

Lee

2007

Genetics

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The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.

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“…NAB1 represents a eukaryotic example of a cytosolic RRM protein being subject to cysteine-based redox control. Apart from C. reinhardtii, NAB1 analogous proteins containing a combination of CSD and RRM domains were only identified in the genomes of closely related algal species C. incerta (14) and Volvox carteri (15). The position of both cysteines is conserved in all 3 genome sequences indicating that the mechanism of redox regulation is conserved at least within the Volvocales taxonomic group of green algae.…”

Section: Discussionmentioning

confidence: 99%

Cysteine modification of a specific repressor protein controls the translational status of nucleus-encoded LHCII mRNAs in Chlamydomonas

Wobbe

Blifernez

Schwarz

et al. 2009

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

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The cytosolic RNA-binding protein NAB1 represses translation of LHCII (light-harvesting complex of photosystem II) encoding mRNAs by sequestration into translationally silent mRNP complexes in the green alga Chlamydomonas reinhardtii. NAB1 contains 2 cysteine residues, Cys-181 and Cys-226, within its C-terminal RRM motif. Modification of these cysteines either by oxidation or by alkylation in vitro was accompanied by a decrease in RNAbinding affinity for the target mRNA sequence. To confirm the relevance of reversible NAB1 cysteine oxidation for the regulation of its activity in vivo, we replaced both cysteines with serines. All examined cysteine single and double mutants exhibited a reduced antenna at PSII caused by a perturbed NAB1 deactivation mechanism, with double mutations and Cys-226 single mutations causing a stronger and more distinctive phenotype compared with the Cys-181 mutation. Our data indicated that the responsible redox control mechanism is mediated by modification of single cysteines. Polysome analyses and RNA co-immunoprecipitation experiments demonstrated the interconnection of the NAB1 thiol state and its activity as a translation repressor in vivo. NAB1 is fully active in its dithiol state and is reversibly deactivated by modification of its cysteines. In summary, this work is an example that cytosolic translation of nucleus encoded photosynthetic genes is regulated via a reversible cysteine-based redox switch in a RNA-binding translation repressor protein.Chlamydomonas reinhardtii ͉ light harvesting antenna ͉ redox control ͉ translation control T o compensate for changes in light intensity or spectral quality, plants have developed several short-term and longterm mechanisms to regulate the amount of light that is captured by each photosystem (1). One important long-term adaptation strategy of plant organisms involves the complex expression regulation of various nuclear-encoded light harvesting complex (Lhcb) genes (1). All levels of LHCII gene expression are targeted by regulation mechanisms (2-5) which rely on a complex retrograde and anterograde communication between plastid, nucleus, and cytosol (6). The cytosolic translation repressor NAB1, which was identified in a Chlamydomonas reinhardtii light acclimation mutant (4), is the center of interest within this work. NAB1 harbors 2 RNA-binding motifs and 1 of these motifs, located at the N terminus, belongs to the highly conserved family of CSD (cold shock domain) domains. Proteins containing a CSD motif are referred to as Y-box proteins and eukaryotic members of this large family generally contain a second auxiliary RNA-binding domain, which modulates the RNA affinity of the protein but can be dispensable for selective RNA recognition (7). In the case of NAB1, the CSD motif is combined with a C-terminal RRM (RNA recognition motif) domain, which was demonstrated not to be essential for selective RNA recognition (4). It was shown that NAB1 binds to the mRNA of LHCBM (major light-harvesting complex of photosystem II) genes, thereby preventi...

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Evolutionary Rates and Expression Level in Chlamydomonas

Cited by 39 publications

References 75 publications

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Cysteine modification of a specific repressor protein controls the translational status of nucleus-encoded LHCII mRNAs in Chlamydomonas

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