Systematics and Evolution of the Algae: Endocytobiosis and Evolution of the Major Algal Lineages

Melkonian, Michael

doi:10.1007/978-3-642-79844-3_16

Cited by 4 publications

(1 citation statement)

References 158 publications

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“…(B) Densitometry of the exposed film: protein levels were calculated in relative percentage; the higher level of CR (gametes) was used as 100% reference. as would be expected for this unicellular chlorophyte (Melkonian 1996). Database searching with the blast algorithm revealed no homology between CR and any protein sequence from prokaryotic genomes (data not shown).…”

Section: Resultsmentioning

confidence: 51%

CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

Zuppini

Barbato

Bergantino

et al. 1999

Journal of Phycology

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The occurrence of calreticulin, the main Ca 2؉ binding protein in the endoplasmic reticulum of eukaryotic cells, was investigated in the unicellular green alga Chlamydomonas reinhardtii Dangeard. The biochemical characterization of a diethylaminoethyl purified extract highlighted the presence, on SDS-PAGE, of a 55-kDa protein that stained blue with the Stains All dye, a diagnostic feature of acidic Ca 2؉ binding proteins. Immunoblot analyses revealed a strong cross-reaction of the Chlamydomonas reinhardtii protein with antibodies to plant calreticulins and the endoplasmic reticulum retention signal HDEL. Furthermore, the 55-kDa protein bound [ 45 Ca 2؉ ] and had an acidic isoelectric point (pI ‫؍‬ 4.9) but was neither glycosylated nor phosphorylated. N-terminal sequencing revealed strong amino acid sequence similarity to calreticulin from other sources. The presence of calreticulin in Chlamydomonas reinhardtii suggested that an endoplasmic reticulum Ca 2؉ buffering mechanism was present in this unicellular chlorophyte. The data suggest an early origin and high conservation of endoplasmic-reticulummediated Ca 2؉ functions in eukaryotes, whereby specific posttranslational modifications of the protein 1 have been specifically acquired in different lineages of photosynthetic eukaryotes. Moreover, northern and western blot analysis experiments showed a regulation of calreticulin expression during Chlamydomonas sexual reproduction with a high abundance of calreticulin mRNA and protein in reproductive cells.

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Section: Resultsmentioning

confidence: 51%

CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

Zuppini

Barbato

Bergantino

et al. 1999

Journal of Phycology

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Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution

Vogl

Badger

Kearney

et al. 2003

Journal of Molecular Evolution

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Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue-green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.

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The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis

1997

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The evolutionary histories of the 12 enzymes that catalyze the reactions of the Calvin cycle in higher-plant chloroplasts are summarized. They are shown to be encoded by a mixture of nuclear genes of cyanobacterial and proteobacterial origin. Moreover, where cytosolic isoforms of these enzymes are found they are almost invariably encoded by genes of clearly endosymbiont origin. We infer that endosymbiosis resulted in functional redundancy that was eliminated through differential gene loss, with intruding eubacterial genes repeatedly replacing pre-existing nuclear counterparts to which they were either functionally or structurally homologous. Our findings fail to support the 'product-specificity corollary', which predicts re-targeting of nuclear-encoded gene products to the organelle from whose genome they originated. Rather it would appear that the enzymes of central carbohydrate metabolism have evolved novel targeting possibilities regardless of their origins. Our findings suggest a new hypothesis to explain organelle genome persistence, based on the testable idea that some organelle-encoded gene products might be toxic when present in the cytosol or other inappropriate cellular compartments.

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Systematics and Evolution of the Algae: Endocytobiosis and Evolution of the Major Algal Lineages

Cited by 4 publications

References 158 publications

CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution

The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis

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Systematics and Evolution of the Algae: Endocytobiosis and Evolution of the Major Algal Lineages

Cited by 4 publications

References 158 publications

CA2+ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

CA2+ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution

The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis

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CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS

CA²⁺ BINDING PROTEIN CALRETICULIN IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): BIOCHEMICAL CHARACTERIZATION, DIFFERENTIAL EXPRESSION DURING SEXUAL REPRODUCTION, AND PHYLOGENETIC ANALYSIS