RESUMO
It is generally accepted that plastids first arose by acquisition of photosynthetic prokaryotic endosymbionts by non-photosynthetic eukaryotic hosts. It is also accepted that photosynthetic eukaryotes were acquired on several occasions as endosymbionts by non-photosynthetic eukaryote hosts to form secondary plastids. In some lineages, secondary plastids were lost and new symbionts were acquired, to form tertiary plastids. Most recent work has been interpreted to indicate that primary plastids arose only once, referred to as a 'monophyletic' origin. We critically assess the evidence for this. We argue that the combination of Ockham's razor and poor taxon sampling will bias studies in favour of monophyly. We discuss possible concerns in phylogenetic reconstruction from sequence data. We argue that improved understanding of lineage-specific substitution processes is needed to assess the reliability of sequence-based trees. Improved understanding of the timing of the radiation of present-day cyanobacteria is also needed. We suggest that acquisition of plastids is better described as the result of a process rather than something occurring at a discrete time, and describe the 'shopping bag' model of plastid origin. We argue that dinoflagellates and other lineages provide evidence in support of this.
Assuntos
Evolução Molecular , Plastídeos/genética , Plastídeos/metabolismo , Transporte de Elétrons , Complexo de Proteínas da Cadeia de Transporte de Elétrons/genética , Complexo de Proteínas da Cadeia de Transporte de Elétrons/metabolismo , Transferência Genética Horizontal , Modelos Biológicos , Fotossíntese , Filogenia , Plastídeos/classificação , SimbioseRESUMO
Frequently, letters, words and sentences are used in undergraduate textbooks and the popular press as an analogy for the coding, transfer and corruption of information in DNA. We discuss here how the converse can be exploited, by using programs designed for biological analysis of sequence evolution to uncover the relationships between different manuscript versions of a text. We point out similarities between the evolution of DNA and the evolution of texts.
Assuntos
Evolução Molecular , Manuscritos como Assunto/história , História do Século XV , Filogenia , Mutação PuntualRESUMO
Frequently, letters, words and sentences are used in undergraduate textbooks and the popular press as an analogy for the coding, transfer and corruption of information in DNA. We discuss here how the converse can be exploited, by using programs designed for biological analysis of sequence evolution to uncover the relationships between different manuscript versions of a text. We point out similarities between the evolution of DNA and the evolution of texts.
Assuntos
DNA/genética , Editoração , FilogeniaRESUMO
We show using PCR that psbC, atpA and petB genes are present in the plastid DNA minicircles from the dinoflagellate Amphidinium operculatum, extending the set of plastid genes identified from this organism. Unusually, the petBand atpA genes are located on the same minicircle. PCR using primers based on the "core" region found on all coding minicircles revealed the existence of a number of DNA minicircles with no apparent coding function. Northern analysis of total RNA from A. operculatum showed that the petB and atpA genes are represented on separate transcripts, despite being encoded in close proximity on the same minicircle. The possibility of transcript editing was investigated by RT-PCR, but psaA, psbA, psbB and atpB transcripts showed no evidence of editing, indicating that GUA can be used as an initiation codon in A. operculatum.
Assuntos
Dinoflagellida/genética , Proteínas de Plantas/genética , Plastídeos/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA Circular/genética , DNA de Protozoário/genética , Genes de Protozoários , Genoma , Dados de Sequência Molecular , ATPases Translocadoras de Prótons/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido NucleicoRESUMO
Plastid DNA was purified from the dinoflagellate Amphidinium operculatum. The genes atpB, petD, psaA, psbA and psbB have been shown to reside on single-gene minicircles of a uniform size of 2.3-2.4 kb. The psaA and psbB genes lack conventional initiation codons in the expected positions, and may use GTA for translation initiation. There are marked biases in codon preference. The predicted PsbA protein lacks the C-terminal extension which is present in all other photosynthetic organisms except Euglena gracilis, and there are other anomalies elsewhere in the predicted amino acid sequences. The non-coding regions of the minicircles contain a "core" region which includes a number of stretches that are highly conserved across all minicircles and modular regions that are conserved within subsets of the minicircles.
Assuntos
Complexo Citocromos b6f , DNA Circular/genética , DNA Circular/isolamento & purificação , DNA de Protozoário/genética , DNA de Protozoário/isolamento & purificação , Dinoflagellida/genética , Complexos de Proteínas Captadores de Luz , Complexo de Proteína do Fotossistema I , Plastídeos/genética , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/genética , Sequência de Bases , Códon/genética , Grupo dos Citocromos b/genética , Genes de Protozoários , Dados de Sequência Molecular , Complexo de Proteínas do Centro de Reação Fotossintética/genética , Complexo de Proteína do Fotossistema II , Filogenia , Proteínas de Protozoários/genética , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido NucleicoAssuntos
Organelas/genética , Plastídeos/genética , Animais , Dano ao DNA , DNA Mitocondrial/genética , Eucariotos/genética , GenomaRESUMO
We have generated secA sequence data from a number of photosynthetic prokaryotes and carried out a phylogenetic analysis using secA sequences from prokaryotes, green plants, and red and brown algae. We have studied the substitution patterns that give rise to the apparent phylogenetic structure. We show that the high AT content of the plastid sequences significantly affects the amino-acid composition. We also show that most of the apparent evidence for an edge separating red and brown plastids from green plants within the phylogenetic tree is due to differences in nucleotide composition. The remaining apparent evidence is likely to be due, at least in part, to differences in the distribution of sites free to vary. We discuss the implications of this study for hypotheses of plastid origins.
Assuntos
Adenosina Trifosfatases/genética , Proteínas de Bactérias/genética , Proteínas de Escherichia coli , Proteínas de Membrana Transportadoras , Filogenia , Plastídeos/genética , Proteínas de Algas/genética , Aminoácidos/análise , Transporte Biológico/genética , Clonagem Molecular , Ácidos Nucleicos/análise , Fotossíntese/genética , Proteínas de Plantas/genética , Canais de Translocação SEC , Proteínas SecA , Análise de Sequência de DNARESUMO
The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.
Assuntos
Modelos Genéticos , Oxigênio/metabolismo , Fotossíntese/genética , Filogenia , Cadeias de MarkovRESUMO
We have identified and sequenced a cDNA containing a complete open reading frame for a putative 340-amino acid precursor of the thylakoidal processing peptidase from Arabidopsis thaliana. The predicted amino acid sequence of the protein includes regions highly conserved among Type I leader peptidases and indicates that the enzyme uses a serine-lysine catalytic dyad mechanism. Phylogenetic analysis indicated a common ancestry of the enzyme with those from oxygenic photosynthetic prokaryotes, suggesting that the cDNA encoded the chloroplast enzyme. The catalytic domain was overexpressed in Escherichia coli, generating a product capable of cleaving the thylakoid-transfer domain from a chloroplast protein. Antibodies to the overexpressed polypeptide cross-reacted with a 30-kDa thylakoid membrane protein.
Assuntos
Arabidopsis/enzimologia , Endopeptidases/genética , Sequência de Aminoácidos , Arabidopsis/genética , Catálise , DNA Complementar , Endopeptidases/química , Endopeptidases/metabolismo , Dados de Sequência Molecular , Filogenia , Homologia de Sequência de AminoácidosRESUMO
Proteins targeted to the thylakoid lumen of plants and cyanobacteria and the periplasmic space of cyanobacteria are synthesised with N-terminal presequences which are removed following translocation across the membrane. These presequences are thought to direct translocation of the preprotein by a sec-type pathway. Detergent extracts of cyanobacterial and chloroplast membranes contain enzymes which are capable of processing precursors to the mature size. We show that the processing of a range of precursors by both cyanobacterial and chloroplast enzymes is inhibited by the penem SB216357. This is the first report of an inhibitor of these enzymes and indicates that they are type 1 signal peptidases.
Assuntos
Cloroplastos/enzimologia , Cianobactérias/enzimologia , Endopeptidases/metabolismo , Lactamas/farmacologia , Inibidores de Proteases/farmacologia , Precursores de Proteínas/metabolismo , Processamento de Proteína Pós-Traducional/efeitos dos fármacos , Cloroplastos/efeitos dos fármacos , Cianobactérias/efeitos dos fármacos , Pisum sativum/enzimologia , Complexo de Proteínas do Centro de Reação Fotossintética/metabolismo , Plastocianina/metabolismoAssuntos
Proteínas de Bactérias/metabolismo , Cianobactérias/metabolismo , Proteínas de Escherichia coli , Proteínas de Membrana Transportadoras , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Proteínas de Bactérias/genética , Transporte Biológico Ativo , Cloroplastos/metabolismo , Cianobactérias/genética , Genes Bacterianos , Membranas Intracelulares/metabolismo , Canais de Translocação SEC , Proteínas SecARESUMO
Cyanobacteria possess cytoplasmic membranes, which are common to all eubacteria, and an additional internal network of thylakoid membranes. We have investigated the distribution of the protein translocation machinery between the two membrane systems. We have demonstrated that leader peptidase activity exists in both membrane systems, suggesting that newly synthesized protein precursors are targeted directly rather than sorted after translocation. Southern blot analysis suggests that the leader peptidase is likely to be a single enzyme common to both membrane systems. We have also shown that cyanobacteria possess a single SecA homologue. These results indicate that the protein translocation machinery in the two membrane systems is likely to be the same and leaves open the question of what mechanism enables the cell to sort proteins between them.