Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment

Wächtershäuser, Günter

doi:10.1016/s0723-2020(98)80058-1

Cited by 33 publications

(16 citation statements)

References 35 publications

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“…The Gϩve signal in the Arabidopsis data most likely ref lects an overall similarity of many proteins in Gϩve genomes to homologues in cyanobacteria. Data from rRNA (44) and protein trees (45)(46)(47), operon organization (48), and lipoprotein components (49) phylogenetically link Gϩves and cyanobacteria. In our view, the Gϩve signal in the Arabidopsis data are most easily attributed to genes that entered the plant lineage through the ancestors of plastids, even though the gene trees recover a Gϩve branch, either because of shared ancestry or lateral transfer of Gϩve and cyanobacterial genes (17).…”

Section: Resultsmentioning

confidence: 99%

Evolutionary analysis ofArabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

Martin

Rujan²,

Richly

et al. 2002

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

1,068

796

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Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only Ϸ5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that Ϸ4,500 of Arabidopsis protein-coding genes (Ϸ18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.

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Section: Resultsmentioning

confidence: 99%

Evolutionary analysis ofArabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

Martin

Rujan²,

Richly

et al. 2002

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

1,068

796

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“…It was Volcanic origin of chemoautotrophic life G. Wächtershäuser 1797 found ( Wächtershäuser 1998b;cf. Lathe et al 2000) that in all sequenced bacterial and archaeal genomes, a number of relatively short conserved gene clusters, mainly for transcription and translation, had different lengths from phyla to phyla and could be organized into overlapping gene cluster alignments, whereby astonishingly long segments of ancestral genome segments of the common ancestors of all Bacteria (BCA; 46 genes) and all Archaea (ACA; 53 genes) can be reconstructed (figure 6).…”

Section: Cellularization (A) Surface Lipophilizationmentioning

confidence: 99%

From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya

Wächtershäuser¹

2006

Phil. Trans. R. Soc. B

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The theory of a chemoautotrophic origin of life in a volcanic iron-sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure-function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.

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“…At the eve of the emergence of the domains of Archaea and Bacteria, the pre-cells were already highly advanced and the result of many millions of years of evolution, with DNA chromosomes having a strict gene order partly conserved to this day, with RNA, ribosomes, replication, transcription, translation, and protein translocation, and with a lipid membrane and a complex metabolism [52]. Lipids with two long-chain lipophilic rests, like phosphoglycerol lipids are chiral, but the enzymes for the synthesis of these chiral lipids would at first not have been enantiospecific, which means that the pre-cell lipids were racemic.…”

Section: Scheme Peptide Cyclementioning

confidence: 99%

On the Chemistry and Evolution of the Pioneer Organism

Wächtershäuser¹

2007

Chemistry & Biodiversity

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229

142

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The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.

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Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment

Cited by 33 publications

References 35 publications

Evolutionary analysis ofArabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

Evolutionary analysis ofArabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya

On the Chemistry and Evolution of the Pioneer Organism

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