Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Mirkin, Boris; Fenner, Trevor; Galperin, Michael Y.; Koonin, Eugene V.

doi:10.1186/1471-2148-3-2

Cited by 320 publications

(145 citation statements)

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“…The last universal common ancestor (LUCA) 2 had a few hundred genes encoding the machinery needed for replication, transcription, and translation; a few transporters and transcriptional regulators; an ATP synthase; and metabolic enzymes for synthesis of amino acids and nucleotides (1,2). In the ensuing 3.8 billion years, the protein repertoire of the LUCA expanded as new folds were discovered, domain fusions led to larger and more complex structures, and families and superfamilies emerged by duplication and divergence of ancestral genes (3).…”

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confidence: 99%

Toward a Systems Biology Perspective on Enzyme Evolution

Copley

2012

Journal of Biological Chemistry

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Large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. Division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. Later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. Enzymes operate in the context of complex metabolic and regulatory networks. The potential for evolution of a new enzyme depends upon the collection of enzymes in a microbe, the topology of the metabolic network, the environmental conditions, and the net effect of trade-offs between the original and novel activities of the enzyme.

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confidence: 99%

Toward a Systems Biology Perspective on Enzyme Evolution

Copley

2012

Journal of Biological Chemistry

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“…Many factors affect the detection of HGT, such as lineage-specific gene loss (18,19), unequal rates of base substitution (1), loss of signal due to amelioration processes (16), and others (1, 15).…”

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Global extent of horizontal gene transfer

Choi

Kim

2007

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

121

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Horizontal gene transfer (HGT) is thought to play an important role in the evolution of species and innovation of genomes. There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT. Here, we present a method of identifying HGT events within a given protein family and estimate the global extent of HGT in all curated protein domain families (Ϸ8,000) listed in the Pfam database. The results suggest four conclusions: (i) for all protein domain families in Pfam, the fixation of genes horizontally transferred is not a rampant phenomenon between organisms with substantial phylogenetic separations (1.1-9.7% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); (ii) however, at the level of domains, >50% of Archaea have one or more protein domains acquired by HGT, and nearly 30 -50% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10%; (iii) HGT will have very little impact in the construction of organism phylogeny, when the construction methods use whole genomes, large numbers of common genes, or SSU rRNAs; and (iv) there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.protein domain family ͉ protein sequence family ͉ lateral gene transfer O ne of the new important concepts that emerged from a large number of genomic sequences in the last decade is that of horizontal gene transfer (HGT): gene transfer among organisms of different species. HGT has been found to have occurred in all three domains: Archaea, Bacteria, and Eukarya. The concept of HGT has been evoked to interpret various evolutionary processes ranging from speciation and the adaptation of organisms to uncertainties in phylogenetic inference of the tree of life (1-9). Although HGT has been regarded as a driving force in the innovation and evolution of genomes, especially in prokaryotes, its extent and impact on the evolutionary process and phylogeny of organisms or species remains controversial (8-10).There have been several methods developed to detect HGT, including (i) difference between gene trees derived from a limited number of gene families and the reference trees such as the small-subunit ribosomal RNA (SSU rRNA) tree (11-13) or whole genome tree (14); (ii) unexpectedly high sequence similarity of a gene from two distant genomes compared with those among homologous genes in closely related genomes (15); and (iii) unusual nucleotide composition or codon usages of a gene compared with the rest of the genes within a genome (16,17). Many factors affect the detection of HGT, such as lineage-specific gene loss (18,19), unequal rates of base substitution (1), loss of signal due to amelioration processes (16), and others (1, 15).It has been suggested that HGT may have been ''rampant'' in primitive genomes (6,20), but, for modern organisms, it may not be a dominant factor in speciation, because HGT has less effect on overall ge...

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“…An efficient algorithm, PARS, (PARsimonious Scenario) for computing the Maximum parsimony over a given phylogenetic tree is given by Mirkin et al (6). Although the assumption in (6) is that the gain and loss penalties are uniform over the tree, the recursive structure of PARS allows the use of node-specific penalties.…”

Section: Maximum Parsimonymentioning

confidence: 99%

“…Although the assumption in (6) is that the gain and loss penalties are uniform over the tree, the recursive structure of PARS allows the use of node-specific penalties.…”

Section: Maximum Parsimonymentioning

confidence: 99%

A Common Approach to Finding the Optimal Scenarios of a Markov Stochastic Process Over a Phylogenetic Tree

Konovski¹

2012

Biotechnology & Biotechnological Equipment

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Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Cited by 320 publications

References 83 publications

Toward a Systems Biology Perspective on Enzyme Evolution

Toward a Systems Biology Perspective on Enzyme Evolution

Global extent of horizontal gene transfer

A Common Approach to Finding the Optimal Scenarios of a Markov Stochastic Process Over a Phylogenetic Tree

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