Chapter 4 : : Whose Sister Lineage?

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Following a review of archaeal genomics, the author wishes to scrutinize the convenient though perhaps misleading construct that is organismic phylogeny. In so doing, the author will address theories of the origin of eukaryotes, theories which look to for answers, thanks to the (largely) accepted rooting of the tree of life in the bacterial branch. Interest in archaeal genomes, as judged by volume in the literature, has focused mainly on the extremely halophilic archaea. The genetic instability appears to be prevalent not only among members of the family but also among members of the order , though the insertion sequences responsible are apparently unrelated. Physical analysis of archaeal nucleoids lags behind the efforts of genetic characterization. Rooting of the tree, using anciently duplicated paralogous sequences further divided from Bacteria by positioning the root in the bacterial branch. The biological species will tend to restrict lateral transfers to specific groups. However, movement of genes from more distantly related organisms is not precluded, even between and . Specific genomes have subsets of these collections and typically possess a number of open reading frames not found anywhere else. Sequence evolution is responsible for the unmatched open reading frames, having erased the evidence of their homologies. Confounding things further are lateral genetic transfer and gene replacement, especially from extinct lineages. Comparative genomic analyses have begun, and they will undoubtedly transform the method of molecular evolutionary study.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4

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Family B DNA Polymerase
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Image of FIGURE 1

Eucaryal origin from the fusion of a bacterium with an archaeon ( ). The arrows indicate the two most important endosymbiotic events to occur since the origin of mitochondria and chloroplasts.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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Image of FIGURE 2

Eucaryal origin from the fusion of a gram-negative bacterium with an archaeon ( ). Although this modification of Fig. 1 helps to explain why are more closely related to gram-positive bacteria than to gram-negative bacteria, one must assume that a burst of evolutionary sequence change occurred shortly after the inception of and that early-branching are artifactually early branching (see text).

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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Image of FIGURE 3

Model of archaeal chimerism ( ) in which owe their metabolic similarity with to a large-scale lateral transfer of bacterial genes.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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Image of FIGURE 4

Fourth Domain model of eucaryal origins (right), based on the hypothesis that (E) are chimerae of (A) and an extinct (daggers) lineage of cytotrophs. If one trims the current phylogenetic tree (left) to the time in question (second from left), one suggests that the world supported an implausibly small microbial biodiversity, unless one accepts that other lineages existed (second from right) which have since gone extinct. Such a lineage may have engulfed an early archaeon, adopting its information processing mechanisms but retaining many of its own genes for fermentative metabolism.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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Image of FIGURE 5

Fourth Domain model, adjusted to take into account the sequence similarities among archaea, gram-positive bacteria, and cyanobacteria. Here, one must suppose that after the divergence of from gram-positive bacteria, redesigned their gene expression mechanisms, resulting in rapid sequence evolution. In this scenario, eucaryal genes are more closely related to archaeal genes or to gram-negative bacterial genes, since any affinity with gram-positive bacterial genes would be outweighed by the closer similarity to archaeal genes. is a gram-negative member of the gram-positive lineage, with the simplest of bacteriochlorophyll (BChl)-based photosynthetic apparatuses. + , addition of depth to the otherwise sheet-like murein sacculus; −, loss of the bacterial outer membrane, characteristic of gram-negative bacteria and believed to be ancestral ( ); AEexpr., invention of the archaeal-eucaryal style of gene expression and loss of peptidoglycan.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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Image of FIGURE 6

General model of the history of life, in which generic traits are largely inherited by descent except for common intraphyletic lateral genetic transfer—hence the thick branches—and occasional interphyletic lateral genetic transfer. The shaded bands represent contemporary gene pools, and the degree of shading indicates both the ease with which cross-kingdom exchanges might have occurred and the impact on all of extant life of such exchanges. The daggers indicate extinct lineages.

Citation: Charlebois R. 1999. : Whose Sister Lineage?, p 63-76. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch4
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