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Chapter 17 : Genetic Inventory: as a Window on Ancestral Proteins

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Genetic Inventory: as a Window on Ancestral Proteins, Page 1 of 2

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Abstract:

The delineation of groups of genes and proteins that trace back to common ancestors derives legitimacy and depth when functions are known and can be assessed for relatedness within any sequence related group. The goal in understanding protein evolution is the reconstruction of past events that have given rise to the inventory of extant proteins. Early ancestral organisms that existed before the separation of the three branches of the tree of life are believed to have possessed many of the functions of cell physiology and metabolism that are found in all living forms today. Molecular phylogeny tries to trace all the speciation events back to the last universal common ancestor. A few proteins have been rearranged and have fused since their initial duplication and divergence, and the separate elements within complex proteins need to be identified and separated. In many of the paralogous modules were clearly distinguishable by inspection of the DARWIN output. To inquire into the descent of the proteins of a family from their ancestral sequence, the authors have studied further the history of individual families. With the many whole-genome-sequencing projects under way today and planned for the future, there will be an abundance of data to be analyzed further along these lines, with the ambitious aim of eventually reconstructing the paths of evolution of all proteins.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Figures

Image of FIGURE 1
FIGURE 1

Distribution of РАМ distances separating sequence-related proteins. Shaded bars, the 11,160 DARWIN matches separated by less than 250 РАМ units and having alignments extending over at least 80 residues; solid bars, the 9,375 matches required to have identities of at least 20%.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 2
FIGURE 2

Schematic view of the different module arrangements found for the 11,160 DARWIN matches. The natures of the family, of the present-day modules, and of the ancestor are indicated for the three cases A, B, and C. “Paralogous” and “single” refer to modules with paralogous (duplication and divergence of the two copies) or nonparalogous (no duplication and unilineal descent) behaviors, respectively, during their evolutionary histories.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 3
FIGURE 3

Distribution of module lengths.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 4
FIGURE 4

Family 439: genealogical tree and module alignment. The DARWIN PhyloTree procedure was used to reconstruct the genealogical tree from the alignment of modules found in proteins b0072, b0118, b0771, and b1276. The matrix of the РАМ distances separating the modules of these different proteins is shown in an inset. NH, nonhomologous; aa, amino acids.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 5
FIGURE 5

Genealogical tree for family 523.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 6
FIGURE 6

Genealogical tree for family 549. PBP, periplasmic binding protein. Thin branches, repressors of type LacI; thick branches, PBP. The PBP with significant sequence similarities to one or several repressors are underlined.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 7
FIGURE 7

Module alignment for families 481 and 500.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Image of FIGURE 8
FIGURE 8

Schematic view comparing evolutionary histories of similar sequences and similar functions. Broken lines indicate putative lineages of descent of each putative ancestor of either the ancestor of one family of paralogous modules or unique modules. Solid lines indicate schematic trees of the determined families of paralogous modules.

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17
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Tables

Generic image for table
TABLE 1

Mean lengths of the different kinds of proteins and modules

Citation: Labedan B, Riley M. 1999. Genetic Inventory: as a Window on Ancestral Proteins, p 311-329. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch17

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