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Chapter 4 : Gene Duplication and Gene Loading
Author:
Renato Fani1
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Affiliations:
1: Dipartimento di Biologia Animale e Genetica, Università degli Studi di Firenze, Via Romana 17–19, I-50125 Florence, Italy
Content Type: Textbook
Publication Year:
2004
Category: Microbial Genetics and Molecular Biology; Bacterial Pathogenesis
Book DOI:
10.1128/9781555817749
Chapter DOI:
10.1128/9781555817749.ch4
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Gene Duplication and Gene Loading, Page 1 of 2
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Abstract:
During the early evolution of life, gene duplication, the production of two copies of a DNA sequence, allowed the rapid diversification of enzymatically catalyzed reactions and an increase in genome size, providing also material for the invention of new enzymatic properties and complex regulatory and developmental patterns. A duplication may involve (i) a part of a gene, (ii) a whole gene, (iii) DNA stretches including two or more genes involved in the same or in different metabolic pathways, (iv) entire operons, (v) a part of a chromosome, (vi) an entire chromosome, and finally (vii) the whole genome. Therefore, any DNA sequence may undergo a duplication event(s), but the fate of the replicate depends on whether it provides an evolutionary advantage to the host cell. Two hypotheses on the origin and evolution of metabolic pathways exist. The first one, the Horowitz retrograde hypothesis, predicts that an entire metabolic route was assembled by successive duplications of an ancestral gene in a backward fashion, starting with the synthesis of the final product, then the penultimate pathway intermediate, and so on down the pathway to the initial precursor. The patchwork hypothesis is based on the duplication(s) of ancestral gene(s) leading to the progressive increasing of specificity of low-specific enzymes, which then may be recruited to catalyze similar reactions in different metabolic pathways or sequential steps in the same route.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
Figures
Gene Duplication and Gene Loading
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Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-1
FIGURE 1
Gene duplication and divergence: formation of paralogs.
10.1128/9781555817749/fig4-1_thmb.gif
10.1128/9781555817749/fig4-1.gif
FIGURE 1
Gene duplication and divergence: formation of paralogs.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-2
FIGURE 2
Evolutionary relationship between orthologous and paralogous genes.
10.1128/9781555817749/fig4-2_thmb.gif
10.1128/9781555817749/fig4-2.gif
FIGURE 2
Evolutionary relationship between orthologous and paralogous genes.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-3
FIGURE 3
Evolution of a paralogous gene family.
10.1128/9781555817749/fig4-3_thmb.gif
10.1128/9781555817749/fig4-3.gif
FIGURE 3
Evolution of a paralogous gene family.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-4
FIGURE 4
Gene elongation: the duplication of an ancestral gene and the subsequent fusion of the two homologs to produce a longer protein.
10.1128/9781555817749/fig4-4_thmb.gif
10.1128/9781555817749/fig4-4.gif
FIGURE 4
Gene elongation: the duplication of an ancestral gene and the subsequent fusion of the two homologs to produce a longer protein.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-5
FIGURE 5
The Horowitz hypothesis. As each intermediate (A through D) becomes exhausted in the primordial soup, the successful organisms evolve the next step in the pathway. Thus, as A is exhausted, ? (the next intermediate) becomes the prime material source, and so on.
10.1128/9781555817749/fig4-5_thmb.gif
10.1128/9781555817749/fig4-5.gif
FIGURE 5
The Horowitz hypothesis. As each intermediate (A through D) becomes exhausted in the primordial soup, the successful organisms evolve the next step in the pathway. Thus, as A is exhausted, ? (the next intermediate) becomes the prime material source, and so on.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-6
FIGURE 6
Patchwork hypothesis on the origin and evolution of metabolic pathways.
10.1128/9781555817749/fig4-6_thmb.gif
10.1128/9781555817749/fig4-6.gif
FIGURE 6
Patchwork hypothesis on the origin and evolution of metabolic pathways.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-7
FIGURE 7
Evolutionary divergence of an ancestral enzyme (E1) with a low specificity catalyzing similar reactions in the same (a) or different (b) metabolic route(s).
10.1128/9781555817749/fig4-7_thmb.gif
10.1128/9781555817749/fig4-7.gif
FIGURE 7
Evolutionary divergence of an ancestral enzyme (E1) with a low specificity catalyzing similar reactions in the same (a) or different (b) metabolic route(s).
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-8
FIGURE 8
Organization of nif genes in Klebsiella pneumoniae.
10.1128/9781555817749/fig4-8_thmb.gif
10.1128/9781555817749/fig4-8.gif
FIGURE 8
Organization of nif genes in Klebsiella pneumoniae.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-9
FIGURE 9
Origin and evolution of nifD, nifE, nifK, and nifN genes found in present-day bacterial and archaeal diazotrophs: a cascade of DNA duplications and divergence.
10.1128/9781555817749/fig4-9_thmb.gif
10.1128/9781555817749/fig4-9.gif
FIGURE 9
Origin and evolution of nifD, nifE, nifK, and nifN genes found in present-day bacterial and archaeal diazotrophs: a cascade of DNA duplications and divergence.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-10
FIGURE 10
Two scenarios depicted for the evolution of the original functions performed by the nifDKEN genes and their ancestor genes.
10.1128/9781555817749/fig4-10_thmb.gif
10.1128/9781555817749/fig4-10.gif
FIGURE 10
Two scenarios depicted for the evolution of the original functions performed by the nifDKEN genes and their ancestor genes.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-11
FIGURE 11
Schematic representation of the E. coli histidine biosynthetic operon (upper) and pathway (lower).
10.1128/9781555817749/fig4-11_thmb.gif
10.1128/9781555817749/fig4-11.gif
FIGURE 11
Schematic representation of the E. coli histidine biosynthetic operon (upper) and pathway (lower).
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
/content/10.1128/9781555817749.chap4.fig4-12
FIGURE 12
Evolutionary origin of the hisA and hisF genes.
10.1128/9781555817749/fig4-12_thmb.gif
10.1128/9781555817749/fig4-12.gif
FIGURE 12
Evolutionary origin of the hisA and hisF genes.
Citation:
Fani R.
2004.
Gene Duplication and Gene Loading,
p 67-81.
In
Miller R, Day M (ed),
Microbial Evolution.
ASM Press, Washington, DC.
doi: 10.1128/9781555817749.ch4
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