- Email: [email protected]
Genetically encoded generators of genetic variants
J O U RN A L OF P R O TE O MI CS 7 2 (2 0 0 9 ) 8 3 6– 8 3 7
a v a i l a b l e a t w w w. s c i e n c e d i r e c t . c o m
w w w. e l s e v i e r. c o m / l o c a t e / j p r o t
Review
Genetically encoded generators of genetic variants Werner Arber⁎ Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
AR TIC LE D ATA
ABSTR ACT
Article history:
Several specific molecular mechanisms contribute to the generation of genetic variants at
Received 14 September 2008
low rates. Some of these mechanisms involve the action of specific gene products as
Accepted 5 November 2008
variation generators. We discuss here known as well as still hypothetical ways by which natural reality may succeed to keep the rates of genetic variation at low levels that insure a
Keywords:
relatively high genetic stability of the individual organisms.
Biological evolution
© 2008 Elsevier B.V. All rights reserved.
Spontaneous mutagenesis Evolution genes DNA recombination and repair DNA acquisition Activities of isomeric conformations
Contents
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837
According to the neo-Darwinian theory, the biological evolution is driven by the availability of genetic variants within populations of individuals. Natural selection, resulting from how individuals can cope with their encountered environments, influences, together with the available genetic variants, the directions that biological evolution takes. Reproductive as well as geographic isolations modulate the evolutionary process. Recent advances in molecular genetics enable us to investigate the molecular mechanisms that generate genetic variants. On the one hand, computational comparisons of DNA sequence domains, of a given gene, of groups of genes, or of entire genomes of more or less evolutionarily related organisms allow us to speculate on the sources of observed differences. On the other hand, case by case studies of the
generation of novel genetic variants is possible with relatively small microbial genomes or for a particular gene. In these studies we define as variants any alterations relative to the parental DNA sequences. However, by far not all such sequence alterations cause a change in the phenotype of the concerned organism; they are often silent or neutral. Changes of the phenotype are frequently unfavorable, detrimental and provide to the organism a selective disadvantage. Rather rarely are DNA sequence alterations favorable, beneficial and provide a selective advantage. In this context, spontaneous mutations have often been seen as replication errors or resulting from accidents occurring to the DNA. This view is now contradicted by results of investigations on the molecular mechanisms of the generation of genetic variants.
⁎ Fax: +41 61 267 21 18. E-mail address: [email protected]. 1874-3919/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.jprot.2008.11.002
J O U RN A L OF P R O TE O MI CS 72 ( 20 0 9 ) 8 3 6– 8 3 7
Solid experimental evidence indicates that several mechanistically different molecular mechanisms contribute to the overall, occasional generation of genetic variants. These sources of genetic variants can be classified into three different natural strategies: local sequence changes affecting one or a few neighboring base pairs, intra-genomic rearrangements of DNA segments, and DNA acquisition by horizontal gene transfer. A theory of molecular evolution [1] is based on these insights, and it postulates that products of so-called evolution genes are involved together with various nongenetic elements in the generation of DNA sequence alterations. The products of evolution genes act either directly as variation generators or as modulators of the rates of genetic variation, while some of these gene products contribute to both of these functions. A good example for the latter statement is provided by bacterial restriction endonucleases. These enzymes keep the acquisition of foreign DNA at low rates, while the DNA fragments resulting from endonucleolytic cleavage are recombinogenic before becoming eliminated by exonucleolytic activities. We thus identify two antagonistic principles: to provide means to keep biological evolution going on and to provide a reasonable genetic stability to populations of organisms. These insights imply a duality of the genome that carries many genes serving for the fulfillment of the individual's life, while other genes primarily serve for the evolutionary expansion of life, for providing and replenishing biodiversity. This was the general message that I gave in my lecture at the 6th Siena meeting on proteomics [2] together with the recommendation that researchers in proteomics should pay special attention to gene products involved in driving biological evolution. Since the rates of generating genetic variants by any of the molecular mechanisms must be kept very low, we raise here the question on how this request is met. Generally speaking, the activities of the evolution genes that we encounter nowadays in nature must have been fine-tuned by secondorder selection [3] in the course of long periods of evolution. Looking at a number of particular gene activities one can observe a multitude of strategies/mechanisms to reach the goal of well balanced activities of the products of evolution genes. These can for example involve different strengths of the transcription promoter, early transcription terminators within the open reading frame and antisense RNA. We also postulate the possible requirement for the gene products to become post-translationally modified or to assume a rare, short-living isomeric conformation in order to become active. In experimental investigations attention should thus be paid to the quantity of protein gene products available as well as to the possibility to obtain a particular enzymatic activity by
837
isomeric or modified forms of the enzyme or of its substrate, which are often DNA sequences. Attention should also be paid to a possible requirement of specific, often environmental ligands for a particular reaction to take place [4]. We are aware that experimental investigations on these questions are impeded by the two boundary conditions that the rates of genetic variation must be kept quite low and that the generation of genetic variants must not be strictly reproducible from case to case. However, experimental work has already provided some evidence on a number of mechanisms and strategies that can satisfy these postulates [5,6]. In conclusion, products of evolution genes may often differ considerably from properties expected for many other, more classical gene products that work efficiently and reproducibly, reliably. More detailed information on molecular mechanisms involved in biological evolution can be found in a few relevant reviews [7–11].
REFERENCES [1] Arber W. Gene products with evolutionary functions. Proteomics 2005;5:2280–4. [2] Arber W. Elements for a theory of molecular evolution. Gene 2003;317:3–11. [3] Weber M. Evolutionary plasticity in prokaryotes: a panglossian view. Biol Philos 1996;11:67–88. [4] Saravanan M, Vasu K, Nagaraja V. Evolution of sequence specificity in a restriction endonuclease by a point mutation. PNAS 2008;105:10344–7. [5] Sengstag C, Shepherd JCW, Arber W. The sequence of the bacteriophage P1 genome region serving as hot target for IS2 insertion. EMBO J 1983;2:1777–81. [6] Iida S, Hiestand-Nauer R. Role of the central dinucleotide at the crossover sites for the selection of quasi sites in DNA inversion mediated by the site-specific Cin recombinase of phage P1. Mol Gen Genet 1987;208:464–8. [7] Arber W. The generation of variation in bacterial genomes. J Mol Evol 1995;40:7–12. [8] Arber W. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 2000;24:1–7. [9] Arber W. Evolution of prokaryotic genomes. Curr Top Microbiol Immunol 2002;264/I:1–14. [10] Arber W. Genetic variation and molecular evolution. In: Meyers RA, editor. Genomics and genetics, vol. 1. Weinheim: Wiley-VCH; 2007. p. 385–406. [11] Arber W. Stochastic genetic variations and their role in biological evolution. In: Arber W, Cabibbo N, Sanchez Sorondo M, editors. Predictability in science: accuracy and limitations. Vatican City: Pontifical Academy of Sciences; 2008. p. 126–40.
a v a i l a b l e a t w w w. s c i e n c e d i r e c t . c o m
w w w. e l s e v i e r. c o m / l o c a t e / j p r o t
Review
Genetically encoded generators of genetic variants Werner Arber⁎ Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
AR TIC LE D ATA
ABSTR ACT
Article history:
Several specific molecular mechanisms contribute to the generation of genetic variants at
Received 14 September 2008
low rates. Some of these mechanisms involve the action of specific gene products as
Accepted 5 November 2008
variation generators. We discuss here known as well as still hypothetical ways by which natural reality may succeed to keep the rates of genetic variation at low levels that insure a
Keywords:
relatively high genetic stability of the individual organisms.
Biological evolution
© 2008 Elsevier B.V. All rights reserved.
Spontaneous mutagenesis Evolution genes DNA recombination and repair DNA acquisition Activities of isomeric conformations
Contents
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837
According to the neo-Darwinian theory, the biological evolution is driven by the availability of genetic variants within populations of individuals. Natural selection, resulting from how individuals can cope with their encountered environments, influences, together with the available genetic variants, the directions that biological evolution takes. Reproductive as well as geographic isolations modulate the evolutionary process. Recent advances in molecular genetics enable us to investigate the molecular mechanisms that generate genetic variants. On the one hand, computational comparisons of DNA sequence domains, of a given gene, of groups of genes, or of entire genomes of more or less evolutionarily related organisms allow us to speculate on the sources of observed differences. On the other hand, case by case studies of the
generation of novel genetic variants is possible with relatively small microbial genomes or for a particular gene. In these studies we define as variants any alterations relative to the parental DNA sequences. However, by far not all such sequence alterations cause a change in the phenotype of the concerned organism; they are often silent or neutral. Changes of the phenotype are frequently unfavorable, detrimental and provide to the organism a selective disadvantage. Rather rarely are DNA sequence alterations favorable, beneficial and provide a selective advantage. In this context, spontaneous mutations have often been seen as replication errors or resulting from accidents occurring to the DNA. This view is now contradicted by results of investigations on the molecular mechanisms of the generation of genetic variants.
⁎ Fax: +41 61 267 21 18. E-mail address: [email protected]. 1874-3919/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.jprot.2008.11.002
J O U RN A L OF P R O TE O MI CS 72 ( 20 0 9 ) 8 3 6– 8 3 7
Solid experimental evidence indicates that several mechanistically different molecular mechanisms contribute to the overall, occasional generation of genetic variants. These sources of genetic variants can be classified into three different natural strategies: local sequence changes affecting one or a few neighboring base pairs, intra-genomic rearrangements of DNA segments, and DNA acquisition by horizontal gene transfer. A theory of molecular evolution [1] is based on these insights, and it postulates that products of so-called evolution genes are involved together with various nongenetic elements in the generation of DNA sequence alterations. The products of evolution genes act either directly as variation generators or as modulators of the rates of genetic variation, while some of these gene products contribute to both of these functions. A good example for the latter statement is provided by bacterial restriction endonucleases. These enzymes keep the acquisition of foreign DNA at low rates, while the DNA fragments resulting from endonucleolytic cleavage are recombinogenic before becoming eliminated by exonucleolytic activities. We thus identify two antagonistic principles: to provide means to keep biological evolution going on and to provide a reasonable genetic stability to populations of organisms. These insights imply a duality of the genome that carries many genes serving for the fulfillment of the individual's life, while other genes primarily serve for the evolutionary expansion of life, for providing and replenishing biodiversity. This was the general message that I gave in my lecture at the 6th Siena meeting on proteomics [2] together with the recommendation that researchers in proteomics should pay special attention to gene products involved in driving biological evolution. Since the rates of generating genetic variants by any of the molecular mechanisms must be kept very low, we raise here the question on how this request is met. Generally speaking, the activities of the evolution genes that we encounter nowadays in nature must have been fine-tuned by secondorder selection [3] in the course of long periods of evolution. Looking at a number of particular gene activities one can observe a multitude of strategies/mechanisms to reach the goal of well balanced activities of the products of evolution genes. These can for example involve different strengths of the transcription promoter, early transcription terminators within the open reading frame and antisense RNA. We also postulate the possible requirement for the gene products to become post-translationally modified or to assume a rare, short-living isomeric conformation in order to become active. In experimental investigations attention should thus be paid to the quantity of protein gene products available as well as to the possibility to obtain a particular enzymatic activity by
837
isomeric or modified forms of the enzyme or of its substrate, which are often DNA sequences. Attention should also be paid to a possible requirement of specific, often environmental ligands for a particular reaction to take place [4]. We are aware that experimental investigations on these questions are impeded by the two boundary conditions that the rates of genetic variation must be kept quite low and that the generation of genetic variants must not be strictly reproducible from case to case. However, experimental work has already provided some evidence on a number of mechanisms and strategies that can satisfy these postulates [5,6]. In conclusion, products of evolution genes may often differ considerably from properties expected for many other, more classical gene products that work efficiently and reproducibly, reliably. More detailed information on molecular mechanisms involved in biological evolution can be found in a few relevant reviews [7–11].
REFERENCES [1] Arber W. Gene products with evolutionary functions. Proteomics 2005;5:2280–4. [2] Arber W. Elements for a theory of molecular evolution. Gene 2003;317:3–11. [3] Weber M. Evolutionary plasticity in prokaryotes: a panglossian view. Biol Philos 1996;11:67–88. [4] Saravanan M, Vasu K, Nagaraja V. Evolution of sequence specificity in a restriction endonuclease by a point mutation. PNAS 2008;105:10344–7. [5] Sengstag C, Shepherd JCW, Arber W. The sequence of the bacteriophage P1 genome region serving as hot target for IS2 insertion. EMBO J 1983;2:1777–81. [6] Iida S, Hiestand-Nauer R. Role of the central dinucleotide at the crossover sites for the selection of quasi sites in DNA inversion mediated by the site-specific Cin recombinase of phage P1. Mol Gen Genet 1987;208:464–8. [7] Arber W. The generation of variation in bacterial genomes. J Mol Evol 1995;40:7–12. [8] Arber W. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 2000;24:1–7. [9] Arber W. Evolution of prokaryotic genomes. Curr Top Microbiol Immunol 2002;264/I:1–14. [10] Arber W. Genetic variation and molecular evolution. In: Meyers RA, editor. Genomics and genetics, vol. 1. Weinheim: Wiley-VCH; 2007. p. 385–406. [11] Arber W. Stochastic genetic variations and their role in biological evolution. In: Arber W, Cabibbo N, Sanchez Sorondo M, editors. Predictability in science: accuracy and limitations. Vatican City: Pontifical Academy of Sciences; 2008. p. 126–40.