Time for acquiring a new gene by duplication.

The partial nucleotide sequence for an Fcreceptor gene from an M-type 76 group A streptococcus was determined. DNA sequence analysis revealed considerable sequence similarity between the Fc-receptor and M-protein genes in their proposed promoter regions, signal sequences, and 3' termini. Additional analysis indicated that the deduced Fc-receptor protein contains a proline-rich region and membrane anchor region highly similar to that of M protein. (7). We previously reported the cloning and expression of an Fc-receptor gene from group A streptococci (8, 9). Our initial results, based on Southern hybridization data, indicated that DNA sequence similarity existed between the Fc-receptor genetic locus (fcrA76) and the M12 gene (emm12) (8). Here we report a partial nucleotide sequence offcrA76 and compare it to several M-protein genes.* Our analysis indicated that the cloned receptor protein (FcRA76) is highly similar to M protein in its secondary structure and in organization of functional domains. Extensive amino acid sequence similarity between FcRA76 and M proteins in their signal peptides was observed. The deduced amino acid sequence also indicated that FcRA76 contains a proline-rich region and a portion of a C-terminal membrane anchor sequence, both similar to that of M6 and M24 proteins (10). From these results, we postulated that streptococci retain a superfamily of genes that encode surface proteins with heterologous functions: a family of immunoglobulin receptors and a family of antiphagocytic M proteins. We proposed that homologous recombination between FcRA76 and M-protein genes is a potential means for streptococci to generate antigenic diversity in their surface proteins. § MATERIALS AND METHODSBacterial Strains, Plasmids, Bacteriophage, and Media. Escherichia coli strains JM83, JM105, and JM109, the plasmid expression vectors pUC9 and pUC19, and phage M13mpl8 and M13mp19 were gifts of J. Messing and have been described (11). E. coli JM83, JM109, and DH5a were grown in LB broth or, after transformation with chimeric pUC plasmids, in LB broth/agar containing ampicillin at 50 jig/ml. E. coli JM105 was grown in M9 medium as described (12). The recombinant plasmid pDH56 and the group A streptococcal strain CS110 have been described (8).Preparation of Streptococcal DNA and Isolation of Plasmid DNA. Preparation of DNA from group A streptococci and of plasmid DNA from E. coli have been described (8).Recombinant DNA Techniques. Restriction endonucleases were purchased from Bethesda Research Laboratories and New England Biolabs, and digestions were performed as recommended by the suppliers. Gel electrophoresis was performed in either 0.7% or 1% agarose gels. The method for transfer of DNA to nitrocellulose has been described (13). Southern (14) and colony (15) blot hybridizations were done using heparin as a blocking agent (16), and standard conditions were used for DNA ligation and radiolabeling and for transformation of E. coli (13).DNA Sequencing and Analysis. Previous results indicated that fcrA76 ...

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“…Gene duplication and subsequent divergence is an important genetic mechanism for the creation of new genes (39) and gene families (40 (Fig. 3) …”

Section: Discussionmentioning

confidence: 99%

Fc-receptor and M-protein genes of group A streptococci are products of gene duplication.

Heath

Cleary

1989

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

136

106

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“…Chimeric structures significantly contribute to the evolution of new genes Population genetic models have been developed to account for the fixation of new genes within a population (Ohta 1988;Clark 1994;Lynch and Force 2000;Lynch et al 2001). Most of them assume that gene duplication generates a new gene copy that is functionally and structurally redundant at birth.…”

Section: A New Perspective On De Novo Originationmentioning

confidence: 99%

On the origin of new genes in Drosophila

Zhou

Zhang²,

Zhang³

et al. 2008

Genome Res.

247

257

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Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the Drosophila melanogaster species subgroup. We find that (1) tandem gene duplication has generated ∼80% of the nascent duplicates that are limited to single species (D. melanogaster or Drosophila yakuba); (2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; (3) de novo gene origination from noncoding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; (4) retroposition is also an important mechanism, and had generated ∼10% of the new genes; (5) ∼30% of the new genes in the D. melanogaster species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and (6) the rate of the origin of new functional genes is estimated to be five to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 globally derived strains for D. melanogaster-specific new genes and reveal that 44.4% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in Drosophila species.

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“…The classical model for the evolution of gene duplicates suggests that one member of most duplicate pairs should mutate to a pseudogene within a few million generations (Haldane 1933;Ohno 1970;Nei and Roychoudhury 1973;Bailey et al 1978;Kimura and King 1979;Takahata and Maruyama 1979;Li 1980;Watterson 1983;Ohta 1988;Clark 1994), and investigations of completely sequenced genomes suggests that duplicate genes usually become silenced within about 4 Myr (Lynch and Conery 2000). Many gene duplicates, however, remain for tens of millions of years after the duplication event (Allendorf et al 1975;Ferris and Whitt 1979;Ahn and Tanksley 1993;Hughes and Hughes 1993;White and Doebley 1998), indicating that other mechanisms must exist to preserve genes, such as the rare evolution of novel positively selected gene functions (Ohno 1970), or the reciprocal sharing of gene subfunctions (Hughes 1994;Force et al 1999;Stoltzfus 1999).…”

mentioning

confidence: 99%

Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish

et al. 2004

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The pufferfish skeleton lacks ribs and pelvic fins, and has fused bones in the cranium and jaw. It has been hypothesized that this secondarily simplified pufferfish morphology is due to reduced complexity of the pufferfish Hox complexes. To test this hypothesis, we determined the genomic structure of Hox clusters in the Southern pufferfish Spheroides nephelus and interrogated genomic databases for the Japanese pufferfish Takifugu rubripes (fugu). Both species have at least seven Hox clusters, including two copies of Hoxb and Hoxd clusters, a single Hoxc cluster, and at least two Hoxa clusters, with a portion of a third Hoxa cluster in fugu. Results support genome duplication before divergence of zebrafish and pufferfish lineages, followed by loss of a Hoxc cluster in the pufferfish lineage and loss of a Hoxd cluster in the zebrafish lineage. Comparative analysis shows that duplicate genes continued to be lost for hundreds of millions of years, contrary to predictions for the permanent preservation of gene duplicates. Gene expression analysis in fugu embryos by in situ hybridization revealed evolutionary change in gene expression as predicted by the duplication-degeneration-complementation model. These experiments rule out the hypothesis that the simplified pufferfish body plan is due to reduction in Hox cluster complexity, and support the notion that genome duplication contributed to the radiation of teleosts into half of all vertebrate species by increasing developmental diversification of duplicate genes in daughter lineages.

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Time for acquiring a new gene by duplication.

Cited by 42 publications

References 33 publications

Fc-receptor and M-protein genes of group A streptococci are products of gene duplication.

Fc-receptor and M-protein genes of group A streptococci are products of gene duplication.

On the origin of new genes in Drosophila

Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish

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