Evolution of novel genes

Long, Manyuan

doi:10.1016/s0959-437x(00)00252-5

Cited by 148 publications

(93 citation statements)

References 69 publications

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“…Mobile modules should also to be able to fold independently (Kolkman and Stemmer, 2001) and be encoded by one exon. This notion of exon shuffling was postulated by Gilbert (1978) and can occur by recombining introns and by retropositioning (Long, 2001). It has been suggested that exon shuffling is essential in the formation of mosaic proteins and, as indicated by Patthy (1999), this became significant with the formation of spliceosomal in-trons, and increasingly so with the evolution of larger and less compacted genomes (larger spliceosomal introns) from protists to humans.…”

Section: Collagen As a Multimodular Proteinmentioning

confidence: 99%

Evolution of collagens

et al. 2002

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The extracellular matrix is often defined as the substance that gives multicellular organisms (from plants to vertebrates) their structural integrity, and is intimately involved in their development. Although the general functions of extracellular matrices are comparable, their compositions are quite distinct. One of the specific components of metazoan extracellular matrices is collagen, which is present in organisms ranging from sponges to humans. By comparing data obtained in diploblastic, protostomic, and deuterostomic animals, we have attempted to trace the evolution of collagens and collagen-like proteins. Moreover, the collagen story is closely involved with the emergence and evolution of metazoa. The collagen triple helix is one of numerous modules that arose during the metazoan radiation which permit the formation of large multimodular proteins. One of the advantages of this module is its involvement in oligomerization, in which it acts as a structural organizer that is not only relatively resistant to proteases but also permits the creation of multivalent supramolecular networks. Anat Rec 268: 302-316, 2002.

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Section: Collagen As a Multimodular Proteinmentioning

confidence: 99%

Evolution of collagens

et al. 2002

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“…The tailoring of existing genetic systems to new uses is called genetic co-option (True and Carrol 2002). Although new genes have been created by assembling normally unrelated genomic segments (e.g., Long 2001;Long and Langley 1993), the observation that the total gene number in complex organisms does not differ greatly from simpler organisms suggests the importance of co-option of pre-existing genetic systems (e.g., Claverie 2001; Betra´n and Long 2002). Furthermore, genetic co-option events have been associated with major changes in organism ecology and life history (e.g., Chen et al 1997; Harris et al 2002).…”

Section: Introductionmentioning

confidence: 99%

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

2004

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Abstract. The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (x) as a measure of selection on the protein, with x = 1, <1, and >1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in x among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different x's between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the e and c globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophilderived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the e and c globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.

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“…Gene duplication, exon shuffling, and retrotransposition events played crucial roles during vertebrate evolution (Long, 2001;McLysaght et al, 2002;Brosius, 2003). About 5% of the human genome is composed of duplicated segments that emerged during the past 35 million years of primate evolution, resulting in the generation of novel protein functions (Courseaux and Nahon, 2001;Taylor and Raes, 2004).…”

Section: Introductionmentioning

confidence: 99%

The Primate-specific Protein TBC1D3 Is Required for Optimal Macropinocytosis in a Novel ARF6-dependent Pathway

Frittoli

Palamidessi

Pizzigoni

et al. 2008

MBoC

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The generation of novel genes and proteins throughout evolution has been proposed to occur as a result of whole genome and gene duplications, exon shuffling, and retrotransposition events. The analysis of such genes might thus shed light into the functional complexity associated with highly evolved species. One such case is represented by TBC1D3, a primatespecific gene, harboring a TBC domain. Because TBC domains encode Rab-specific GAP activities, TBC-containing proteins are predicted to play a major role in endocytosis and intracellular traffic. Here, we show that the TBC1D3 gene originated late in evolution, likely through a duplication of the RNTRE locus, and underwent gene amplification during primate speciation. Despite possessing a TBC domain, TBC1D3 is apparently devoid of Rab-GAP activity. However, TBC1D3 regulates the optimal rate of epidermal growth factor-mediated macropinocytosis by participating in a novel pathway involving ARF6 and RAB5. In addition, TBC1D3 binds and colocalize to GGA3, an ARF6-effector, in an ARF6-dependent manner, and synergize with it in promoting macropinocytosis, suggesting that the two proteins act together in this process. Accordingly, GGA3 siRNA-mediated ablation impaired TBC1D3-induced macropinocytosis. We thus uncover a novel signaling pathway that appeared after primate speciation. Within this pathway, a TBC1D3:GGA3 complex contributes to optimal propagation of signals, ultimately facilitating the macropinocytic process. INTRODUCTIONGene duplication, exon shuffling, and retrotransposition events played crucial roles during vertebrate evolution (Long, 2001;McLysaght et al., 2002;Brosius, 2003). About 5% of the human genome is composed of duplicated segments that emerged during the past 35 million years of primate evolution, resulting in the generation of novel protein functions (Courseaux and Nahon, 2001;Taylor and Raes, 2004).One of the cellular processes, whose regulation has became more and more complex and tightly regulated during evolution is endocytosis. Endocytosis serves to maintain cellular and organismal homeostasis by mediating the uptake of fluids, solutes, and signaling molecules and their receptors. Multiple mechanisms of endocytosis operate within a single cell (Conner and Schmid, 2003). Among them, two major categories are phagocytosis and pinocytosis, which mediate the uptake of particles or of fluid, respectively (Conner and Schmid, 2003).Pinocytosis encompasses a variety of different membraneentry routes and is invariably characterized by the relatively small size (50 -150 nm) of the internalized particles. Large volumes of fluid are, instead, engulfed by extension, folding, and closure of plasma membranes (PM) through a process termed macropinocytosis (Swanson and Watts, 1995). Macropinocytosis displays many similarities to phagocytosis; the biochemical and cellular components of these endocytic mechanisms have been best characterized in hematopoietic cells, in processes such as phagocytosis by macrophages in response to Fc receptor stimulation, or ma...

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Evolution of novel genes

Cited by 148 publications

References 69 publications

Evolution of collagens

Evolution of collagens

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

The Primate-specific Protein TBC1D3 Is Required for Optimal Macropinocytosis in a Novel ARF6-dependent Pathway

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