Downloaded from genome. cshlporg on June 20, 2011-Published by Cold Spring Harbor Laboratory Press Evolution of new genes implications of the majority of these plant chimeric genes remain almost bound to provide a new function), is the emergence of new to be explored, an interesting class of functional chimeric genesgenes"from scratch. In other words, new genes arise from pre- that involve fusions of mitochondrial retroposed gene copies and viously nonfunctional genomic sequence, unrelated to any pre- nuclear genes was identified in flowering plants (Nugent and existing genic material(Fig 3) Palmer 1991; Liu et al. 2009). Specifically, it was shown that mi- tochondrial g became relocated to the nuclear genome, De novo emergence of protein-coding probably via RNA intermediates (Nugent and Palmer 1991), The de novo origin of entire protein-coding genes was long con- forming chimeras with preexisting nuclear genes. Notably, in sidered to be highly unlikely. For instance in agreement with his many cases the ancestral nuclear genes provided targeting signals contemporary gene duplication advocates, Frangois Jacob noted in for import of the mitochondrion-derived protein back into mito- an influential essay that the"probability that a functional protein chondria(Liu et al. 2009). Thus, this type of gene fusion readily would appear de novo by random association of amino acids is allowed for transfer of mitochondrial genes into the nucleus while practically zero"and that therefore the"creation of entirely new mitochondrial functions could be maintained nucleotide sequence could not be of any importance in the pro- duction of new information"Jacob 1977) Transcription-mediated gene fusions In spite of these notions, recent work has uncovered a number of new protein-coding genes that apparently arose from previously In addition to the genome-based juxtapositions and "permanent. noncoding (and nonrepetitive) DNA sequences. Probably the first exons from independent consecutive genes in the genome at the gene family that emerged in an Old World primate ancestor transcription level by intergenic splicing(Fig 2B). Given that this Johnson et al. 2001). Although the details regarding the emer- mechanism draws from exons of preexisting genes, it does not gence of the original coding sequence remain unclear, the lack of nteresting to discuss here, given that it gives rise to new tran. johnson et a. (2001) revealed that the ancestor of this gene family times be fixed as new genes in the genome through secondary massively expanded by segmental duplication in hominoids, and that the various morpheus gene copies show spectacular signatures cents(see below). Transcription-mediated gene fusion was long of positive selection in their coding sequences, suggestive of ex- ought to be exceedingly rare, but after the discovery of in- ceedingly high rates of adaptive protein evolution. Although the genome-wide surveys unearthed large numbers of transcription. determined, the strong selective pressures associated with their et al. 2007). Notably, many of these chimeras involve fusions of protein-coding exons from adjacent genes. But although their encoded proteins pression levels are sometimes relatively high(Denoeud et al Other studies have followed suit and have provided a more 2007)and individual characterizations suggest specific subcellular tailed picture of de novo gene origination. For example, 14 de lovO-originated genes have been identified in Drosophila(Levine localizations of encoded products with respect to the proteins et al. 2006: Zhou et al. 2008), the majority of which are specifically encoded by the involved partner genes(Thomson et al. 2000 Pradet-Balade et al. 2002), the functional and evolutionary po- tential of these fused transcripts remains to be explored. Also, their evolutionary origin(presumably through the emergence and fix ation of intergenic splice sites)and level of selective preservation Proto ORF with frame disruptions etween species have yet to be documented. Interestingly, how- ver, at least one of the transcription-induced chimeric mRNAs was Mutations abolish frame disruptions shown to have become fixed in the genome during evolution as a separate new gene through the process of retroposition(Fig 2B Akiva et al. 2006). Babushok et al.(2007) showed that this new tact proto- ORF retrogene(termed PIP5K1A)emerged in the common hominoid ancestor, became specifically expressed in testes, experienc Promoter acquisition and transcriptional activation itive selection, and shows significant affinity for cellular ubiquitinated proteins(reflecting a modified activity of one of the parental proteins), which suggests a new and beneficial functional role of the encoded protein in apes Origin of protein-coding genes from scratch. New coding Gene origination from scratch en reading frames (proto-ORFs: thin blue bars) acquire muta- As noted above, the origin of new genes was long believed to ntimately linked to the process of gene duplication(Ohno 1970). activation of ORFs(through acquisition of promoters located in the Consistent with this notion(and as discussed in this review), new 5'flanking region) genes were usually found to be associated with duplicated genomic ing genes(Large blue n,(pink right-angled arrow) TSS,(tra raw material in one way or another. Yet, what one would probably box untranslated ssequence. Note that the transcriptional activation intuitively associate with true gene"birth"and what could, argu- step may, alternatively, also precede the formation of complete fune ably, be considered the most intriguing mode(also because it onally relevant ORFs Genome Research 1319implications of the majority of these plant chimeric genes remain to be explored, an interesting class of functional chimeric genes that involve fusions of mitochondrial retroposed gene copies and nuclear genes was identified in flowering plants (Nugent and Palmer 1991; Liu et al. 2009). Specifically, it was shown that mi￾tochondrial genes became relocated to the nuclear genome, probably via RNA intermediates (Nugent and Palmer 1991), forming chimeras with preexisting nuclear genes. Notably, in many cases the ancestral nuclear genes provided targeting signals for import of the mitochondrion-derived protein back into mito￾chondria (Liu et al. 2009). Thus, this type of gene fusion readily allowed for transfer of mitochondrial genes into the nucleus while mitochondrial functions could be maintained. Transcription-mediated gene fusions In addition to the genome-based juxtapositions and ‘‘permanent’’ fusions of genes or gene fragments described above, recent work uncovered an alternative gene fusion mechanism that combines exons from independent consecutive genes in the genome at the transcription level by intergenic splicing (Fig. 2B). Given that this mechanism draws from exons of preexisting genes, it does not represent a true process of new gene formation, but is nevertheless interesting to discuss here, given that it gives rise to new tran￾scription units with potentially novel functions that may some￾times be fixed as new genes in the genome through secondary events (see below). Transcription-mediated gene fusion was long thought to be exceedingly rare, but after the discovery of in￾dividual cases early in the past decade (e.g., Thomson et al. 2000), genome-wide surveys unearthed large numbers of transcription￾induced chimeras (Akiva et al. 2006; Parra et al. 2006; Denoeud et al. 2007). Notably, many of these chimeras involve fusions of protein-coding exons from adjacent genes. But although their expression levels are sometimes relatively high (Denoeud et al. 2007) and individual characterizations suggest specific subcellular localizations of encoded products with respect to the proteins encoded by the involved partner genes (Thomson et al. 2000; Pradet-Balade et al. 2002), the functional and evolutionary po￾tential of these fused transcripts remains to be explored. Also, their evolutionary origin (presumably through the emergence and fix￾ation of intergenic splice sites) and level of selective preservation between species have yet to be documented. Interestingly, how￾ever, at least one of the transcription-induced chimeric mRNAs was shown to have become fixed in the genome during evolution as a separate new gene through the process of retroposition (Fig. 2B; Akiva et al. 2006). Babushok et al. (2007) showed that this new retrogene (termed PIP5K1A) emerged in the common hominoid ancestor, became specifically expressed in testes, experienced a phase of intense positive selection, and shows significant affinity for cellular ubiquitinated proteins (reflecting a modified activity of one of the parental proteins), which suggests a new and beneficial functional role of the encoded protein in apes. Gene origination from scratch As noted above, the origin of new genes was long believed to be intimately linked to the process of gene duplication (Ohno 1970). Consistent with this notion (and as discussed in this review), new genes were usually found to be associated with duplicated genomic raw material in one way or another. Yet, what one would probably intuitively associate with true gene ‘‘birth’’ and what could, argu￾ably, be considered the most intriguing mode (also because it is almost bound to provide a new function), is the emergence of new genes ‘‘from scratch.’’ In other words, new genes arise from pre￾viously nonfunctional genomic sequence, unrelated to any pre￾existing genic material (Fig. 3). De novo emergence of protein-coding genes The de novo origin of entire protein-coding genes was long con￾sidered to be highly unlikely. For instance, in agreement with his contemporary gene duplication advocates, Francxois Jacob noted in an influential essay that the ‘‘probability that a functional protein would appear de novo by random association of amino acids is practically zero’’ and that therefore the ‘‘creation of entirely new nucleotide sequence could not be of any importance in the pro￾duction of new information’’ (Jacob 1977). In spite of these notions, recent work has uncovered a number of new protein-coding genes that apparently arose from previously noncoding (and nonrepetitive) DNA sequences. Probably the first such case described in the literature is presented by the morpheus gene family that emerged in an Old World primate ancestor (Johnson et al. 2001). Although the details regarding the emer￾gence of the original coding sequence remain unclear, the lack of any corresponding orthologous sequences outside of Old World primates suggest a de novo origin for this gene family. Notably, Johnson et al. (2001) revealed that the ancestor of this gene family massively expanded by segmental duplication in hominoids, and that the various morpheus gene copies show spectacular signatures of positive selection in their coding sequences, suggestive of ex￾ceedingly high rates of adaptive protein evolution. Although the precise functional roles of the morpheus genes have not yet been determined, the strong selective pressures associated with their evolution suggest important and rapidly evolving functions of the encoded proteins in humans and apes. Other studies have followed suit and have provided a more detailed picture of de novo gene origination. For example, 14 de novo-originated genes have been identified in Drosophila (Levine et al. 2006; Zhou et al. 2008), the majority of which are specifically Figure 3. Origin of protein-coding genes from scratch. New coding regions may emerge de novo from noncoding genomic sequences. First, proto-open reading frames (proto-ORFs; thin blue bars) acquire muta￾tions (point substitutions, insertions/deletions; yellow stars) that remove, bit by bit, frame-disrupting nucleotides (red wedges). Transcriptional activation of ORFs (through acquisition of promoters located in the 59 flanking region) encoding proteins with potentially useful functions may allow for the evolution of novel protein-coding genes. (Large blue box) Functional exon, (pink right-angled arrow) TSS, (transparent pink box) untranslated 59 sequence. Note that the transcriptional activation step may, alternatively, also precede the formation of complete func￾tionally relevant ORFs. Evolution of new genes Genome Research 1319 www.genome.org Downloaded from genome.cshlp.org on June 20, 2011 - Published by Cold Spring Harbor Laboratory Press