- Email: [email protected]
Symbiont Genes in Host Genomes: Fragments with a Future?
Cell Host & Microbe
Previews (Mitsiades et al., 2001), it will be important to determine whether epithelialmesenchymal signaling is involved in the survival phenotype reported by Mimuro et al. and others. The present study by Mimuro and colleagues has enhanced our understanding of the complex and active interplay that occurs between H. pylori and epithelial cells. However, it is clear that there are still many viable questions regarding the biology of H. pylori and mechanisms by which this bacterium is able to manipulate the highly regulated organization of the gastric epithelium, which over time can promote the progression from normal gastric mucosa to gastric adenocarcinoma.
REFERENCES Blaser, M.J., Perez-Perez, G.I., Kleanthous, H., Cover, T.L., Peek, R.M., Chyou, P.H., Stemmermann, G.N., and Nomura, A. (1995). Cancer Res. 55, 2111–2115.
Mimuro, H., Suzuki, T., Nagai, S., Rieder, G., Suzuki, M., Nagai, T., Fujita, Y., Nagamatsu, K., Ishijima, N., Koyasu, S., et al. (2007). Cell Host & Microbe 2, this issue, 250–263.
Craig, R.W. (2002). Leukemia 16, 444–454.
Mitsiades, N., Yu, W.H., Poulaki, V., Tsokos, M., and Stamenkovic, I. (2001). Cancer Res. 61, 577–581.
Crawford, H.C., Krishna, U.S., Israel, D.A., Matrisian, L.M., Washington, M.K., and Peek, R.M., Jr. (2003). Gastroenterology 125, 1125–1136.
Nagase, H., and Woessner, J.F., Jr. (1999). J. Biol. Chem. 274, 21491–21494.
Karam, S., and Leblond, C.P. (1995). Microsc. Res. Tech. 31, 193–214.
Peek, R.M., Jr., and Crabtree, J.E. (2006). J. Pathol. 208, 233–248.
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S.W., et al. (2007). Nature 445, 915–918.
Varro, A., Kenny, S., Hemers, E., McCaig, C., Przemeck, S., Wang, T.C., Bodger, K., and Pritchard, D.M. (2007). Am. J. Physiol. Gastrointest. Liver Physiol. 292, G1133–G1140.
McCaig, C., Duval, C., Hemers, E., Steele, I., Pritchard, D.M., Przemeck, S., Dimaline, R., Ahmed, S., Bodger, K., Kerrigan, D.D., et al. (2006). Gastroenterology 130, 1754–1763.
Wroblewski, L.E., Noble, P.J., Pagliocca, A., Pritchard, D.M., Hart, C.A., Campbell, F., Dodson, A.R., Dockray, G.J., and Varro, A. (2003). J. Cell Sci. 116, 3017–3026.
Symbiont Genes in Host Genomes: Fragments with a Future? Mark Blaxter1,* 1Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, King’s Buildings, University of Edinburgh, West Mains Road, Edinburgh, Scotland EH9 3JT, UK *Correspondence: [email protected] DOI 10.1016/j.chom.2007.09.008
While lateral transfer is the rule in the evolutionary history of bacterial and archaeal genes, events of transfer from prokaryotes to eukaryotes are rare. Germline-transmitted animal symbionts, such as Wolbachia pipientis, are well placed to participate in such transfers. In a recent issue of Science, Dunning Hotopp et al. identified instances of transfer of Wolbachia DNA to host genomes. It is unknown whether these transfers represent innovation in animal evolution.
Lateral gene transfer (LGT; also known as horizontal gene transfer) is a major feature of bacterial and archaeal genome evolution. Through this mechanism, lineages can acquire important functions wholesale from other lineages, and thus improve their relative fitness. While LGT has an ancient history in prokaryotes, it is an ongoing process, as evidenced by the emergence of drug-resistant pathogens in human communities. In contrast, lateral gene transfer in eukaryotes appears to be rare. For animals, the early segregation of germline cells in development is likely to make LGT events
rarer than in eukaryotes without a segregated germline. One textbook example, the acquisition of cellulase genes by termites from a bacterial source, has recently been shown to be erroneous (Davison and Blaxter, 2005), and initial excitement about ‘‘bugs in our genome’’ from the initial analysis of the human genome (Lander et al., 2001) has evaporated, as these genes have been shown to be present in other eukaryotes and thus more probably part of the core eukaryote genome (Salzberg et al., 2001). Is LGT a significant, ongoing process in animal genomes?
Animals can be infected with germline-transmitted symbionts, and these bacterial genomes are thus in just the right position to be donors in LGT events. There are several groups of animal germline symbionts, and the best studied are the a-proteobacterial Wolbachia parasites of arthropods and nematodes. First discovered in mosquitoes, Wolbachia pipientis induces a range of reproductive manipulation phenotypes in infected hosts (such as mating type incompatibility, feminization of genetic males, and induction of parthenogenesis) that increase the relative fitness of the host, and thus
Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc. 211
Cell Host & Microbe
Previews
Figure 1. The Fate of Laterally Transferred Genes A DNA fragment laterally transferred from an intracellular germline symbiont to the nucleus of an eukaryotic cell (top) can either be degraded by neutral mutation, and play no significant part in the evolution of the eukaryotic host genome (left), or become integrated into the host genome and provide a novel function (right) by acquiring eukaryotic promoter elements and RNA processing signals. The Wolbachia insertions thus far described fit the left-hand model, while the rhizosphere bacterial genes acquired by plant parasitic nematodes fit the right-hand model. The images below represent Drosophila melanogaster, the filarial nematode Brugia malayi, and a cartoon of a transmission electron micrograph of a Meloidogyne sp. nematode within a root showing the feeding stylet (in the center) used to penetrate cell walls with the aid of laterally transferred gene products.
the fitness of its germline parasite. Many arthropod species are infected, mostly hexapods, but also chelicerates and crustaceans. In the 1990s it emerged that Wolbachia germline symbionts were also present in a restricted group of parasitic nematodes, the filaria (including major human parasites such as those causing river blindness and elephantiasis). In these nematodes, the Wolbachia have what appears to be a mutualistic relationship with their hosts (Fenn and Blaxter, 2004).
In a recent issue of Science, Dunning Hotopp et al. (2007) built on two previous reports of the presence of Wolbachia-derived DNA sequences in a beetle (Kondo et al., 2002) and a filarial nematode (Fenn et al., 2006), by screening whole-genome shotgun data from a wide range of nematodes and arthropods for signs of nuclear insertions of Wolbachia DNA. In the genomes of 23 insects, one tick, and two nematodes they found evidence for 22 insertions in five species. The insertions were verified by reamplifica-
212 Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc.
tion and sequencing from genomic DNA, and in the case of a large insertion in the fruit fly Drosophila ananasse by in situ hybridization to the nuclear chromosome. All of the species in which insertions were found were known to be infected with Wolbachia. Six arthropods known to carry Wolbachia had no insertions. In addition, fragments of Wolbachia DNA were identified in introns of a previously sequenced gene from a filarial nematode. Thus, infected animals can carry fragments, sometimes large fragments, of Wolbachia DNA in their nuclear genomes. Is this significant in evolutionary terms? An LGT with evolutionary significance would show two features: (1) longevity and (2) integration into the host’s biology. These Wolbachia insertions do not display either feature. There is no evidence of maintenance over long evolutionary periods. The arthropod insertions all have high identity to extant Wolbachia genomes, suggesting very recent insertion. In contrast, the nematode insertions are different from extant Wolbachia but have accumulated many mutations rendering them nonfunctional (Fenn et al., 2006). Many of the arthropod junctional fragments derive from insertion of Drosophila transposons, a pattern also suggestive of nonfunctional DNA. In addition, if this process was important in the evolution of the hosts, we would expect to see Wolbachia-like genes in species that do not now have Wolbachia but did in the past, or insertions that are present in sister taxa following an insertion in an ancestral organism. Neither was observed. Integration into host biology remains to be demonstrated. Dunning Hotopp et al., in Wolbachia-cured but insertion-containing D. ananasse, identified RNA transcripts from 28 of 1208 genes in the Wolbachia genome (Dunning Hotopp et al., 2007), but whether these transcripts are translated and have biological meaning is unknown. Thus, the Wolbachia insertions resemble another well-described feature of animal genomes: the presence of nonfunctional fragments (or even complete copies) of mitochondrial genome DNA (Richly and Leister, 2004). These numts (nuclear mitochondrial fragments) are transients in the animal
Cell Host & Microbe
Previews genome, decaying by mutation to become yet more noncoding, nongenic DNA. It is likely that the Wolbachia insertions are just another flavor of numt-like elements, and interesting for their rarity rather than their evolutionary significance. Whether the Wolbachia insertions have been or will be evolutionarily significant remains to be proven. However, another group of nematodes provides examples of well-supported bacterial-animal LGT events that have demonstrable biological importance. Many tylenchid nematodes are parasites of plants and have a life cycle that includes migration and establishment of a permanent feeding site within the tissues of their hosts. To do this they modify plant cell walls and transform plant cells to make unique structures. These plant parasitic nematodes have been shown to secrete a range of plant cell wall degrading and modifying enzymes that appear to have a bacterial origin (Scholl et al., 2003; Smant et al., 1998). These glucanases and pectate lyases are not found in other animals, and the classes of enzymes
found in the nematodes are more like those of rhizosphere bacteria than of plants, and robustly cluster within clades of bacterial homologs in phylogenetic analyses. Examination of the genes encoding these enzymes shows that they have been integrated into the host: they have eukaryotic introns and produce capped mRNAs (Figure 1). They appear to be an ancient acquisition, as orthologous genes have been found in many related species of plant-parasitic nematodes (Scholl et al., 2003). The process has been continuing, as different groups of plant parasite have different suites of LGTacquired genes. Evolutionarily significant LGT from bacteria to animals has occurred and is likely ongoing.
Dunning Hotopp, J.C., Clark, M.E., Oliveira, D.C.S.G., Foster, J.M., Fischer, P., Torres, M.C.M., Giebel, J.D., Kumar, N., Ishmael, N., Wang, S., et al. (2007). Science 317, 1753– 1756. Published online Aug 30, 2007. 10. 1126/science.1142490. Fenn, K., and Blaxter, M. (2004). Trends Ecol. Evol. 19, 163–166. Fenn, K., Conlon, C., Jones, M., Quail, M.A., Holroyd, N.E., Parkhill, J., and Blaxter, M. (2006). PLoS Pathog. 2, e94. 10.1371/journal. ppat.0020094. Kondo, N., Nikoh, N., Ijichi, N., Shimada, M., and Fukatsu, T. (2002). Proc. Natl. Acad. Sci. USA 99, 14280–14285. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Nature 409, 860–921. Richly, E., and Leister, D. (2004). Mol. Biol. Evol. 21, 1081–1084. Salzberg, S.L., White, O., Peterson, J., and Eisen, J.A. (2001). Science 292, 1903– 1906.
ACKNOWLEDGMENTS Thanks to Graham Stone and Katelyn Fenn for critical comments.
REFERENCES Davison, A., and Blaxter, M. (2005). Mol. Biol. Evol. 22, 1273–1284.
Scholl, E.H., Thorne, J.L., McCarter, J.P., and Bird, D.M. (2003). Genome Biol. 4, R39. Smant, G., Stokkermans, J.P., Yan, Y., de Boer, J.M., Baum, T.J., Wang, X., Hussey, R.S., Gommers, F.J., Henrissat, B., Davis, E.L., et al. (1998). Proc. Natl. Acad. Sci. USA 95, 4906–4911.
Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc. 213
Previews (Mitsiades et al., 2001), it will be important to determine whether epithelialmesenchymal signaling is involved in the survival phenotype reported by Mimuro et al. and others. The present study by Mimuro and colleagues has enhanced our understanding of the complex and active interplay that occurs between H. pylori and epithelial cells. However, it is clear that there are still many viable questions regarding the biology of H. pylori and mechanisms by which this bacterium is able to manipulate the highly regulated organization of the gastric epithelium, which over time can promote the progression from normal gastric mucosa to gastric adenocarcinoma.
REFERENCES Blaser, M.J., Perez-Perez, G.I., Kleanthous, H., Cover, T.L., Peek, R.M., Chyou, P.H., Stemmermann, G.N., and Nomura, A. (1995). Cancer Res. 55, 2111–2115.
Mimuro, H., Suzuki, T., Nagai, S., Rieder, G., Suzuki, M., Nagai, T., Fujita, Y., Nagamatsu, K., Ishijima, N., Koyasu, S., et al. (2007). Cell Host & Microbe 2, this issue, 250–263.
Craig, R.W. (2002). Leukemia 16, 444–454.
Mitsiades, N., Yu, W.H., Poulaki, V., Tsokos, M., and Stamenkovic, I. (2001). Cancer Res. 61, 577–581.
Crawford, H.C., Krishna, U.S., Israel, D.A., Matrisian, L.M., Washington, M.K., and Peek, R.M., Jr. (2003). Gastroenterology 125, 1125–1136.
Nagase, H., and Woessner, J.F., Jr. (1999). J. Biol. Chem. 274, 21491–21494.
Karam, S., and Leblond, C.P. (1995). Microsc. Res. Tech. 31, 193–214.
Peek, R.M., Jr., and Crabtree, J.E. (2006). J. Pathol. 208, 233–248.
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S.W., et al. (2007). Nature 445, 915–918.
Varro, A., Kenny, S., Hemers, E., McCaig, C., Przemeck, S., Wang, T.C., Bodger, K., and Pritchard, D.M. (2007). Am. J. Physiol. Gastrointest. Liver Physiol. 292, G1133–G1140.
McCaig, C., Duval, C., Hemers, E., Steele, I., Pritchard, D.M., Przemeck, S., Dimaline, R., Ahmed, S., Bodger, K., Kerrigan, D.D., et al. (2006). Gastroenterology 130, 1754–1763.
Wroblewski, L.E., Noble, P.J., Pagliocca, A., Pritchard, D.M., Hart, C.A., Campbell, F., Dodson, A.R., Dockray, G.J., and Varro, A. (2003). J. Cell Sci. 116, 3017–3026.
Symbiont Genes in Host Genomes: Fragments with a Future? Mark Blaxter1,* 1Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, King’s Buildings, University of Edinburgh, West Mains Road, Edinburgh, Scotland EH9 3JT, UK *Correspondence: [email protected] DOI 10.1016/j.chom.2007.09.008
While lateral transfer is the rule in the evolutionary history of bacterial and archaeal genes, events of transfer from prokaryotes to eukaryotes are rare. Germline-transmitted animal symbionts, such as Wolbachia pipientis, are well placed to participate in such transfers. In a recent issue of Science, Dunning Hotopp et al. identified instances of transfer of Wolbachia DNA to host genomes. It is unknown whether these transfers represent innovation in animal evolution.
Lateral gene transfer (LGT; also known as horizontal gene transfer) is a major feature of bacterial and archaeal genome evolution. Through this mechanism, lineages can acquire important functions wholesale from other lineages, and thus improve their relative fitness. While LGT has an ancient history in prokaryotes, it is an ongoing process, as evidenced by the emergence of drug-resistant pathogens in human communities. In contrast, lateral gene transfer in eukaryotes appears to be rare. For animals, the early segregation of germline cells in development is likely to make LGT events
rarer than in eukaryotes without a segregated germline. One textbook example, the acquisition of cellulase genes by termites from a bacterial source, has recently been shown to be erroneous (Davison and Blaxter, 2005), and initial excitement about ‘‘bugs in our genome’’ from the initial analysis of the human genome (Lander et al., 2001) has evaporated, as these genes have been shown to be present in other eukaryotes and thus more probably part of the core eukaryote genome (Salzberg et al., 2001). Is LGT a significant, ongoing process in animal genomes?
Animals can be infected with germline-transmitted symbionts, and these bacterial genomes are thus in just the right position to be donors in LGT events. There are several groups of animal germline symbionts, and the best studied are the a-proteobacterial Wolbachia parasites of arthropods and nematodes. First discovered in mosquitoes, Wolbachia pipientis induces a range of reproductive manipulation phenotypes in infected hosts (such as mating type incompatibility, feminization of genetic males, and induction of parthenogenesis) that increase the relative fitness of the host, and thus
Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc. 211
Cell Host & Microbe
Previews
Figure 1. The Fate of Laterally Transferred Genes A DNA fragment laterally transferred from an intracellular germline symbiont to the nucleus of an eukaryotic cell (top) can either be degraded by neutral mutation, and play no significant part in the evolution of the eukaryotic host genome (left), or become integrated into the host genome and provide a novel function (right) by acquiring eukaryotic promoter elements and RNA processing signals. The Wolbachia insertions thus far described fit the left-hand model, while the rhizosphere bacterial genes acquired by plant parasitic nematodes fit the right-hand model. The images below represent Drosophila melanogaster, the filarial nematode Brugia malayi, and a cartoon of a transmission electron micrograph of a Meloidogyne sp. nematode within a root showing the feeding stylet (in the center) used to penetrate cell walls with the aid of laterally transferred gene products.
the fitness of its germline parasite. Many arthropod species are infected, mostly hexapods, but also chelicerates and crustaceans. In the 1990s it emerged that Wolbachia germline symbionts were also present in a restricted group of parasitic nematodes, the filaria (including major human parasites such as those causing river blindness and elephantiasis). In these nematodes, the Wolbachia have what appears to be a mutualistic relationship with their hosts (Fenn and Blaxter, 2004).
In a recent issue of Science, Dunning Hotopp et al. (2007) built on two previous reports of the presence of Wolbachia-derived DNA sequences in a beetle (Kondo et al., 2002) and a filarial nematode (Fenn et al., 2006), by screening whole-genome shotgun data from a wide range of nematodes and arthropods for signs of nuclear insertions of Wolbachia DNA. In the genomes of 23 insects, one tick, and two nematodes they found evidence for 22 insertions in five species. The insertions were verified by reamplifica-
212 Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc.
tion and sequencing from genomic DNA, and in the case of a large insertion in the fruit fly Drosophila ananasse by in situ hybridization to the nuclear chromosome. All of the species in which insertions were found were known to be infected with Wolbachia. Six arthropods known to carry Wolbachia had no insertions. In addition, fragments of Wolbachia DNA were identified in introns of a previously sequenced gene from a filarial nematode. Thus, infected animals can carry fragments, sometimes large fragments, of Wolbachia DNA in their nuclear genomes. Is this significant in evolutionary terms? An LGT with evolutionary significance would show two features: (1) longevity and (2) integration into the host’s biology. These Wolbachia insertions do not display either feature. There is no evidence of maintenance over long evolutionary periods. The arthropod insertions all have high identity to extant Wolbachia genomes, suggesting very recent insertion. In contrast, the nematode insertions are different from extant Wolbachia but have accumulated many mutations rendering them nonfunctional (Fenn et al., 2006). Many of the arthropod junctional fragments derive from insertion of Drosophila transposons, a pattern also suggestive of nonfunctional DNA. In addition, if this process was important in the evolution of the hosts, we would expect to see Wolbachia-like genes in species that do not now have Wolbachia but did in the past, or insertions that are present in sister taxa following an insertion in an ancestral organism. Neither was observed. Integration into host biology remains to be demonstrated. Dunning Hotopp et al., in Wolbachia-cured but insertion-containing D. ananasse, identified RNA transcripts from 28 of 1208 genes in the Wolbachia genome (Dunning Hotopp et al., 2007), but whether these transcripts are translated and have biological meaning is unknown. Thus, the Wolbachia insertions resemble another well-described feature of animal genomes: the presence of nonfunctional fragments (or even complete copies) of mitochondrial genome DNA (Richly and Leister, 2004). These numts (nuclear mitochondrial fragments) are transients in the animal
Cell Host & Microbe
Previews genome, decaying by mutation to become yet more noncoding, nongenic DNA. It is likely that the Wolbachia insertions are just another flavor of numt-like elements, and interesting for their rarity rather than their evolutionary significance. Whether the Wolbachia insertions have been or will be evolutionarily significant remains to be proven. However, another group of nematodes provides examples of well-supported bacterial-animal LGT events that have demonstrable biological importance. Many tylenchid nematodes are parasites of plants and have a life cycle that includes migration and establishment of a permanent feeding site within the tissues of their hosts. To do this they modify plant cell walls and transform plant cells to make unique structures. These plant parasitic nematodes have been shown to secrete a range of plant cell wall degrading and modifying enzymes that appear to have a bacterial origin (Scholl et al., 2003; Smant et al., 1998). These glucanases and pectate lyases are not found in other animals, and the classes of enzymes
found in the nematodes are more like those of rhizosphere bacteria than of plants, and robustly cluster within clades of bacterial homologs in phylogenetic analyses. Examination of the genes encoding these enzymes shows that they have been integrated into the host: they have eukaryotic introns and produce capped mRNAs (Figure 1). They appear to be an ancient acquisition, as orthologous genes have been found in many related species of plant-parasitic nematodes (Scholl et al., 2003). The process has been continuing, as different groups of plant parasite have different suites of LGTacquired genes. Evolutionarily significant LGT from bacteria to animals has occurred and is likely ongoing.
Dunning Hotopp, J.C., Clark, M.E., Oliveira, D.C.S.G., Foster, J.M., Fischer, P., Torres, M.C.M., Giebel, J.D., Kumar, N., Ishmael, N., Wang, S., et al. (2007). Science 317, 1753– 1756. Published online Aug 30, 2007. 10. 1126/science.1142490. Fenn, K., and Blaxter, M. (2004). Trends Ecol. Evol. 19, 163–166. Fenn, K., Conlon, C., Jones, M., Quail, M.A., Holroyd, N.E., Parkhill, J., and Blaxter, M. (2006). PLoS Pathog. 2, e94. 10.1371/journal. ppat.0020094. Kondo, N., Nikoh, N., Ijichi, N., Shimada, M., and Fukatsu, T. (2002). Proc. Natl. Acad. Sci. USA 99, 14280–14285. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Nature 409, 860–921. Richly, E., and Leister, D. (2004). Mol. Biol. Evol. 21, 1081–1084. Salzberg, S.L., White, O., Peterson, J., and Eisen, J.A. (2001). Science 292, 1903– 1906.
ACKNOWLEDGMENTS Thanks to Graham Stone and Katelyn Fenn for critical comments.
REFERENCES Davison, A., and Blaxter, M. (2005). Mol. Biol. Evol. 22, 1273–1284.
Scholl, E.H., Thorne, J.L., McCarter, J.P., and Bird, D.M. (2003). Genome Biol. 4, R39. Smant, G., Stokkermans, J.P., Yan, Y., de Boer, J.M., Baum, T.J., Wang, X., Hussey, R.S., Gommers, F.J., Henrissat, B., Davis, E.L., et al. (1998). Proc. Natl. Acad. Sci. USA 95, 4906–4911.
Cell Host & Microbe 2, October 2007 ª2007 Elsevier Inc. 213