Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin s... more Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.
APOBEC3 (A3) proteins are of considerable interest because most are potent DNA cytidine deaminase... more APOBEC3 (A3) proteins are of considerable interest because most are potent DNA cytidine deaminases that have the capacity to restrict the replication and/or edit the sequences of a wide variety of parasitic elements, including many retroviruses and retrotransposons (reviewed in references 5, 8-10, and 14). Likely substrates include (i) lentiviruses, such as human immunodeficiency virus type 1, human immunodeficiency virus type 2, simian immunodeficiency virus, maedi-visna virus, feline immunodeficiency virus, and equine infectious anemia virus; (ii) alpha-, beta-, gamma-, and deltaretroviruses, such as Rous sarcoma virus, Mason-Pfizer monkey virus or mouse mammary tumor virus, murine leukemia virus or feline leukemia virus, and human T-cell leukemia virus or bovine leukemia virus, respectively; (iii) spumaviruses, such as primate foamy virus and feline foamy virus; (iv) hepadnaviruses, such as hepatitis B virus; (v) endogenous retroviruses and long terminal repeat retrotransposons, such as human endogenous retrovirus K, murine intracisternal A particle, murine MusD, and porcine endogenous retrovirus; (vi) non-long terminal repeat retroposons, such as L1 and Alu; and (vii) DNA viruses, such as adenoassociated virus and human papillomavirus. Over the past few years, there has also been an increasing appreciation for the multiple, distinct mechanisms that parasitic elements use to coexist with the A3 proteins of their hosts. Together, these observations indicate that the evolution of the A3 proteins has been driven by a requirement to minimize the spread of exogenous and endogenous genetic threats. The likelihood that the A3 proteins might exist solely for this purpose has been supported recently by studies indicating that A3-deficient mice have no obvious phenotypes apart from a notable increase in susceptibility to retrovirus infection .
Sandler and Novitski first pointed out in 1957 that chromosomes could selfishly exploit meiotic a... more Sandler and Novitski first pointed out in 1957 that chromosomes could selfishly exploit meiotic asymmetries to maximize their own transmission, in a process termed 'meiotic drive'. However, since then, only post-meiotic processes of non-Mendelian inheritance have received serious scientific attention in studies of transmission distortion. A recent study by Fishman and Willis puts the focus squarely back on meiotic drive. They found completely biased transmission of a centromere-linked locus from an outcrossing Mimulus species over that from an inbred species, providing the first direct evidence that centromeres can act as general, powerful meiotic drivers. This study suggests that, although difficult to detect experimentally, female meiotic drive is a major evolutionary force in nature.
R1 and R2 retrotransposable elements are stable components of the 28S rRNA genes of arthropods. W... more R1 and R2 retrotransposable elements are stable components of the 28S rRNA genes of arthropods. While each retrotransposition event leads to incremental losses of rDNA unit expression, little is known about the selective consequences of these elements on the host genome. Previous reports suggested that in the abnormal abdomen (aa) phenotype of Drosophila mercatorum, high levels of rDNA insertions (R1) in conjunction with the under-replication locus (ur), enable the utilization of different ecological conditions via a population level shift to younger age. We have sequenced the R1 and R2 elements of D. mercatorum and show that the levels of R1-and R2-inserted rDNA units were inaccurately scored in the original studies of aa, leading to several misinterpretations. In particular, contrary to earlier reports, aa flies differentially underreplicate R1-and R2-inserted rDNA units, like other species of Drosophila. However, aa flies do not undergo the lower level of underreplication of their functional rDNA units (general underreplication) that is seen in wild-type strains. The lack of general underreplication is expected to confer a selective advantage and, thus, can be interpreted as an adaptation to overcome high levels of R1 and R2 insertions. These results allow us to reconcile some of the apparently contradictory effects of aa and the bobbed phenotype found in other species of Drosophila.
Ty3 is a gypsy-type, retrovirus-like element found in the budding yeast Saccharomyces cerevisiae.... more Ty3 is a gypsy-type, retrovirus-like element found in the budding yeast Saccharomyces cerevisiae. In cells overexpressing Ty3 under the GAL1 upstream activation sequence, Ty3 RNA, proteins, and DNA are made. Elucidation of the molecular masses and amino-terminal sequences of protease and reverse transcriptase indicated the existence of an additional intervening domain, designated J, in the Ty3 Gag3-Pol3p polyprotein. A region analogous to J can be found in many retrotransposable elements closely related to Ty3; however, J does not correspond to any of the highly conserved retroviral protein domains. Ty3 mutants deleted for the J-coding region showed moderately reduced transposition frequency but greatly reduced levels of Ty3 DNA. These results show that under galactose regulation, the Ty3 J domain is not absolutely essential.
Proceedings of the National Academy of Sciences of the United States of America, 1997
The ␣-and -karyopherins (Kaps), also called importins, mediate the nuclear transport of proteins... more The ␣-and -karyopherins (Kaps), also called importins, mediate the nuclear transport of proteins. All ␣-Kaps contain a central domain composed of eight approximately 40 amino acid, tandemly arranged, armadillolike (Arm) repeats. The number and order of these repeats have not changed since the common origin of fungi, plants, and mammals. Phylogenetic analysis suggests that the various ␣-Kaps fall into two groups, ␣1 and ␣2. Whereas animals encode both types, the yeast genome encodes only an ␣1-Kap. The -Kaps are characterized by 14-15 tandemly arranged HEAT motifs. We show that the Arm repeats of ␣-Kaps and the HEAT motifs of -Kaps are similar, suggesting that the ␣-Kaps and -Kaps (and for that matter, all Arm and HEAT repeat-containing proteins) are members of the same protein superfamily. Phylogenetic analysis indicates that there are at least three major groups of -Kaps, consistent with their proposed cargo specificities. We present a model in which an ␣-independent -Kap progenitor gave rise to the ␣-dependent -Kaps and the ␣-Kaps.
8 the hippocampus in vitro 1-3 . Although the mechanisms by which Dzȋ causes neuronal death are no... more 8 the hippocampus in vitro 1-3 . Although the mechanisms by which Dzȋ causes neuronal death are not fully understood, in vitro results suggest that an increase in oxidative stress and destabilization of calcium homeostasis 2,3 are involved.
Eukaryotic and prokaryotic genomes encode either Type I or Type II Ribonuclease H (RNH) which is ... more Eukaryotic and prokaryotic genomes encode either Type I or Type II Ribonuclease H (RNH) which is important for processing RNA primers that prime DNA replication in almost all organisms. This review highlights the important role that Type I RNH plays in the life cycle of many retroelements, and its utility in tracing early events in retroelement evolution. Many retroelements utilize host genome-encoded RNH, but several lineages of retroelements, including some non-LTR retroposons and all LTR retrotransposons, encode their own RNH domains. Examination of these RNH domains suggests that all LTR retrotransposons acquired an enzymatically weak RNH domain that is missing an important catalytic residue found in all other RNH enzymes. We propose that this reduced activity is essential to ensure correct processing of the poly-purine tract (PPT), which is an important step in the life cycle of these retrotransposons. Vertebrate retroviruses appear to have reacquired their RNH domains, which are catalytically more active, but their ancestral RNH domains (found in other LTR retrotransposons) have degenerated to give rise to the tether domains unique to vertebrate retroviruses. The tether domain may serve to control the more active RNH domain of vertebrate retroviruses. Phylogenetic analysis of the RNH domains is also useful to "date" the relative ages of LTR and non-LTR retroelements. It appears that all LTR retrotransposons are as old as, or younger than, the "youngest" lineages of non-LTR retroelements, suggesting that LTR retrotransposons arose late in eukaryotes.
Nucleocytoplasmic transport is a broadly conserved process across eukaryotes. Despite its essenti... more Nucleocytoplasmic transport is a broadly conserved process across eukaryotes. Despite its essential function and conserved mechanism, components of the nuclear transport apparatus have been implicated in genetic conflicts in Drosophila, especially in the male germ line. The best understood case is represented by a truncated RanGAP gene duplication that is part of the segregation distorter system in Drosophila melanogaster. Consistent with the hypothesis that the nuclear transport pathway is at the heart of mediating genetic conflicts, both nucleoporins and directionality imposing components of nuclear transport have previously been shown to evolve under positive selection. Here, we present a comprehensive phylogenomic analysis of importins (karyopherins) in Drosophila evolution. Importins are adaptor molecules that physically mediate the transport of cargo molecules and comprise the third component of the nuclear transport apparatus. We find that importins have been repeatedly gained and lost throughout various stages of Drosophila evolution, including two intriguing examples of an apparently coincident loss and gain of nonorthologous and noncanonical importin-a. Although there are a few signatures of episodic positive selection, genetic innovation in importin evolution is more evident in patterns of recurrent gene birth and loss specifically for function in Drosophila testes, which is consistent with their role in supporting host genomes defense against segregation distortion.
Progress in molecular and subcellular biology, 2009
Centromeres are far more complex and evolutionarily labile than expected based on their conserved... more Centromeres are far more complex and evolutionarily labile than expected based on their conserved, essential function. The rapid evolution of both centromeric DNA and proteins strongly argue that centromeres are locked in an evolutionary conflict to increase their odds of transmission during asymmetric (female) meiosis. Evolutionary success for “cheating” centromeres can result in highly deleterious consequences for the species, either in terms of skewed sex ratios or male sterility. Centromeric proteins evolve rapidly to suppress the deleterious effects of “centromere-drive.” This chapter summarizes the mounting evidence in favor of the centromere-drive model, and its implications for centromere evolution in taxa with variations in meiosis.
Centromere-drive is a process where centromeres compete for transmission through asymmetric "fema... more Centromere-drive is a process where centromeres compete for transmission through asymmetric "female" meiosis for inclusion into the oocyte. In symmetric "male" meiosis, all meiotic products form viable germ cells. Therefore, the primary incentive for centromere-drive, a potential transmission bias, is believed to be missing from male meiosis. In this article, we consider whether male meiosis also bears the primary cost of centromere-drive. Because different taxa carry out different combinations of meiotic programs (symmetric + asymmetric, symmetric only, asymmetric only), it is possible to consider the evolutionary consequences of centromere-drive in the context of these differing systems. Groups with both types of meiosis have large, rapidly evolving centromeric regions, and their centromeric histones (CenH3s) have been shown to evolve under positive selection, suggesting roles as suppressors of centromere-drive. In contrast, taxa with only symmetric male meiosis have shown no evidence of positive selection in their centromeric histones. In this article, we present the first evolutionary analysis of centromeric histones in ciliated protozoans, a group that only undergoes asymmetric "female" meiosis. We find no evidence of positive selection acting on CNA1, the CenH3 of Tetrahymena species. Cytological observations of a panel of Tetrahymena species are consistent with dynamic karyotype evolution in this lineage. Our findings suggest that defects in male meiosis, and not mitosis or female meiosis, are the primary selective force behind centromere-drive suppression. Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive.
Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous de... more Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous defense against viral infections. Viral recognition determinants in intrinsic immunity genes are expected to evolve rapidly as host genes adapt to changing viruses, resulting in a signature of adaptive evolution. Zinc-finger antiviral protein (ZAP) from rats was discovered to be an intrinsic immunity gene that can restrict murine leukemia virus, and certain alphaviruses and filoviruses. Here, we used an approach combining molecular evolution and cellular infectivity assays to address whether ZAP also acts as a restriction factor in primates, and to pinpoint which protein domains may directly interact with the virus. We find that ZAP has evolved under positive selection throughout primate evolution. Recurrent positive selection is only found in the poly(ADP-ribose) polymerase (PARP)-like domain present in a longer human ZAP isoform. This PARP-like domain was not present in the previously identified and tested rat ZAP gene. Using infectivity assays, we found that the longer isoform of ZAP that contains the PARP-like domain is a stronger suppressor of murine leukemia virus expression and Semliki forest virus infection. Our study thus finds that human ZAP encodes a potent antiviral activity against alphaviruses. The striking congruence between our evolutionary predictions and cellular infectivity assays strongly validates such a combined approach to study intrinsic immunity genes. Citation: Kerns JA, Emerman M, Malik HS (2008) Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein. PLoS Genet 4(1): e21.
Proceedings of the National Academy of Sciences of the United States of America, 2005
Primate genomes encode a variety of innate immune strategies to defend themselves against retrovi... more Primate genomes encode a variety of innate immune strategies to defend themselves against retroviruses. One of these, TRIM5␣, can restrict diverse retroviruses in a species-specific manner. Thus, whereas rhesus TRIM5␣ can strongly restrict HIV-1, human TRIM5␣ only has weak HIV-1 restriction. The biology of TRIM5␣ restriction suggests that it is locked in an antagonistic conflict with the proteins encoding the viral capsid. Such antagonistic interactions frequently result in rapid amino acid replacements at the proteinprotein interface, as each genetic entity vies for evolutionary dominance. By analyzing its evolutionary history, we find strong evidence for ancient positive selection in the primate TRIM5␣ gene. This selection is strikingly variable with some of the strongest selection occurring in the human lineage. This history suggests that TRIM5␣ evolution has been driven by antagonistic interactions with a wide variety of viruses and endogenous retroviruses that predate the origin of primate lentiviruses. A 13-aa ''patch'' in the SPRY protein domain bears a dense concentration of positively selected residues, potentially implicating it as an antiviral interface. By using functional studies of chimeric TRIM5␣ genes, we show that this patch is generally essential for retroviral restriction and is responsible for most of the species-specific antiretroviral restriction activity. Our study highlights the power of evolutionary analyses, in which positive selection identifies not only the age of genetic conflict but also the interaction interface where this conflict plays out.
The ability to mount an interferon response on sensing viral infection is a critical component of... more The ability to mount an interferon response on sensing viral infection is a critical component of mammalian innate immunity. Several viruses directly antagonize viral sensing pathways to block activation of the host immune response. Here, we show that recurrent viral antagonism has shaped the evolution of the host protein MAVS-a crucial component of the viral-sensing pathway in primates. From sequencing and phylogenetic analyses of MAVS from 21 simian primates, we found that MAVS has evolved under strong positive selection. We focused on how this positive selection has shaped MAVS' susceptibility to Hepatitis C virus (HCV). We functionally tested MAVS proteins from diverse primate species for their ability to resist antagonism by HCV, which uses its protease NS3/4A to cleave human MAVS. We found that MAVS from multiple primates are resistant to inhibition by the HCV protease. This resistance maps to single changes within the protease cleavage site in MAVS, which protect MAVS from getting cleaved by the HCV protease. Remarkably, most of these changes have been independently acquired at a single residue 506 that evolved under positive selection. We show that ''escape'' mutations lower affinity of the NS3 protease for MAVS and allow it to better restrict HCV replication. We further show that NS3 proteases from all other primate hepaciviruses, including the highly divergent GBV-A and GBV-C viruses, are functionally similar to HCV. We conclude that convergent evolution at residue 506 in multiple primates has resulted in escape from antagonism by hepaciviruses. Our study provides a model whereby insights into the ancient history of viral infections in primates can be gained using extant host and virus genes. Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV.
Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin s... more Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.
APOBEC3 (A3) proteins are of considerable interest because most are potent DNA cytidine deaminase... more APOBEC3 (A3) proteins are of considerable interest because most are potent DNA cytidine deaminases that have the capacity to restrict the replication and/or edit the sequences of a wide variety of parasitic elements, including many retroviruses and retrotransposons (reviewed in references 5, 8-10, and 14). Likely substrates include (i) lentiviruses, such as human immunodeficiency virus type 1, human immunodeficiency virus type 2, simian immunodeficiency virus, maedi-visna virus, feline immunodeficiency virus, and equine infectious anemia virus; (ii) alpha-, beta-, gamma-, and deltaretroviruses, such as Rous sarcoma virus, Mason-Pfizer monkey virus or mouse mammary tumor virus, murine leukemia virus or feline leukemia virus, and human T-cell leukemia virus or bovine leukemia virus, respectively; (iii) spumaviruses, such as primate foamy virus and feline foamy virus; (iv) hepadnaviruses, such as hepatitis B virus; (v) endogenous retroviruses and long terminal repeat retrotransposons, such as human endogenous retrovirus K, murine intracisternal A particle, murine MusD, and porcine endogenous retrovirus; (vi) non-long terminal repeat retroposons, such as L1 and Alu; and (vii) DNA viruses, such as adenoassociated virus and human papillomavirus. Over the past few years, there has also been an increasing appreciation for the multiple, distinct mechanisms that parasitic elements use to coexist with the A3 proteins of their hosts. Together, these observations indicate that the evolution of the A3 proteins has been driven by a requirement to minimize the spread of exogenous and endogenous genetic threats. The likelihood that the A3 proteins might exist solely for this purpose has been supported recently by studies indicating that A3-deficient mice have no obvious phenotypes apart from a notable increase in susceptibility to retrovirus infection .
Sandler and Novitski first pointed out in 1957 that chromosomes could selfishly exploit meiotic a... more Sandler and Novitski first pointed out in 1957 that chromosomes could selfishly exploit meiotic asymmetries to maximize their own transmission, in a process termed 'meiotic drive'. However, since then, only post-meiotic processes of non-Mendelian inheritance have received serious scientific attention in studies of transmission distortion. A recent study by Fishman and Willis puts the focus squarely back on meiotic drive. They found completely biased transmission of a centromere-linked locus from an outcrossing Mimulus species over that from an inbred species, providing the first direct evidence that centromeres can act as general, powerful meiotic drivers. This study suggests that, although difficult to detect experimentally, female meiotic drive is a major evolutionary force in nature.
R1 and R2 retrotransposable elements are stable components of the 28S rRNA genes of arthropods. W... more R1 and R2 retrotransposable elements are stable components of the 28S rRNA genes of arthropods. While each retrotransposition event leads to incremental losses of rDNA unit expression, little is known about the selective consequences of these elements on the host genome. Previous reports suggested that in the abnormal abdomen (aa) phenotype of Drosophila mercatorum, high levels of rDNA insertions (R1) in conjunction with the under-replication locus (ur), enable the utilization of different ecological conditions via a population level shift to younger age. We have sequenced the R1 and R2 elements of D. mercatorum and show that the levels of R1-and R2-inserted rDNA units were inaccurately scored in the original studies of aa, leading to several misinterpretations. In particular, contrary to earlier reports, aa flies differentially underreplicate R1-and R2-inserted rDNA units, like other species of Drosophila. However, aa flies do not undergo the lower level of underreplication of their functional rDNA units (general underreplication) that is seen in wild-type strains. The lack of general underreplication is expected to confer a selective advantage and, thus, can be interpreted as an adaptation to overcome high levels of R1 and R2 insertions. These results allow us to reconcile some of the apparently contradictory effects of aa and the bobbed phenotype found in other species of Drosophila.
Ty3 is a gypsy-type, retrovirus-like element found in the budding yeast Saccharomyces cerevisiae.... more Ty3 is a gypsy-type, retrovirus-like element found in the budding yeast Saccharomyces cerevisiae. In cells overexpressing Ty3 under the GAL1 upstream activation sequence, Ty3 RNA, proteins, and DNA are made. Elucidation of the molecular masses and amino-terminal sequences of protease and reverse transcriptase indicated the existence of an additional intervening domain, designated J, in the Ty3 Gag3-Pol3p polyprotein. A region analogous to J can be found in many retrotransposable elements closely related to Ty3; however, J does not correspond to any of the highly conserved retroviral protein domains. Ty3 mutants deleted for the J-coding region showed moderately reduced transposition frequency but greatly reduced levels of Ty3 DNA. These results show that under galactose regulation, the Ty3 J domain is not absolutely essential.
Proceedings of the National Academy of Sciences of the United States of America, 1997
The ␣-and -karyopherins (Kaps), also called importins, mediate the nuclear transport of proteins... more The ␣-and -karyopherins (Kaps), also called importins, mediate the nuclear transport of proteins. All ␣-Kaps contain a central domain composed of eight approximately 40 amino acid, tandemly arranged, armadillolike (Arm) repeats. The number and order of these repeats have not changed since the common origin of fungi, plants, and mammals. Phylogenetic analysis suggests that the various ␣-Kaps fall into two groups, ␣1 and ␣2. Whereas animals encode both types, the yeast genome encodes only an ␣1-Kap. The -Kaps are characterized by 14-15 tandemly arranged HEAT motifs. We show that the Arm repeats of ␣-Kaps and the HEAT motifs of -Kaps are similar, suggesting that the ␣-Kaps and -Kaps (and for that matter, all Arm and HEAT repeat-containing proteins) are members of the same protein superfamily. Phylogenetic analysis indicates that there are at least three major groups of -Kaps, consistent with their proposed cargo specificities. We present a model in which an ␣-independent -Kap progenitor gave rise to the ␣-dependent -Kaps and the ␣-Kaps.
8 the hippocampus in vitro 1-3 . Although the mechanisms by which Dzȋ causes neuronal death are no... more 8 the hippocampus in vitro 1-3 . Although the mechanisms by which Dzȋ causes neuronal death are not fully understood, in vitro results suggest that an increase in oxidative stress and destabilization of calcium homeostasis 2,3 are involved.
Eukaryotic and prokaryotic genomes encode either Type I or Type II Ribonuclease H (RNH) which is ... more Eukaryotic and prokaryotic genomes encode either Type I or Type II Ribonuclease H (RNH) which is important for processing RNA primers that prime DNA replication in almost all organisms. This review highlights the important role that Type I RNH plays in the life cycle of many retroelements, and its utility in tracing early events in retroelement evolution. Many retroelements utilize host genome-encoded RNH, but several lineages of retroelements, including some non-LTR retroposons and all LTR retrotransposons, encode their own RNH domains. Examination of these RNH domains suggests that all LTR retrotransposons acquired an enzymatically weak RNH domain that is missing an important catalytic residue found in all other RNH enzymes. We propose that this reduced activity is essential to ensure correct processing of the poly-purine tract (PPT), which is an important step in the life cycle of these retrotransposons. Vertebrate retroviruses appear to have reacquired their RNH domains, which are catalytically more active, but their ancestral RNH domains (found in other LTR retrotransposons) have degenerated to give rise to the tether domains unique to vertebrate retroviruses. The tether domain may serve to control the more active RNH domain of vertebrate retroviruses. Phylogenetic analysis of the RNH domains is also useful to "date" the relative ages of LTR and non-LTR retroelements. It appears that all LTR retrotransposons are as old as, or younger than, the "youngest" lineages of non-LTR retroelements, suggesting that LTR retrotransposons arose late in eukaryotes.
Nucleocytoplasmic transport is a broadly conserved process across eukaryotes. Despite its essenti... more Nucleocytoplasmic transport is a broadly conserved process across eukaryotes. Despite its essential function and conserved mechanism, components of the nuclear transport apparatus have been implicated in genetic conflicts in Drosophila, especially in the male germ line. The best understood case is represented by a truncated RanGAP gene duplication that is part of the segregation distorter system in Drosophila melanogaster. Consistent with the hypothesis that the nuclear transport pathway is at the heart of mediating genetic conflicts, both nucleoporins and directionality imposing components of nuclear transport have previously been shown to evolve under positive selection. Here, we present a comprehensive phylogenomic analysis of importins (karyopherins) in Drosophila evolution. Importins are adaptor molecules that physically mediate the transport of cargo molecules and comprise the third component of the nuclear transport apparatus. We find that importins have been repeatedly gained and lost throughout various stages of Drosophila evolution, including two intriguing examples of an apparently coincident loss and gain of nonorthologous and noncanonical importin-a. Although there are a few signatures of episodic positive selection, genetic innovation in importin evolution is more evident in patterns of recurrent gene birth and loss specifically for function in Drosophila testes, which is consistent with their role in supporting host genomes defense against segregation distortion.
Progress in molecular and subcellular biology, 2009
Centromeres are far more complex and evolutionarily labile than expected based on their conserved... more Centromeres are far more complex and evolutionarily labile than expected based on their conserved, essential function. The rapid evolution of both centromeric DNA and proteins strongly argue that centromeres are locked in an evolutionary conflict to increase their odds of transmission during asymmetric (female) meiosis. Evolutionary success for “cheating” centromeres can result in highly deleterious consequences for the species, either in terms of skewed sex ratios or male sterility. Centromeric proteins evolve rapidly to suppress the deleterious effects of “centromere-drive.” This chapter summarizes the mounting evidence in favor of the centromere-drive model, and its implications for centromere evolution in taxa with variations in meiosis.
Centromere-drive is a process where centromeres compete for transmission through asymmetric "fema... more Centromere-drive is a process where centromeres compete for transmission through asymmetric "female" meiosis for inclusion into the oocyte. In symmetric "male" meiosis, all meiotic products form viable germ cells. Therefore, the primary incentive for centromere-drive, a potential transmission bias, is believed to be missing from male meiosis. In this article, we consider whether male meiosis also bears the primary cost of centromere-drive. Because different taxa carry out different combinations of meiotic programs (symmetric + asymmetric, symmetric only, asymmetric only), it is possible to consider the evolutionary consequences of centromere-drive in the context of these differing systems. Groups with both types of meiosis have large, rapidly evolving centromeric regions, and their centromeric histones (CenH3s) have been shown to evolve under positive selection, suggesting roles as suppressors of centromere-drive. In contrast, taxa with only symmetric male meiosis have shown no evidence of positive selection in their centromeric histones. In this article, we present the first evolutionary analysis of centromeric histones in ciliated protozoans, a group that only undergoes asymmetric "female" meiosis. We find no evidence of positive selection acting on CNA1, the CenH3 of Tetrahymena species. Cytological observations of a panel of Tetrahymena species are consistent with dynamic karyotype evolution in this lineage. Our findings suggest that defects in male meiosis, and not mitosis or female meiosis, are the primary selective force behind centromere-drive suppression. Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive.
Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous de... more Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous defense against viral infections. Viral recognition determinants in intrinsic immunity genes are expected to evolve rapidly as host genes adapt to changing viruses, resulting in a signature of adaptive evolution. Zinc-finger antiviral protein (ZAP) from rats was discovered to be an intrinsic immunity gene that can restrict murine leukemia virus, and certain alphaviruses and filoviruses. Here, we used an approach combining molecular evolution and cellular infectivity assays to address whether ZAP also acts as a restriction factor in primates, and to pinpoint which protein domains may directly interact with the virus. We find that ZAP has evolved under positive selection throughout primate evolution. Recurrent positive selection is only found in the poly(ADP-ribose) polymerase (PARP)-like domain present in a longer human ZAP isoform. This PARP-like domain was not present in the previously identified and tested rat ZAP gene. Using infectivity assays, we found that the longer isoform of ZAP that contains the PARP-like domain is a stronger suppressor of murine leukemia virus expression and Semliki forest virus infection. Our study thus finds that human ZAP encodes a potent antiviral activity against alphaviruses. The striking congruence between our evolutionary predictions and cellular infectivity assays strongly validates such a combined approach to study intrinsic immunity genes. Citation: Kerns JA, Emerman M, Malik HS (2008) Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein. PLoS Genet 4(1): e21.
Proceedings of the National Academy of Sciences of the United States of America, 2005
Primate genomes encode a variety of innate immune strategies to defend themselves against retrovi... more Primate genomes encode a variety of innate immune strategies to defend themselves against retroviruses. One of these, TRIM5␣, can restrict diverse retroviruses in a species-specific manner. Thus, whereas rhesus TRIM5␣ can strongly restrict HIV-1, human TRIM5␣ only has weak HIV-1 restriction. The biology of TRIM5␣ restriction suggests that it is locked in an antagonistic conflict with the proteins encoding the viral capsid. Such antagonistic interactions frequently result in rapid amino acid replacements at the proteinprotein interface, as each genetic entity vies for evolutionary dominance. By analyzing its evolutionary history, we find strong evidence for ancient positive selection in the primate TRIM5␣ gene. This selection is strikingly variable with some of the strongest selection occurring in the human lineage. This history suggests that TRIM5␣ evolution has been driven by antagonistic interactions with a wide variety of viruses and endogenous retroviruses that predate the origin of primate lentiviruses. A 13-aa ''patch'' in the SPRY protein domain bears a dense concentration of positively selected residues, potentially implicating it as an antiviral interface. By using functional studies of chimeric TRIM5␣ genes, we show that this patch is generally essential for retroviral restriction and is responsible for most of the species-specific antiretroviral restriction activity. Our study highlights the power of evolutionary analyses, in which positive selection identifies not only the age of genetic conflict but also the interaction interface where this conflict plays out.
The ability to mount an interferon response on sensing viral infection is a critical component of... more The ability to mount an interferon response on sensing viral infection is a critical component of mammalian innate immunity. Several viruses directly antagonize viral sensing pathways to block activation of the host immune response. Here, we show that recurrent viral antagonism has shaped the evolution of the host protein MAVS-a crucial component of the viral-sensing pathway in primates. From sequencing and phylogenetic analyses of MAVS from 21 simian primates, we found that MAVS has evolved under strong positive selection. We focused on how this positive selection has shaped MAVS' susceptibility to Hepatitis C virus (HCV). We functionally tested MAVS proteins from diverse primate species for their ability to resist antagonism by HCV, which uses its protease NS3/4A to cleave human MAVS. We found that MAVS from multiple primates are resistant to inhibition by the HCV protease. This resistance maps to single changes within the protease cleavage site in MAVS, which protect MAVS from getting cleaved by the HCV protease. Remarkably, most of these changes have been independently acquired at a single residue 506 that evolved under positive selection. We show that ''escape'' mutations lower affinity of the NS3 protease for MAVS and allow it to better restrict HCV replication. We further show that NS3 proteases from all other primate hepaciviruses, including the highly divergent GBV-A and GBV-C viruses, are functionally similar to HCV. We conclude that convergent evolution at residue 506 in multiple primates has resulted in escape from antagonism by hepaciviruses. Our study provides a model whereby insights into the ancient history of viral infections in primates can be gained using extant host and virus genes. Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV.
Uploads
Papers by Harmit Malik