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Venomous snakes are important subjects of study in evolution, ecology, and biomedicine. Many venomous snakes have alpha-neurotoxins (α-neurotoxins) in their venom. These toxins bind the alpha-1 nicotinic acetylcholine receptor (nAChR) at the neuromuscular junction, causing paralysis and asphyxia. Several venomous snakes and their predators have evolved resistance to α-neurotoxins. The resistance is conferred by steric hindrance from N-glycosylated asparagines at amino acids 187 or 189, by an arginine at position 187 that has been hypothesized to either electrostatically repulse positively charged neurotoxins or sterically interfere with α-neurotoxin binding, or proline replacements at positions 194 or 197 of the nAChR ligand-binding domain to inhibit α-neurotoxin binding through structural changes in the receptor. Here, we analyzed this domain in 148 vertebrate species, and assessed its amino acid sequences for resistance-associated mutations. Of these sequences, 89 were sequenced de novo. We find widespread convergent evolution of the N-glycosylation form of resistance in several taxa including venomous snakes and their lizard prey, but not in the snake-eating birds studied. We also document new lineages with the arginine form of inhibition. Using an in vivo assay in four species, we provide further evidence that N-glycosylation mutations reduce the toxicity of cobra venom. The nAChR is of crucial importance for normal neuromuscular function and is highly conserved throughout the vertebrates as a result. Our research shows that the evolution of α-neurotoxins in snakes may well have prompted arms races and mutations to this ancient receptor across a wide range of sympatric vertebrates. These findings underscore the inter-connectedness of the biosphere and the ripple effects that one adaption can have across global ecosystems.
Muzaffar A. Khan; Daniel Dashevsky; Harald Kerkkamp; Dušan Kordiš; Merijn A. G. De Bakker; Roel Wouters; Jory Van Thiel; Bianca Op Den Brouw; Freek J. Vonk; R. Manjunatha Kini; Jawad Nazir; Bryan G. Fry; Michael K. Richardson. Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates. Toxins 2020, 12, 638 .
AMA StyleMuzaffar A. Khan, Daniel Dashevsky, Harald Kerkkamp, Dušan Kordiš, Merijn A. G. De Bakker, Roel Wouters, Jory Van Thiel, Bianca Op Den Brouw, Freek J. Vonk, R. Manjunatha Kini, Jawad Nazir, Bryan G. Fry, Michael K. Richardson. Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates. Toxins. 2020; 12 (10):638.
Chicago/Turabian StyleMuzaffar A. Khan; Daniel Dashevsky; Harald Kerkkamp; Dušan Kordiš; Merijn A. G. De Bakker; Roel Wouters; Jory Van Thiel; Bianca Op Den Brouw; Freek J. Vonk; R. Manjunatha Kini; Jawad Nazir; Bryan G. Fry; Michael K. Richardson. 2020. "Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates." Toxins 12, no. 10: 638.
The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.
Sabina Ott Rutar; Dusan Kordis. Analysis of the RNA virome of basal hexapods. PeerJ 2020, 8, e8336 .
AMA StyleSabina Ott Rutar, Dusan Kordis. Analysis of the RNA virome of basal hexapods. PeerJ. 2020; 8 ():e8336.
Chicago/Turabian StyleSabina Ott Rutar; Dusan Kordis. 2020. "Analysis of the RNA virome of basal hexapods." PeerJ 8, no. : e8336.
The only hitherto known biological role of yeast Saccharomyces cerevisiae Tum1 protein is in the tRNA thiolation pathway. The mammalian homologue of the yeast TUM1 gene, the thiosulfate sulfurtransferase (a.k.a. rhodanese) Tst, has been proposed as an obesity-resistance and antidiabetic gene. To assess the role of Tum1 in cell metabolism and the putative functional connection between lipid metabolism and tRNA modification, we analysed evolutionary conservation of the rhodanese protein superfamily, investigated the role of Tum1 in lipid metabolism, and examined the phenotype of yeast strains expressing the mouse homologue of Tum1, TST. We analysed evolutionary relationships in the rhodanese superfamily and established that its members are widespread in bacteria, archaea and in all major eukaryotic groups. We found that the amount of sterol esters was significantly higher in the deletion strain tum1Δ than in the wild-type strain. Expression of the mouse TST protein in the deletion strain did not rescue this phenotype. Moreover, although Tum1 deficiency in the thiolation pathway was complemented by re-introducing TUM1, it was not complemented by the introduction of the mouse homologue Tst. We further showed that the tRNA thiolation pathway is not involved in the regulation of sterol ester content in S. cerevisiae, as overexpression of the tEUUC, tKUUU and tQUUG tRNAs did not rescue the lipid phenotype in the tum1Δ deletion strain, and, additionally, deletion of the key gene for the tRNA thiolation pathway, UBA4, did not affect sterol ester content. The rhodanese superfamily of proteins is widespread in all organisms, and yeast TUM1 is a bona fide orthologue of mammalian Tst thiosulfate sulfurtransferase gene. However, the mouse TST protein cannot functionally replace yeast Tum1 protein, neither in its lipid metabolism-related function, nor in the tRNA thiolation pathway. We show here that Tum1 protein is involved in lipid metabolism by decreasing the sterol ester content in yeast cells, and that this function of Tum1 is not exerted through the tRNA thiolation pathway, but through another, currently unknown pathway.
Katja Uršič; Mojca Ogrizović; Dušan Kordiš; Klaus Natter; Uroš Petrovič. Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae. BMC Microbiology 2017, 17, 1 -9.
AMA StyleKatja Uršič, Mojca Ogrizović, Dušan Kordiš, Klaus Natter, Uroš Petrovič. Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae. BMC Microbiology. 2017; 17 (1):1-9.
Chicago/Turabian StyleKatja Uršič; Mojca Ogrizović; Dušan Kordiš; Klaus Natter; Uroš Petrovič. 2017. "Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae." BMC Microbiology 17, no. 1: 1-9.
Molecular domestications of transposable elements have occurred repeatedly during the evolution of eukaryotes. Mammals possess numerous single copy domesticated genes that have originated from the intronless multicopy transposable elements. The genesis and regulatory wiring of the Metaviridae-derived domesticated genes have been explained through phylogenomic analysis of more than 90 chordate genomes. Phylogenomic analysis has demonstrated that major diversification of these domesticated genes occurred in the ancestor of placental mammals. Mammalian domesticated genes have originated in several steps by independent domestication events. The analysis of active Metaviridae lineages in amniotes has demonstrated that domesticated genes originated from retroelement remains. The analysis of syntenic loci has shown that diverse domesticated genes and their chromosomal positions were fully established in the ancestor of placental mammals. During the domestication process, de novo acquisition of regulatory regions was crucial for the survival of the novel domesticated genes. The origin and evolution of de novo acquired promoters and untranslated regions in diverse mammalian domesticated genes have been explained by comparative analysis of orthologous gene loci. The origin of placental mammal-specific innovations and adaptations, such as placenta and newly evolved brain functions, was most probably connected to the regulatory wiring of domesticated genes and their rapid fixation in the ancestor of placental mammals.
Dušan Kordiš. The Life History of Domesticated Genes Illuminates the Evolution of Novel Mammalian Genes. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts 2017, 147 -162.
AMA StyleDušan Kordiš. The Life History of Domesticated Genes Illuminates the Evolution of Novel Mammalian Genes. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. 2017; ():147-162.
Chicago/Turabian StyleDušan Kordiš. 2017. "The Life History of Domesticated Genes Illuminates the Evolution of Novel Mammalian Genes." Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts , no. : 147-162.
Natural toxins are a threat to health but have also turned out to be very useful. Among the most illustrative examples are the deadly botulinum toxins that are used today in numerous therapeutic applications. The essential condition for a toxin to be used as a medicament or a research tool is to understand about how it interferes with the victim’s physiology. In this chapter, a group of snake venom toxins is described, the β-neurotoxins, whose mechanism of action at the molecular level is still not completely understood, leaving their medical potential yet to be exploited. As explained, these molecules have evolved by a process of accelerated evolution from harmless digestive enzymes, the secreted phospholipases A2, to potent toxins that block synaptic signaling in vertebrate skeletal muscles. To advance the insight into the molecular basis of action of β-neurotoxins, the results of the most recent investigations have been examined critically. A draft picture of how β-neurotoxins poison the nerve terminal is presented. Important details, including the identity of β-neurotoxicity-linked receptors, pathways by which β-neurotoxins cross plasma and mitochondrial membranes, and intracellular regulation of their enzymatic activity, are however still unknown. Unraveling these issues should provide considerable support for clarifying the functions and dysfunctions of mammalian secreted phospholipases A2 in the nervous system.
Dušan Kordiš; Igor Križaj. Secreted Phospholipases A2 with β-Neurotoxic Activity. Organotypic Models in Drug Development 2017, 67 -86.
AMA StyleDušan Kordiš, Igor Križaj. Secreted Phospholipases A2 with β-Neurotoxic Activity. Organotypic Models in Drug Development. 2017; ():67-86.
Chicago/Turabian StyleDušan Kordiš; Igor Križaj. 2017. "Secreted Phospholipases A2 with β-Neurotoxic Activity." Organotypic Models in Drug Development , no. : 67-86.
S1 family of serine peptidases is the largest family of peptidases. They are specifically inhibited by the Kunitz/BPTI inhibitors. Kunitz domain is characterized by the compact 3D structure with the most important inhibitory loops for the inhibition of S1 peptidases. In the present study we analysed the action of site-specific positive selection and its impact on the structurally and functionally important parts of the snake venom Kunitz/BPTI family of proteins. By using numerous models we demonstrated the presence of large numbers of site-specific positively selected sites that can reach between 30–50% of the Kunitz domain. The mapping of the positively selected sites on the 3D model of Kunitz/BPTI inhibitors has shown that these sites are located in the inhibitory loops 1 and 2, but also in the Kunitz scaffold. Amino acid replacements have been found exclusively on the surface, and the vast majority of replacements are causing the change of the charge. The consequence of these replacements is the change in the electrostatic potential on the surface of the Kunitz/BPTI proteins that may play an important role in the precise targeting of these inhibitors into the active site of S1 family of serine peptidases.
Vera Župunski; Dušan Kordiš. Strong and widespread action of site-specific positive selection in the snake venom Kunitz/BPTI protein family. Scientific Reports 2016, 6, 37054 .
AMA StyleVera Župunski, Dušan Kordiš. Strong and widespread action of site-specific positive selection in the snake venom Kunitz/BPTI protein family. Scientific Reports. 2016; 6 (1):37054.
Chicago/Turabian StyleVera Župunski; Dušan Kordiš. 2016. "Strong and widespread action of site-specific positive selection in the snake venom Kunitz/BPTI protein family." Scientific Reports 6, no. 1: 37054.
Natural toxins are a threat to health but have also turned out to be very useful. Among the most illustrative examples are the deadly botulinum toxins that are used today in numerous therapeutic applications. The essential condition for a toxin to be used as a medicament or a research tool is to understand about how it interferes with the victim’s physiology. In this chapter, a group of snake venom toxins is described, the β-neurotoxins, whose mechanism of action at the molecular level is still not completely understood, leaving their medical potential yet to be exploited. As explained, these molecules have evolved by a process of accelerated evolution from harmless digestive enzymes, the secreted phospholipases A2, to potent toxins that block synaptic signaling in vertebrate skeletal muscles. To advance the insight into the molecular basis of action of β-neurotoxins, the results of the most recent investigations have been examined critically. A draft picture of how β-neurotoxins poison the nerve terminal is presented. Important details, including the identity of β-neurotoxicity-linked receptors, pathways by which β-neurotoxins cross plasma and mitochondrial membranes, and intracellular regulation of their enzymatic activity, are however still unknown. Unraveling these issues should provide considerable support for clarifying the functions and dysfunctions of mammalian secreted phospholipases A2 in the nervous system.
Dušan Kordiš; Igor Križaj. Secreted Phospholipases A2 with β-Neurotoxic Activity. Organotypic Models in Drug Development 2015, 1 -15.
AMA StyleDušan Kordiš, Igor Križaj. Secreted Phospholipases A2 with β-Neurotoxic Activity. Organotypic Models in Drug Development. 2015; ():1-15.
Chicago/Turabian StyleDušan Kordiš; Igor Križaj. 2015. "Secreted Phospholipases A2 with β-Neurotoxic Activity." Organotypic Models in Drug Development , no. : 1-15.
Molecular domestications of transposable elements have occurred repeatedly during the evolution of eukaryotes. Vertebrates, especially mammals, possess numerous single copy domesticated genes (DGs) that have originated from the intronless multicopy transposable elements. However, the origin and evolution of the retroelement-derived DGs (RDDGs) that originated from Metaviridae has been only partially elucidated, due to absence of genome data or to limited analysis of a single family of DGs. We traced the genesis and regulatory wiring of the Metaviridae-derived DGs through phylogenomic analysis, using whole-genome information from more than 90 chordate genomes. Phylogenomic analysis of these DGs in chordate genomes provided direct evidence that major diversification has occurred in the ancestor of placental mammals. Mammalian RDDGs have been shown to originate in several steps by independent domestication events and to diversify later by gene duplications. Analysis of syntenic loci has shown that diverse RDDGs and their chromosomal positions were fully established in the ancestor of placental mammals. By analysis of active Metaviridae lineages in amniotes, we have demonstrated that RDDGs originated from retroelement remains. The chromosomal gene movements of RDDGs were highly dynamic only in the ancestor of placental mammals. During the domestication process, de novo acquisition of regulatory regions is shown to be a prerequisite for the survival of the DGs. The origin and evolution of de novo acquired promoters and untranslated regions in diverse mammalian RDDGs have been explained by comparative analysis of orthologous gene loci. The origin of placental mammal-specific innovations and adaptations, such as placenta and newly evolved brain functions, was most probably connected to the regulatory wiring of DGs and their rapid fixation in the ancestor of placental mammals.
Janez Kokošar; Dušan Kordiš. Genesis and Regulatory Wiring of Retroelement-Derived Domesticated Genes: A Phylogenomic Perspective. Molecular Biology and Evolution 2013, 30, 1015 -1031.
AMA StyleJanez Kokošar, Dušan Kordiš. Genesis and Regulatory Wiring of Retroelement-Derived Domesticated Genes: A Phylogenomic Perspective. Molecular Biology and Evolution. 2013; 30 (5):1015-1031.
Chicago/Turabian StyleJanez Kokošar; Dušan Kordiš. 2013. "Genesis and Regulatory Wiring of Retroelement-Derived Domesticated Genes: A Phylogenomic Perspective." Molecular Biology and Evolution 30, no. 5: 1015-1031.
Investigations of TEs in sauropsid genomes over the last four decades have provided an insight into the TE repertoires of all major extant sauropsid lineages. Invaluable information concerning the diversity, activity, and repetitive landscapes in sauropsids has emerged from analyses of the chicken and Anolis genomes and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many active TE families, the extant avian genomes have few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals. In sauropsid genomes, TEs have been active for hundreds of millions of years, and as such have had a large impact on the genetic diversity and genome architectures.
Dušan Kordiš. The Repetitive Landscape of Sauropsid Genomes. Evolutionary Biology: Mechanisms and Trends 2012, 243 -263.
AMA StyleDušan Kordiš. The Repetitive Landscape of Sauropsid Genomes. Evolutionary Biology: Mechanisms and Trends. 2012; ():243-263.
Chicago/Turabian StyleDušan Kordiš. 2012. "The Repetitive Landscape of Sauropsid Genomes." Evolutionary Biology: Mechanisms and Trends , no. : 243-263.
Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.
Dušan Kordiš; Janez Kokošar. What Can Domesticated Genes Tell Us about the Intron Gain in Mammals? International Journal of Evolutionary Biology 2012, 2012, 1 -7.
AMA StyleDušan Kordiš, Janez Kokošar. What Can Domesticated Genes Tell Us about the Intron Gain in Mammals? International Journal of Evolutionary Biology. 2012; 2012 ():1-7.
Chicago/Turabian StyleDušan Kordiš; Janez Kokošar. 2012. "What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?" International Journal of Evolutionary Biology 2012, no. : 1-7.
Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures.
Dušan Kordiš. Extensive intron gain in the ancestor of placental mammals. Biology Direct 2011, 6, 59 -59.
AMA StyleDušan Kordiš. Extensive intron gain in the ancestor of placental mammals. Biology Direct. 2011; 6 (1):59-59.
Chicago/Turabian StyleDušan Kordiš. 2011. "Extensive intron gain in the ancestor of placental mammals." Biology Direct 6, no. 1: 59-59.
Transposable elements (TEs) have profound effects on the structure, function and evolution of their host genomes. Our knowledge about these agents of genomic change in sauropsids, a sister group of mammals that includes all extant reptiles and birds, is still very limited. Invaluable information concerning the diversity, activity and repetitive landscapes in sauropsids has recently emerged from analyses of the draft genomes of chicken and Anolis and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many young, active TE families, the extant avian genomes have very few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals, being more similar in diversity to that of lower vertebrates. The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context.
D. Kordis. Transposable Elements in Reptilian and Avian (Sauropsida) Genomes. Cytogenetic and Genome Research 2009, 127, 94 -111.
AMA StyleD. Kordis. Transposable Elements in Reptilian and Avian (Sauropsida) Genomes. Cytogenetic and Genome Research. 2009; 127 (2-4):94-111.
Chicago/Turabian StyleD. Kordis. 2009. "Transposable Elements in Reptilian and Avian (Sauropsida) Genomes." Cytogenetic and Genome Research 127, no. 2-4: 94-111.
The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea.
Dušan Kordiš; Vito Turk. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes. BMC Evolutionary Biology 2009, 9, 266 -266.
AMA StyleDušan Kordiš, Vito Turk. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes. BMC Evolutionary Biology. 2009; 9 (1):266-266.
Chicago/Turabian StyleDušan Kordiš; Vito Turk. 2009. "Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes." BMC Evolutionary Biology 9, no. 1: 266-266.
L1 retrotransposons constitute the largest single component of mammalian genomes. In contrast to the single remaining lineage of L1 retrotransposons in mammalian genomes, some teleost fishes contain a highly diverse L1 retrotransposon repertoire. Major evolutionary changes in L1 retrotransposon repertoires have therefore taken place in the land vertebrates (Tetrapoda). The lack of sequence data for L1 retrotransposons in the basal living Tetrapoda lineages prompted an investigation of their distribution and evolution in the genomes of the key tetrapod lineages, amphibians and reptiles, and in lungfishes. In this study, we combined genome database searches with PCR analysis to demonstrate that L1 retrotransposons are present in the genomes of lungfishes, amphibians, and lepidosaurs. Phylogenomic analysis shows that the genomes of Deuterostomia possess three highly divergent groups of L1 retrotransposons, with distinct distribution patterns. The analysis of L1 diversity shows the presence of a very large number of diverse L1 families, each with very low copy numbers, at the time of the origin of tetrapods. During the evolution of synapsids, all but one L1 lineage have been lost. This study establishes that the loss of L1 diversity and explosion in copy numbers occurred in the synapsid ancestors of mammals, and was most probably caused by severe population bottlenecks.
Dušsan Kordiš; Nika Lovšin; Franc Gubenšek. Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia. Systematic Biology 2006, 55, 886 -901.
AMA StyleDušsan Kordiš, Nika Lovšin, Franc Gubenšek. Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia. Systematic Biology. 2006; 55 (6):886-901.
Chicago/Turabian StyleDušsan Kordiš; Nika Lovšin; Franc Gubenšek. 2006. "Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia." Systematic Biology 55, no. 6: 886-901.
Chromoviruses, chromodomain-containing retrotransposons, are the only Metaviridae (Ty3/gypsy group of retrotransposons) clade with a Eukaryota-wide distribution. They have a common evolutionary origin and are the most prolific and diverse Metaviridae clade. The fusion of a retrotransposon and a chromodomain, was most probably responsible for their extreme evolutionary success in Eukaryota. Analysis of the massive amount of genome sequence data for different eukaryotic lineages has provided an in depth insight into the diversity, evolution, neofunctionalization, high rate of genomic turnover and origin of chromoviruses in Eukaryota. This review attempts to summarise the unique aspects of chromoviruses from a genomic perspective.
Dušan Kordiš. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 2005, 347, 161 -173.
AMA StyleDušan Kordiš. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene. 2005; 347 (2):161-173.
Chicago/Turabian StyleDušan Kordiš. 2005. "A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses." Gene 347, no. 2: 161-173.
The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.
Benjamin Gorinšek; Franc Gubenšek; Dušan Kordiš. Evolutionary Genomics of Chromoviruses in Eukaryotes. Molecular Biology and Evolution 2004, 21, 781 -798.
AMA StyleBenjamin Gorinšek, Franc Gubenšek, Dušan Kordiš. Evolutionary Genomics of Chromoviruses in Eukaryotes. Molecular Biology and Evolution. 2004; 21 (5):781-798.
Chicago/Turabian StyleBenjamin Gorinšek; Franc Gubenšek; Dušan Kordiš. 2004. "Evolutionary Genomics of Chromoviruses in Eukaryotes." Molecular Biology and Evolution 21, no. 5: 781-798.
The evolution of the novel L2 clade of non-long terminal repeat (LTR) retrotransposons and their evolutionary dynamics in Deuterostomia has been examined. The short-term evolution of long interspersed nuclear element 2s (LINE2s) has been studied in 18 reptilian species by analysis of a PCR amplified 0.7-kb fragment encoding the palm/fingers subdomain of reverse transcriptase (RT). Most of the reptilian LINE2s examined are inactive since they contain multiple stop codons, indels, or frameshift mutations that disrupt the RT. Analysis of reptilian LINE2s has shown a high degree of sequence divergence and an unexpectedly large number of deletions. The evolutionary dynamics of LINE2s in reptiles has been found to be complex. LINE2s are shown to form a novel clade of non-LTR retrotransposons that is well separated from the CR1 clade. This novel L2 clade is more widely distributed than previously thought, and new representatives have been discovered in echinoderms, insects, teleost fishes, Xenopus, Squamata, and marsupials. There is an apparent absence of LINE2s from different vertebrate classes, such as cartilaginous fishes, Archosauria (birds and crocodiles), and turtles. Whereas the LINE2s are present in echinoderms and teleost fishes in a conserved form, in most tetrapods only highly degenerated pseudogenes can be found. The predominance of inactive LINE2s in Tetrapoda indicates that, in the host genomes, only inactive copies are still present. The present data indicate that the vertical inactivation of LINE2s might have begun at the time of Tetrapoda origin, 400 MYA. The evolutionary dynamics of the L2 clade in Deuterostomia can be described as a gradual vertical inactivation in Tetrapoda, stochastic loss in Archosauria and turtles, and strict vertical transmission in echinoderms and teleost fishes.
Nika Lovšin; Franc Gubenšek; Dušan Kordi. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia. Molecular Biology and Evolution 2001, 18, 2213 -2224.
AMA StyleNika Lovšin, Franc Gubenšek, Dušan Kordi. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia. Molecular Biology and Evolution. 2001; 18 (12):2213-2224.
Chicago/Turabian StyleNika Lovšin; Franc Gubenšek; Dušan Kordi. 2001. "Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia." Molecular Biology and Evolution 18, no. 12: 2213-2224.
This study examined the evolutionary dynamics of Bov-B LINEs in vertebrates and the evolution of the RTE clade of non-LTR retrotransposons. The first full-length reptilian Bov-B LINE element is described; it is 3.2 kb in length, with a structural organization typical of the RTE clade of non-LTR retrotransposons. The long-term evolution of Bov-B LINEs was studied in 10 species of Squamata by analysis of a PCR-amplified 1.8-kb fragment encoding part of apurinic/apyrimidinic endonuclease, the intervening domain, and the palm/fingers subdomain of reverse transcriptase. A very high level of conservation in Squamata Bov-B long interspersed nuclear elements has been found, reaching 86% identity in the nearly 600 amino acids of ORF2. The same level of conservation exists between the ancestral snake lineage and Ruminantia. Such a high level is exceptional when compared with the level of conservation observed in nuclear and mitochondrial proteins and in other transposable elements. The RTE clade has been found to be much more widely distributed than previously thought, and novel representatives have been discovered in plants, brown algae, annelids, crustaceans, mollusks, echinoderms, and teleost fishes. Evolutionary relationships in the RTE clade were deduced at the amino acid level from three separate regions of ORF2. By using different independent methods, including the divergence-versus-age analysis, several examples of horizontal transfer in the RTE clade were recognized, with important implications for the existence of HT in non-LTR retrotransposons.
Vera Župunski; Franc Gubenšek; Dušan Kordis. Evolutionary Dynamics and Evolutionary History in the RTE Clade of Non-LTR Retrotransposons. Molecular Biology and Evolution 2001, 18, 1849 -1863.
AMA StyleVera Župunski, Franc Gubenšek, Dušan Kordis. Evolutionary Dynamics and Evolutionary History in the RTE Clade of Non-LTR Retrotransposons. Molecular Biology and Evolution. 2001; 18 (10):1849-1863.
Chicago/Turabian StyleVera Župunski; Franc Gubenšek; Dušan Kordis. 2001. "Evolutionary Dynamics and Evolutionary History in the RTE Clade of Non-LTR Retrotransposons." Molecular Biology and Evolution 18, no. 10: 1849-1863.
Animal toxins comprise a diverse array of proteins that have a variety of biochemical and pharmacological functions. A large number of animal toxins are encoded by multigene families. From studies of several toxin multigene families at the gene level the picture is emerging that most have been functionally diversified by gene duplication and adaptive evolution. The number of pharmacological activities in most toxin multigene families results from their adaptive evolution. The molecular evolution of animal toxins has been analysed in some multigene families, at both the intraspecies and interspecies levels. In most toxin multigene families, the rate of non-synonymous to synonymous substitutions (dN/dS) is higher than one. Thus natural selection has acted to diversify coding sequences and consequently the toxin functions. The selection pressure for the rapid adaptive evolution of animal toxins is the need for quick immobilization of the prey in classical predator and prey interactions. Currently available evidence for adaptive evolution in animal toxin multigene families will be considered in this review.
Dušan Kordiš; Franc Gubenšek. Adaptive evolution of animal toxin multigene families. Gene 2000, 261, 43 -52.
AMA StyleDušan Kordiš, Franc Gubenšek. Adaptive evolution of animal toxin multigene families. Gene. 2000; 261 (1):43-52.
Chicago/Turabian StyleDušan Kordiš; Franc Gubenšek. 2000. "Adaptive evolution of animal toxin multigene families." Gene 261, no. 1: 43-52.
Danuta Babula; Malgorzata Ruminska; Jan Sadowski; Josep M. Folch; Ramona Natacha Pena; Agustina Coll; Armand Sánchez; James M. H. Kijas; Leif Andersson; Dušan Kordiš; Franc Gubenšek; Gregor Majdič; Tomaž Snoj; Aleš Horvat; Janko Mrkun; Marian Kosec; Vojteh Cestnik; Juan F. Medrano; Andrea Johnson; Edward J. DePeters; Alma Isias; Matjaž Ursič; Jelka Zabavnik. Abstracts. Pflügers Archiv - European Journal of Physiology 2000, 439, r23 -r24.
AMA StyleDanuta Babula, Malgorzata Ruminska, Jan Sadowski, Josep M. Folch, Ramona Natacha Pena, Agustina Coll, Armand Sánchez, James M. H. Kijas, Leif Andersson, Dušan Kordiš, Franc Gubenšek, Gregor Majdič, Tomaž Snoj, Aleš Horvat, Janko Mrkun, Marian Kosec, Vojteh Cestnik, Juan F. Medrano, Andrea Johnson, Edward J. DePeters, Alma Isias, Matjaž Ursič, Jelka Zabavnik. Abstracts. Pflügers Archiv - European Journal of Physiology. 2000; 439 (S1):r23-r24.
Chicago/Turabian StyleDanuta Babula; Malgorzata Ruminska; Jan Sadowski; Josep M. Folch; Ramona Natacha Pena; Agustina Coll; Armand Sánchez; James M. H. Kijas; Leif Andersson; Dušan Kordiš; Franc Gubenšek; Gregor Majdič; Tomaž Snoj; Aleš Horvat; Janko Mrkun; Marian Kosec; Vojteh Cestnik; Juan F. Medrano; Andrea Johnson; Edward J. DePeters; Alma Isias; Matjaž Ursič; Jelka Zabavnik. 2000. "Abstracts." Pflügers Archiv - European Journal of Physiology 439, no. S1: r23-r24.