Limits...
Early mesozoic coexistence of amniotes and hepadnaviridae.

Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H - PLoS Genet. (2014)

Bottom Line: Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene.We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs.Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden.

ABSTRACT
Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic "fossil" is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote-HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.

Show MeSH

Related in: MedlinePlus

An evolutionary scenario for the emergence of the oncogenic X gene.(A) The genome of the HBV ancestor contained neither an X nor X-like ORF, given that avian and crocodilian eHBVs lack an X-like ORF, despite the fact that it is thought to be expressed in some closely related avihepadnaviruses [20]. X (+2 frame) and X-like (+3 frame) are encoded in different reading frames relative to the part of pol they overlap with (+1 frame), which strongly suggests that these ORFs are non-homologous and the X-like protein emerged in the ancestor of avihepadnaviruses. Independently, the X protein arose in orthohepadnaviruses via overprinting (4.) after a segmental duplication (1.), a partial deletion (2.), and a frameshifting mutation (3.) in one region of the HBV genome. Only the part of the HBV genome between the ribonuclease H (RNH) and the terminal protein (TP) domains of the pol ORF is shown, including structural elements such as direct repeats (DR; purple vertical lines) and the RNA encapsidation signal (ε; orange box). (B) Translated sequence alignment of the X-like ORF sensu Chang et al. [20] indicates presence of multiple internal stop codons in avian and crocodilian eHBVs, resulting in potential translation products <30 aa. Stop codon positions (asterisks) are highlighted with grey boxes if they are conserved between eHBVs, start codon positions for the longest possible ORF are highlighted by circles. Even when assuming that nonconventional start codons are used as suggested for DHBV [20], potential eHBV X-like proteins would comprise just a portion of the DHBV X-like protein. (C) Sequence similarity between translated preC/C 5′ end region (incl. in-frame aa sites upstream of the start codon) and translated central region of the preC/C ORF might be a potential remnant of an ancient segmental duplication of the first two thirds of the preC/C ORF. Amino acid residues with dark grey background are conserved between the start and the middle part of the preC/C ORF and thus constitute a potentially duplicated amino acid motif. (D) Schematic illustration of the proposed evolutionary steps of X ORF emergence [(1.) to (4.)] described in (A) that potentially led to the extant genome organization of orthohepadnaviruses. Black rectangles illustrate the location of the duplicated amino acid motif shown in (C).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4263362&req=5

pgen-1004559-g004: An evolutionary scenario for the emergence of the oncogenic X gene.(A) The genome of the HBV ancestor contained neither an X nor X-like ORF, given that avian and crocodilian eHBVs lack an X-like ORF, despite the fact that it is thought to be expressed in some closely related avihepadnaviruses [20]. X (+2 frame) and X-like (+3 frame) are encoded in different reading frames relative to the part of pol they overlap with (+1 frame), which strongly suggests that these ORFs are non-homologous and the X-like protein emerged in the ancestor of avihepadnaviruses. Independently, the X protein arose in orthohepadnaviruses via overprinting (4.) after a segmental duplication (1.), a partial deletion (2.), and a frameshifting mutation (3.) in one region of the HBV genome. Only the part of the HBV genome between the ribonuclease H (RNH) and the terminal protein (TP) domains of the pol ORF is shown, including structural elements such as direct repeats (DR; purple vertical lines) and the RNA encapsidation signal (ε; orange box). (B) Translated sequence alignment of the X-like ORF sensu Chang et al. [20] indicates presence of multiple internal stop codons in avian and crocodilian eHBVs, resulting in potential translation products <30 aa. Stop codon positions (asterisks) are highlighted with grey boxes if they are conserved between eHBVs, start codon positions for the longest possible ORF are highlighted by circles. Even when assuming that nonconventional start codons are used as suggested for DHBV [20], potential eHBV X-like proteins would comprise just a portion of the DHBV X-like protein. (C) Sequence similarity between translated preC/C 5′ end region (incl. in-frame aa sites upstream of the start codon) and translated central region of the preC/C ORF might be a potential remnant of an ancient segmental duplication of the first two thirds of the preC/C ORF. Amino acid residues with dark grey background are conserved between the start and the middle part of the preC/C ORF and thus constitute a potentially duplicated amino acid motif. (D) Schematic illustration of the proposed evolutionary steps of X ORF emergence [(1.) to (4.)] described in (A) that potentially led to the extant genome organization of orthohepadnaviruses. Black rectangles illustrate the location of the duplicated amino acid motif shown in (C).

Mentions: Annotation suggests that an X or X-like ORF is absent in non-avian eHBVs, while the genomes of orthohepadnaviruses and avihepadnaviruses appear to contain an X and X-like gene, respectively (Fig. 4A). Even when aligning the translated sequences of eHBVs in the region homologous to the putative X-like ORF of avihepadnaviruses [20], all eHBVs and even several extant avian HBVs exhibit several internal stop codons at conserved positions (Fig. 4B), suggesting that an X-like ORF never existed in these unrelated HBV lineages. While it remains unclear whether the putative X-like gene in DHBV has a function [58], it is interesting to note that the ribonuclease H (RNH) domain (partially overlapping with the X/X-like ORF region) has a moderate GC content in eHBVs and avihepadnaviruses (S3 Figure), while mammalian HBV genomes exhibit a conserved X gene and a highly elevated GC content of the RNH domain.


Early mesozoic coexistence of amniotes and hepadnaviridae.

Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H - PLoS Genet. (2014)

An evolutionary scenario for the emergence of the oncogenic X gene.(A) The genome of the HBV ancestor contained neither an X nor X-like ORF, given that avian and crocodilian eHBVs lack an X-like ORF, despite the fact that it is thought to be expressed in some closely related avihepadnaviruses [20]. X (+2 frame) and X-like (+3 frame) are encoded in different reading frames relative to the part of pol they overlap with (+1 frame), which strongly suggests that these ORFs are non-homologous and the X-like protein emerged in the ancestor of avihepadnaviruses. Independently, the X protein arose in orthohepadnaviruses via overprinting (4.) after a segmental duplication (1.), a partial deletion (2.), and a frameshifting mutation (3.) in one region of the HBV genome. Only the part of the HBV genome between the ribonuclease H (RNH) and the terminal protein (TP) domains of the pol ORF is shown, including structural elements such as direct repeats (DR; purple vertical lines) and the RNA encapsidation signal (ε; orange box). (B) Translated sequence alignment of the X-like ORF sensu Chang et al. [20] indicates presence of multiple internal stop codons in avian and crocodilian eHBVs, resulting in potential translation products <30 aa. Stop codon positions (asterisks) are highlighted with grey boxes if they are conserved between eHBVs, start codon positions for the longest possible ORF are highlighted by circles. Even when assuming that nonconventional start codons are used as suggested for DHBV [20], potential eHBV X-like proteins would comprise just a portion of the DHBV X-like protein. (C) Sequence similarity between translated preC/C 5′ end region (incl. in-frame aa sites upstream of the start codon) and translated central region of the preC/C ORF might be a potential remnant of an ancient segmental duplication of the first two thirds of the preC/C ORF. Amino acid residues with dark grey background are conserved between the start and the middle part of the preC/C ORF and thus constitute a potentially duplicated amino acid motif. (D) Schematic illustration of the proposed evolutionary steps of X ORF emergence [(1.) to (4.)] described in (A) that potentially led to the extant genome organization of orthohepadnaviruses. Black rectangles illustrate the location of the duplicated amino acid motif shown in (C).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263362&req=5

pgen-1004559-g004: An evolutionary scenario for the emergence of the oncogenic X gene.(A) The genome of the HBV ancestor contained neither an X nor X-like ORF, given that avian and crocodilian eHBVs lack an X-like ORF, despite the fact that it is thought to be expressed in some closely related avihepadnaviruses [20]. X (+2 frame) and X-like (+3 frame) are encoded in different reading frames relative to the part of pol they overlap with (+1 frame), which strongly suggests that these ORFs are non-homologous and the X-like protein emerged in the ancestor of avihepadnaviruses. Independently, the X protein arose in orthohepadnaviruses via overprinting (4.) after a segmental duplication (1.), a partial deletion (2.), and a frameshifting mutation (3.) in one region of the HBV genome. Only the part of the HBV genome between the ribonuclease H (RNH) and the terminal protein (TP) domains of the pol ORF is shown, including structural elements such as direct repeats (DR; purple vertical lines) and the RNA encapsidation signal (ε; orange box). (B) Translated sequence alignment of the X-like ORF sensu Chang et al. [20] indicates presence of multiple internal stop codons in avian and crocodilian eHBVs, resulting in potential translation products <30 aa. Stop codon positions (asterisks) are highlighted with grey boxes if they are conserved between eHBVs, start codon positions for the longest possible ORF are highlighted by circles. Even when assuming that nonconventional start codons are used as suggested for DHBV [20], potential eHBV X-like proteins would comprise just a portion of the DHBV X-like protein. (C) Sequence similarity between translated preC/C 5′ end region (incl. in-frame aa sites upstream of the start codon) and translated central region of the preC/C ORF might be a potential remnant of an ancient segmental duplication of the first two thirds of the preC/C ORF. Amino acid residues with dark grey background are conserved between the start and the middle part of the preC/C ORF and thus constitute a potentially duplicated amino acid motif. (D) Schematic illustration of the proposed evolutionary steps of X ORF emergence [(1.) to (4.)] described in (A) that potentially led to the extant genome organization of orthohepadnaviruses. Black rectangles illustrate the location of the duplicated amino acid motif shown in (C).
Mentions: Annotation suggests that an X or X-like ORF is absent in non-avian eHBVs, while the genomes of orthohepadnaviruses and avihepadnaviruses appear to contain an X and X-like gene, respectively (Fig. 4A). Even when aligning the translated sequences of eHBVs in the region homologous to the putative X-like ORF of avihepadnaviruses [20], all eHBVs and even several extant avian HBVs exhibit several internal stop codons at conserved positions (Fig. 4B), suggesting that an X-like ORF never existed in these unrelated HBV lineages. While it remains unclear whether the putative X-like gene in DHBV has a function [58], it is interesting to note that the ribonuclease H (RNH) domain (partially overlapping with the X/X-like ORF region) has a moderate GC content in eHBVs and avihepadnaviruses (S3 Figure), while mammalian HBV genomes exhibit a conserved X gene and a highly elevated GC content of the RNH domain.

Bottom Line: Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene.We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs.Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden.

ABSTRACT
Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic "fossil" is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote-HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.

Show MeSH
Related in: MedlinePlus