Limits...
Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans.

Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK - PLoS ONE (2011)

Bottom Line: However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older.A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking.Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR) regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5' and 3' LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

Show MeSH

Related in: MedlinePlus

Phylogenetic tree of full-length HERV-K (HML-2) LTR sequences.The clustering of the HERV-K 5′ and 3′ LTR sequences of each insertion suggests that gene conversion is rare in the HERV-K family. Each HERV is indicated by its name (K106 for HERV-K106). HERV taxa that may have undergone gene conversion are indicated in red. HERV-K115 5′LTR clusters with HERV-K109 suggesting a gene conversion occurred between these two HERV-K members. HERV-K10, HERV-K HML2HOM, and HERV-K110 are sometimes referred to as HERV-K107, HERV-K108, and HERV-K18, respectively. HERV-K110 was used to root the phylogeny because it is present in both Humans and Gorillas [16].
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3102101&req=5

pone-0020234-g001: Phylogenetic tree of full-length HERV-K (HML-2) LTR sequences.The clustering of the HERV-K 5′ and 3′ LTR sequences of each insertion suggests that gene conversion is rare in the HERV-K family. Each HERV is indicated by its name (K106 for HERV-K106). HERV taxa that may have undergone gene conversion are indicated in red. HERV-K115 5′LTR clusters with HERV-K109 suggesting a gene conversion occurred between these two HERV-K members. HERV-K10, HERV-K HML2HOM, and HERV-K110 are sometimes referred to as HERV-K107, HERV-K108, and HERV-K18, respectively. HERV-K110 was used to root the phylogeny because it is present in both Humans and Gorillas [16].

Mentions: It has previously been hypothesized that gene conversion may be rampant amongst HERV loci [19]. Pervasive gene conversion would prevent us from applying a molecular clock to these data, since observed sequence variation between LTR regions would be attributed to recombination rather than the stepwise accumulation of mutations predicted by the neutral theory of evolution [20]. We reconstructed a maximum likelihood phylogeny of all HERV-K LTRs to determine the prevalence of gene conversion between insertions in the HERV-K family (Figure 1). The clustering of the 5′ and 3′ LTR sequences associated with each insertion locus in our phylogeny suggests that gene conversion is rare among HERV-Ks, with the single exception of HERV-K115. Evidence of a gene conversion event in HERV-K115 has been reported previously [17], [19].


Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans.

Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK - PLoS ONE (2011)

Phylogenetic tree of full-length HERV-K (HML-2) LTR sequences.The clustering of the HERV-K 5′ and 3′ LTR sequences of each insertion suggests that gene conversion is rare in the HERV-K family. Each HERV is indicated by its name (K106 for HERV-K106). HERV taxa that may have undergone gene conversion are indicated in red. HERV-K115 5′LTR clusters with HERV-K109 suggesting a gene conversion occurred between these two HERV-K members. HERV-K10, HERV-K HML2HOM, and HERV-K110 are sometimes referred to as HERV-K107, HERV-K108, and HERV-K18, respectively. HERV-K110 was used to root the phylogeny because it is present in both Humans and Gorillas [16].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102101&req=5

pone-0020234-g001: Phylogenetic tree of full-length HERV-K (HML-2) LTR sequences.The clustering of the HERV-K 5′ and 3′ LTR sequences of each insertion suggests that gene conversion is rare in the HERV-K family. Each HERV is indicated by its name (K106 for HERV-K106). HERV taxa that may have undergone gene conversion are indicated in red. HERV-K115 5′LTR clusters with HERV-K109 suggesting a gene conversion occurred between these two HERV-K members. HERV-K10, HERV-K HML2HOM, and HERV-K110 are sometimes referred to as HERV-K107, HERV-K108, and HERV-K18, respectively. HERV-K110 was used to root the phylogeny because it is present in both Humans and Gorillas [16].
Mentions: It has previously been hypothesized that gene conversion may be rampant amongst HERV loci [19]. Pervasive gene conversion would prevent us from applying a molecular clock to these data, since observed sequence variation between LTR regions would be attributed to recombination rather than the stepwise accumulation of mutations predicted by the neutral theory of evolution [20]. We reconstructed a maximum likelihood phylogeny of all HERV-K LTRs to determine the prevalence of gene conversion between insertions in the HERV-K family (Figure 1). The clustering of the 5′ and 3′ LTR sequences associated with each insertion locus in our phylogeny suggests that gene conversion is rare among HERV-Ks, with the single exception of HERV-K115. Evidence of a gene conversion event in HERV-K115 has been reported previously [17], [19].

Bottom Line: However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older.A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking.Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR) regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5' and 3' LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

Show MeSH
Related in: MedlinePlus