Transcript Document

THLBA105
Epistatic effect and positive selection
in the HIV-1 vif gene are linked with
APOBEC3G/F neutralization activity
Élcio Leal 1, Shiori Yabe 3, Hirohisa Kishino 3, Maria Clara Bizinoto 2, Leonardo
de Oliveira Martins 4, Mariana Leão de Lima 2, Edsel Renata Morais 2,
Ricardo Sobhie Diaz 2, Luiz Mário Janini 2
1
Federal University of Pará, Belém, Brazil
Federal University of São Paulo, São Paulo, Brazil
3 Graduate School of Agriculture and Life Sciences, University of Tokyo, Japan
4 Bioinformatics and Molecular Evolution Laboratory, Department of Biochemistry, Genetics and Immunology,
University of Vigo, Spain
2
APOBEC (apolipoprotein B mRNA-editing
catalytic polypeptide) 3G/F and vif
Innate Immunity
APOBEC 3G
APOBEC 3F
C
U
G A
Hypermutation
vif
TAA
TGA = x
TAG
Proteasomal
degration
Viral extinction
To explore in more detail the host-virus
evolutionary interaction at the population
level, we evaluated the influence of A3G
polymorphisms in the HIV-1 diversification
and disease status.
Methods:
•400 Patients
•CD4 + T cell counts and Viral load
•7 SNPs A3G (2 PCR fragments of 6.5 and 8 kb
•vif gene sequencing
•Hypermutation detection in the integrase
region (HA yellow into agarose gel)
Methods (cntd):
•vif phylogenetic inference
•Population dynamics
•Bayesian skyline plot method (Neτ)
•Bayesian Markov chain Monte Carlo coalescent
framework
•Recombination detection using Bayesian
approach (biomc2)
•Positive selection dN/dS (Yang, Z., 2007 Mol Biol Evol 24: 1586-1591)
•Co-evolving sites BGM (Poon, et al., 2007, PLoS Comput Biol 3: e231)
•Vif sites versus CD4 levels (permutation test)
•A3G SNPs versus viral phylogenies (Bayesian
framework, BaTS)
Results:
•36% of samples were hypermutated (integras
•80% B, 16% BF, 3% C, 1% F, 1 sample AG
•mean diversity, measured by pairwise distances assuming the HKY
model, was 0.0931±0.0006 for clade B, and 0.0493±0.001 for
C (vif)
•No single vif amino acid positions were significantly associated with
the CD4+T counts.
•No A3G polymorphism correlation with vif genealogies
SNP -571 correlated with CD4+ T cell counts (Mann-Whitney test p-value=0.0076)
C/G tend to have lower CD4+ T cell counts compared to C/C individuals
Results:
•Peak of vif recombination in sites that are essential to recognize and
neutralizes 3G complexes.
•Positively selected sites between APOBEC3 binding sites (WKSLVK
and YRHHY) of the vif gene
Positively selected sites within BC-Box and Cullin5-Box (region that
binds cellular elongin B and C to form complexes that trigger the
ubiquitination and proteasomal degradation of the A3G proteins)
•Co-evolving sites concentrated in a CTL region and within BC box
•Epistatic sites located in two distinct regions of the vif gene
•Epistatic codons associated with CD4 levels
Results:
•Peak of vif recombination in sites that are essential to recognize and
neutralizes 3G complexes
•Positively selected sites between APOBEC3 binding sites (WKSLVK
and YRHHY) of the vif gene
•Positively selected sites within BC-Box and Cullin5-Box (region that
binds cellular elongin B and C to form complexes that trigger the
ubiquitination and proteasomal degradation of the A3G proteins)
•Co-evolving sites concentrated in a CTL region and within BC box
•Epistatic sites located in two distinct regions of the vif gene
•Epistatic codons associated with CD4 levels
HIV-1 vif gene
Consensus subtype B
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
HIV-1 vif gene
(Positively selected sites)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Positive selected sites >1 and p<0.99
HIV-1 vif gene
(Co-evolving sites)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Positive selected sites >1 and p<0.99
Co-evolving sites detected by BGM
HIV-1 vif gene
(Co-evolving sites)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Positive selected sites >1 and p<0.99
Co-evolving sites detected by BGM
HIV-1 vif gene
(Co-evolving sites)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Positive selected sites >1 and p<0.99
Co-evolving sites detected by BGM
HIV-1 vif gene
(Epistatic sites x CD4 levels)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Co-evolving sites detected by BGM
Positive selected sites >1 and p<0.99
Epistatic sites associated with CD4+ T cell count levels
HIV-1 vif gene
(Epistatic sites x CD4 levels)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Co-evolving sites detected by BGM
Positive selected sites >1 and p<0.99
Epistatic sites associated with CD4+ T cell count levels
HIV-1 vif gene
(Epistatic sites x CD4 levels)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Co-evolving sites detected by BGM
Positive selected sites >1 and p<0.99
Epistatic sites associated with CD4+ T cell count levels
HIV-1 vif gene
(Epistatic sites x CD4 levels)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Co-evolving sites detected by BGM
Positive selected sites >1 and p<0.99
Epistatic sites associated with CD4+ T cell count levels
HIV-1 vif gene
(Epistatic sites x CD4 levels)
(A3F)
(A3G)
(A3G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYISKKAKGWFYRHHYESTHPRI
(A3)
SSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKRRYSTQVDPDLAD
BC-BOX
QLIHLYYFDCFSESAIRNAILGHIVRPRCEYQAGHNKVGSLQYLALTALIKPKKIQ
Cullin-BOX
KPPLPSVRKLTEDRWNKPQKTKGHRGSHTMNGH
CTL/CD8 epitope regions
Co-evolving sites detected by BGM
Positive selected sites >1 and p<0.99
Epistatic sites associated with CD4+ T cell count levels
Conclusions:
Most of the adaptive evolution in the vif gene probably
was to optimize A3G/F and cellular proteins (i.e.,
elongins) binding and recognition.
Acknowledgements:
Laboratory work performed at the Retrovirology laboratory
of Federal University of Sao Paulo Brazil
This work was supported by FAPESP, (Foundation for the
Support of Research in the State of Sao Paulo; grant no.
06/50109-5) and by the Japan Society for the Promotion of
Science (SPS KAKENHI) Grant-in-Aid for Scientific
Research (B) 19300094.