Title:Molecular and Genetic Characterization of Natural Variants of HIV-1 Nef Gene from North India and its Functional Implication in Down-Regulation of MHC-I and CD-4
Volume: 19
Issue: 2
Author(s): J. Singh*, L. Ronsard, M. Pandey, R. Kapoor, V. G. Ramachandran and A. C. Banerjea
Affiliation:
- National Institute of Immunology, New Delhi,India
Keywords:
Cluster of Differentiation-4 (CD4), functional domain, genetic variations, human immunodeficiency virus (HIV),
major histocompatibility complex-1 (MHC-1), Nef.
Abstract: Background: HIV-1 Nef is an important accessory protein with multiple effector functions.
Genetic studies of the HIV-1 Nef gene show extensive genetic diversity and the functional
studies have been carried out mostly with Nef derived from regions dominated by subtype B
(North America & Europe).
Objective: This study was carried out to characterize genetic variations of the Nef gene from
HIV-1 infected individuals from North India and to find out their functional implications.
Methods: The unique representative variants were sub-cloned in a eukaryotic expression vector
and further characterized with respect to their ability to downregulate cell surface expression of
CD4 and MHC-1 molecules.
Results: The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus
subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology
to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of
the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying
the importance of mutations in Nef variants. Intracellular stability of Nef variants differed
greatly when compared with wild type Nef B and C. There were some variants that possessed mutations
in the functional domains of Nef and responsible for its differential CD4 and MHC-1 downregulation
activity.
Conclusion: We observed enhanced biological activities in some of the variants, perhaps arising
from amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation
activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a
population to become the most abundant after a single selection event.
