Virology as Biosystematics: Towards Understanding the Viral Infection Biology

Large numbers of virus species exist in the realm of nature, and are now classified into distinct sub-groups based on their biochemical and biological characteristics (Knipe et al., 2007). Viruses are unique in their genomic composition, nucleocapsid/ virion morphology, replication strategy, and/or target host. Even though viruses represent the smallest entity encoding a genetic program and are strictly dependent on hosts for their replication, they adapt themselves in a species-specific and dexterous manner to infect or persist in a wide variety of living things. In the course of interaction with hosts, viruses somehow find ecologica

Strategy of HIV‐1 for survival : mutation, adaptation and evolution

Viruses are the smallest self-replicating organisms in nature. Without a metabolic system of their own, they survive in their hosts by ably utilizing host’s cellular machinery. To this end, viruses must continue to mutate and adapt in host’s varying environments. This adaptation ability is a fundamental property of viruses, closely linking to their survival. Understanding molecular bases for viral mutation and adaptation would certainly lead to the establishment of novel strategies against viruses. HIV‐１ exhibits a narrow host range, and disease-inducing infections are observed only in human population. The important question “Why and how does HIV‐１ cause disease only in human?” must be demonstratively solved. To address this issue, HIV‐１infection models for AIDS are essential. Since valid animal models for this purpose have not been established yet, we now aim at constructing a novel class of HIV‐１（HIV‐１rmt）that infects experimental macaques and causes AIDS. Recent studies suggested that HIV‐１ emerged in human population following repeated species transmission/adaptation to new hosts of different SIVs from various hosts. Generation of HIV‐１rmt could be considered as an opposite process to HIV‐１ emergence, i.e., adapting human-specific HIV‐１to replicate in new host macaques. HIV‐１rmt is a good model virus to determine functional and structural changes for survival in new hosts. To overcome species barrier, we modified HIV‐１genome by using two techniques : virus adaption and assisted evolution. Finally, we successfully constructed HIV‐１rmt clones which can antagonize all intrinsic restriction factors in macaque cells. Moreover, virological analyses of growth-enhancing mutations appeared in adaptation processes of the prototype HIV‐１rmt led to the identification of novel genomic regulatory elements for Vif expression. Our experimental system using HIV‐１rmt and macaque cells provides pivotal information on molecular bases for species-specific HIV‐１ replication, and would thus contribute to understanding the HIV‐１pathogenesis

The Fourth Major Restriction Factor Against HIV/SIV

Human and simian immunodeficiency viruses (HIV/SIVs) carry a unique set of accessory proteins that enhance virus replication in an optimized manner. These viral proteins specific to HIV/SIVs are designated Vif, Vpx, Vpr, Vpu, and Nef, and are functional in certain cell types (Malim and Emerman, 2008; Fujita et al., 2010). While viruses of the HIV-1 group do not encode Vpx, the other HIV-2/SIVs are unable to replicate in cells of the myeloid lineage such as monocyte-derived dendritic cells (MDDCs) and macrophages (MDMs) in the absence of Vpx (Fujita et al., 2010). Vpx and its structural close relative Vpr are leas

Nucleotide Variations Affect vif/Vif Expression

Vif is required for HIV-1 replication in natural target cells by counteracting host restriction factors, APOBEC3 (A3) proteins. We recently demonstrated that Vif expression level can be changed by naturally occurring single-nucleotide variations within SA1D2prox of the HIV-1 genome. We also found that levels for vif/vpr mRNAs are inversely correlated. While amino acid sequence per se is critical for functionality, Vif expression level modulated by signal sequences in its coding region is likely to be important as well. There are two splicing sites in the region involved in vpr expression. To reveal possible fluctuations of Vif-expression level, we examined SA1D2prox and vif gene by chimeric approaches using HIV-1 subtypes B and C with distinct anti-A3 activity. In this report, recombinant clones in subtype B backbone carrying chimeric sequences with respect to SA1D2prox/vif and those within the vif-coding region were generated. Of these, clones containing vif-coding sequence of subtype C, especially its 3′ region, expressed vif/Vif at a decreased level but did at an increased level for vpr/Vpr. Clones with reduced vif/Vif level grew similarly or slightly better than a parental clone in weakly A3G-positive cells but more poorly in highly A3G-expressing cells. Three clones with this property were also tested for their A3-degrading activity. One of the clones appeared to have some defect in addition to the poor ability to express vif/Vif. Taken all together, our results show that natural variations in the SA1D2prox and vif-coding region can change the Vif-expression level and affect the HIV-1 replication potential

Interdomain Linker of HIV/SIV Gag-CA

Gag proteins underlie retroviral replication by fulfilling numerous functional roles at various stages during viral life cycle. Out of the four mature proteins, Gag-capsid (CA) is a major component of viral particles, and has been most well studied biogenetically, biochemically and structurally. Gag-CA is composed of two structured domains, and also of a short stretch of disordered and flexible interdomain linker. While the two domains, namely, N-terminal and C-terminal domains (NTD and CTD), have been the central target for Gag research, the linker region connecting the two has been poorly studied. We recently have performed systemic mutational analyses on the Gag-CA linker region of HIV-1 by various experimental and in silico systems. In total, we have demonstrated that the linker region acts as a cis-modulator to optimize the Gag-related viral replication process. We also have noted, during the course of conducting the research project, that HIV-1 and SIVmac, belonging to distinct primate lentiviral lineages, share a similarly biologically active linker region with each other. In this brief article, we summarize and report the results obtained by mutational studies that are relevant to the functional significance of the interdomain linker of HIV/SIV Gag-CA. Based on this investigation, we discuss about the future directions of the research in this line

Complete Genome Sequences of Human Immunodeficiency Type 1 Viruses Genetically Engineered To Be Tropic for Rhesus Macaques

We have constructed two human immunodeficiency type 1 (HIV-1) derivatives, CXCR4 tropic and CCR5 tropic, that replicate in rhesus macaques. They are genetically engineered to be resistant to macaque restriction factors against HIV-1, including TRIM5α, APOBEC3, and tetherin proteins. The two HIV-1 variants described here are fundamental clones aiming for rhesus infection studies of HIV-1

Structural Dynamics of Retroviral Genome and the Packaging

Retroviruses can cause diseases such as AIDS, leukemia, and tumors, but are also used as vectors for human gene therapy. All retroviruses, except foamy viruses, package two copies of unspliced genomic RNA into their progeny viruses. Understanding the molecular mechanisms of retroviral genome packaging will aid the design of new anti-retroviral drugs targeting the packaging process and improve the efficacy of retroviral vectors. Retroviral genomes have to be specifically recognized by the cognate nucleocapsid domain of the Gag polyprotein from among an excess of cellular and spliced viral mRNA. Extensive virological and structural studies have revealed how retroviral genomic RNA is selectively packaged into the viral particles. The genomic area responsible for the packaging is generally located in the 5′ untranslated region (5′ UTR), and contains dimerization site(s). Recent studies have shown that retroviral genome packaging is modulated by structural changes of RNA at the 5′ UTR accompanied by the dimerization. In this review, we focus on three representative retroviruses, Moloney murine leukemia virus, human immunodeficiency virus type 1 and 2, and describe the molecular mechanism of retroviral genome packaging