Visualizing the viral burden: phenotypic and functional alterations of T cells and APCs during persistent infection

Persistent viral infections continue to present major public health problems. Failure to achieve virus control confronts the immune system with a chronic viral burden that may involve immune cells themselves and directly compromise the functionality of effector lymphocytes and APCs. In this study we use the lymphocytic choriomeningitis virus system for persistent viral infection of its natural murine host and use analytical techniques for direct ex vivo visualization of virus-infected immune cells. We report that virtually all cells of the immune system can be infected, but the distribution of the viral burden is differentially allocated to lymphocyte and APC subsets of defined phenotypes. Importantly, the profile of immune cell infection found in the blood is broadly representative for the pattern of cellular infection in most organs and is independent of the presence of Abs or complement. By direct comparison of virus-infected and uninfected cell subsets, we demonstrate that lymphocytic choriomeningitis virus-infected T cells show preferential activation, skewed cytokine profiles, and increased apoptosis. In contrast, increased activation of APCs is generalized and independent of the presence of viral Ag. Our data indicate that specific patterns of immune cell infection are associated with distinct forms of immunostimulatory and immunosuppressive alterations that may provide insights into autoimmune processes associated with infectious disease and offer clues for therapeutic interventions aimed at restoration of complete immunity.     

Bone alterations during HIV infection

Osteopenia and osteoporosis are common in HIV-1-infected individuals and represent a challenge in clinical and therapeutic management. Since the mechanisms underlying this degenerative process are largely unsettled and it has not yet been determined whether bone dysfunction is linked to HIV-1-mediated direct and/or indirect effects on osteoblasts/osteoclasts cross-talk regulation, this brief review analyzes an array of mechanisms that could account for the dramatic bone derangement (bone loss and osteopenia/osteoporosis) during the course of HIV-1 infection.     

Persistent vesicular stomatitis virus infection mediates base substitutions in viral RNA termini.

We have sequenced (via a product RNA) the 3' RNA terminus of a defective interfering particle that was generated from the standard virus isolated from a culture of BHK-21 cells persistently infected with vesicular stomatitis virus for over 5 years. By hybridization and RNA sequencing, seven mutations were identified in the 46 nucleotides at the terminus of this defective-interfering-particle RNA. It is likely that these mutations are a reflection of altered protein-nucleic acid interactions that the virus has evolved to maintain its persistently infected carrier state in vitro.     

Characterization of homologous defective interfering RNA during persistent infection of Vero cells with Japanese encephalitis virus

It has been suggested that defective interfering (DI) RNA contributes to the persistence of Japanese en-cephalitis virus (JEV). In this study, we characterized molecular and biological aspects of the DI RNA and its relation to viral persistence. We identified a homolo-gous DI virus intimately associated with JEV persis-tence in Vero cells. The production of DI RNA during undiluted serial passages of JEV coincided with the appearance of cells refractory to acute infection with JEV. We also established a Vero cell clone with a per-sistent JEV infection in which the DI RNA co-replicated efficiently at the expense of helper virus. The infectious virus yield of the clone fluctuated dur-ing its growth depending upon the amount of DI RNA accumulated in the previous replication cycle. Identifi-cation of the corresponding negative-sense RNA of the DI RNA indicated that the DI RNA functioned as a replication unit. Most of the DI RNA molecules re-tained their open reading frames despite a large dele-tion, encompassing most of the prM, the entire E, and the 5' half of the NS1 gene. Taken together, these ob-servations suggest that the generation of homologous DI RNA during successive JEV acute infections in Vero cells probably participates actively in persistent JEV infection.     

Calcium exchange and structural changes during the photosynthetic oxygen evolving cycle

PSII catalyzes the oxidation of water and reduction of plastoquinone in oxygenic photosynthesis. PSII contains an oxygen-evolving complex, which is located on the lumenal side of the PSII reaction center and which contains manganese, calcium, and chloride. Four sequential photooxidation reactions are required to generate oxygen. This process produces five Sn-states, where n refers to the number of oxidizing equivalents stored. Calcium is required for oxygen production. Strontium is the only divalent cation that replaces calcium and maintains activity. In our previous FT-IR work, we assessed the effect of strontium substitution on substrate-limited PSII preparations, which were inhibited at the S3 to S0 transition. In this work, we report reaction-induced FT-IR studies of hydrated PSII preparations, which undergo the full S-state cycle. The observed difference FT-IR spectra reflect long-lived photoinduced conformational changes in the oxygen-evolving complex; strontium exchange identifies vibrational bands sensitive to substitutions at the calcium site. During the S1' to S2' transition, the data are consistent with an electrostatic or structural perturbation of the calcium site. During the S3' to S0' and S0' to S1' transitions, the data are consistent with a perturbation of a hydrogen bonding network, which contains calcium, water, and peptide carbonyl groups. To explain our data, persistent shifts in divalent cation coordination must occur when strontium is substituted for calcium. A modified S-state model is proposed to explain these results and results in the literature.     

Hemophagocytic macrophages harbor Salmonella enterica during persistent infection

Salmonella enterica subspecies can establish persistent, systemic infections in mammals, including human typhoid fever. Persistent S. enterica disease is characterized by an initial acute infection that develops into an asymptomatic chronic infection. During both the acute and persistent stages, the bacteria generally reside within professional phagocytes, usually macrophages. It is unclear how salmonellae can survive within macrophages, cells that evolved, in part, to destroy pathogens. Evidence is presented that during the establishment of persistent murine infection, macrophages that contain S. enterica serotype Typhimurium are hemophagocytic. Hemophagocytic macrophages are characterized by the ingestion of non-apoptotic cells of the hematopoietic lineage and are a clinical marker of typhoid fever as well as certain other infectious and genetic diseases. Cell culture assays were developed to evaluate bacterial survival in hemophagocytic macrophages. S. Typhimurium preferentially replicated in macrophages that pre-phagocytosed viable cells, but the bacteria were killed in macrophages that pre-phagocytosed beads or dead cells. These data suggest that during persistent infection hemophagocytic macrophages may provide S. Typhimurium with a survival niche.     

Role of the host cell in persistent viral infection: Coevolution of L cells and reovirus during persistent infection

Mutant L cells, designated LR cells, were isolated after “curing” a persistently infected cell line (L/C) with antireovirus serum. The LR cells were shown to be virus-free; no reovirus was detectable by infectious center assays, plaque assays, presence of viral proteins, presence of viral dsRNA and immunofluorescence studies. Persistent infections were readily established in LR cells following infection with either cloned, low passage wild-type reovirus or cloned, low passage reovirus isolated from carrier cultures. Reovirus isolated from carrier cultures, however, grew much better than wild-type reovirus in LR cells and showed complete dominance over wild-type reovirus in coinfection experiments. Infection of LR cells with wild-type reovirus resulted in a low-level persistent infection with inefficient viral replication; these mutant L cells were partially resistant to infection with wild-type reovirus. In contrast, infection of the mutant L cells with virus isolated from the persistently infected cells resulted in a persistent infection accompanied with efficient viral replication. Infection of the original L cells with either wild-type reovirus or reovirus isolated from the persistently infected cells resulted in a lytic infection with no surviving cells. Thus the host cell plays a crucial role in the maintenance of persistent reovirus infection. Our results show that there is a coevolution of both mutant L cells and mutant reovirus during persistent infection.     

Blocked and unblocked 5' termini in reovirus genome RNA

Uniformly ³²P-labeled, double-stranded genome RNA isolated from purified reovirus contains two types of 5′-terminal sequences. One strand contains a phosphatase-resistant 5′-terminal structure, XpppG^*pCpU, which is also present in the viral mRNA. The 5′ blocking group, X, is removed by β-elimination indicating that it is a nucleoside containing free 2′,3′-hydroxyls. G^*pC is an alkaline-resistant, 2′-O-methylated sequence. The other strand contains a phosphatase-sensitive 5′ sequence, ppGpPupPyp. The results are discussed in relation to blocked 5′-terminal structures in other viral and cellular RNAs.     

Characterization of genetic changes occurring in attenuated poliovirus 2 during persistent infection in mouse central nervous systems.

Genomic changes occurring in the attenuated W-2 strain of poliovirus 2 during persistent infection of the central nervous system of immunosuppressed mice were analyzed. The RNase T1 oligonucleotide fingerprints of 34 different viruses, isolated from the brains and spinal cords of paralyzed and nonparalyzed mice during a 105-day period, were used to quantitate and compare the mutations occurring in each isolate. Although mice were inoculated with plaque-purified virus, genetically distinct viruses were recovered from the central nervous system. The number of oligonucleotide changes occurring in isolates from paralyzed mice generally was greater than that observed in isolates from nonparalyzed mice. However, differences in the extent of mutation in isolates from the two groups of mice did not appear to be related to the level of virus replication. In paralyzed mice, the number of oligonucleotide changes on average was greater in viruses isolated during the first 60 days of the infection than in the last 45 days. The number of oligonucleotide changes was essentially constant throughout the infection, however, in viruses isolated from the brains of nonparalyzed mice. In addition, several specific oligonucleotide changes were found only in viruses isolated from paralyzed animals.     

Phosphorylation of the termini of Cauliflower mosaic virus precapsid protein is important for productive infection

Cauliflower mosaic virus (CaMV) coat protein precursor (pre-CP) has 489 amino acids (p57) and is processed by the viral proteinase into three major forms: p44, p39, and p37. The N- and C-terminal extensions of pre-CP are released during maturation by the virus-encoded proteinase. We showed that these extensions are phosphorylated at several sites by host casein kinase II (CKII). We have identified the phosphorylated amino acids using an in vitro phosphorylation assay and tested the effect of mutation of these sites on viral infectivity. Mutation of serines S66, S68, and S72 to alanine in the N-terminal extension abolished phosphorylation of the protein in vitro. Also, mutation of all S and T residues in the C-terminus (450 to 489) made this region insensitive to CKII. Amino acid substitutions also were introduced into a full-length infectious clone of CaMV. Mutated forms of the virus with S66, S68, and S72 substituted with A or D showed a delay in symptom development and affected the infectivity of the virus. However, a mutant with an A substitution of all the S and T residues of the C-terminal extension of CP was not infectious. These results suggest that phosphorylation of the N- and C-termini of CaMV pre-CP plays an important role in the initiation of viral infection.     

Positively charged termini of the L2 minor capsid protein are necessary for papillomavirus infection

Coexpression of bovine papillomavirus L1 with L2 mutants lacking either eight N-terminal or nine C-terminal amino acids that encode positively charged domains resulted in wild-type levels of viral genome encapsidation. Despite wild-type binding to the cell surface, the resulting virions were noninfectious. An L2 mutant encoding a scrambled version of the nine C-terminal residues restored infectivity, in contrast to an L2 mutant encoding a scrambled version of the N-terminal residues.     

Evaluating conformational changes in protein structures binding RNA

Many protein-RNA recognition events are known to exhibit conformational changes from qualitative observations of individual complexes. However, a quantitative estimation of conformational changes is required if protein-RNA docking and template-based methods for RNA binding site prediction are to be developed. This study presents the first quantitative evaluation of conformational changes that occur when proteins bind RNA. The analysis of twelve RNA-binding proteins in the bound and unbound states using error-scaled difference distance matrices is presented. The binding site residues are mapped to each structure, and the conformational changes that affect these residues are evaluated. Of the twelve proteins four exhibit greater movements in nonbinding site residues, and a further four show the greatest movements in binding site residues. The remaining four proteins display no significant conformational change. When interface residues are found to be in conformationally variable regions of the protein they are typically seen to move less than 2 A between the bound and unbound conformations. The current data indicate that conformational changes in the binding site residues of RNA binding proteins may not be as significant as previously suggested, but a larger data set is required before wider conclusions may be drawn. The implications of the observed conformational changes for protein function prediction are discussed.