A Single Amino Acid Substitution in a Segment of the CA Protein within Gag That Has Similarity to Human Immunodeficiency Virus Type 1 Blocks Infectivity of a Human Endogenous Retrovirus K Provirus in the Human Genome

Human endogenous retrovirus K (HERV-K) is the most intact retrovirus in the human genome. However, no single HERV-K provirus in the human genome today appears to be infectious. Since the Gag protein is the central component for the production of retrovirus particles, we investigated the abilities of Gag from two HERV-K proviruses to support production of virus-like particles and viral infectivity. HERV-K113 has full-length open reading frames for all viral proteins, while HERV-K101 has a full-length gag open reading frame and is expressed in human male germ cell tumors. The Gag of HERV-K101 allowed production of viral particles and infectivity, although at lower levels than observed with a consensus sequence Gag. Thus, including HERV-K109, at least two HERV-K proviruses in human genome today have functional Gag proteins. In contrast, HERV-K113 Gag supported only very low levels of particle production, and no infectivity was detectable due to a single amino acid substitution (I516M) near the extreme C terminus of the CA protein within Gag. The sequence of this portion of HERV-K CA showed similarities to that of human immunodeficiency virus type 1 and other primate immunodeficiency viruses. The extreme C terminus of CA may be a general determinant of retrovirus particle production. In addition, precise mapping of the defects in HERV-K proviruses as was done here identifies the key polymorphisms that need to be analyzed to assess the possible existence of infectious HERV-K alleles within the human population.Approximately 8% of the human genome comprises endogenous retroviruses (ERVs) (33, 59). These viruses infect germ lineage cells and thereby enter the genome of the host species. Thus, endogenous proviruses (the integrated form of retroviral DNA) are transmitted from parents to offspring in genomic DNA. If ERV genomes are intact, viral particles may be generated that can reinfect the germ line and form proviruses at new positions in the host genome. However, ERVs are subject to the same mutagenic processes over evolutionary time as any cellular gene. In the absence of selective pressure on the host to maintain intact viral genomes, endogenous retroviral proviruses accrue mutations over evolutionary time that inactivate viral infectivity. Most of the ERVs in the human genome have converted to solo long terminal repeats (solo LTRs), which are the product of homologous recombination between LTRs at the ends of the complete viral genome. Other types of mutations, such as nucleotide substitutions, insertions, and deletions, can also affect ERV proviruses, and many of the retroviral proviruses in the human genome have been inactivated by such mutations, which created premature stop codons or frameshifts in viral open reading frames (ORFs). The vast majority of the ERVs present in humans today (and perhaps all of them) have incurred mutations that inactivated viral infectivity.One provirus that exists in the genome of approximately 20% of humans, human ERV K113 (HERV-K113, referred to here as K113), has full-length ORFs for all viral proteins (8, 63). However, this provirus does not appear to be infectious, as the pol and env genes of K113 do not support infectivity (9, 19, 20). K113 belongs to a subset of HERV-K called HML-2 (43). Since the human and chimpanzee lineages diverged about 6 million years ago (52), the only proviruses that entered the genome of the human lineage belong to this subgroup, although other members of this subgroup entered the germ line prior to the divergence of the human and chimpanzee lineages (8, 27, 44, 63). The human-specific proviruses of this subgroup are the most intact retroviruses in the human genome. Infectious HERV-K particles have been generated using two different approaches based on their DNA sequences. HERV-KCON (K-CON) was constructed based on the consensus sequence of human-specific HERV-K proviruses (34). Infectious HERV-K particles were also generated by combining pieces from three separate proviruses, HERV-K109 (K109) gag-pro, HERV-K115 pol, and HERV-K108 (K108) env (20). Thus, it may be that no single provirus is infectious, but recombination and/or genetic complementation among multiple genomic proviruses may be required to produce infectious HERV-K particles. This raises the questions of whether multiple functional HERV-K components exist in the human genome today and how close these components are to being able to form a functional viral genome that might be capable of reinfecting human cells.To begin addressing these issues, we examined two of the full-length HERV-K gag genes that exist in the human genome today. Like all retroviruses, HERV-K contains the four genes necessary for viral replication: gag, pro, pol, and env. The human-specific HERV-K proviruses exist in two forms, type I and type II (38, 39). The type II proviruses contain gag, pro, pol, and env plus an accessory gene, rec, that encodes a protein (Rec) that functions in nuclear export of unspliced viral RNA in a manner analogous to that of human immunodeficiency virus type 1 (HIV-1) Rev (12, 40, 41, 65, 66). In type I proviruses, the pol and env genes are fused in frame by a 292-bp deletion that includes the first coding exon of rec, and the viruses encode an additional protein called Np9 (5, 48). The gag genes are relevant to whether HERV-K components in the human genome today might form an infectious virus, as the Gag protein is sufficient to produce virus-like particles (VLPs) in the absence of other viral proteins (4). Formation of such particles is an essential step for subsequent viral replication. Therefore, we decided to investigate whether Gag proteins from K113 and a second provirus, HERV-K101 (K101), are active in functional assays.     

Identification of Unusual E6 and E7 Proteins within Avian Papillomaviruses: Cellular Localization,Biophysical Characterization,and Phylogenetic Analysis

Papillomaviruses (PVs) are a large family of small DNA viruses infecting mammals, reptiles, and birds. PV infection induces cell proliferation that may lead to the formation of orogenital or skin tumors. PV-induced cell proliferation has been related mainly to the expression of two small oncoproteins, E6 and E7. In mammalian PVs, E6 contains two 70-residue zinc-binding repeats, whereas E7 consists of a natively unfolded N-terminal region followed by a zinc-binding domain which folds as an obligate homodimer. Here, we show that both the novel francolin bird PV Francolinus leucoscepus PV type 1 (FlPV-1) and the chaffinch bird PV Fringilla coelebs PV contain unusual E6 and E7 proteins. The avian E7 proteins contain an extended unfolded N terminus and a zinc-binding domain of reduced size, whereas the avian E6 proteins consist of a single zinc-binding domain. A comparable single-domain E6 protein may have existed in a common ancestor of mammalian and avian PVs. Mammalian E6 C-terminal domains are phylogenetically related to those of single-domain avian E6, whereas mammalian E6 N-terminal domains seem to have emerged by duplication and subsequently diverged from the original ancestral domain. In avian and mammalian cells, both FlPV-1 E6 and FlPV-1 E7 were evenly expressed in the cytoplasm and the nucleus. Finally, samples of full-length FlPV-1 E6 and the FlPV-1 E7 C-terminal zinc-binding domain were prepared for biophysical analysis. Both constructs were highly soluble and well folded, according to nuclear magnetic resonance spectroscopy measurements.Papillomaviruses (PVs) are nonenveloped, epitheliotropic, double-stranded DNA viruses that cause a variety of diseases in a multitude of hosts. Based on available whole-genome sequences and subgenomic amplicons, more than 200 human and over 55 nonhuman mammalian PV types have been described (7, 34, 35, 37, 38). To date, two avian PV types have been characterized (37, 38).The genomic organizations of the PVs are remarkably similar. The genome is ca. 8 kb in length and comprises an upstream regulatory region (URR), the early genes (E1, E2, E4, E6, and E7), and the late genes that encode the capsid proteins (L1 and L2). Although most PVs code for these seven open reading frames (ORFs), only the URR, the replicative proteins E1 and E2 (and possibly the E4 gene), and the capsid proteins L1 and L2 are strictly conserved in all PVs (11).Upon infection of the stratified squamous epithelia, PV gene expression is linked to the differentiation state of the infected epithelium cells. The expression of early PV proteins, in particular E6 and E7, primes the proliferation of the infected epithelium. This proliferation, which is absolutely required for viral replication, may become malignant depending on the PV strain considered. Several “high-risk” mucosal human PV (HPV) strains (predominantly HPV type 16 [HPV-16], HPV-18, and HPV-45) have been shown to be responsible for cervical cancer (19).The ability of PVs to induce proliferation of the infected cells has been attributed mainly to two small “oncoproteins,” E6 and E7. In genital high-risk HPVs, these proteins play a prominent role in cell immortalization and transformation (31). In most mammalian PVs, E6 is a small protein of about 150 amino acids, with two conserved N- and C-terminal zinc-binding domains, E6N and E6C, respectively (12). The solution structure of the HPV-16 E6C domain was recently determined (23). The sequence alignments pointed to a structural similarity between the E6C and E6N domains, suggesting that a single-domain protein possessing the same fold might have once existed. Earlier phylogenetic studies had suggested that gene duplication may have given rise to the current double-domain E6 proteins (5). Interestingly, although the E6 ORF has been found in most mammalian PVs (with the exception of bovine papillomavirus type 3 [BPV-3], BPV-4, BPV-6, HPV-101, and HPV-103 [3, 7]), it was not detected in the two avian PVs previously sequenced (37, 38).In this study, we present the full sequence of the genome of a novel PV from a francolin bird (Francolinus leucoscepus PV type 1 [FlPV-1]) and compare it to the two other avian PV genomes known to date (Psittacus erithacus PV [PePV] and Fringilla coelebs PV [FPV]). In light of recent structural data, we compare the unusual avian E6 and E7 ORFs to their mammalian orthologs. We describe the expression and purification of recombinant avian PV E6 and E7 proteins, their biophysical characterization, and cellular localization. Finally, we use phylogenetic techniques to investigate the evolutionary history of the E6 protein family.     

Zooplankton, phytoplankton and the microbial food web in two turbid and two clearwater shallow lakes in Belgium

Components of the pelagic food web in four eutrophic shallow lakes in two wetland reserves in Belgium (Blankaart and De Maten) were monitored during the course of 1998–1999. In each wetland reserve, a clearwater and a turbid lake were sampled. The two lakes in each wetland reserve had similar nutrient loadings and occurred in close proximity of each other. In accordance with the alternative stable states theory, food web structure differed strongly between the clearwater and turbid lakes. Phytoplankton biomass was higher in the turbid than the clearwater lakes. Whereas chlorophytes dominated the phytoplankton in the turbid lakes, cryptophytes were the most important phytoplankton group in the clearwater lakes. The biomass of microheterotrophs (bacteria, heterotrophic nanoflagellates and ciliates) was higher in the turbid than the clearwater lakes. Biomass and community composition of micro- and macrozooplankton was not clearly related to water clarity. The ratio of macrozooplankton to phytoplankton biomass – an indicator of zooplankton grazing pressure on phytoplankton – was higher in the clearwater when compared to the turbid lakes. The factors potentially regulating water clarity, phytoplankton, microheterotrophs and macrozooplankton are discussed. Implications for the management of these lakes are discussed.     

Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region

Background  

The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2), followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts.     

Involvement of the platelet-activating factor receptor in host defense against Streptococcus pneumoniae during postinfluenza pneumonia

Although influenza infection alone may lead to pneumonia, secondary bacterial infections are a much more common cause of pneumonia. Streptococcus pneumoniae is the most frequently isolated causative pathogen during postinfluenza pneumonia. Considering that S. pneumoniae utilizes the platelet-activating factor receptor (PAFR) to invade the respiratory epithelium and that the PAFR is upregulated during viral infection, we here used PAFR gene-deficient (PAFR-/-) mice to determine the role of this receptor during postinfluenza pneumococcal pneumonia. Viral clearance was similar in wild-type and PAFR-/- mice, and influenza virus was completely removed from the lungs at the time mice were inoculated with S. pneumoniae (day 14 after influenza infection). PAFR-/- mice displayed a significantly reduced bacterial outgrowth in their lungs, a diminished dissemination of the infection, and a prolonged survival. Pulmonary levels of IL-10 and KC were significantly lower in PAFR-/- mice, whereas IL-6 and TNF-alpha were only trendwise lower. These data indicate that the pneumococcus uses the PAFR leading to severe pneumonia in a host previously exposed to influenza A.     

Phytoplankton growth rates in the freshwater tidal reaches of the Schelde estuary (Belgium) estimated using a simple light-limited primary production model

During the course of 1996, phytoplankton was monitored in the turbid, freshwater tidal reaches of the Schelde estuary. Using a simple light-limited primary production model, phytoplankton growth rates were estimated to evaluate whether phytoplankton could attain net positive growth rates and whether growth rates were high enough for a bloom to develop. Two phytoplankton blooms were observed in the freshwater tidal reaches. The first bloom occurred in March and was mainly situated in the most upstream reaches of the freshwater tidal zone, suggesting that it was imported from the tributary river Schelde. The second bloom occurred in July and August. This summer bloom was situated more downstream in the freshwater tidal reaches and appeared to have developed within the estuary. A comparison between phytoplankton growth rates estimated using a simple primary production model and flushing rate of the water indicated that no net increase in phytoplankton biomass was possible in March while phytoplankton could theoretically increase its biomass by 20% per day during summer. Chlorophyllaconcentrations at all times decreased strongly at salinities between 5–10 psu. This decline was ascribed to a combination of salinity stress and light limitation. Phytoplankton biomass and estimated annual net production were much higher in the freshwater tidal zone compared to the brackish reaches of the estuary (salinity > 10 psu) despite mixing depth to euphotic depth ratios being similar. Possible reasons for this high production include high nutrient concentrations, low zooplankton grazing pressure and import of phytoplankton blooms from the tributary rivers.     

Phytoplankton–bacterioplankton interactions in a neotropical floodplain lake (Laguna Bufeos,Bolivia)

Laguna Bufeos is a floodplain lake of the river Ichilo, a tributary of the Amazon basin situated in Bolivia. Nutrient addition assays involving whole water (<200 μm) as well as fractionated water (<0.8 μm) treatments were carried out in incubation tubes to test whether bacterial growth is limited by the availability of inorganic nutrients and to test whether bacteria are able to utilize inorganic nutrients directly or are stimulated by inorganic nutrients through increased production of phytoplankton. The assays were carried out during two extreme hydrological conditions, the high-water and the low-water period. During the high-water period experiment, neither N or P limited bacterial growth rates. During the low-water period, bacterial growth was P limited. Bacterial growth was stimulated in the fractionated as well as in the whole water treatments, indicating that bacterial growth was directly stimulated by P. Bacterial growth corrected for grazing losses (determined by means of dilution experiments) was significantly higher in the fractionated water containing only bacteria when compared to the whole water containing also grazers and phytoplankton. This suggests that bacterial growth was suppressed by competition with phytoplankton rather than stimulated through the production of dissolved organic matter by phytoplankton.