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Soil to genomics: the Streptomyces chromosome.

The 8-9-Mb Streptomyces chromosome is linear, with a "core" containing essential genes and "arms" carrying conditionally adaptive genes that can sustain large deletions in the laboratory. Bidirectional chromosome replication from a central oriC is completed by "end-patching," primed from terminal proteins covalently bound to the free 5'-ends. Plasmid-mediated conjugation involves movement of double-stranded DNA by proteins resembling other bacterial motor proteins, probably via hyphal tip fusion, mediated by these transfer proteins. Circular plasmids probably transfer chromosomes by transient integration, but linear plasmids may lead the donor chromosome end-first into the recipient by noncovalent association of ends. Transfer of complete chromosomes may be the rule. The recipient mycelium is colonized by intramycelial spreading of plasmid copies, under the control of plasmid-borne "spread" genes. Chromosome partition into prespore compartments of the aerial mycelium is controlled in part by actin- and tubulin-like proteins, resembling MreB and FtsZ of other bacteria.

Bacterial Proteins↗

Popliteomeniscal fascicle tears causing symptomatic lateral compartment knee pain: diagnosis by the figure-4 test and treatment by open repair.

BACKGROUND: Injuries to the popliteomeniscal fascicles of the lateral meniscus are difficult to identify from physical examination and magnetic resonance imaging scans. To our knowledge, there have been no described physical examination techniques to identify symptomatic isolated popliteomeniscal fascicle tears. The popliteomeniscal fascicles have been demonstrated to be important for lateral meniscus stability, and it has been reported that tears can lead to painful symptoms. HYPOTHESIS: Popliteomeniscal fascicle tears cause symptomatic lateral compartment knee pain and can be diagnosed by physical examination. Surgical repair can improve patient function. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: Six patients with isolated tears of the popliteomeniscal fascicles, which caused lateral joint line knee pain, were identified by positive figure-4 test results. RESULTS: All patients were found to have replication of their symptoms while placing the affected knee in the figure-4 position and were found to have lateral meniscal hypermobility due to tears of the popliteomeniscal fascicles on arthroscopic examination. All patients had an open repair of the popliteomeniscal fascicles of the lateral meniscus with complete resolution of their symptoms at a mean follow-up of 3.8 years postoperatively. CONCLUSIONS: The figure-4 test was found to be useful in identifying the source of lateral compartment knee pain due to popliteomeniscal fascicle tears. Open repair of isolated popliteomeniscal fascicle tears was also found to be effective in resolving lateral compartment knee pain due to popliteomeniscal fascicle tears.

Adult↗

Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution and involved in maintenance of the mitochondrial genome.

A novel protein family (p14.5, or YERO57c/YJGFc) highly conserved throughout evolution has recently been identified. The biological role of these proteins is not yet well characterized. Two members of the p14.5 family are present in the yeast Saccharomyces cerevisiae. In this study, we have characterized some of the biological functions of the two yeast proteins. Mmf1p is a mitochondrial matrix factor, and homologous Mmf1p factor (Hmf1p) copurifies with the soluble cytoplasmic fraction. Deltammf1 cells lose mitochondrial DNA (mtDNA) and have a decreased growth rate, while Deltahmf1 cells do not display any visible phenotype. Furthermore, we demonstrate by genetic analysis that Mmf1p does not play a direct role in replication and segregation of the mtDNA. rho(+) Deltammf1 haploid cells can be obtained when tetrads are directly dissected on medium containing a nonfermentable carbon source. Our data also indicate that Mmf1p and Hmf1p have similar biological functions in different subcellular compartments. Hmf1p, when fused with the Mmf1p leader peptide, is transported into mitochondria and is able to functionally replace Mmf1p. Moreover, we show that homologous mammalian proteins are functionally related to Mmf1p. Human p14.5 localizes in yeast mitochondria and rescues the Deltammf1-associated phenotypes. In addition, fractionation of rat liver mitochondria showed that rat p14.5, like Mmf1p, is a soluble protein of the matrix. Our study identifies a biological function for Mmf1p and furthermore indicates that this function is conserved between members of the p14.5 family.

Amino Acid Sequence↗

Analysis of p21CDKN1A recruitment to DNA excision repair foci in the UV-induced DNA damage response.

The cyclin-dependent kinase (CDK) inhibitor p21CDKN1A (also known as p21(waf1/cip1)) is a well known player of the G1 and G2 phase cell cycle checkpoints, which are activated in response to DNA damage. In addition, p21 interacts directly with proliferating cell nuclear antigen (PCNA), thereby inhibiting DNA replication. More controversial is the role of p21 in DNA repair, since both inhibition of and requirement for nucleotide excision repair have been suggested. Since the DNA repair process occurs at discrete nuclear foci in a chromatin-bound compartment, a suitable extraction procedure is necessary to investigate the association of p21 with PCNA in these structures. This chapter focuses on biochemical and immunofluorescence methods to analyze the recruitment of p21 protein to DNA repair foci. Cellular fractionation and subsequent nuclear extraction procedures are described for Western blot analysis of p21 recruitment, as well as for protein-protein interaction studies. An in situ extraction protocol is also described for immunofluorescence microscopy and flow cytometric analyses of nuclear localization and cell cycle distribution of p21 recruited to DNA repair foci. The combination of these methodologies is extremely powerful to investigate in more detail the role of p21 in the UV-induced DNA damage response.

Cell Cycle↗

Regulation of minute virus of mice NS1 replicative functions by atypical PKClambda in vivo.

Minute virus of mice NS1 protein is a multifunctional phosphoprotein endowed with a variety of enzymatic and regulatory activities necessary for progeny virus particle production. To regulate all of its different functions in the course of a viral infection, NS1 has been proposed to be modulated by posttranslational modifications, in particular, phosphorylation. Indeed, it was shown that the NS1 phosphorylation pattern is altered during the infectious cycle and that the biochemical profile of the protein is dependent on the phosphorylation state of the polypeptide. Moreover, in vitro approaches have identified members of the protein kinase C (PKC) family, in particular, atypical PKC, as regulators of viral DNA replication through the phosphorylation of NS1 residues T435 and S473, thereby activating the protein for DNA unwinding activities. In order to substantiate these findings in vivo, we produced NS1 in the presence of a dominant-negative PKClambda mutant and characterized the purified protein in vitro. The NS1 protein produced under these conditions was found to be only partially phosphorylated and as a consequence to be deficient for viral DNA replication. However, it could be rescued for this viral function by treatment with recombinant activated PKClambda. Our data clearly demonstrate that NS1 is a target for PKClambda phosphorylation in vivo and that this modification is essential for the helicase activity of the viral polypeptide. In addition, the phosphorylation of NS1 at residues T435 and S473 appeared to occur mainly in the nucleus, providing further evidence for the involvement of PKClambda which, unlike PKCzeta, accumulates in the nuclear compartment of infected cells.

Animals↗

Nuclear matrix proteins as structural and functional components of the mitotic apparatus.

The eukaryotic nucleus is a membrane-enclosed compartment containing the genome and associated organelles supported by a complex matrix of nonhistone proteins. Identified as the nuclear matrix, this component maintains spatial order and provides the structural framework needed for DNA replication, RNA synthesis and processing, nuclear transport, and steroid hormone action. During mitosis, the nucleoskeleton and associated chromatin is efficiently dismantled, packaged, partitioned, and subsequently reassembled into daughter nuclei. The dramatic dissolution of the nucleus is accompanied by the assembly of a mitotic apparatus required to facilitate the complex events associated with nuclear division. Until recently, little was known about the fate or disposition of nuclear matrix proteins during mitosis. The availability of specific molecular probes and imaging techniques, including confocal microscopy and improved immunoelectron microscopy using resinless sections and related procedures, has enabled investigators to identify and map the distribution of nuclear matrix proteins throughout the cell cycle. This chapter will review the structure, function, and distribution of the protein NuMA (nuclear matrix mitotic apparatus) and other nuclear matrix proteins that depart the nucleus during the interphase/mitosis transition to become structural and functional components within specific domains of the mitotic apparatus.

Animals↗

Regulation of the tonsil cytokine milieu favors HIV susceptibility.

Mucosal associated lymphoid tissues are major targets of HIV during early infection and disease progression but can also provide a viral safe haven during highly active antiretroviral therapy. Among these tissues, the tonsils remain enigmatic regarding their status as primary and/or secondary sites of retroviral infection. To dissect the mechanisms underlying susceptibility to HIV in this compartment, isolated tonsil cells were studied for phenotypic and functional characteristics, which may account for their permissiveness to infection. For this, tonsil cells and PBMC were infected in parallel with HIV, and viral replication was monitored by p24 ELISA. Our results demonstrate that unstimulated tonsil cells were more readily infected than PBMC with HIV. Phenotypic characterization of the tonsil cells revealed heterogeneous lymphoid populations but with increased expression of early activation markers and the viral co-receptor CXCR4, relative to PBMC, all of which may contribute to viral susceptibility. Furthermore, the cytokine microenvironment appeared to be key in facilitating HIV infection and tonsil-secreted products enhanced HIV infection in PBMC. Of the cytokines detected in the tonsil supernatants, TH2 cytokines, particularly IL-4, promoted HIV infection and replication. Interestingly, this TH2 profile appeared to dominate, even in the presence of the TH1 cytokine IFNgamma and the anti-viral factor IFNalpha, likely due to the enhanced expression of suppressor of cytokine signaling (SOCS) proteins, which may disengage IFN signaling. These and other local environmental factors may render tonsil cells increasingly susceptible to HIV infection.

Cytokines↗

Morphometric analyses of adrenal gland growth in fetal and neonatal sheep. III. Volumes of the major organelles within zona fasciculata steroidogenic cells.

We have undertaken a morphometric analysis of the distribution patterns of the major subcellular organelles of the zona fasciculata in fetal (53, 100, 130, 144 days) and neonatal (2 days) sheep as they may be expressed as volume densities, volumes per cell, volumes per 100 microns 3 of cytoplasm per cell, and volumes per mm3 of steroidogenic cells per gland. Data obtained indicate that certain of the volume densities and the 3 other volume indicators of the 6 organelles considered change with gestational age. While the volume of mitochondria per cell increased in late gestation because of cellular hypertrophy, the real time volumes of mitochondria per unit volume of cell or gland did not vary significantly during the period of development studied. The volume of the SER, however, changed markedly, being minimal at 100 days fetal development (0.68 gestation) and increasing, probably initially during the 123-130 day (0.84-0.88 gestation) period, until the end of the fetal period (term = 147 days). The SER exhibited the most marked variability in the three volume indicators, the volumes correlating closely with cell size and steroidogenic capability. The RER volumes altered little, decreasing per 100 microns 3 of cytoplasm from mid-gestation, probably as a reflection of the cell maturity state attained. Changes in the distribution of the Golgi apparatus paralleled those of the SER; but the lipid storage droplets were sparse and their volumes constant. In the fetal sheep, the Golgi apparatus appears to be a significant component of the steroidogenic organelle complex, while the lipid droplet compartment does not. Consideration of growth during the 2nd major growth phase of the adrenal cortex (from before 0.85 gestation), as expressed in mitotic events, showed that at 130 days (0.88 gestation) cellular replication was randomly spread through the zona fasciculata, whereas at 144 days (0.98 gestation) mitoses were twice as prevalent in the outer half of that zone as they were in the inner half. At 130 and 144 days, the cells of the outer half of the zona fasciculata contained significantly more smooth endoplasmic reticulum than did those of the inner half. The maturation of the zona fasciculata, which allows the maximal production of cortisol in late pregnancy, thus occurs in a centripetal direction. This may result from the fact that the outer cells of the zona fasciculata are first in contact with the rising levels of ACTH and cortisol, two primary determinants of its growth and differentiation during the last 3 weeks of gestation.

Animals↗

Detection of HIV-specific cell-mediated cytotoxicity in the peripheral blood from infected children.

Cytotoxic T lymphocytes may play a significant role in containing the spread of HIV in infected individuals. Although HIV-infection is associated with immune suppression, a vigorous T lymphocyte response has been detected in infected adults. HIV can be transmitted from mother to child, either during pregnancy, when differentiation of the T lymphoid compartment is ongoing, or at birth when the neonate immune system is partially competent. The shorter asymptomatic period of pediatric infection could be related to differences in the host immune control of viral replication. HIV-specific cell-mediated cytotoxicity (CMC) from fresh and in vitro stimulated PBMC of HIV-infected children was measured. CD8+CD3+ T lymphocytes were found to be the major effector population. The vast majority of children examined had detectable HIV-specific CMC. A cross-sectional analysis of CMC responses as a function of clinical status revealed that 71% of asymptomatic children (CDC stage P1) recognized the Env protein, 14% the Gag protein, but none of them recognized the Pol protein. Cytolytic activities directed against these three proteins were detected in two thirds of paucisymptomatic children (P2A). In contrast, symptomatic children (P2B-F) did not show cytolytic activities toward the Gag and Pol proteins, and only 20% recognized the Env protein. In contrast in vitro generated secondary CTL were consistently detected at all stages of disease, even in children with low CD4+ cells counts.

Amino Acid Sequence↗

Rabbit conjunctival and corneal epithelial cells belong to two separate lineages.

PURPOSE: This study investigated rabbit conjunctival and corneal epithelial cells to determine if they belong to two separate lineages. METHODS: Rabbit corneal, limbal, and conjunctival epithelial cells were isolated and grown in Dulbecco's minimum essential media and 20% fetal bovine serum in the presence of mitomycin-treated 3T3 feeder cells. After reaching 80% confluence, 3T3 feeder cells and any contaminating fibroblasts were removed, and epithelial cells were resuspended in fresh Dulbecco's minimum essential media. Aliquots containing 5x10(6) cells were placed subcutaneously into the flanks of athymic mice, which subsequently formed small nodules. At 2, 4, 6, 8, 14, 21, and 28 days, athymic mice were killed and the nodules (epithelial cyst) were excised for light and transmission electron microscopic examination and histochemical and cell kinetic analyses. RESULTS: Within 2 days after injection of single-cell suspensions, cells aggregated to form cysts lined with a stratified squamous epithelium, the structure of which resembled the original in vivo donor sites by 8 days. Limbal- and corneal-derived cysts were comprised only of glycogen-rich stratified epithelial cells. In contrast, only cysts arising from cultured conjunctival cells contained periodic acid-Schiff-positive cells with a goblet cell structure interspersed among stratified epithelial cells. Furthermore, cystic epithelium of conjunctival origin did not accumulate glycogen. CONCLUSIONS: To determine whether distinct phenotypes are caused by intrinsic divergence or by environmental modulation, the behavior of cells can be monitored in an identical in vivo growth environment. The athymic mouse provides such a permissive growth environment for cultured corneal, limbal, and conjunctival epithelial cells. All these cells reproduced their in vivo phenotype when placed in the athymic mouse. Thus, these findings provide the strongest evidence to date that the corneal-limbal lineage is distinct from the conjunctival lineage. These data also support the idea that the progenitor of goblet cells does not reside in the corneal-limbal epithelial compartment.

Animals↗

Protein-protein interactions between hepatitis C virus nonstructural proteins.

Replication of the hepatitis C virus (HCV) genome has been proposed to take place close to the membrane of the endoplasmic reticulum in membrane-associated replicase complexes, as is the case with several other plus-strand RNA viruses, such as poliovirus and flaviviruses. The most obvious benefits of this property are the possibility of coupling functions residing in different polypeptidic chains and the sequestration of viral proteins and nucleic acids in a distinct cytoplasmic compartment with high local concentrations of viral components. Indeed, HCV nonstructural (NS) proteins were clearly colocalized in association with membranes derived from the endoplasmic reticulum. This observation, together with the demonstration of the existence of several physical interactions between HCV NS proteins, supports the idea of assembly of a highly ordered multisubunit protein complex(es) probably involved in the replication of the viral genome. The objective of this study, therefore, was to examine all potential interactions between HCV NS proteins which could result in the formation of a replication complex(es). We identified several interacting viral partners by using a glutathione S-transferase pull-down assay, by in vitro and ex vivo coimmunoprecipitation experiments in adenovirus-infected Huh-7 cells allowing the expression of HCV NS proteins, and, finally, by using the yeast two-hybrid system. In addition, by confocal laser scanning microscopy, NS proteins were clearly shown to colocalize when expressed together in Huh-7 cells. We have been able to demonstrate the existence of a complex network of interactions implicating all six NS proteins. Our observations confirm previously described associations and identify several novel homo- and heterodimerizations.

Dimerization↗

Structure and function in the nucleus: subnuclear trafficking of DNA replication factors.

The traditional view of the eukaryotic cell nucleus as a more or less amorphous milieu in which proteins and nucleic acids are freely floating has been challenged by an ever increasing number of reports uncovering highly organized structures where biological processes are concentrated together with their corresponding factors. The identification and utilization of protein domains that are necessary and sufficient for targeting to different subnuclear compartments have begun to elucidate the molecular principles underlying this structural organization and its dynamic behavior. The combination of biochemical, cell biology, and biophysical approaches to study nuclear structure and function should help to elucidate how these higher-order structures organize and coordinate countless enzymatic activities in time and space within the mammalian nucleus. J. Cell Biochem. Suppls. 32/33:15-23, 1999.

Animals↗

ORF1a-encoded replicase subunits are involved in the membrane association of the arterivirus replication complex.

Among the functions of the replicase of equine arteritis virus (EAV; family Arteriviridae, order Nidovirales) are important viral enzyme activities such as proteases and the putative RNA polymerase and RNA helicase functions. The replicase is expressed in the form of two polyproteins (open reading frame 1a [ORF1a] and ORF1ab), which are processed into 12 nonstructural proteins by three viral proteases. In immunofluorescence assays, the majority of these cleavage products localized to the perinuclear region of the cell. A dense granular and vesicular staining was observed, which strongly suggested membrane association. By using confocal microscopy and double-label immunofluorescence, the distribution of the EAV replicase was shown to overlap with that of PDI, a resident protein of the endoplasmic reticulum and intermediate compartment. An in situ labeling of nascent viral RNA with bromo-UTP demonstrated that the membrane-bound complex in which the replicase subunits accumulate is indeed the site of viral RNA synthesis. A number of ORF1a-encoded hydrophobic domains were postulated to be involved in the membrane association of the arterivirus replication complex. By using various biochemical methods (Triton X-114 extraction, membrane purification, and sodium carbonate treatment), replicase subunits containing these domains were shown to behave as integral membrane proteins and to be membrane associated in infected cells. Thus, contribution to the formation of a membrane-bound scaffold for the viral replication-transcription complex appears to be an important novel function for the arterivirus ORF1a replicase polyprotein.

Animals↗

Determinants for membrane association of the hepatitis C virus RNA-dependent RNA polymerase.

The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), represented by nonstructural protein 5B (NS5B), is believed to form a membrane-associated RNA replication complex together with other nonstructural proteins and as yet unidentified host components. However, the determinants for membrane association of this essential viral enzyme have not been defined. By double label immunofluorescence analyses, NS5B was found in the endoplasmic reticulum (ER) or an ER-like modified compartment both when expressed alone or in the context of the entire HCV polyprotein. The carboxyl-terminal 21 amino acid residues were necessary and sufficient to target NS5B or a heterologous protein to the cytosolic side of the ER membrane. This hydrophobic domain is highly conserved among 269 HCV isolates analyzed and predicted to form a transmembrane alpha-helix. Association of NS5B with the ER membrane occurred by a posttranslational mechanism that was ATP-independent. These features define the HCV RdRp as a new member of the tail-anchored protein family, a class of integral membrane proteins that are membrane-targeted posttranslationally via a carboxyl-terminal insertion sequence. Formation of the HCV replication complex, therefore, involves specific determinants for membrane association that represent potential targets for antiviral intervention.

Amino Acid Sequence↗

Antiviral profile of HIV inhibitors in macrophages: implications for therapy.

Macrophages (M/M) are identified as the second cellular target of HIV and a crucial virus reservoir. M/M are persistently infected cells and not susceptible to the HIV cytophatic effects typical of infected CD4+ T-lymphocytes. HIV replication in M/M is a crucial pathogenetic event during the whole course of the disease. Moreover, the dynamics of HIV-1 replication and cumulative virus production is quite different in M/M and CD4+ T-lymphocytes in the presence or in the absence of antiviral drugs. Thus, for their unique cellular characteristics, the activity of anti-HIV compounds could be different in M/M than in CD4+ T-lymphocytes. Indeed, nucleoside analogues inhibitors of HIV-reverse transcriptase (NRTIs) show potent antiviral activity in macrophages, although the limited penetration of these compounds in sequestered body compartments and the scarce phosphorylation ability of macrophages, suggest that a phosphate group linked to NRTIs may confer a greater anti-HIV activity in such cells. The antiviral activity of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in macrophages is similar to that found in CD4-lymphocytes. Interestingly, protease inhibitors (PIs), acting at post-integrational stages of virus replication, are the only drugs able to interfere with virus production and release from macrophages with established and persistent HIV infection. For these reasons, a careful analysis of the distribution of antiviral drugs, and the assessment of their activity in cells of macrophage lineage, represent key factors in the development of therapeutic strategies aimed to the treatment of the HIV-infected patients.

Anti-HIV Agents↗

Aspects of biochemical effects by hyperthermia.

Hyperthermia caused an immediate decrease of DNA, RNA, and protein synthesis. The latter process was most sensitive. Initiation of DNA synthesis at the transition from G1-to S-phase and at the start of new replication units were inhibited. These effects were responsible for the growth delay of cells and were potentiated with irradiation. The immediate inhibition of protein synthesis was due mainly to a disaggregation of the synthesizing mechanisms. It led to a decrease of enzyme activities with a short biological half-life, e.g., ornithine decarboxylase. Lysosomal hydrolytic activities might be enhanced after hyperthermia and contribute to tissue damage. During hyperthermia, glycogen breakdown and glucose turnover through glycolysis and the citrate cycle were apparently increased, but after hyperthermia, respiration and glycolysis were reduced. No lactate accumulation occurred, but other acidic metabolites were enhanced and could induce a metabolic acidosis hours later. A glucose load potentiated the effects on respiration and glycolysis. Immediately after hyperthermia, a lactate accumulation was observed under these conditions. A formula is given by which the ratios of reduced to oxidized substrates might indicate the redox state in different cellular compartments, with oxygen pressure, and during other metabolic conditions. Such changes of the intracellular milieu are important for the thermosensitivity of cells.

Animals↗

Adult small intestinal stem cells: identification, location, characteristics, and clinical applications.

There are few systems which enable adult tissue stem cells to be studied. However, the gastrointestinal tract with its high degree of polarity, well-defined cell migratory pathways, and dynamic cell replacement is a model tissue providing unique opportunities for stem cell study. Lineage tracking indicates that all cell replacement originates at well-defined stem cell positions, with an associated slower cell cycle. Radiobiological studies suggest a hierarchical stem cell compartment (actual and potential stem cells). Actual stem cells have an intolerance of genotoxic damage and die via apoptosis. Stem cells also selectively sort the old and new DNA strands at division, retaining the replication error free strands in the stem cell daughter. High genotoxic sensitivity and selective sorting of old and new DNA strands, provides extremely effective protective mechanisms against both replication and random errors. This provides a new explanation for the low cancer risk in the small intestine.

Adult↗

Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study.

The mammalian nucleus is a highly organised organelle that contains many subcompartments with roles in DNA replication and repair, gene expression and RNA processing. Cajal and promyelocytic leukaemia (PML) bodies are discrete nuclear structures with specific molecular signatures. RNA polymerase II and many transcription factors have been identified within these compartments by immunofluorescence microscopy, suggesting a role in polymerase II assembly or transcriptional activity. Here, we have examined the presence of different phosphorylated forms of polymerase II and newly made RNA in Cajal and PML bodies using high-resolution imaging of ultrathin cryosections (approximately 120 nm thick) with fluorescence and electron microscopes. We show that Cajal bodies contain polymerase II phosphorylated on Ser5, and not the Ser2-phosphorylated (active) form or newly made RNA. The presence of polymerase II in the absence of transcriptional activity suggests that Cajal bodies have roles in polymerase assembly or transport, but not in gene transcription. PML bodies contain no detectable polymerase II or nascent RNA in HeLa cells, at the resolution achieved by electron microscopy, but are often surrounded by these markers at distances>25 nm. These results support the view that although PML bodies are present in transcriptionally active areas of the nucleus, they are not generally sites of polymerase II assembly, transport or activity.

Antibodies↗