Structural analysis of conserved oligomeric Golgi complex subunit 2

The conserved oligomeric Golgi (COG) complex is strongly implicated in retrograde vesicular trafficking within the Golgi apparatus. Although its mechanism of action is poorly understood, it has been proposed to function by mediating the initial physical contact between transport vesicles and their membrane targets. An analogous role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex essential for trafficking to the plasma membrane. Here we report the solution structure of a large portion of yeast Cog2p, one of eight subunits composing the COG complex. The structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. This finding provides the first structural evidence that COG, like the exocyst and potentially other tethering complexes, is constructed from helical bundles. These structures may represent platforms for interaction with other trafficking proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs.     

Selection of highly metastatic rat MTLn2 mammary adenocarcinoma cell variants using in vitro growth response to transferrin

We previously found that the proliferative response to transferrin and the expression of transferrin receptors (TfR) on the cell surface of various rat 13762NF mammary adenocarcinoma cell sublines correlated with their spontaneous metastatic capability. To further assess the involvement of transferrin and TfR in metastasis, transferrin-responsive cells were selected from the poorly-metastatic, low-transfferin responsive 13762NF MTLn2 subline. When maintained in low serum (0.3%) conditions, MTLn2 cells failed to survive. However, if like medium was supplemented with 0.5 μmg/ml rat transferrin, some colonies emerged, presumably due to their ability to proliferate in response to the added transferrin. The surviving cells were expanded and exposed to ten or 20 similar cycles of transferrin growth selection to obtain the sublines MTLn2-Tf10 and MTLn2-Tf20, respectively. The MTLn2-Tf20 cells proliferated in response to transferrin at a rate similar to that of the high metastatic 13762NF sublines. Using immunofluorescent staining, Scatchard analysis, and affinity isolation of TfR, we discovered that the MTLn2-Tf20 cells had 5 to 6 times more TfR than did the parental MTLn2 line. When injected into the mammary fat pads of rats, the MTLn2-Tf20 line metastasized to the axillary lymph node in seven out of ten animals and to the lungs in six out of ten (median number = 13). No metastases were seen in the MTLn2 parental line. The MTLn2-Tf10 cells showed intermediate properties compared with the MTLn2 and MTLn2-Tf20 cells. The results indicate that variant cells with a high response to transferrin may be more metastatic than the bulk cells in a poorly metastatic population. The selection of cells with high levels of TfR and a higher proliferative response to transferrin results in sublines with greater potentials for spontaneous metastasis. J. Cell. Physiol. 174:48–57, 1998. © 1998 Wiley-Liss, Inc.     

Cyclooxygenase regulates human oropharyngeal carcinomas via the proinflammatory cytokine IL-6: a general role for inflammation?

High levels of prostaglandins are produced in human oropharyngeal carcinoma (OPC). Five human OPC cell lines tested expressed both isoforms of cyclooxygenases (COX). The pan-COX inhibitor ketorolac continuously and significantly decreased PGE(2) production and IL-6 and IL-8 levels in all OPC cell lines tested, but did not affect IL-1alpha, GM-CSF levels, or in vitro tumor cell growth. In contrast, ketorolac reduced OPC growth in vivo. The OPC cell lines used express the IL-6 receptor, and IL-6 stimulation of these cells causes transduction to occur via STAT3 pathway activation. Coincubation with OPC cell lines with conditioned medium from a TPA-exposed HL-60 cells stimulated growth proportional to the IL-6 levels measured in the conditioned medium. This growth effect was specifically inhibited by anti-IL-6 antibody. These results are consistent with cytokine products of inflammatory cells having paracrine growth effects on OPC. If chronic inflammation plays a role in promoting the development of OPC, this mechanism may also apply to other epithelial tumor systems modulated by COX activity.     

Neuroprotection by brain-derived neurotrophic factor is mediated by extracellular signal-regulated kinase and phosphatidylinositol 3-kinase.

Apoptosis is a form of programmed cell death that plays a pivotal role during development and in the homeostasis of the adult nervous systems. However, mechanisms that regulate neuronal apoptosis are not well defined. Here, we report that brain-derived neurotrophic factor (BDNF) protects cortical neurons against apoptosis induced by camptothecin or serum deprivation and activates the extracellular-signal-regulated kinase (ERK) and the phosphatidylinositol 3-kinase (PI 3-kinase) pathways. Using pharmacological agents and transient transfection with dominant interfering or constitutive active components of the ERK or the PI 3-kinase pathway, we demonstrate that the ERK pathway plays a major role in BDNF neuroprotection against camptothecin. Furthermore, ERK is activated in cortical neurons during camptothecin-induced apoptosis, and inhibition of ERK increases apoptosis. In contrast, the PI 3-kinase pathway is the dominant survival mechanism for serum-dependent survival under normal culture conditions and for BDNF protection against serum withdrawal. These results suggest that the ERK pathway is one of several neuroprotective mechanisms that are activated by stress to counteract death signals in central nervous system neurons. Furthermore, the relative contribution of the ERK and PI 3-kinase pathways to neuronal survival may depend on the type of cellular injury.     

The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution

The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic ¹³C/¹²C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO₂ fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth’s atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO₂-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.Subject terms: Bacterial evolution, Applied microbiology, Biogeochemistry     

Evidence for a core gut microbiota in the zebrafish

Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.     

The hyphal tip structure of Basidiobolus sp.: a zygomycete fungus of uncertain phylogeny

To date, among the zygomycete fungi that have been examined, a Spitzenk?rper has not been reported. In this paper, the cytoplasmic order of hyphal tip cells of Basidiobolus sp.,?a zygomycete genus of uncertain phylogeny, has been examined using light microscopy and transmission electron microscopy methods. With phase-contrast light optics, a phase-dark body was observed at the tips of growing hyphae of Basidiobolus sp. The hyphal apex also showed high affinity for FM4-64 labelling resulting in an intense fluorescence signal. The phase-dark inclusion exhibited independent motility within the hyphal apex and its presence and position were correlated to the rate and direction of hyphal growth. The hyphal apex of Basidiobolus sp. did not contain γ-tubulin. Ultrastructural observations revealed a dense cluster of vesicles at the hyphal apex. These results suggest that the growing hypha of Basidiobolus sp. contains a Spitzenk?rper, a character generally attributed to members of the ascomycete and basidiomycete fungi and not to zygomycete fungi.     

16S rRNA phylogenetic analysis and quantification of <Emphasis Type="Italic">Korarchaeota</Emphasis> indigenous to the hot springs of Kamchatka,Russia

The candidate archaeal division Korarchaeota is known primarily from deeply branching sequences of 16S rRNA genes PCR-amplified from hydrothermal springs. Parallels between the phylogeny of these genes and the geographic locations where they were identified suggested that Korarchaeota exhibit a high level of endemism. In this study, the influence of geographic isolation and select environmental factors on the diversification of the Korarchaeota was investigated. Fourteen hot springs from three different regions of Kamchatka, Russia were screened by PCR using Korarchaeota-specific and general Archaea 16S rRNA gene-targeting primers, cloning, and sequencing. Phylogenetic analyses of these sequences with Korarchaeota 16S rRNA sequences previously identified from around the world suggested that all Kamchatka sequences cluster together in a unique clade that subdivides by region within the peninsula. Consistent with endemism, 16S rRNA gene group-specific quantitative PCR of all Kamchatka samples detected only the single clade of Korarchaeota that was found by the non-quantitative PCR screening. In addition, their genes were measured in only low numbers; small Korarchaeota populations would present fewer chances for dispersal to and colonization of other sites. Across the entire division of Korarchaeota, common geographic locations, temperatures, or salinities of identification sites united sequence clusters at different phylogenetic levels, suggesting varied roles of these factors in the diversification of Korarchaeota.