Met receptor overexpression and oncogenic Ki-ras mutation cooperate to enhance tumorigenicity of colon cancer cells in vivo

We have investigated the influence of Ki-ras oncogene on Met/hepatocyte growth factor (HGF) receptor signaling in human carcinoma cells. The model system used in these studies included the DLD-1 colon cancer cell line with a mutated Ki-ras allele, and the DKO-4 cell line generated from DLD-1, with its mutant Ki-ras allele inactivated by targeted disruption. These cell lines were transduced with cDNAs of either active Met receptor or dominant negative Met receptor. As compared to the DLD-1 cells, constitutive overexpression of Met receptor in this cell line (DLD-1-Met) resulted in increased tumorigenicity in SCID mice. In contrast, overexpression of Met in DKO-4 cells (DKO-4-Met) that have lost oncogenic Ras activity demonstrated suppressed tumorigenicity with respect to the parent DKO-4 cell line. Tumors formed by the DLD-1-Met cells showed increased levels of mitogen-activated protein kinase (MAPK) and lower levels of apoptosis compared to the DKO-4-Met tumors. Overexpression of the dominant negative Met receptor cDNA decreased the Met phosphorylation levels in both DLD-1 and DKO-4 cells, but only suppressed tumorigenicity in the DKO-4 cell line. In vitro, HGF stimulation of DLD-1 cells resulted in a prolonged duration of MAPK activation, while DKO-4 cells exhibited a rapid attenuation of MAPK phosphorylation. The results suggest that Ki-ras mutations and HGF signaling cooperate to enhance tumor growth by increased duration of MAPK activation and decreased apoptosis in human carcinoma cells.     

Crystal structure of a beta-catenin/APC complex reveals a critical role for APC phosphorylation in APC function

The tumor suppressor adenomatous polyposis coli (APC) plays a critical role in the turnover of cytosolic beta-catenin, the key effector of the canonical Wnt signaling pathway. APC contains seven 20 amino acid (20 aa) beta-catenin binding repeats that are required for beta-catenin turnover. We have determined the crystal structure of beta-catenin in complex with a phosphorylated APC fragment containing two 20 aa repeats. Surprisingly, one single phosphorylated 20 aa repeat, together with its flanking regions, covers the entire structural groove of beta-catenin and may thus compete for beta-catenin binding with all other beta-catenin armadillo repeat partners. Our biochemical studies show that phosphorylation of the APC 20 aa repeats increases the affinity of the repeats for beta-catenin by 300- to 500-fold and the phosphorylated 20 aa repeats prevent beta-catenin binding to Tcf. Our work suggests that the phosphorylation of the APC 20 aa repeats could be a critical switch for APC function.     

Seed-specific promoters direct gene expression in non-seed tissue

The organ specificity of four promoters that are known to direct seed-specific gene expression was tested. Whereas the phaseolin (phas)- and legumin B4 (leB4)-promoters were from genes encoding 7S and 11S globulins from Phaseolus vulgaris and Vicia faba, respectively, the usp- and the sbp-promoters were from non-storage protein genes of V. faba. The expression of different promoter-reporter gene fusions was followed either by RT-PCR or by registering the reporter enzyme activity in organs of transgenic tobacco, pea, narbon bean, or linseed. In addition to seeds, the promoters directed reporter gene expression in pollen and in seed coats. USP-, vicilin- and legumin-mRNA were detected by RT-PCR in pollen of Pisum sativum and V. faba. Expression during microsporogenesis and embryogenesis seems to be a general character of various seed protein genes.     

Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2

We recently described two protein G variants (NuG1 and NuG2) with redesigned first hairpins that were almost twice as stable, folded 100-fold faster, and had a switched folding mechanism relative to the wild-type protein. To test the structural accuracy of our design algorithm and to provide insights to the dramatic changes in the kinetics and thermodynamics of folding, we have now determined the crystal structures of NuG1 and NuG2 to 1.8 A and 1.85 A, respectively. We find that they adopt hairpin structures that are closer to the computational models than to wild-type protein G; the RMSD of the NuG1 hairpin to the design model and the wild-type structure are 1.7 A and 5.1 A, respectively. The crystallographic B factor in the redesigned first hairpin of NuG1 is systematically higher than the second hairpin, suggesting that the redesigned region is somewhat less rigid. A second round of structure-based design yielded new variants of NuG1 and NuG2, which are further stabilized by 0.5 kcal/mole and 0.9 kcal/mole.     

Reconstitution of beta 1-adrenoceptor-dependent adenylate cyclase from purified components.

In continuation of our efforts to reconstitute from purified components into lipid vesicles the signal transmission chain from beta 1-adrenoceptors to adenylate cyclase, we now report on the total reconstitution of the hormone-dependent adenylate cyclase. In these reconstitution experiments we have employed the purified adenylate cyclase (C) from bovine brain and rabbit heart, the stimulatory GTP-binding protein (GS) purified from turkey erythrocytes and rabbit liver and the beta 1-adrenoceptor (R) from turkey erythrocytes. Several detergents were compared with respect to their suitability to allow reconstitution of subunits into phospholipid vesicles. While octyl-polyoxyethylene (octyl-POE) was almost as potent as lauroyl-sucrose for preparation of vesicles containing GS.C, the latter detergent was clearly superior for vesicles enabling productive R.GS and R.GS.C coupling. The catalytic subunit from either bovine brain or rabbit heart was equally efficient in reconstitution. However, GS from turkey erythrocytes and rabbit liver revealed significant differences in RGS and RGS.C containing vesicles. While isoproterenol-induced activation of GS by GTP gamma S was first order in both instances, kon with turkey GS was 0.12 min-1, whereas kon with rabbit liver GS was 0.6 min-1. Moreover, GTP gamma S activation of erythrocyte GS was significantly more dependent on the presence of hormone than that of liver GS, confirming observations made on the native membrane-bound system. Compared with stimulation by isoproterenol (GTP gamma S) (4-fold), stimulation by isoproterenol/GTP was modest (1.3- to 1.6-fold).(ABSTRACT TRUNCATED AT 250 WORDS)     

Browning affects pelagic productivity in northern lakes by surface water warming and carbon fertilization

Global change impacts important environmental drivers for pelagic gross primary production (GPP) in northern lakes, such as temperature, light, nutrient, and inorganic carbon availability. Separate and/or synergistic impacts of these environmental drivers on pelagic GPP remain largely unresolved. Here, we assess key drivers of pelagic GPP by combining detailed depth profiles of summer pelagic GPP with environmental and climatic data across 45 small and shallow lakes across northern Sweden (20 boreal, 6 subarctic, and 19 arctic lakes). We found that across lakes summer pelagic GPP was strongest associated with lake water temperatures, lake carbon dioxide (CO₂) concentrations impacted by lake water pH, and further moderated by dissolved organic carbon (DOC) concentrations influencing light and nutrient conditions. We further used this dataset to assess the extent of additional DOC-induced warming of epilimnia (here named internal warming), which was especially pronounced in shallow lakes (decreasing 0.96°C for every decreasing m in average lake depth) and increased with higher concentrations of DOC. Additionally, the total pools and relative proportion of dissolved inorganic carbon and DOC, further influenced pelagic GPP with drivers differing slightly among the boreal, subarctic and Arctic biomes. Our study provides novel insights in that global change affects pelagic GPP in northern lakes not only by modifying the organic carbon cycle and light and nutrient conditions, but also through modifications of inorganic carbon supply and temperature. Considering the large-scale impacts and similarities of global warming, browning and recovery from acidification of lakes at higher latitudes throughout the northern hemisphere, these changes are likely to operate on a global scale.     

Tissue-based absolute quantification using large-scale TMT and LFQ experiments

Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored. Here, we compare traditional intensity-based absolute quantification (iBAQ) proteome abundance ranking to an analogous method using reporter ion proteome abundance ranking with data from an experiment where LFQ and TMT were measured on the same samples. This new TMT method substitutes reporter ion intensities for MS1 feature intensities in the iBAQ framework. Additionally, we compared LFQ-iBAQ values to TMT-iBAQ values from two independent large-scale tissue atlas datasets (one LFQ and one TMT) using robust bottom-up proteomic identification, normalisation and quantitation workflows.     

Transforming growth factor beta and cyclosporin A inhibit the inducible activity of the interleukin-2 gene in T cells through a noncanonical octamer-binding site.

Transforming growth factor beta (TGF-beta) has a growth-inhibitory effect on numerous different cell types of the immune system, including T lymphocytes. We show in this study that the inhibitory action of TGF-beta on T lymphocytes is accompanied by a block of interleukin 2 (IL-2) gene expression which is mediated, at least in part, by inhibition of IL-2 promoter/enhancer activity. The functional analysis of cis-regulatory (proto-enhancer) elements of the IL-2 enhancer/promoter region showed that the most TGF-beta-responsive element maps to its so-called upstream promoter site. The proto-enhancer activity of the upstream promoter site element is also inhibited by cyclosporin A. The upstream promoter site DNA harbors two noncanonical, closely linked binding sequences for octamer and AP-1-like factors. Both sites are involved in the establishment of IL-2 enhancer activity. Since the activity of genuine octamer sites but not that of AP-1-binding sites is also impaired by TGF-beta and cyclosporin A in El4 T lymphoma cells, we conclude that both immunosuppressives interfere with the activity but not the DNA binding of octamer factors in T lymphocytes.     

The vegetation of roadside verges with respect to environmental gradients in southern New Zealand

Abstract. A survey of the vegetation of roadside verges was made across the southern part of the South Island of New Zealand. Samples were taken at 10-km intervals along selected roads providing a climatic range from the suboceanic conditions of the east coast into semi-arid Central Otago, and from Central Otago through the Southern Alps to the hyper-oceanic areas of high rainfall on the west Coast. The variation in the floristic composition is associated mainly with variation in rainfall, continentality, altitude, soil acidity, soil organic matter, and presence of forest. Sites in the arable and pastoral regions on the eastern side of the Southern Alps support a herbaceous vegetation consisting mostly of exotic species of European origin, with a few native grasses scattered through the drier and less fertile sites. A greater proportion of native species is found at higher altitudes. Roadside vegetation in the area of high rainfall to the west is characterized by indigenous ferns and woody species, although vegetation adjacent to cleared areas is more similar to that on roadsides adjacent to farmland on the east coast. The pattern of distribution of both native and exotic species is strongly related to altitudinal and climatic gradients, and the environmental responses of the exotic species are similar to those recorded in Europe. This suggests a colonization of all available sites by the exotic species, despite the relatively short time since their introduction to New Zealand, rather than an incomplete invasion.