Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast‐cancer cell lines

Secreted proteins play a pivotal role in cellular functions. To better understand malignant behavior, we adapted stable isotopic labeling with amino acids in cell culture technology to identify and quantify proteins differentially released into the extracellular media by a pair of normal and malignant breast‐cancer cell lines. Approximately 380 non‐redundant proteins were quantified in serum‐free media. Of the assigned proteins, 62% are classified secreted in protein databases and an additional 25% are designated secreted in the literature. A number of growth factors were found differentially regulated. Tumor necrosis factor, pigment epithelial‐differentiating factor and stem‐cell growth factor precursor showed decreased expression in breast‐cancer cell line, whereas Inhibin beta and macrophage migration inhibitory factor show increased expression. Interestingly, protease inhibitors, including plasma protease (C1) inhibitor, PZP precursor, and SerpinE2 were significantly down‐regulated in cancer cell line as were angiostatic factors from extracellular matrix (ECM) such as endorepillin. Further, the C‐terminal fragment of type XVIII collagen, endostatin, a potent angiostatic factor, was down‐regulated as well whereas extracellular collagens and osteoblast‐specific factor 2 (OSF‐2), were up‐regulated. Differential expression and secretion of SerpinE2 and OSF‐2 were confirmed using Western blotting. These results corroborate models of invasive tumors sustained by elaborate coordination of stromal cells via chemokines and growth factors, while protease inhibitors remodel the ECM to stimulate angiogenesis.     

Imputation of missing genotypes: an empirical evaluation of IMPUTE

Background

Polymorphism in genes of regulating enzymes, transporters and receptors of the neurotransmitters of the central nervous system have been associated with altered behaviour, and single nucleotide polymorphisms (SNPs) represent the most frequent type of genetic variation. The serotonin and dopamine signalling systems have a central influence on different behavioural phenotypes, both of invertebrates and vertebrates, and this study was undertaken in order to explore genetic variation that may be associated with variation in behaviour.

Results

Single nucleotide polymorphisms in canine genes related to behaviour were identified by individually sequencing eight dogs (Canis familiaris) of different breeds. Eighteen genes from the dopamine and the serotonin systems were screened, revealing 34 SNPs distributed in 14 of the 18 selected genes. A total of 24,895 bp coding sequence was sequenced yielding an average frequency of one SNP per 732 bp (1/732). A total of 11 non-synonymous SNPs (nsSNPs), which may be involved in alteration of protein function, were detected. Of these 11 nsSNPs, six resulted in a substitution of amino acid residue with concomitant change in structural parameters.

Conclusion

We have identified a number of coding SNPs in behaviour-related genes, several of which change the amino acids of the proteins. Some of the canine SNPs exist in codons that are evolutionary conserved between five compared species, and predictions indicate that they may have a functional effect on the protein. The reported coding SNP frequency of the studied genes falls within the range of SNP frequencies reported earlier in the dog and other mammalian species. Novel SNPs are presented and the results show a significant genetic variation in expressed sequences in this group of genes. The results can contribute to an improved understanding of the genetics of behaviour.     

Phospholipid transfer is a prerequisite for PLTP-mediated HDL conversion

Phospholipid transfer protein (PLTP) is an important regulator of high-density lipoprotein (HDL) metabolism. The two main functions of PLTP are transfer of phospholipids between lipoprotein particles and modulation of HDL size and composition in a process called HDL conversion. These PLTP-mediated processes are physiologically important in the transfer of surface remnants from lipolyzed triglyceride-rich lipoproteins to nascent HDL particles and in the generation of prebeta-HDL, the initial acceptor of excess peripheral cell cholesterol. The aim of the study presented here was to investigate the interrelationship between the two functions of PLTP. Plasma PLTP was chemically modified using diethylpyrocarbonate or ethylmercurithiosalicylate. The modified proteins displayed a dose-dependent decrease in phospholipid transfer activity and a parallel decrease in the ability to cause HDL conversion. Two recombinant PLTP mutant proteins, defective in phospholipid transfer activity due to a mutation in the N-terminal lipid-binding pocket, were produced, isolated, and incubated together with radioactively labeled HDL(3). HDL conversion was analyzed using three methods: native gradient gel electrophoresis, ultracentrifugation, and crossed immunoelectrophoresis. The results demonstrate that the mutant proteins (i) are able to induce only a modest increase in HDL particle size compared to the wild-type protein, (ii) are unable to release apoA-I from HDL(3), and (iii) do not generate prebeta-mobile particles following incubation with HDL(3). These data suggest that phospholipid transfer is a prerequisite for HDL conversion and demonstrate the close interrelationship between the two main activities of PLTP.     

Improved Fermentation Performance of a Lager Yeast after Repair of Its AGT1 Maltose and Maltotriose Transporter Genes

The use of more concentrated, so-called high-gravity and very-high-gravity (VHG) brewer''s worts for the manufacture of beer has economic and environmental advantages. However, many current strains of brewer''s yeasts ferment VHG worts slowly and incompletely, leaving undesirably large amounts of maltose and especially maltotriose in the final beers. α-Glucosides are transported into Saccharomyces yeasts by several transporters, including Agt1, which is a good carrier of both maltose and maltotriose. The AGT1 genes of brewer''s ale yeast strains encode functional transporters, but the AGT1 genes of the lager strains studied contain a premature stop codon and do not encode functional transporters. In the present work, one or more copies of the AGT1 gene of a lager strain were repaired with DNA sequence from an ale strain and put under the control of a constitutive promoter. Compared to the untransformed strain, the transformants with repaired AGT1 had higher maltose transport activity, especially after growth on glucose (which represses endogenous α-glucoside transporter genes) and higher ratios of maltotriose transport activity to maltose transport activity. They fermented VHG (24° Plato) wort faster and more completely, producing beers containing more ethanol and less residual maltose and maltotriose. The growth and sedimentation behaviors of the transformants were similar to those of the untransformed strain, as were the profiles of yeast-derived volatile aroma compounds in the beers.The main fermentable sugars in brewer''s wort are maltose (ca. 60% of the total), maltotriose (ca. 25%), and glucose (ca. 15%). In traditional brewery fermentations, worts of about 11° Plato (°P) are used, corresponding to a total fermentable sugar concentration of about 80 g · liter⁻¹. Many modern breweries ferment high-gravity worts (15 to 17°P), and there are efforts to raise the concentration to 25°P, corresponding to a total sugar concentration of about 200 g · liter⁻¹. Industrial use of such very-high-gravity (VHG) worts is attractive because it offers increased production capacity from the same-size brew house and fermentation facilities, decreased energy consumption, and decreased labor, cleaning, and effluent costs (34, 35).Whereas glucose, which is used first, is transported into yeast cells by facilitated diffusion, the α-glucosides maltose and maltotriose are carried by proton symporters (2, 26, 39). Maltose transport seems to have a high level of control over the fermentation rate. Thus, during the early and middle stages of fermentation of brewer''s wort by a lager yeast, the specific rate of maltose consumption was the same as the specific zero-trans maltose uptake rate measured off line with each day''s yeast in each day''s wort spiked with [¹⁴C]maltose (27). Furthermore, introducing a constitutive MAL61 (maltose transporter) gene into a brewer''s yeast on a multicopy plasmid accelerated the fermentation of high-gravity worts (17). Maltotriose is the last sugar to be used in brewing fermentations, and significant amounts of residual maltotriose sometimes remain in beer, causing economic losses (lower yield of ethanol on wort carbohydrate) and possibly undesirable organoleptic effects. The problem of residual sugars in beer is more serious when high-gravity and VHG worts are used. Some, but not all, maltose transporters can also carry maltotriose. The MALx1 genes (x = 1 to 4 and 6) encode transporters that carry maltose efficiently but are generally believed to have little or no activity toward maltotriose (1, 3, 13, 30), although substantial activity toward maltotriose was reported by Day et al. (4). Some yeast strains contain a gene 57% identical to MAL11 that is usually known as AGT1 but is recorded in the Saccharomyces Genome Database (SGDB) as MAL11. The Agt1 transporter has relatively high activity toward maltotriose, as well as maltose (13), and similar K_m values (4 to 5 mM) for these two substrates (4). Alves et al. (1) found that the specific deletion of AGT1 from several Saccharomyces cerevisiae strains also containing at least one MALx1 gene (MAL21, MAL31, and/or MAL41) abolished their ability to transport maltotriose but did not decrease their maltose transport activity. These results supported the belief that the Mal21, Mal31, and Mal41 transporters cannot carry maltotriose, though it remains possible that there are differences between Malx1 transporters from different strains. The same group has also shown (33) that overexpression of AGT1 on a multicopy plasmid in an industrial yeast strain with a very limited ability to ferment maltotriose provided the strain with increased maltotriose uptake activity and the ability to ferment maltotriose efficiently. In 2005, a novel kind of α-glucoside transporter was independently found by two groups (6, 30) in some industrial strains of brewer''s, baker''s, and distiller''s yeasts. These transporters are coded by MTT1 (also called MTY1) genes, which are 90 and 54% identical to the MAL31 and AGT1 genes, respectively. The Mtt1 transporters have high activity toward maltotriose and are the only known α-glucoside transporters with lower K_m values for maltotriose than for maltose (30).Before the discovery of the MTT1 genes, Vidgren et al. (36) sequenced AGT1 genes from two apparently unrelated lager strains and two apparently unrelated ale strains of brewer''s yeast. Surprisingly, at that time (because other maltotriose transporters were not known), the AGT1 genes from the lager strains contained an insertion of one nucleotide, resulting in a premature stop codon, and encoded a truncated, nonfunctional 394-amino-acid polypeptide, whereas those from the ale strains encoded full-length 616-amino-acid transporters. This premature stop codon was later shown (37) to be present in AGT1 genes from all eight of the lager strains tested but was not in any of the four ale strains tested, whereas MTT1 genes were present in all of the lager strains tested but in none of the ale strains tested.In the present work, we have tested whether lager fermentations can be accelerated and residual maltotriose levels decreased by repairing the defective AGT1 genes of lager strains with appropriate DNA sequences from ale strains. Furthermore, the MALx1 and AGT1 genes are repressed by glucose and induced by α-glucosides (9, 16, 19, 25), so that replacing the native AGT1 promoter with a constitutive S. cerevisiae promoter might also increase α-glucoside transport activity and accelerate wort fermentations. The objectives of the present work were to confirm that α-glucoside transport has a high level of control over the rate and extent of wort fermentation and to create a genetically modified lager yeast strain that has improved fermentation performance but contains only Saccharomyces DNA.     

Spatial partitioning of secretory cargo from Golgi resident proteins in live cells

Background  

To maintain organelle integrity, resident proteins must segregate from itinerant cargo during secretory transport. However, Golgi resident enzymes must have intimate access to secretory cargo in order to carry out glycosylation reactions. The amount of cargo and associated membrane may be significant compared to the amount of Golgi membrane and resident protein, but upon Golgi exit, cargo and resident are efficiently sorted. How this occurs in live cells is not known.