Hemocyanin of the molluscan Concholepas concholepas exhibits an unusual heterodecameric array of subunits

We describe here the structure of the hemocyanin from the Chilean gastropod Concholepas concholepas (CCH), emphasizing some attributes that make it interesting among molluscan hemocyanins. CCH exhibits a predominant didecameric structure as revealed by electron microscopy and a size of 8 MDa by gel filtration, and, in contrast with other mollusc hemocyanins, its stabilization does not require additional Ca(2+) and/or Mg(2+) in the medium. Polyacrylamide gel electrophoresis studies, analyses by a MonoQ FPLC column, and Western blots with specific monoclonal antibodies showed that CCH is made by two subunits noncovalently linked, named CCH-A and CCH-B, with molecular masses of 405 and 350 kDa, respectively. Interestingly, one of the subunits undergoes changes within the macromolecule; we demonstrated that CCH-A has an autocleavage site that under reducing conditions is cleaved to yield two polypeptides, CCH-A1 (300 kDa) and CCH-A2 (108 kDa), whereas CCH-B remains unchanged. The CCH-A nick occurs at 4 degrees C, increases at 37 degrees C, and is not inhibited by the addition of protease inhibitors and/or divalent cations. Since the CCH structure is a heterodimer, we investigated whether subunits would be either intermingled, forming heterodecamers, or assembled as two homogeneous decamers. Light scattering and electron microscope studies of the in vitro reassociation of purified CCH subunits demonstrated that the sole addition of Mg(2+) is needed for its reassembly into the native decameric molecule; no homodecamer reorganization was found with either CCH-A or CCH-B subunits alone. Our evidence showed that C. concholepas hemocyanin is an unusual example of heterodecameric organization.     

Humic substances biological activity at the plant-soil interface: From environmental aspects to molecular factors

Humic substances (HS) represent the organic material mainly widespread in nature. HS have positive effects on plant physiology by improving soil structure and fertility and by influencing nutrient uptake and root architecture. The biochemical and molecular mechanisms underlying these events are only partially known. HS have been shown to contain auxin and an “auxin-like” activity of humic substances has been proposed, but support to this hypothesis is fragmentary. In this review article, we are giving an overview of available data concerning molecular structures and biological activities of humic substances, with special emphasis on their hormone-like activities.Key words: auxin, humic substances, root, soil, sustainable agriculture     

Interaction between PPARgamma2 variants and gender on the modulation of body weight

Conflicting results have been reported regarding the effect of the peroxisome proliferator-activated receptor-gamma-2 (PPARgamma2) Pro12Ala polymorphism, (singly or in combination with the silent C1431T polymorphism) on BMI. Gender-based dimorphism has been evidenced for genes that affect BMI, but few and conflicting data are available regarding PPARgamma2. We sought to investigate whether the Pro12Ala interacts with gender in modulating BMI in 566 nondiabetic unrelated white subjects (men:women = 211:355, age 36.59 +/- 11.85; BMI 25.36 +/- 4.53). In the whole study population, BMI, fasting glucose and insulin levels, and lipid profile were similar in Ala12 carriers (i.e., XA) and Pro/Pro homozygous subjects. Among the men, but not among the women, X/Ala individuals showed higher BMI (25.9 +/- 3.6 vs. 28.2 +/- 4.9, P = 0.006) and risk of obesity (odds ratio = 2.85, 95% confidence interval = 1.07-7.62). A significant gene-gender interaction in modulating BMI was observed (P = 0.039). Among the men, but not among the women, those carrying Ala-T haplotype (i.e., containing both Ala12 and T1431 variants) showed the highest BMI (haplo-score = 3.72, P = 0.0014). Our data indicate that in whites from Italy the PPARgamma2 Pro12Ala polymorphism interacts with gender in modulating BMI, thereby replicating some, but not all, earlier data obtained in different populations. Whether the PPARgamma2-gender interaction is a general phenomenon across different populations, is still an open question, the answer to which requires additional, specifically designed, studies.     

Genomic-enabled prediction with classification algorithms

Pearson''s correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait–environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen''s kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets) and the best RE in the same 13 data sets, with values ranging from 0.393 to 0.948 (statistically significant in 12 data sets). RR produced the best mean for both κ and RE in one data set (0.148 and 0.381, respectively). Regarding the wheat data sets, SVC-lin presented the best κ in 12 of the 16 data sets, with outcomes ranging from 0.280 to 0.580 (statistically significant in 4 data sets) and the best RE in 9 data sets ranging from 0.484 to 0.821 (statistically significant in 5 data sets). SVC-rbf (0.235), RR (0.265) and RHKS (0.422) gave the best κ in one data set each, while RHKS and BL tied for the last one (0.234). Finally, BL presented the best RE in two data sets (0.738 and 0.750), RFR (0.636) and SVC-rbf (0.617) in one and RHKS in the remaining three (0.502, 0.458 and 0.586). The difference between the performance of SVC-lin and that of the rest of the models was not so pronounced at higher percentiles of the distribution. The behaviour of regression and classification algorithms varied markedly when selection was done at different thresholds, that is, κ and RE for each algorithm depended strongly on the selection percentile. Based on the results, we propose classification method as a promising alternative for GS in plant breeding.     

Identification of a microRNA (miR-663a) induced by ER stress and its target gene PLOD3 by a combined microRNome and proteome approach

Introduction

MicroRNAs (miRs) regulate gene expression to support important physiological functions. Significant evidences suggest that miRs play a crucial role in many pathological events and in the cell response to various stresses.

Methods

With the aim to identify new miRs induced by perturbation of intracellular calcium homeostasis, we analysed miR expression profiles of thapsigargin (TG)-treated cells by microarray. In order to identify miR-663a-regulated genes, we evaluated proteomic changes in miR-663a-overexpressing cells by two-dimensional differential in-gel electrophoresis coupled to mass spectrometric identification of the differentially represented proteins. Microarray and proteomic analyses were supported by biochemical validation.

Results

Results of microarray revealed 24 differentially expressed miRs; among them, miR-663a turned out to be by ER stress and under the control of the PERK pathway of the unfolded protein response. Proteomic analysis revealed that PLOD3, which is the gene encoding for collagen-modifying lysyl hydroxylase 3 (LH3), is regulated by miR-663a. Luciferase reporter assays demonstrated that miR-663a indeed reduces LH3 expression by targeting to 3′-UTR of PLOD3 mRNA. Interestingly, miR-663a inhibition of LH3 expression generates reduced extracellular accumulation of type IV collagen, thus suggesting the involvement of miR-663a in modulating collagen 4 secretion in physiological conditions and in response to ER stress.

Conclusion

The finding of the ER stress-induced PERK-miR-663a pathway may have important implications in the understanding of the molecular mechanisms underlying the function of this miR in normal and/or pathological conditions.

     

Defective Rac-mediated proliferation and survival after targeted mutation of the beta1 integrin cytodomain

Cell matrix adhesion is required for cell proliferation and survival. Here we report that mutation by gene targeting of the cytoplasmic tail of beta1 integrin leads to defective proliferation and survival both in vivo and in vitro. Primary murine embryonic fibroblasts (MEFs) derived from mutant homozygotes display defective cell cycle coupled to impaired activation of the FAK-PI3K-Akt and Rac-JNK signaling pathways. Expression in homozygous MEFs of a constitutively active form of Rac is able to rescue proliferation, survival, and JNK activation. Moreover, although showing normal Erk phosphorylation, mutant cells fail to display Erk nuclear translocation upon fibronectin adhesion. However, expression of the constitutively activated form of Rac restores Erk nuclear localization, suggesting that adhesion-dependent Rac activation is necessary to integrate signals directed to promote MAPK activity. Altogether, our data provide the evidence for an epistatic interaction between the beta1 integrin cytoplasmic domain and Rac, and indicate that this anchorage-dependent signaling pathway is crucial for cell growth control.     

Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS

Estrogen receptor α (ER-α) is a key mediator of estrogen actions in breast cancer (BC) cells. Understanding the effects of ligand-activated ER-α in target cells requires identification of the molecular partners acting in concert with this nuclear receptor to transduce the hormonal signal. We applied tandem affinity purification (TAP), glycerol gradient centrifugation and MS analysis to isolate and identify proteins interacting with ligand-activated ER-α in MCF-7 cell nuclei. This led to the identification of 264 ER-associated proteins, whose functions highlight the hinge role of ER-α in the coordination of multiple hormone-regulated nuclear processes in BC cells.     

A new psoralen derivative with enlarged antiproliferative properties

Following our results with benzopsoralens as potent photochemotherapeutic agents, we report the antiproliferative evaluation of nitrogenated isoster upon and without UVA irradiation. The evaluated pyridazinopsoralen showed a higher photochemotherapeutic activity with respect to the well-known drug, 8-MOP, and a significant cytotoxicity, also in the dark. This result enlarges the interest in this tetracyclic psoralen derivative skeleton in the search of new anticancer agents.