Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome.

Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].

Spermine deficiency shifts the balance between jasmonic acid and salicylic acid-mediated defence responses in Arabidopsis.

Polyamines are small aliphatic polycations present in all living organisms. In plants, the most abundant polyamines are putrescine (Put), spermidine (Spd) and spermine (Spm). Polyamine levels change in response to different pathogens, including Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). However, the regulation of polyamine metabolism and their specific contributions to defence are not fully understood. Here we report that stimulation of Put biosynthesis by Pst DC3000 is dependent on coronatine (COR) perception and jasmonic acid (JA) signalling, independently of salicylic acid (SA). Conversely, lack of Spm in spermine synthase (spms) mutant stimulated galactolipids and JA biosynthesis, and JA signalling under basal conditions and during Pst DC3000 infection, whereas compromised SA-pathway activation and defence outputs through SA-JA antagonism. The dampening of SA responses correlated with COR and Pst DC3000-inducible deregulation of ANAC019 expression and its key SA-metabolism gene targets. Spm deficiency also led to enhanced disease resistance to the necrotrophic fungal pathogen Botrytis cinerea and stimulated endoplasmic reticulum (ER) stress signalling in response to Pst DC3000. Overall, our findings provide evidence for the integration of polyamine metabolism in JA- and SA-mediated defence responses, as well as the participation of Spm in buffering ER stress during defence.

Putrescine elicits ROS-dependent activation of the salicylic acid pathway in Arabidopsis thaliana.

Polyamines are small amines that accumulate during stress and contribute to disease resistance through as yet unknown signaling pathways. Using a comprehensive RNA-sequencing analysis, we show that early transcriptional responses triggered by each of the most abundant polyamines (putrescine, spermidine, spermine, thermospermine and cadaverine) exhibit specific quantitative differences, suggesting that polyamines (rather than downstream metabolites) elicit defense responses. Signaling by putrescine, which accumulates in response to bacteria that trigger effector triggered immunity (ETI) and systemic acquired resistance (SAR), is largely dependent on the accumulation of hydrogen peroxide, and is partly dependent on salicylic acid (SA), the expression of ENHANCED DISEASE SUSCEPTIBILITY (EDS1) and NONEXPRESSOR of PR GENES1 (NPR1). Putrescine elicits local SA accumulation as well as local and systemic transcriptional reprogramming that overlaps with SAR. Loss-of-function mutations in arginine decarboxylase 2 (ADC2), which is required for putrescine synthesis and copper amine oxidase (CuAO), which is involved in putrescine oxidation, compromise basal defenses, as well as putrescine and pathogen-triggered systemic resistance. These findings confirm that putrescine elicits ROS-dependent SA pathways in the activation of plant defenses.

Effectiveness and quality of life 10 years after transobturator suburethral tape surgery for stress urinary incontinence.

AIM: We aimed to measure the effectiveness and quality of life (QoL) 10 years after transobturator suburethral tape surgery. METHODS: We carried out a prospective observational study of 42 women assessed 10 years after surgical intervention with the transobturator technique. The main outcome measures were subjective and objective cure or improvement, complications, and changes in QoL. RESULTS: The median abdominal leak point pressure had been 92 (82-113) mL H2 O prior to surgery. Thirty-six women (85.7%) remained cured (negative cough test) and 13 (31%) reported urine leakage during physical activity, percentages which were similar to those at a previous assessment at the 5th year. Urgency urinary incontinence was reported by 18 women (42.9%), 16 of whom required the use of anticholinergic drugs. Nineteen women had undergone some form of surgical pelvic reconstruction concomitantly with the TOT procedure, four of whom presented with relapse. The QoL tests indicated that cure and improvement persisted in 85.7% (n = 36, Urogenital Distress Inventory-6) and 92.9% (n = 39, Incontinence Impact Questionnaire-7) of the 42 evaluable women, respectively. CONCLUSION: Rates of objective and subjective effectiveness remained stable after 10 years of surgery and QoL did not deteriorate significantly during that interval. The increase in urgency incontinence needs to be further investigated.

Preservatives in Personal Hygiene and Cosmetic Products, Topical Medications, and Household Cleaners in Spain. / Conservantes en productos de higiene y cosméticos, medicamentos tópicos y productos de limpieza doméstica en España.

INTRODUCTION: Preservatives are added to cosmetic, household cleaning, and other industrial products to prevent the growth of microorganisms. Unfortunately, exposure to these substances can cause sensitization. MATERIAL AND METHODS: Between January and June 2015, we analyzed the ingredients of 2300 products commercially available in Spain to identify the frequency of a wide variety of preservatives in different product categories. We analyzed 1093 skin care and cosmetic products sold exclusively in pharmacies (dermocosmetics), 458 household cleaning and personal hygiene and cosmetic products sold in supermarkets, 636 topical medications, and 113 cosmetic products sold in a herbal shop. RESULTS: Phenoxyethanol, citric acid, sodium benzoate, and potassium sorbate were very common in all the cosmetic product categories. Parabens were present in 16.1% of dermocosmetic products, 14.45% of cosmetic products available in supermarkets, 0.88% of cosmetic products available in the herbal shop, 5.18% of topical medications, and in none of the cleaning products. Isothiazolinones were identified in 2.56% of dermocosmetic products, 18% of cosmetic products in supermarkets, 7.9% of cosmetic products in the herbal shop, 63.63% of household cleaners, and in none of the topical medications. Formaldehyde releasers were detected in 5.76% of dermocosmetic products, 6.42% of cosmetic products sold in supermarkets, 7.96% of cosmetic products sold in the herbal shop, 3.93% of topical medications, and 16.74% of household cleaners. CONCLUSIONS: Evaluation of the presence of preservatives in everyday products allows us to indirectly estimate exposure levels to each one. Measures restricting the use of the most problematic preservatives need to be strengthened.

[GnRH analogues for the treatment of fibroids]. / Análogos de la GnRH en el tratamiento de los miomas.

Uterine fibroids are benign tumors that are very common in women and may present significant symptoms in 20%-50% of cases. When they require action, their traditional management has been surgery (hysterectomy or fibroidectomy); however medical alternatives have been proposed, given that surgery is associated with a certain morbidity and mortality and involves healthcare costs. Within the pharmacological management of uterine fibroids, GnRH analogues are the best known and most commonly used drugs, although their indications are limited by the side effects associated with long-term treatment. Their primary indication is based on preoperative treatment (to hysterectomy or fibroidectomy) and in selected cases of patients close to menopause or who want more conservative management. These analogues are able to significantly reduce the uterine volume, the size of the fibroid and their accompanying symptoms. Their main disadvantage, however, lies in the reversibility of their effect when treatment is discontinued, along with the side effects associated with hypoestrogenism, such as climacteric symptoms and loss of bone mass. "Add-back" therapies, which associate low-dose estrogens to aGnRH, allow for extended use thanks to decreased side effects without affecting the benefits.