Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation

Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.

Influência do estímulo por PAF no perfil de abundância proteica em neutrófilos : uma abordagem proteômica

Tese (doutorado)—Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, 2015.

Breast cancer

Breast cancer remains one of the leading causes of cancer morbidity and mortality. Despite significant advances in treatment of breast cancer a substantial proportion of women affected by this disease succumb to it. Survival of patients with advanced disease, chemoresistant tumors or a suboptimal response to endocrine therapy is significantly shortened. Hence, further understanding of disease pathogenesis is required to enhance the arsenal of approaches to cure this deadly ailment. Recent advances in biochemistry, molecular cell biology and cancer research highlighted the importance of dysregulation of protein synthesis, translation, in the development and progression of tumors. This dysregulation appears to take place at an early stage of translation, called translation initiation, that is a highly controlled and rate-limiting step of the protein synthesis. In this chapter we summarize decades of knowledge accumulated in regards to the role of translation and its regulation in the development and progression of breast cancer. We then extensively discuss applications of this knowledge in diagnosis and treatment of breast cancer.

Tools For Spatiotemporally Specific Proteomic Analysis In Multicellular Organisms

The emergence of mass spectrometry-based proteomics has revolutionized the study of proteins and their abundances, functions, interactions, and modifications. However, in a multicellular organism, it is difficult to monitor dynamic changes in protein synthesis in a specific cell type within its native environment. In this thesis, we describe methods that enable the metabolic labeling, purification, and analysis of proteins in specific cell types and during defined periods in live animals. We first engineered a eukaryotic phenylalanyl-tRNA synthetase (PheRS) to selectively recognize the unnatural L-phenylalanine analog p-azido-L-phenylalanine (Azf). Using Caenorhabditis elegans, we expressed the engineered PheRS in a cell type of choice (i.e. body wall muscles, intestinal epithelial cells, neurons, pharyngeal muscles), permitting proteins in those cells -- and only those cells -- to be labeled with azides. Labeled proteins are therefore subject to "click" conjugation to cyclooctyne-functionalized affnity probes, separation from the rest of the protein pool and identification by mass spectrometry. By coupling our methodology with heavy isotopic labeling, we successfully identified proteins -- including proteins with previously unknown expression patterns -- expressed in targeted subsets of cells. While cell types like body wall or pharyngeal muscles can be targeted with a single promoter, many cells cannot; spatiotemporal selectivity typically results from the combinatorial action of multiple regulators. To enhance spatiotemporal selectivity, we next developed a two-component system to drive overlapping -- but not identical -- patterns of expression of engineered PheRS, restricting labeling to cells that express both elements. Specifically, we developed a split-intein-based split-PheRS system for highly efficient PheRS-reconstitution through protein splicing. Together, these tools represent a powerful approach for unbiased discovery of proteins uniquely expressed in a subset of cells at specific developmental stages.

Anabolic resistance does not explain sarcopenia in patients with type 2 diabetes mellitus, compared with healthy controls, despite reduced mTOR pathway activity

Background Ageing and type 2 diabetes mellitus (T2DM) are risk factors for skeletal muscle loss. We investigated whether anabolic resistance to feeding might underlie accelerated muscle loss in older people with T2DM and whether dysregulated mTOR signalling was implicated. Subjects 8 obese men with T2DM, and 12 age-matched controls were studied (age 68±3 vs. 68±6y; BMI: 30±2 vs. 27±5 kg·m-2). Methods Body composition was measured by dual-X-ray absorptiometry. Insulin and glucose were clamped at post-absorptive concentrations (13±2 vs. 9±3 mU·l-1; 7.4±1.9 vs. 4.6±0.4 mmol·l-1; T2DM vs. controls). Fractional synthetic rates (FSR) of myofibrillar and sarcoplasmic proteins were measured as the rate of incorporation of [13C] leucine during a primed, constant infusion of [1-13C] α-ketoisocaproic acid, 3 h after 10 or 20g of essential amino acids (EAA) were orally administered. Protein expression of total and phosphorylated mTOR signalling proteins was determined by Western blot analysis. Results Despite a significantly lower appendicular lean mass index and a greater fat mass index in T2DM vs. controls, basal myofibrillar and sarcoplasmic and post-prandial myofibrillar FSR were similar. After 20g EAA, stimulation of sarcoplasmic FSR was slightly blunted in T2DM patients. Furthermore, feeding 20g EAA increased phosphorylation of mTOR, p70S6k and 4E-BP1 by 60-100% in controls with no response observed in T2DM. Conclusions There was clear dissociation between changes in mTOR signalling versus changes in protein synthesis rates. However, the intact anabolic response of myofibrillar FSR to feeding in both groups suggests anabolic resistance may not explain accelerated muscle loss in T2DM.

The mitochondrial elongation factor LeEF-Tsmt is regulated during tomato fruit ripening and upon wounding and ethylene treatment.

A gene encoding an elongation factor LeEF-Tsmt that participates in the protein synthesis process in mitochondria shows strong expression in ripening fruit as compared to other organs. It is strongly up-regulated during the first stages of the ripening process in parallel with the climacteric rise in respiration. LeEF-Tsmt expression is stimulated by ethylene, wounding and high temperature but ethylene-insensitive mutants exhibit normal expression. Transgenic fruit have been generated in which LeEF-Tsmt has been constitutively up- and down-regulated. Surprisingly, altering the expression of the gene by genetic transformation with antisense and sense LeEF-Tsmt constructs did not affect the pattern of respiration and ethylene production during ripening and upon wounding. In addition, expression of the alternative oxidase gene which is known to play an important role in respiratory climacteric was not affected. Possible reasons for the absence of effect on respiration of variations of LeEF-Tsmt gene expression are discussed.

Modeling Alzheimer disease with iPSCs and mouse model for the identification of risk factors, new targets, and potential therapeutical strategies

Alzheimer's disease (AD) is the most common neurodegenerative disease in elderly. Donepezil is the first-line drug used for AD. In section one, the experimental activity was oriented to evaluate and characterize molecular and cellular mechanisms that contribute to neurodegeneration induced by the Aβ1-42 oligomers (Aβ1-42O) and potential neuroprotective effects of the hybrids feruloyl-donepezil compound called PQM130. The effects of PQM130 were compared to donepezil in a murine AD model, obtained by intracerebroventricular (i.c.v.) injection of Aβ1-42O. The intraperitoneal administration of PQM130 (0.5-1 mg/kg) after i.c.v. Aβ1-42O injection improved learning and memory, protecting mice against spatial cognition decline. Moreover, it reduced oxidative stress, neuroinflammation and neuronal apoptosis, induced cell survival and protein synthesis in mice hippocampus. PQM130 modulated different pathways than donepezil, and it is more effective in counteracting Aβ1-42O damage. The section two of the experimental activity was focused on studying a loss of function variants of ABCA7. GWA studies identified mutations in the ABCA7 gene as a risk factor for AD. The mechanism through which ABCA7 contributes to AD is not clear. ABCA7 regulates lipid metabolism and critically controls phagocytic function. To investigate ABCA7 functions, CRISPR/Cas9 technology was used to engineer human iPSCs and to carry the genetic variant Y622*, which results in a premature stop codon, causing ABCA7 loss-of-function. From iPSCs, astrocytes were generated. This study revealed the effects of ABCA7 loss in astrocytes. ABCA7 Y622* mutation induced dysfunctional endocytic trafficking, impairing Aβ clearance, lipid dysregulation and cell homeostasis disruption, alterations that could contribute to AD. Though further studies are needed to confirm the PQM130 neuroprotective role and ABCA7 function in AD, the provided results showed a better understanding of AD pathophysiology, a new therapeutic approach to treat AD, and illustrated an innovative methodology for studying the disease.

Comprendere come lo stato genetico di TP53 influenza la risposta al deficit indotto sul Complesso I mitocondriale come terapia anticancro

Il Complesso I (CI) mitocondriale è uno dei target metabolici più promettenti nelle terapie anti- cancro. In particolare, la metformina è un inibitore noto del CI, capace di inibire la crescita delle cellule tumorali, ma non di eradicare la patologia. Recentemente, l’associazione metformina ed ipoglicemia si è rivelata letale per i tumori, sebbene l’efficacia terapeutica del trattamento sinergico possa essere influenzata dall’accumulo di alterazioni genetiche nei più noti drivers della tumorigenesi. Abbiamo così investigato l’effetto dello stress metabolico indotto dalla restrizione di glucosio in un pannello di linee cellulari tumorali con un severo deficit sul CI e con un diverso stato genetico di TP53. Il deficit del CI associato alla carenza di glucosio inducono un abbattimento dei livelli di espressione della proteina p53 mutata, ma non della controparte wild-type. Il fenomeno biologico osservato non dipende né da un blocco trascrizionale, né dall’innesco di vie di degradazione intracellulare, come proteasoma ed autofagia. La scomparsa di p53 mutata, invece, sembra dipendere da un blocco generale della sintesi proteica, verosimilmente indotto dallo stress energetico e nutrizionale. Nella controparte p53 wild-type, invece, si osserva solo una parziale riduzione della sintesi proteica, suggerendo l’innesco di possibili vie di adattamento per compensare il danno sul CI. La carenza di amminoacidi è una caratteristica dei tumori solidi che potrebbe essere esacerbata in condizioni di deficit generali della catena respiratoria mitocondriale. In particolare, l’inibizione del CI causa auxotrofia da aspartato, metabolita limitante per la proliferazione, condizione che potrebbe generare il blocco della sintesi proteica osservato. L’incremento di espressione dei livelli del trasportatore aspartato/glutatammato mediata da p53 mutata compensa l’auxotrofia da aspartato, identificando un meccanismo di adattamento al deficit del CI. Dunque, i risultati ottenuti sottolineano l’importanza di implementare la terapia anti-complesso I nel cancro, poiché il diverso stato di p53 può alterare l’efficacia del trattamento.

Specificità, efficacia e risposte adattative mediate da mutazioni dell'oncosoppressore TP53 degli inibitori del Complesso I mitocondriale nella terapia oncologica personalizzata: dai meccanismi molecolari allo sviluppo di modelli preclinici avanzati

L'inibizione del complesso respiratorio I (CI) è una strategia antitumorale emergente, sebbene la specificità e l’efficacia di nuovi farmaci restino poco investigate. La generazione di modelli cellulari tumorali nulli per il CI rivela la specificità di EVP 4593 e BAY 872243 nell’indurre gli effetti antiproliferativi non associati all’apoptosi, selettivamente via CI, riducendo eventuali effetti collaterali. Studi preliminari in vivo evidenziano un rallentamento della crescita tumorale negli animali trattati con EVP 4593, il quale emerge come l’inibitore più potente. Per il suo ruolo nella riprogrammazione metabolica, e la sua elevata frequenza di mutazioni nelle neoplasie umane, sono stati investigati i potenziali meccanismi di adattamento alla terapia anti-CI sulla base dello stato mutazionale di TP53. L’auxotrofia da aspartato, un hallmark metabolico delle cellule tumorali con un danno al CI, causa un blocco della sintesi proteica mTORC1-dipendente nelle linee cellulari con una p53 mutata o nulla, inducendo un collasso metabolico. Viceversa, l'attivazione del sensore energetico AMPK promuove un recupero parziale della sintesi di aspartato in linee cellulari con la forma wild type di P53, che è in grado di sostenere una migliore anaplerosi attraverso SCO2, fattore di assemblaggio del complesso respiratorio IV. Al fine di traslare questi risultati in un modello preclinico, si è ottimizzato l’ottenimento di colture di tumori umani espiantati tramite il bioreattore U-CUP. Il modello scelto è stato quello di carcinoma sieroso ad alto grado dell’ovaio (HGSOC), a partire da tessuto congelato, per l’elevata frequenza di mutazioni driver in TP53. I tessuti congelati preservano l'eterogeneità delle componenti cellulari del tessuto di origine e sono caratterizzati da cellule in attiva proliferazione senza attivazione di apoptosi. Dati preliminari mostrano un trend di riduzione dell’area tumorale nei tessuti trattati con EVP 4593 e supportano l’utilizzo del modello preclinico nello studio di nuovi inibitori del CI sfruttando materiale primario di pazienti oncologici.

Role of Shiga toxins in the pathogenesis of hemolytic uremic syndrome

During the pathogenesis of hemolytic uremic syndrome (HUS), a severe sequela of Shiga toxin (Stx)-producing Escherichia coli (STEC) gastrointestinal infections, before the toxin acts on the target endothelial cells of the kidney and brain, several Stx forms are transported in the bloodstream: free Stx; Stx bound to circulating cells through Gb3Cer and TLR4 receptors; and Stx associated to blood cell-derived microvesicles. The latter form is mainly responsible for the development of life-threatening HUS in 15% of STEC-infected patients. Stx consist of five B subunits non-covalently bound to a single A subunit (uncleaved Stx) which can be cleaved in two fragments (A1 and A2) held by a disulfide bond (cleaved Stx). After reduction, the enzymatically active A1 fragment responsible for toxicity is released. Cleaved and uncleaved Stx are biologically active but functionally different, thus their presence in patients’ blood could affect the onset of HUS. Currently, there are no effective therapies for the treatment of STEC-infected patients and the gold standard strategies available for the diagnosis are very expensive and time-consuming. In this thesis, by exploiting the resolving power of SERS technology (Amplified Raman Spectroscopy on Surfaces), a plasmonic biosensor was developed as effective diagnostic tool for early detection of Stx in patients’ sera. An acellular protein synthesis system for detecting cleaved Stx2a in human serum based on its greater translation inhibition after treatment with reducing agents was developed and used to identify cleaved Stx in STEC-infected patients’ sera. Pathogenic microvesicles from Stx2a-challenged blood from healthy donors were isolated and characterized. The antibiotic NAB815, acting as inhibitor of toxin binding to TLR4 expressed by circulating cells, was found to be effective in impairing the formation of blood cell-derived microvesicles containing Stx2a, also having a protective effect in cellular models. This approach could be proposed as an innovative treatment for HUS prevention.

The p.A2215D Thyroglobulin Gene Mutation Leads to Deficient Synthesis and Secretion of the Mutated Protein and Congenital Hypothyroidism with Wide Phenotype Variation

Context: Thyroglobulin (TG) is a large glycoprotein and functions as a matrix for thyroid hormone synthesis. TG gene mutations give rise to goitrous congenital hypothyroidism (CH) with considerable phenotype variation. Objectives: The aim of the study was to report the genetic screening of 15 patients with CH due to TG gene mutations and to perform functional analysis of the p. A2215D mutation. Design: Clinical evaluation and DNA sequencing of the TG gene were performed in all patients. TG expression was analyzed in the goitrous tissue of one patient. Human cells were transfected with expression vectors containing mutated and wild-type human TG cDNA. Results: All patients had an absent rise of serum TG after stimulation with recombinant human TSH. Sequence analysis revealed three previously described mutations (p. A2215D, p. R277X, and g. IVS30 + 1G > T), and two novel mutations (p. Q2142X and g. IVS46-1G > A). Two known (g. IVS30 + 1G/p. A2215D and p. A2215D/p. R277X) and one novel (p. R277X/g. IVS46-1G > A) compound heterozygous constellations were also identified. Functional analysis indicated deficiency in TG synthesis, reduction of TG secretion, and retention of the mutant TG within the cell, leading to an endoplasmic reticulum storage disease, whereas small amounts of mutant TG were still secreted within the cell system. Conclusion: All studied patients were either homozygous or heterozygous for TG gene mutations. Two novel mutations have been detected, and we show that TG mutation p. A2215D promotes the retention of TG within the endoplasmic reticulum and reduces TG synthesis and secretion, causing mild hypothyroidism. In the presence of sufficient iodine supply, some patients with TG mutations are able to compensate the impaired hormonogenesis and generate thyroid hormone. (J Clin Endocrinol Metab 94: 2938-2944, 2009)

Synthesis, identification, characterization, stability, solubility, and protein binding of ester derivatives of salicylic acid and diflunisal

O-Acyl esters were prepared from salicylic acid and diflunisal by esterification with the appropriate acyl anhydride (in the presence of sulfuric acid at 80 degrees C) or acyl chloride (in the presence of pyridine at 0 degrees C). Synthesis, identification and characterization of these compounds is described. In vitro hydrolysis, solubility and protein binding studies of these O-acyl esters were performed. For the diflunisal esters, the melting points fell as the side chain was increased from ethyl to pentyl. The melting points showed no significant difference as the length of the side chain was increased from pentyl to heptyl. The aspirin analogues showed a similar trend, The relationship between solubility and carbon chain length agreed closely with that for the melting points with carbon chain length. In vitro non-enzymatic hydrolysis studies concluded that: (1) hydrolysis rate constants generally decreased with carbon chain length; (2) the diflunisal esters have shorter half lives compared with their salicylate counterparts; and (3) the in vitro hydrolysis of these compounds was retarded by the presence of bovine serum albumin. Protein binding experiments showed that the strength of binding of the aspirin and diflunisal analogues to bovine serum albumin increased with carbon chain length. (C) 1997 Elsevier Science B.V.

Synthesis of an analog of the thyroid hormone-binding protein transthyretin via regioselective chemical ligation

Transthyretin is an essential protein responsible for the transport of thyroid hormones and retinol in human serum and is also implicated in the amyloid diseases familial amyloidotic polyneuropathy and senile systemic amyloidosis. Its folding properties and stabilization by ligands are of current interest due to their importance in understanding and combating these diseases, Here we report the solid phase synthesis of the monomeric unit of a transthyretin analog (equivalent to 127 amino acids) using t-Boc chemistry and peptide ligation and its folding to form a functional 54-kDa tetramer, The monomeric unit of the protein was chemically synthesized in three parts (positions 1-51, 54-99, and 102-127) and ligated using a chemoselective thioether ligation chemistry. The synthetic protein was folded and assembled to a tetrameric structure in the presence of transthyretin's native ligand, thyroxine, as shown by gel filtration chromatography, native gel electrophoresis, transthyretin antibody recognition, and thyroid hormone binding. Other folding products included a high molecular weight aggregate as well as a transient dimeric species. This represents one of the largest macromolecules chemically synthesized to date and demonstrates the potential of protein chemical synthesis for investigations of protein-ligand interactions.

A cassette ligation strategy with thioether replacement of three Gly-Gly peptide bonds: Total chemical synthesis of the 101 residue protein early pregnancy factor [psi(CH2S)(28-29,56-57,76-77)]

The 101 residue protein early pregnancy factor (EPF), also known as human chaperonin 10, was synthesized from four functionalized, but unprotected, peptide segments by a sequential thioether ligation strategy. The approach exploits the differential reactivity of a peptide-NHCH2CH2SH thiolate with XCH2CO-peptides, where X = Cl or I/Br. Initial model studies with short functionalized (but unprotected) peptides showed a significantly faster reaction of a peptide-NHCH2CH2SH thiolate with a BrCH2CO-peptide than with a CICH2CO-peptide, where thiolate displacement of the halide leads to chemoselective formation of a thioether surrogate for the Gly-Gly peptide bond. This rate difference was used as the basis of a novel sequential ligation approach to the synthesis of large polypeptide chains. Thus, ligation of a model bifunctional N-alpha-chloroacetyl, C-terminal thiolated peptide with a second N-alpha-bromoacetyl peptide demonstrated chemoselective bromide displacement by the thiol group. Further investigations showed that the relatively unreactive N-alpha-chloroacetyl peptides could be activated by halide exchange using saturated KI solutions to yield the highly reactive No-iodoacetyl peptides. These findings were used to formulate a sequential thioether ligation strategy for the synthesis of EPF, a 101 amino acid protein containing three Gly-Gly sites approximately equidistantly spaced within the peptide chain. Four peptide segments or cassettes comprising the EPF protein sequence (BrAc-[EPF 78-101] 12, ClAc-[EPF 58-75]-[NHCH2CH2SH] 13, ClAc-[EPF 30-55]-[NHCH2CH2SH] 14, and Ac-[EPF 1-27]-[NHCH2CH2SH] 15) of EPF were synthesized in high yield and purity using Boc SPPS chemistry. In the stepwise sequential ligation strategy, reaction of peptides 12 and 13 was followed by conversion of the N-terminal chloroacetyl functional group to an iodoacetyl, thus activating the product peptide for further ligation with peptide 14. The process of ligation followed by iodoacetyl activation was repeated to yield an analogue of EPF (EPF psi(CH2S)(28-29,56-57,76-77)) 19 in 19% overall yield.

Synthesis and structural analysis of the N-terminal domain of the thyroid hormone-binding protein transthyretin

Transthyretin (TTR) is a 55 kDa protein responsible for the transport of thyroid hormones and retinol in human serum. Misfolded forms of the protein are implicated in the amyloid diseases familial amyloidotic polyneuropathy and senile systemic amyloidosis. Its folding properties and stabilization by ligands are of current interest due to their importance in understanding and combating these diseases. To assist in such studies we developed a method for the solid phase synthesis of the monomeric unit of a TTR analogue and its folding to form a functional 55 kDa tetramer. The monomeric unit of the protein was chemically synthesized in three parts, comprising amino acid residues 151, 5499 and 102127, and ligated using chemoselective thioether ligation chemistry. The synthetic protein was folded and assembled to a tetrameric structure in the presence of the TTRs native ligand, thyroxine, as shown by gel filtration chromatography, native gel electrophoresis, TTR antibody recognition and thyroid hormone binding. In the current study the solution structure of the first of these fragment peptides, TTR(151) is examined to determine its intrinsic propensity to form beta-sheet structure, potentially involved in amyloid fibril formation by TTR. Despite the presence of extensive beta-structure in the native form of the protein, the Nterminal fragment adopts an essentially random coil conformation in solution.