RESUMO
Cyanobacteria and microalgae are oxygen-producing photosynthetic unicellular organisms encompassing a great diversity of species, which are able to grow under all types of extreme environments and exposed to a wide variety of predators and microbial pathogens. The antibacterial compounds described for these organisms include alkaloids, fatty acids, indoles, macrolides, peptides, phenols, pigments and terpenes, among others. This review presents an overview of antibacterial peptides isolated from cyanobacteria and microalgae, as well as their synergism and mechanisms of action described so far. Antibacterial cyanopeptides belong to different orders, but mainly from Oscillatoriales and Nostocales. Cyanopeptides have different structures but are mainly cyclic peptides. This vast peptide repertoire includes ribosomal and abundant non-ribosomal peptides, evaluated by standard conventional methodologies against pathogenic Gram-negative and Gram-positive bacteria. The antibacterial activity described for microalgal peptides is considerably scarcer, and limited to protein hydrolysates from two Chlorella species, and few peptides from Tetraselmis suecica. Despite the promising applications of antibacterial peptides and the importance of searching for new natural sources of antibiotics, limitations still persist for their pharmaceutical applications.
Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Cianobactérias/química , Microalgas/química , Proteínas de Algas/química , Proteínas de Algas/isolamento & purificação , Proteínas de Algas/farmacologia , Animais , Antibacterianos/química , Antibacterianos/isolamento & purificação , Antibacterianos/farmacologia , Anti-Inflamatórios não Esteroides/química , Anti-Inflamatórios não Esteroides/isolamento & purificação , Anti-Inflamatórios não Esteroides/farmacologia , Anti-Hipertensivos/química , Anti-Hipertensivos/isolamento & purificação , Anti-Hipertensivos/farmacologia , Peptídeos Catiônicos Antimicrobianos/isolamento & purificação , Peptídeos Catiônicos Antimicrobianos/farmacologia , Antineoplásicos/química , Antineoplásicos/isolamento & purificação , Antineoplásicos/farmacologia , Proteínas de Bactérias/química , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/farmacologia , Sinergismo Farmacológico , Eucariotos/química , Humanos , Técnicas de Síntese em Fase SólidaRESUMO
We systematically predict the internal flexibility of the S3 segment, one of the most mobile elements in the voltage-sensor domain. By analyzing the primary amino acid sequences of V-sensor containing proteins, including Hv1, TPC channels and the voltage-sensing phosphatases, we established correlations between the local flexibility and modes of activation for different members of the VGIC superfamily. Taking advantage of the structural information available, we also assessed structural aspects to understand the role played by the flexibility of S3 during the gating of the pore. We found that S3 flexibility is mainly determined by two specific regions: (1) a short NxxD motif in the N-half portion of the helix (S3a), and (2) a short sequence at the beginning of the so-called paddle motif where the segment has a kink that, in some cases, divide S3 into two distinct helices (S3a and S3b). A good correlation between the flexibility of S3 and the reported sensitivity to temperature and mechanical stretch was found. Thus, if the channel exhibits high sensitivity to heat or membrane stretch, local S3 flexibility is low. On the other hand, high flexibility of S3 is preferentially associated to channels showing poor heat and mechanical sensitivities. In contrast, we did not find any apparent correlation between S3 flexibility and voltage or ligand dependence. Overall, our results provide valuable insights into the dynamics of channel-gating and its modulation.
Assuntos
Eucariotos/metabolismo , Canais Iônicos/química , Canais Iônicos/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Eucariotos/química , Eucariotos/classificação , Eucariotos/genética , Ativação do Canal Iônico , Canais Iônicos/genética , Ligantes , Filogenia , Conformação Proteica , Alinhamento de SequênciaRESUMO
BACKGROUND: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport. To validate the new version and to demonstrate its improved performance, we tested snoReport 2.0 in different organisms. RESULTS: Results of the training and test phases of boxes H/ACA and C/D snoRNAs, in both versions of snoReport, are discussed. Validation on real data was performed to evaluate the predictions of snoReport 2.0. Our program was applied to a set of previously annotated sequences, some of them experimentally confirmed, of humans, nematodes, drosophilids, platypus, chickens and leishmania. We significantly improved the predictions for vertebrates, since the training phase used information of these organisms, but H/ACA box snoRNAs identification was improved for the other ones. CONCLUSION: We presented snoReport 2.0, to predict H/ACA box and C/D box snoRNAs, an efficient method to find true positives and avoid false positives in vertebrate organisms. H/ACA box snoRNA classifier showed an F-score of 93 % (an improvement of 10 % regarding the previous version), while C/D box snoRNA classifier, an F-Score of 94 % (improvement of 14 %). Besides, both classifiers exhibited performance measures above 90 %. These results show that snoReport 2.0 avoid false positives and false negatives, allowing to predict snoRNAs with high quality. In the validation phase, snoReport 2.0 predicted 67.43 % of vertebrate organisms for both classes. For Nematodes and Drosophilids, 69 % and 76.67 %, for H/ACA box snoRNAs were predicted, respectively, showing that snoReport 2.0 is good to identify snoRNAs in vertebrates and also H/ACA box snoRNAs in invertebrates organisms.
Assuntos
Biologia Computacional/métodos , Eucariotos/genética , RNA Nucleolar Pequeno/química , Máquina de Vetores de Suporte , Animais , Sequência de Bases , Biologia Computacional/instrumentação , Eucariotos/química , Humanos , Dados de Sequência Molecular , RNA Nucleolar Pequeno/genética , Vertebrados/genéticaRESUMO
BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. RESULTS: By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. CONCLUSIONS: The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.
Assuntos
Biologia Computacional/métodos , Eucariotos/genética , Genômica/métodos , MicroRNAs/química , Animais , Biologia Computacional/instrumentação , Simulação por Computador , Eucariotos/química , Genoma , Genômica/instrumentação , Humanos , Aprendizado de Máquina , MicroRNAs/genética , Conformação de Ácido Nucleico , Plantas/química , Plantas/genéticaRESUMO
Phosphatidylglycerol and phospholipids derived from it are widely distributed throughout the three domains of life. Cardiolipin is the best characterized of these phospholipids, and plays a key role in the response to environmental variations. Phosphatidylglycerol-derived phospholipids confer cell membranes with a wide range of responses, including changes in surface charge, fluidity, flexibility, morphology, biosynthesis and remodeling, that adapt the cell to these situations. Furthermore, the synthesis and remodeling of these phospholipids is finely regulated, highlighting the importance of these lipids in cell homeostasis and responses during stressful situations. In this article, we review the most important roles of these anionic phospholipids across domains, focusing on the biophysical basis by which these phospholipids are used in stress responses.
Assuntos
Archaea/fisiologia , Bactérias/metabolismo , Cardiolipinas/biossíntese , Eucariotos/fisiologia , Fosfatidilgliceróis/biossíntese , Apoptose/fisiologia , Archaea/química , Bactérias/química , Cardiolipinas/química , Membrana Celular/química , Membrana Celular/metabolismo , Eucariotos/química , Mitofagia/fisiologia , Fosfatidilgliceróis/química , Estresse FisiológicoRESUMO
Posttranslational modification of proteins plays a key role in the regulation of a plethora of metabolic functions. Protein modification by mono-ADP-ribosylation was first described as a mechanism of action of bacterial toxins. Since these pioneering studies, the number of pathways regulated by ADP-ribosylation in organisms from all domains of life expanded significantly. However, in only a few cases the full regulatory ADP-ribosylation circuit is known. Here, we review the system where mono-ADP-ribosylation regulates the activity of an enzyme: the regulation of nitrogenase in bacteria. When the nitrogenase product, ammonium, becomes available, the ADP-ribosyltransferase (DraT) covalently links an ADP-ribose moiety to a specific arginine residue on nitrogenase switching-off nitrogenase activity. After ammonium exhaustion, the ADP-ribosylhydrolase (DraG) removes the modifying group, restoring nitrogenase activity. DraT and DraG activities are reversibly regulated through interaction with PII signaling proteins . Bioinformatics analysis showed that DraT homologs are restricted to a few nitrogen-fixing bacteria while DraG homologs are widespread in Nature. Structural comparisons indicated that bacterial DraG is closely related to Archaea and mammalian ADP-ribosylhydrolases (ARH). In all available structures, the ARH active site consists of a hydrophilic cleft carrying a binuclear Mg(2+) or Mn(2+) cluster, which is critical for catalysis.
Assuntos
Adenosina Difosfato Ribose/metabolismo , Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Eucariotos/enzimologia , Nitrogenase/metabolismo , ADP Ribose Transferases/genética , ADP Ribose Transferases/metabolismo , Animais , Bactérias/química , Bactérias/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Eucariotos/química , Eucariotos/genética , Regulação Enzimológica da Expressão Gênica , Humanos , Nitrogenase/química , Nitrogenase/genética , Processamento de Proteína Pós-TraducionalRESUMO
A laboratory culture of Ankistrodesmus gracilis algae was evaluated by studyingthe biology of the species and its chemical composition in a traditional medium (CHU12)and in two alternative culture media, NPK (20-5-20) and macrophyte (Eichhornia crassipes)+ NPK, in three different types of recipients (fiberglass, carboy and plastic bag). First peakin the growth curve of Ankistrodesmus gracilis occurred on the ninth day in macrophyte+ NPK medium (74.16 x 105 cells mL-1) in a fiberglass recipient. However, highest density(p < 0.01) was reported in medium CHU12 (122.87 x 105 cells mL-1) in a plastic bag on thetwelfth day. Cell density was over 70 x 105 cells mL-1 starting on the twelfth day. Growthrate of A. gracilis was similar (p > 0.05) in culture media in the three recipients. Protein andfiber were similar (p > 0.05) in the treatments, but lipids were higher (p < 0.05) in NPK.Nitrate, ammonia, total phosphorus and orthophosphate contents were over 1 mg L-1 inNPK (p < 0.01). Results show that alternative media, such as NPK and macrophyte+ NPK, are possible for large-scale culture of A. gracilis cultured in three types of recipients.Costs are low, occupying less space when cultured in plastic bags and in the laboratory. (AU)
O objetivo do estudo foi avaliar os aspectos biológicos e a composição químicada alga Ankistrodesmus gracilis em laboratório utilizando um meio tradicional (CHU12) e doismeios alternativos, NPK (20-5-20) e macrófita (Eichhornia crassipes) + NPK em trêsdiferentes tipos de recipientes (cuba de fibra de vidro translúcido, garrafões e saco plástico).O primeiro pico de densidade celular de Ankistrodesmus gracilis ocorreu no nono dia da curvade crescimento em meio macrófita+NPK (74,16 x 105 células mL-1) no recipiente de fibrade vidro, porém a maior densidade (p < 0,01) foi observada no meio CHU12 (122,87 x 105células mL-1) em saco plástico no décimo segundo dia, a partir do qual a densidade celularpermaneceu acima de 70 x 105 células mL-1. A taxa de crescimento de A. gracilis foi similar(p > 0,05) nos três recipientes e meios de cultivo. Os teores de proteína e fibra foramsimilares (p > 0,05) nos tratamentos utilizados, já os de lipídios foram mais elevados (p < 0,05)no meio NPK. Os teores médios de nitrato, amônia, fósforo total e ortofosfato estiveramacima de 1 mg L-1 no meio NPK (p < 0,01). Os resultados obtidos neste estudo indicam apossibilidade do uso de meios alternativos como o NPK e macrophyte +NPK para o cultivode A. gracilis em larga escala cultivados nos três tipos de recipientes, porém, em saco plásticoo custo é baixo e ocupa menos espaço em cultivo de laboratório.(AU)
Assuntos
Eucariotos/química , Euglena gracilisRESUMO
A structural study of the carbohydrates from Coccomyxa mucigena, the symbiotic algal partner of the lichenized fungus Peltigera aphthosa, was carried out. It produced an O-methylated mannogalactan, with a (1-->6)-linked beta-galactopyranose main-chain partially substituted at O-3 by beta-Galp, 3-OMe-alpha-Manp or alpha-Manp units. There were no similarities with polysaccharides previously found in the lichen thallus of P. aphthosa. Moreover, the influence of lichenization in polysaccharide production by symbiotic microalgae and the nature of the photobiont in carbohydrate production in lichen symbiosis are also discussed.
Assuntos
Ascomicetos/fisiologia , Eucariotos/química , Simbiose , Cromatografia Gasosa , Cromatografia em Gel , Cromatografia Líquida de Alta Pressão , Eucariotos/fisiologia , Espectroscopia de Ressonância Magnética , MetilaçãoRESUMO
Copper complexation in marine systems is mainly controlled by organic matter, partially produced by micro- and macroalgae that release exudates with the capacity to bind metals. This feature is important as it influences bioavailability, bioaccumulation, toxicity, and transport of copper through biological membranes. The release of Cu-complexing ligands by seaweeds cultured under copper excess was studied in the laboratory. Five macroalgae belonging to different functional groups were used, including the filamentous Chaetomorphafirma (Chlorophyta), the foliose Ulvalactuca (Chlorophyta) and Porphyra columbina (Rhodophyta), the corticated Gelidium lingulatum (Rhodophyta), and the leathery Lessonia nigrescens (Phaeophyceae). The concentration of ligands and their copper-binding strength (logK') of exudates released by each species was determined by anodic stripping voltammetry (ASV). The selected algae released exudates in a wide range of concentration (42-117 nM) after 48h of culture, and addition of 157nM copper increased the production of ligands up to 8 times. A relationship between structural complexity or thallus thickness and the amount of ligands released was not observed. The binding strength (logK') varied among species from 7.6 to 8.9, a response that was not modified by exposure to sub-lethal copper excess. The kelp L. nigrescens showed a fast response to copper excess, releasing ligands that reduced toxicity of the metal in hours. Results suggest that intertidal and shallow subtidal macroalgae might have been overlooked regarding their role as producers of organic ligands and, therefore, as modulators of metal complexing capacity in coastal waters.
Assuntos
Disponibilidade Biológica , Cobre/metabolismo , Ligantes , Alga Marinha/química , Adsorção , Sítios de Ligação , Cobre/química , Monitoramento Ambiental , Eucariotos/química , Metais/metabolismo , Phaeophyceae/química , Rodófitas/química , Alga Marinha/metabolismoRESUMO
Tobago's fringing coral reefs (FR) and Buccoo Reef Complex (BRC) can be affected locally by wastewater and stormwater, and regionally by the Orinoco River. In 2001, seasonal effects of these inputs on water-column nutrients and phytoplankton (Chl a), macroalgal C:N:P and delta(15)N values, and biocover at FR and BRC sites were examined. Dissolved inorganic nitrogen (DIN, particularly ammonium) increased and soluble reactive phosphorus (SRP) decreased from the dry to wet season. Wet season satellite and Chl a data showed that Orinoco runoff reaching Tobago contained chromophoric dissolved organic matter (CDOM) but little Chl a, suggesting minimal riverine nutrient transport to Tobago. C:N ratios were lower (16 vs. 21) and macroalgal delta(15)N values higher (6.6 per thousand vs. 5.5 per thousand) in the BRC vs. FR, indicating relatively more wastewater N in the BRC. High macroalgae and low coral cover in the BRC further indicated that better wastewater treatment could improve the health of Tobago's coral reefs.