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Given the limitation of technologies, the subcellular localizations of proteins are difficult to identify. Predicting the subcellular localization and the intercellular distribution patterns of proteins in accordance with their specific biological roles, including validated functions, relationships with other proteins, and even their specific sequence characteristics, is necessary. The computational prediction of protein subcellular localizations can be performed on the basis of the sequence and the functional characteristics. In this study, the protein–protein interaction network, functional annotation of proteins and a group of direct proteins with known subcellular localization were used to construct models. To build efficient models, several powerful machine learning algorithms, including two feature selection methods, four classification algorithms, were employed. Some key proteins and functional terms were discovered, which may provide important contributions for determining protein subcellular locations. Furthermore, some quantitative rules were established to identify the potential subcellular localizations of proteins. As the first prediction model that uses direct protein annotation information (i.e., functional features) and STRING-based protein–protein interaction network (i.e., network features), our computational model can help promote the development of predictive technologies on subcellular localizations and provide a new approach for exploring the protein subcellular localization patterns and their potential biological importance Given the limitation of technologies, the subcellular localizations of proteins are difficult to identify. Predicting the subcellular localization and the intercellular distribution patterns of proteins in accordance with their specific biological roles, including validated functions, relationships with other proteins, and even their specific sequence characteristics, is necessary. The computational prediction of protein subcellular localizations can be performed on the basis of the sequence and the functional characteristics. In this study, the protein-protein interaction network, functional annotation of proteins and a group of direct proteins with known subcellular localization were used to construct models. To build efficient models, several powerful machine learning algorithms, including two feature selection methods, four classification algorithms, were employed. Some key proteins and functional terms were discovered, which may provide important contributions for determining protein subcellular locations. Furthermore, some quantitative rules were established to identify the potential subcellular localizations of proteins. As the first prediction model that uses direct protein annotation information (i.e., functional features) and STRING-based protein-protein interaction network (i.e., network features), our computational model can help promote the development of predictive technologies on subcellular localizations and provide a new approach for exploring the protein subcellular localization patterns and their potential biological importance.

Type I Baeyer&ndash, Villiger monooxygenases (BVMOs) are flavin-dependent monooxygenases that catalyze the oxidation of ketones to esters or lactones, a reaction otherwise performed in chemical processes by employing hazardous and toxic peracids. Even though various BVMOs are extensively studied for their promising role in industrial biotechnology, there is still a demand for enzymes that are able to retain activity at high saline concentrations. To this aim, and based on comparative in silicoanalyses, we cloned HtBVMO from the extremely halophilic archaeon Haloterrigena turkmenica DSM 5511. When expressed in standard mesophilic cell factories, proteins adapted to hypersaline environments often behave similarly to intrinsically disordered polypeptides. Nevertheless, we managed to express HtBVMO in Escherichia coli and could purify it as active enzyme. The enzyme was characterized in terms of its salt-dependent activity and resistance to some water&ndash, organic-solvent mixtures. Although HtBVMO does not seem suitable for industrial applications, it provides a peculiar example of an alkalophilic and halophilic BVMO characterized by an extremely negative charge. Insights into the behavior and structural properties of such salt-requiring may contribute to more efficient strategies for engineering the tuned stability and solubility of existing BVMOs.

The Gram-positive bacterium Bacillus subtilis encounters nutrient limitations and osmotic stress in its natural soil ecosystem. To ensure survival and sustain growth, highly integrated adaptive responses are required. Here, we investigated the system-wide response of B.subtilis to different, simultaneously imposed stresses. To address the anticipated complexity of the cellular response networks, we combined chemostat experiments under conditions of carbon limitation, salt stress and osmoprotection with multi-omics analyses of the transcriptome, proteome, metabolome and fluxome. Surprisingly, the flux through central carbon and energy metabolism is very robust under all conditions studied. The key to achieve this robustness is the adjustment of the biocatalytic machinery to compensate for solvent-induced impairment of enzymatic activities during osmotic stress. Specifically, increased production of several enzymes of central carbon metabolism compensates for their reduced activity in the presence of high salt. A major response of the cell during osmotic stress is the production of the compatible solute proline. This is achieved through the concerted adjustment of multiple reactions around the 2-oxoglutarate node, which drives metabolism towards the proline precursor glutamate. The fine-tuning of the transcriptional and metabolic networks involves functional modules that overarch the individual pathways.

Central metabolism is a coordinated network that is regulated at multiple levels by resource availability and by environmental and developmental cues. Its genetic architecture has been investigated by mapping metabolite quantitative trait loci (QTL). A more direct approach is to identify enzyme activity QTL, which distinguishes between cis-QTL in structural genes encoding enzymes and regulatory trans-QTL. Using genome-wide association studies, we mapped QTL for 24 enzyme activities, nine metabolites, three structural components, and biomass in Arabidopsis thaiiana. We detected strong cis-QTL for five enzyme activities. A cis-QTL for UDP-glucose pyrophosphorylase activity in the UGP1 promoter is maintained through balancing selection. Variation in acid invertase activity reflects multiple evolutionary events in the promoter and coding region of VAC-INV. cis-QTL were also detected for ADP-glucose pyrophosphorylase, fumarase, and phosphoglucose isomerase activity. We detected many trans-QTL, including transcription factors, E3 ligases, protein targeting components, and protein kinases, and validated some by knockout analysis. trans-QTL are more frequent but tend to have smaller individual effects than cis-QTL. We detected many colocalized QTL, including a multitrait QTL on chromosome 4 that affects six enzyme activities, three metabolites, protein, and biomass. These traits are coordinately modified by different ACCELERATED CELL DEATH6 alleles, revealing a trade-off between metabolism and defense against biotic stress.

O objetivo deste trabalho foi analisar o efeito de diferentes temperaturas na atividade respiratória, enzimática e em processos relacionados à qualidade fisiológica de sementes de arroz, bem como utilizar a relação entre esses parâmetros como forma de caracterizar o início do processo de deterioração de sementes. As sementes foram expostas por 24 h às temperaturas de 15; 25; 30 e 35 ºC, e conduzidas aos testes de germinação, primeira contagem de germinação, índice de velocidade de germinação, comprimento e massa seca da parte aérea e raiz, condutividade elétrica, atividade respiratória e enzimática. O delineamento experimental foi inteiramente casualizado, com quatro repetições, sendo as médias comparadas pelo teste de Tukey (p < 0,05) com posterior análise de regressão polinomial. As sementes de arroz apresentaram diminuição na germinação e no vigor a partir de temperaturas superiores a 25 ºC. A atividade respiratória aumentou com o aumento de temperatura, o mesmo ocorreu com a atividade das enzimas aos cinco dias após a semeadura (variando de 14,55 a 59,86 µmol de NAD+g-1 MF min-1 para a malato desidrogenase e de 0,25 a 0,57 µmol de NADPH g-1 MF min-1 para a glicose-6-fosfato desidrogenase). Portanto, pode-se concluir que os testes bioquímicos avaliados podem ser utilizados para identificar o início do processo deteriorativo das sementes de arroz e que temperaturas superiores a 25 ºC depreciam a qualidade destas sementes. The purpose of this research was to analyze the effect of different temperatures on the respiratory activity, enzymatic and in process related to the physiological quality of rice seeds, and use the relationship between these parameters to characterize the beginning of the deterioration process of seeds. The seeds were exposed during 24 h and conducted tests for germination, first count germination, index the germination speed, length and dry weight of shoot and roots, electrical conductivity, respiratory activity and activity of the enzymes. The experiment was completely randomized with four replicates and the averages compared by Tukey test (p < 0.05) with subsequent analysis of regression. Rice seeds showed that the germination and vigor were reduced above 25 ºC temperatures. Respiratory activity increased with increasing temperature, the same occurred with study enzymes activity in at five days after sowing (ranging from 14.55 at 59.86 µmol of NAD+ g-1 MF min-1 for at malate dehydrogenase and 0.25 at 0.57 µmol of at NADPH g-1 MF min-1 for glucose-6-phosphate dehydrogenase). Therefore, it can be concluded that the evaluated biochemical tests can be used to identify the beginning of the deteriorating process of rice seeds and that temperatures above 25 ºC can depreciate the quality of these seeds.

Made available in DSpace on 2019-09-12T16:53:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2009 Universidade Federal do Rio de Janeiro (UFRJ) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Ministério do Meio Ambiente (MMA) Secretariat of the Inter-Ministry Commission for Marine Resources (SeCIRM) The potential aerobic ATP-generating pathway and the argininolytic capacity of the Antarctic bivalve Laternula elliptica in its main tissues were measured by the specific activity of the enzymes malate dehydrogenase (MDH), citrate synthase (CS) and arginase. The kidney showed the major potential for aerobic ATP-generating pathway and argininolytic capacity. High levels of CS and MDH activities indicated that renal tissue can be involved in activities that require a lot of energy such as excretion of metabolic end products, amino acids catabolism or even gluconeogenic activities related to inter-tissue metabolism. The fact that kidneys are the main site for arginase activity is very unusual for mollusks and could be related to the living habits of L. elliptica. Genetic expression of the L. elliptica renal arginase could be controlling the levels of l-arginine and forming urea in the excretory organ, which may not have its physiological functions directly affected by the seasonal retraction of its siphons. Compared to the bivalve Dreissena polymorpha, renal arginase of L. elliptica is more resistant to inhibition by copper and cadmium. This could be related to naturally high levels of these metals in the Antarctic marine environment and its bioaccumulation in the renal tissue of L. elliptica, as a probable advantage to its environmental adaptation. Different from other Antarctic animals that feed on Krill, the arginase of L. elliptica is much more sensitive to fluoride inhibition. However, diet composition of L. elliptica would be expected to be variable site to site and its high sensitivity to fluoride inhibition may be a matter of concern in areas near ornithogenic soils subjected to ice-melting processes. [Rodrigues, Edson; da Silva Santos, Marcela Rosana; Rodrigues Junior, Edson; Gannabathula, Vani] Universidade de Taubaté (Unitau), Biochem Lab, Basic Inst Biosci, BR-12030180 Taubate, SP, Brazil [Lavrado, Helena Passeri] Univ Fed Rio de Janeiro, UFRJ, CCS, BR-21949900 Rio De Janeiro, Brazil

The Gram-positive bacterium Bacillus subtilis encounters nutrient limitations and osmotic stress in its natural soil ecosystem. To ensure survival and sustain growth, highly integrated adaptive responses are required. Here, we investigated the system-wide response of B.subtilis to different, simultaneously imposed stresses. To address the anticipated complexity of the cellular response networks, we combined chemostat experiments under conditions of carbon limitation, salt stress and osmoprotection with multi-omics analyses of the transcriptome, proteome, metabolome and fluxome. Surprisingly, the flux through central carbon and energy metabolism is very robust under all conditions studied. The key to achieve this robustness is the adjustment of the biocatalytic machinery to compensate for solvent-induced impairment of enzymatic activities during osmotic stress. Specifically, increased production of several enzymes of central carbon metabolism compensates for their reduced activity in the presence of high salt. A major response of the cell during osmotic stress is the production of the compatible solute proline. This is achieved through the concerted adjustment of multiple reactions around the 2-oxoglutarate node, which drives metabolism towards the proline precursor glutamate. The fine-tuning of the transcriptional and metabolic networks involves functional modules that overarch the individual pathways.

The monoclonal a-70-kDa heat shock protein (hsp70) antibody recognizes in crude extracts from watermelon ( Citrullus vulgaris ) cotyledons two hsps with molecular masses of 70 and 72 kDa. Immunocytochemistry on watermelon cotyledon tissue and on isolated glyoxysomes identified hsp70s in the matrix of glyoxysomes and plastids. Affinity purification and partial amino acid determination revealed the 70-kDa protein to share high sequence identity with cytosolic hsp70s from a number of plant species, while the 72 kDa protein was very similar to plastid hsp70s from pea and cucumber. A full-length cDNA clone encoding the 72-kDa hsp70 was isolated and identified two start methionines in frame within the N-terminal presequence leading either to an N-terminal extension of 67 amino acids or to a shorter one of 47 amino acids. The longer presequence was necessary and sufficient to target a reporter protein into watermelon proplastids in vitro . The shorter extension starting from the second methionine within the long version harbored a consensus peroxisomal targeting signal (RT-X 5 -KL) that directed in vivo a reporter protein into peroxisomes of the yeast Hansenula polymorpha . Peroxisomal targeting was however prevented, when the 67-residue presequence was fused to the reporter protein, indicating that the peroxisomal targeting signal 2 information is hidden in this context. We propose that the 72-kDa hsp70 is encoded by a single gene, but targeted alternatively into two organelles by the modulated use of its presequence.

A correct interpretation of isozyme patterns can be seriously hampered by the lack of supporting genetic data. The availability of the complete genome sequence of Phytophthora ramorum, enabled us to correlate isozyme profiles with the gene models predicted for these enzymes. Thirty-nine P. ramorum strains were characterised employing isozyme analysis on malate dehydrogenase (MDH), NADP-dependent malic enzyme (MDHP), 6-phosphogluconate dehydrogenase (PGD), glucosephosphate isomerase (GPI) and lactate dehydrogenase (LDH) comprising nine putative loci. One isozyme band was enzymatically stained for PGD whereas multiple bands were detected for GPI, MDH, MDHP and LDH. All putative loci were monomorphic except for Ldh-2. Genome mining revealed that the assembled genome sequences of P. ramorum and P. sojae each contain one Gpi and one Pgd gene model. For MDH, two gene models were identified, encoding a cytosolic and mitochondrial type, respectively. Also for MDHP P. ramorum has two gene models that are both duplicated in P. sojae. Both species contain six Ldh gene models, including pseudogenes. The Ldh gene models are clustered and located in regions that show a high level of conserved synteny. This study demonstrates that insight into the gene models encoding isozymes helps to interpret isozyme profiles in Phytophthora.

A triple cysteine mutant of sorghum leaf NADP-malate dehydrogenase has been constructed by site-directed mutagenesis, combining the previously obtained mutation of the two N-terminal cysteines with the mutation of the most internal of the two C-terminal cysteines. The construct, over-expressed in E. coli, yielded an always active, dithiol-insensitive enzyme. It can be concluded that the dithiol activation of the unmodified enzyme involves a maximum of two different disulfides per subunit, and that none of the mutated cysteines is implicated in catalysis.