Aspergillus niger G proteins: subcellular localization

Aspergillus niger postmitochondrial fraction, which contains high GTPase activity and high GTP binding capacity, has been subjected to subcellular fractionation on a sucrose gradient. A cytosolic and four membranous populations have been separated according to their relative density. The main difficulty has been the characterization of the plasma membrane of the fungus. This fraction, which does not contain any typical enzyme, has been identified after iodination of the outer proteins of protoplasts from A. niger. The immunological detection has shown the occurrence of cytosolic G proteins and membranous small G proteins located not only in the plasma membrane but also in the membranes of the endoplasmic reticulum.     

Predicting subcellular localization of proteins using machine-learned classifiers

MOTIVATION: Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy and most particularly breadth of coverage. Rather than using sequence information alone, we have explored the use of database text annotations from homologs and machine learning to substantially improve the prediction of subcellular location. RESULTS: We have constructed five machine-learning classifiers for predicting subcellular localization of proteins from animals, plants, fungi, Gram-negative bacteria and Gram-positive bacteria, which are 81% accurate for fungi and 92-94% accurate for the other four categories. These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service.     

Identification of the subcellular localization of mycobacterial proteins using localization motifs

Mycobacterium, the most common disease-causing genus, infects billions of people and is notoriously difficult to treat. Understanding the subcellular localization of mycobacterial proteins can provide essential clues for protein function and drug discovery. In this article, we present a novel approach that focuses on local sequence information to identify localization motifs that are generated by a merging algorithm and are selected based on a binomially distributed model. These localization motifs are employed as features for identifying the subcellular localization of mycobacterial proteins. Our approach provides more accurate results than previous methods and was tested on an independent dataset recently obtained from an experimental study to provide a first and reasonably accurate prediction of subcellular localization. Our approach can also be used for large-scale prediction of new protein entries in the UniportKB database and of protein sequences obtained experimentally. In addition, our approach identified many local motifs involved with the subcellular localization that also interact with the environment. Thus, our method may have widespread applications both in the study of the functions of mycobacterial proteins and in the search for a potential vaccine target for designing drugs.     

Validating subcellular localization prediction tools with mycobacterial proteins

Background  

The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins.     

PSLpred: prediction of subcellular localization of bacterial proteins

SUMMARY: We developed a web server PSLpred for predicting subcellular localization of gram-negative bacterial proteins with an overall accuracy of 91.2%. PSLpred is a hybrid approach-based method that integrates PSI-BLAST and three SVM modules based on compositions of residues, dipeptides and physico-chemical properties. The prediction accuracies of 90.7, 86.8, 90.3, 95.2 and 90.6% were attained for cytoplasmic, extracellular, inner-membrane, outer-membrane and periplasmic proteins, respectively. Furthermore, PSLpred was able to predict approximately 74% of sequences with an average prediction accuracy of 98% at RI = 5. AVAILABILITY: PSLpred is available at http://www.imtech.res.in/raghava/pslpred/     

Predicting subcellular localization of proteins in a hybridization space

MOTIVATION: The localization of a protein in a cell is closely correlated with its biological function. With the number of sequences entering into databanks rapidly increasing, the importance of developing a powerful high-throughput tool to determine protein subcellular location has become self-evident. In view of this, the Nearest Neighbour Algorithm was developed for predicting the protein subcellular location using the strategy of hybridizing the information derived from the recent development in gene ontology with that from the functional domain composition as well as the pseudo amino acid composition. RESULTS: As a showcase, the same plant and non-plant protein datasets as investigated by the previous investigators were used for demonstration. The overall success rate of the jackknife test for the plant protein dataset was 86%, and that for the non-plant protein dataset 91.2%. These are the highest success rates achieved so far for the two datasets by following a rigorous cross-validation test procedure, suggesting that such a hybrid approach (particularly by incorporating the knowledge of gene ontology) may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. AVAILABILITY: The software would be made available on sending a request to the authors.     

Exercise preconditioning against hydrogen peroxide-induced oxidative damage in proteins of rat myocardium

Both regular physical exercise and low levels of H(2)O(2) administration result in increased resistance to oxidative stress. We measured the accumulation of reactive carbonyl derivatives and the activities of proteasome complex and DT-diaphorase in cardiac muscle of trained and untrained rats after chronic i.p. administration of 1 ml t-butyl H(2)O(2) (1 mmol/kg for 3 weeks every second day). Twenty-four rats were randomly assigned to a control group administered with saline, control administered with H(2)O(2), and exercised administered either saline or H(2)O(2). The activity of DT-diaphorase significantly increased in H(2)O(2) administered and exercised groups, indicating that an increase in H(2)O(2) levels stimulate the activity of this enzyme. The cardiac muscle of H(2)O(2) administered nonexercised animals accumulated significantly more carbonyl than control group (P < 0.05). The exercise and H(2)O(2) administration resulted in less oxidatively modified protein than found in nonexercised groups (P < 0.05). The peptide-like activity of proteasome complex was induced by the treatment of H(2)O(2) and exercise and exercise potentiate the effect of H(2)O(2). On the other hand, the chymotrypsin-like and trypsin-like activities were stimulated only by physical training and H(2)O(2) administration. The data suggest that chronic administration of H(2)O(2) after exercise training decreases the accumulation of carbonyl groups below the steady-state level and induces the activity of proteasome and DT-diaphorase. Hence, the stimulating effect of physical exercise on free radical generation is an important phenomenon of the exercise-induced adaptation process since it increases resistance to oxidative stress. Regular exercise training is a valuable physiological means of preconditioning the myocardium to prolonged oxidative stress.     

A switching system regulating subcellular localization of nuclear proteins using a viral protease

We explored a novel approach to the functional regulation of nuclear proteins; altering their subcellular localization. To anchor a nuclear protein, beta-galactosidase with the nuclear localization signal of SV40 (nbeta-gal), within the cytoplasm, nbeta-gal was fused to the transmembrane domain of granulocyte colony-stimulating factor receptor (G-CSFR), a membrane protein. To liberate the nbeta-gal portion from the fusion protein, we used a protease derived from a plant virus, whose recognition sequence was inserted between the G-CSFR and nbeta-gal. Western analysis showed that the chimeric protein was cleaved in the presence of the protease in 293 cells and that the fusion protein without the recognition sequence remained intact. This chimeric protein was localized exclusively in the cytoplasm as visualized by X-gal staining and immunofluorescence microscopy. In contrast, when expressed together with the protease, beta-gal was predominantly detected in the nuclei. Moreover, we isolated 293-cell clones constitutively expressing the protease, indicating that this protease is not cytotoxic. These results suggest that the viral protease-mediated alteration of subcellular localization can potentially regulate the function of nuclear proteins.     

Quantitative proteomic approach to study subcellular localization of membrane proteins

As proteins within cells are spatially organized according to their role, knowledge about protein localization gives insight into protein function. Here, we describe the LOPIT technique (localization of organelle proteins by isotope tagging) developed for the simultaneous and confident determination of the steady-state distribution of hundreds of integral membrane proteins within organelles. The technique uses a partial membrane fractionation strategy in conjunction with quantitative proteomics. Localization of proteins is achieved by measuring their distribution pattern across the density gradient using amine-reactive isotope tagging and comparing these patterns with those of known organelle residents. LOPIT relies on the assumption that proteins belonging to the same organelle will co-fractionate. Multivariate statistical tools are then used to group proteins according to the similarities in their distributions, and hence localization without complete centrifugal separation is achieved. The protocol requires approximately 3 weeks to complete and can be applied in a high-throughput manner to material from many varied sources.     

Pyruvate prevents hydrogen peroxide-induced apoptosis

Studies were carried out to investigate the protective effects of pyruvate, a key glycolytic intermediate and α-keto-monocarboxylate, against oxidative stress-induced apoptosis. Oxidative stress was induced by treating mouse thymocytes with 25 μM hydrogen peroxide for 15 min at 37°C under 5% CO₂ in air. Pre- and post-treatment of cells with 10 mM pyruvate inhibited morphological changes, internucleosomal DNA fragmentation, and translocation of phosphatidylserine to the plasma membrane surface, which are characteristic features of apoptosis. L-lactate (10 mM) and acetate (10 mM) were ineffective in inhibiting apoptosis and appeared to be toxic to the cells under similar conditions. The results suggest that pyruvate has therapeutic potential for use in the treatment of oxidative stress-induced disorders associated with increased apoptosis.     

A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology

Based on the recent development in the gene ontology and functional domain databases, a new hybridization approach is developed for predicting protein subcellular location by combining the gene product, functional domain, and quasi-sequence-order effects. As a showcase, the same prokaryotic and eukaryotic datasets, which were studied by many previous investigators, are used for demonstration. The overall success rate by the jackknife test for the prokaryotic set is 94.7% and that for the eukaryotic set 92.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross-validation test procedure, suggesting that such a hybrid approach may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. The very high success rates also reflect the fact that the subcellular localization of a protein is closely correlated with: (1). the biological objective to which the gene or gene product contributes, (2). the biochemical activity of a gene product, and (3). the place in the cell where a gene product is active.     

Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing

As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we have developed and tested a strategy that allows their systematic and fast subcellular localization. We have used a novel cloning technology to rapidly generate N- and C-terminal green fluorescent protein fusions of cDNAs to examine the intracellular localizations of >100 expressed fusion proteins in living cells. The entire analysis is suitable for automation, which will be important for scaling up throughput. For >80% of these new proteins a clear intracellular localization to known structures or organelles could be determined. For the cDNAs where bioinformatic analyses were able to predict possible identities, the localization was able to support these predictions in 75% of cases. For those cDNAs where no homologies could be predicted, the localization data represent the first information.     

A catalytic antioxidant metalloporphyrin blocks hydrogen peroxide-induced mitochondrial DNA damage

Reactive oxygen species (ROS) have been implicated as the cause of cumulative damage to DNA, proteins and lipids that can ultimately result in cell death. A common problem when measuring oxidative DNA damage has been the introduction of modifications in the native state of the molecule by many DNA isolation methods. We circumvented this problem by employing direct PCR (DPCR) of whole cell lysates. DPCR of mouse lung fibroblasts performed better than PCRs containing template acquired by phenol/chloroform extraction or a commercially available genomic DNA isolation kit. We investigated the direct use of whole cell preparations in the polymerase chain reaction (PCR) to detect hydrogen peroxide (H₂O₂)-mediated DNA damage. We observed a concentration-dependent decrease in amplification efficiency of a 4.3 kb mitochondrial (mt)DNA target in H₂O₂-treated mouse lung fibroblasts (MLFs). At low doses the efficiency of amplification returns to control levels over 24 h. We detected no change in amplification efficiency of a plasmid control containing our mtDNA target under any of the culture conditions employed in these studies. Treatment of MLFs with the catalytic antioxidant manganese(III) meso-tetrakis(4-benzoic acid)porphyrin (MnTBAP) attenuates the effects of H₂O₂ exposure. When quantitated with an external standard the use of DPCR in tandem with a PCR amplification efficiency assay provides a powerful approach to assess oxidative mtDNA damage.     

Molecular characterization and subcellular localization of salt-inducible lipid transfer proteins in rice

Rice (Oryza sativa L.) is a salt-sensitive species. Salt stress can cause injury to the plant cellular membrane. Plant lipid transfer proteins (LTPs) are abundant lipid binding proteins that are important in membrane vesicle biogenesis and trafficking, however, the biological importance of LTPs on salt-stress response in rice remains unclear. Therefore, salt-responsive rice LTPs were identified and characterized in this study. Microarray analysis showed seven genes positively regulated by salinity, including five Ltp genes (LtpII.3, LtpII.5, LtpII.6, LtpV.1, and LtpV.2) and two Ltp-like (LtpL; LtpL1, and LtpL2) genes. Amino acid alignment revealed that all these Ltp and LtpL genes contained the N-terminal signal peptide. Apart from LtpL1, all salt-inducible Ltp genes had the conserved eight cysteine residue motifs backbone. Verification of gene expression to different stimuli in rice seedlings revealed that salt-regulated Ltp genes differentially responded to drought, cold, H₂O₂, abscisic acid (ABA) and CaCl₂. Furthermore, the expression of Ltp and LtpL genes was tissue-specifically regulated by ABA-dependent and independent pathway. In silico analysis of a 1.5-kb 5’-upstream region of these genes showed regulatory cis-elements associated with ABA, calcium, and cold/drought responses. Three LtpII subfamily genes, including LtpII.3, LtpII.5, and LtpII.6, were strictly expressed in flowers and seeds, and LtpIII.1 mRNA strongly accumulated in stem tissue. Subcellular localization analysis of LTP-DsRed fusion proteins revealed that the five LTPs and two LTPLs localized at the endoplasmic reticulum. The results provide new clues to further understanding the biological functions of Ltp genes.     

Expression and subcellular localization of Spred proteins in mouse and human tissues

Spred-1 and Spred-2 (Sprouty-related protein with an EVH1 domain) are recently described members of the EVH1 (Ena/VASP-homology domain 1) family. Both Spred-1 and Spred-2 are membrane-associated substrates of receptor tyrosine kinases and they act as negative regulators of the Ras pathway upon growth factor stimulation. Since the Spred family members seem to exert overlapping molecular functions, the isotype-specific function of each member remains enigmatic. To date, no comprehensive expression profiling of Spred proteins has been shown. Therefore, we compared mRNA and protein expression patterns of Spred-1 and Spred-2 systematically in mouse organs. Furthermore, we focused on the tissue-specific expression of Spred-2 in adult human tissues, the subcellular localization, and the potential role of Spred-2 in the organism. Our studies show that expression patterns of Spred-1 and Spred-2 differ markedly among various tissues and cell types. In mouse, Spred-1 and Spred-2 were found to be expressed predominantly in brain, whereas Spred-2 was found to be more widely expressed in various adult tissues than Spred-1. In humans, Spred-2 was found to be strongly expressed in glandular epithelia and, at the subcellular level, its immunoreactivity was associated with secretory vesicles. Using confocal microscopy we found Spred-2 to be strongly colocalized with Rab11 and, to a lesser extent, with Rab5a GTPase, an observation that was not made for Spred-1. We conclude that the two members of the recently discovered Spred protein family, Spred-1 and Spred-2, show a highly specific expression pattern in various tissues reflecting a specific physiological role for the individual Spred isoforms in these tissues. Furthermore, it becomes most likely that Spred-2 is involved in the regulation of secretory pathways.     

Sex differences in expression and subcellular localization of heart rhythm determinant proteins

To evaluate sex differences in protein expression in the heart, we performed Western blot studies on a subset of Heart Rhythm Determinant (HRD) proteins. We examined key components of a variety of types of mechanical and electrical junctions including, connexin43, plakophilin-2, N-cadherin and plakoglobin, ankyrin-2 and actin. We describe novel findings in sex differences in cardiac protein expression and membrane localization. For most proteins examined, sex differences were significantly more pronounced in the membrane compartment than in overall expression. These studies extend our previous findings in microarray studies to demonstrate that sex differences in gene expression are likely to confer distinct functional properties on male and female myocardium.     

Generation of optimized yellow and red fluorescent proteins with distinct subcellular localization

Fluorescent proteins (FPs) have revolutionized many aspects of cell biology and have become indispensable research tools. Today's increasingly complex experiments aiming to understand biological systems strongly depend on the availability of combinations of multiple FPs, which allow their distinguishable simultaneous detection in the same cell or tissue. Recently, the VENUS and DsRed. T4 FPs were described as the latest generation of yellow and red FPs. To increase the combinatorial possibilities when using these optimized FPs, we have generated and successfully tested seven new forms of VENUS and DsRed. T4 proteins with distinct subcellular localization. To facilitate their use as markers in biological experiments, bicistronic expression constructs, which have been optimized for robust expression in almost all mammalian developmental stages and cell types, were produced for the new FPs. In addition, several plasmids were created, which contain all necessary elements for inserting the reading frames of these FPs into specific gene loci in knock-in experiments without disrupting the reading frame of the endogenous gene.