Current Protein & Peptide Science

ISSN: 1389-2037

Current Protein and Peptide Science
Volume 11, Number 8, December 2010

Contents

Hot Topic

Fungal Model Systems to Understand the Mechanisms Unravelling the Oxidative Stress Response
Guest Editor: Maria Angeles de la Torre Ruiz


Editorial Pp. 651


Proteomic Strategies for the Analysis of Carbonyl Groups on Proteins Pp. 652-658
V. Irazusta, A. Moreno-Cermeño, E. Cabiscol, J. Tamarit and J. Ros
[Abstract] [Full Text Article]


Structural and Functional Diversity of Glutaredoxins in Yeast Pp. 659-668
E. Herrero, G. Bellí and C. Casas
[Abstract] [Full Text Article]


How Budding Yeast Sense and Transduce the Oxidative Stress Signal and the Impact in Cell Growth and Morphogenesis Pp. 669-679
M.A. de la Torre-Ruiz, A. Mozo-Villarías, N. Pujol and M.I. Petkova
[Abstract] [Full Text Article]


Cell Integrity Signaling and Response to Stress in Fission Yeast Pp. 680-692
P. Pérez and J. Cansado
[Abstract] [Full Text Article]


The Role of MAPK Signal Transduction Pathways in the Response to Oxidative Stress in the Fungal Pathogen Candida albicans: Implications in Virulence Pp. 693-703
C.H. de Dios, E. Román, R.A. Monge and J. Pla
[Abstract] [Full Text Article]


Adaptative and Developmental Responses to Stress In Aspergillus nidulans Pp. 704-718
O. Etxebeste, U. Ugalde and E.A. Espeso
[Abstract] [Full Text Article]


General Articles


The Roles of the A- and B-Chains of Human Relaxin-2 and -3 on Their Biological Activity Pp. 719-724
M.A. Hossain and J.D. Wade
[Abstract] [Full Text Article]


Cysteine Protease Inhibitors: from Evolutionary Relationships to Modern Chemotherapeutic Design for the Treatment of Infectious Diseases Pp. 725-743
E.C.Y. Toh, N.L. Huq, S.G. Dashper and E.C. Reynolds
[Abstract] [Full Text Article]


Compacting Proteins: Pros and Cons of Osmolyte-Induced Folding Pp. 744-751
E.P. Melo, N. Estrela, C. Lopes, A.C. Matias, E. Tavares and V. Ochoa-Mendes
[Abstract] [Full Text Article]


Applications and Modifications of 1,2,3,4-Tetrahydroisoquinoline-3-Carboxylic Acid (Tic) in Peptides and Peptidomimetics Design and Discovery Pp. 752-758
Y. Zhang, H. Fang and W. Xu
[Abstract] [Full Text Article]


Erbin, a Negative Regulator in Diverse Signal Pathways Pp. 759-638
L. Dan, M. Shi, H. Duan, C. Han and N. Guo
[Abstract] [Full Text Article]




Abstracts


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Editorial:

Oxidative stress occurs as a consequence of aerobic life. ROS (Reactive oxygen species) cause important cellular damage to prokaryotic and eukaryotic cells. Oxidation of different molecules in eukaryotic cells is the cause of many human diseases; examples of them include atherosclerosis, Parkinson´s and Alzheimer´s diseases, mental disorders and others. During decades, researchers have been developing new strategies to counteract the pernicious effects of the oxidative stress. One of the main important cues of these studies is to know and to characterise at the molecular level all the cellular processes involved in cell sensing, signalling, transduction and the adaptive responses to oxidative stress. The characterisation of early and late responses and the adaptive mechanism to oxidants, are of major interest in order to develop new antioxidants and drugs to counteract the noxious effects of oxidative stress. Moreover, since oxidative stress is one of the main causes of aging and cell death, knowledge of those processes circumventing aging is tour aim in order to extend human life. In this special issue, an overview of the current knowledge of different aspects of oxidative stress it is shown, developed upon the study of different fungal systems. Fungi are microorganisms. As unicellular systems, they are relatively easy to manipulate and modify genetically. Fungi are eukaryotic cells. Consequently they are suitable model systems since they present a high degree of similarity with human cells. In addition, yeast data bases are the most extended, containing the most complete genetic information to date.

The model systems reviewed in the current issue include Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus nidulans. S. cerevisiae is a very well known model system. Studies based in this system have contributed to extend the knowledge of the molecular mechanisms circumventing oxidative stress by using genomic and proteomic approaches. It is a very suitable model to study biochemical and molecular mechanisms related to antioxidant enzymes, glutaredoxins and thioredoxins, among others. Moreover, in the past decades many advances have been achieved in the study of the processes of sensing and transducing the oxidative signal to the nucleus, along with various mechanisms of cellular responses and adaptation to oxidative stress. These mechanisms include those related to the actin cytoskeleton remodelling and in general to morphogenetic processes. In parallel, and with similar relevance, a huge number of studies have been developed with Schizosaccharomyces pombe, another very well known yeast system. In fact, both yeast models, S. cerevisiae and S. pombe, have largely contributed to increase the knowledge of these responses, as detailed in this issue. Candida albincans is a diploid unicellular eukaryotic system whose study complements the knowledge obtained from the haploids systems S. cerevisiae and S. pombe. Of special relevance in microbiology is the study of the oxidative stress in the context of Candida albicans virulence, since this yeast can be an opportunistic pathogen. In this respect, the study of those mechanisms developed by Candida albicans in the oxidative stress response, can favour the identification of different specific cellular targets in order to design new drugs that block the proliferation of possible fungal pathogens. Aspergillus nidulans is a nascent cellular model that is importantly contributing to increase the knowledge of the oxidative stress responses and in general of the signal transduction mechanisms associated whit it. Again, A. nidulans, as in the case of C. albincas, can offer more information related to microbial virulence as for example the development of new antifungal drugs.

M.A. de la Torre-Ruiz
Guest Editor


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Proteomic Strategies for the Analysis of Carbonyl Groups on Proteins
V. Irazusta, A. Moreno-Cermeño, E. Cabiscol, J. Tamarit and J. Ros

Oxidative stress is caused by an imbalance between formation and destruction of reactive oxygen species. Analysis of the reaction products of reactive oxygen species in biomolecules is an indirect way of determining the existence of oxidative stress. In this context, the formation of carbonyl groups in proteins has been one of the most studied oxidative stress markers because of its stability and easy detection. Various proteomic tools offer great potential for the discovery of new proteins susceptible to oxidative stress, determination of quantitative changes in the profile of these modifications under different biological conditions, and characterization of the type of modification a particular protein has suffered. This paper reviews the different approaches used for the detection of protein carbonyls and the proteomic tools that can be used to identify them.


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Structural and Functional Diversity of Glutaredoxins in Yeast
E. Herrero, G. Bellí and C. Casas

Glutaredoxins are defined as thiol disulfide oxidoreductases that reduce disulfide bonds employing reduced glutathione as electron donor. They constitute a complex family of proteins with a diversity of enzymatic and functional properties. Thus, dithiol glutaredoxins are able to reduce disulfide bonds and deglutathionylate mixed disulfides between glutathione and cysteine protein residues. They could act regulating the redox state of sulfhydryl residues of specific proteins, while thioredoxins (another family of thiol disulfide oxidoreductases which employ NADPH as electron donor) would be the general sulfhydryl reductants. Some dithiol glutaredoxins such as human Grx2 form dimers bridged by one iron-sulfur cluster, which acts as a sensor of oxidative stress, therefore regulating the activity of the glutaredoxin. The ability to interact with iron-sulfur clusters as ligands is also characteristic of monothiol glutaredoxins with a CGFS-type active site. These do not display thiol oxidoreductase activity, but have roles in iron homeostasis. The three members of this subfamily in Saccharomyces cerevisiae participate in the synthesis of the iron-sulfur clusters in mitochondria (Grx5), or in signalling the iron status inside the cell for regulation of iron uptake and intracellular iron relocalization (Grx3 and Grx4). Such a role in iron metabolism seems to be evolutionary conserved. Fungal cells also contain membrane-associated glutaredoxins structurally and enzymatically similar to dithiol glutaredoxins, which may act as redox regulators at the early stages of the protein secretory machinery.


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How Budding Yeast Sense and Transduce the Oxidative Stress Signal and the Impact in Cell Growth and Morphogenesis
M.A. de la Torre-Ruiz, A. Mozo-Villarías, N. Pujol and M.I. Petkova

The eukaryotic microorganism Saccharomyces cerevisiae is a current model system in which to study the signal transduction pathways involved in the oxidative stress response. In this review we present the current evidence demonstrating that in S. cerevisiae several MAPK and signalling routes participate in this response (PKC1-MAPK, TOR, RAS-PKA-cAMP). The signalling processes converge in the activation of a number of transcription factors (Yap1, Skn7, Rlm1, Msn2/Msn4, Sfp1, among others) required for the expression of certain genes involved in the oxidative stress response. Another important output of these signalling pathways is the actin cytoskeleton, a known target for oxidation and whose organisation needs to be tightly controlled since it is essential for the integrity of the cell. We know about the existence of different levels of cross-talk between these signalling pathways, which gives strength to the enormous importance of keeping a correct redox homeostasis in cells. S cerevisiae maintains a safeguard mechanism assuring that cells always respond properly to oxidation, by means of mechanisms described in the current review.


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Cell Integrity Signaling and Response to Stress in Fission Yeast
P. Pérez and J. Cansado

Cellular responses to external signals are regulated by conserved mitogen-activated protein (MAP) kinase signaling cascades. These pathways are triggered by a vast range of stimuli. They phosphorylate numerous proteins, produce significant changes in the gene expression, and regulate diverse processes ranging from proliferation and differentiation to apoptosis in all eukaryotic cells. Three conserved MAP kinase signaling pathways have been identified in the fission yeast Schizosaccharomyces pombe. In this article, we present an overview of two of those pathways that regulate the response of fission yeast to stress and maintain cell integrity. The structure of these signaling modules and the function of the pathways, including the regulation by endogenous inhibitors, are discussed.


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The Role of MAPK Signal Transduction Pathways in the Response to Oxidative Stress in the Fungal Pathogen Candida albicans: Implications in Virulence
C.H. de Dios, E. Román, R.A. Monge and J. Pla

In recent years, Mitogen-Activated Protein Kinase (MAPK) pathways have emerged as major regulators of cellular physiology. In the fungal pathogen Candida albicans, three different MAPK pathways have been characterized in the last years. The HOG pathway is mainly a stress response pathway that is activated in response to osmotic and oxidative stress and also participates regulating other pathways. The SVG pathway (or mediated by the Cek1 MAPK) is involved in cell wall formation under vegetative and filamentous growth, while the Mkc1-mediated pathway is involved in cell wall integrity. Oxidative stress is one of the types of stress that every fungal cell has to face during colonization of the host, where the cell encounters both hypoxia niches (i.e. gut) and high concentrations of reactive oxygen species (upon challenge with immune cells). Two pathways have been shown to be activated in response to oxidative stress: the HOG pathway and the Mkc1-mediated pathway while the third, the Cek1 pathway is deactivated. The timing, kinetics, stimuli and functional responses generated upon oxidative stress differ among them; however, they have essential functional consequences that severely influence pathogenesis. MAPK pathways are, therefore, valuable targets to be explored in antifungal research.


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Adaptative and Developmental Responses to Stress In Aspergillus nidulans
O. Etxebeste, U. Ugalde and E.A. Espeso

Development in the ascomycete A. nidulans is principally determined by environmental signals. Adaptability to oxidative stimuli can derive in changes of growth patterns and/or the activation of sexual or asexual reproductive cycles but this model fungus might also respond to high osmotic or salt concentrations, the redox state, the availability and quantity of carbon or nitrogen sources and the degree or quality of illumination. Since each cell within the colony follows a single morphogenetic program at a time, all these environmental cues might be sensed and integrated into a limited number of intracellular signals which, finally, would activate the required morphogenetic program and repress the others. This signaling mainly occurs through stress response pathways. The present review aims to summarize the available knowledge on how these pathways transduce environmental stimuli to mediate morphological changes in Aspergillus nidulans.


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The Roles of the A- and B-Chains of Human Relaxin-2 and -3 on Their Biological Activity
M.A. Hossain and J.D. Wade

Two members of the human insulin/relaxin superfamily, relaxins-2 and 3 (H2 and H3 respectively), are separated by nearly 75 years in terms of chronological identification but are both the subject of intense recent biological study. The physiological effects of H2 relaxin include vasodilatory, anti-inflammatory, extracellular matrix remodeling, and angiogenic and anti-ischemic. Because of its potent systemic and renal vasodilatory effects, it is currently undergoing phase III clinical trial for the treatment of acute heart failure. In contrast, H3 relaxin is a highly conserved neuropeptide that has rapidly emerged as an important regulator of homeostatic physiology and complex behaviors. Because of their immense clinical potential, an understanding of the structural features that control their functions is critical for rational drug design and development. The native receptor for H2 relaxin is RXFP1. It also strongly binds to the related receptor, RXFP2. The native receptor for H3 relaxin is the unrelated receptor, RXFP3; however, it also has high affinity for another related receptor, RXFP4. Interestingly, H3 relaxin also has a high affinity for RXFP1 and can interact with RXFP2 with a significantly lower affinity. H3 relaxin thus interacts with all four of the relaxin family receptors. Previous studies have shown that H2 and H3 relaxins interact with their receptors primarily using their B-chain specific residues. However, more recent studies suggest that the role of the respective A and B chains for their activity is both peptide- and receptor-dependent. This mini-review summarizes these recent findings on the structure-activity relationships of H2 and H3 relaxins.


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Cysteine Protease Inhibitors: from Evolutionary Relationships to Modern Chemotherapeutic Design for the Treatment of Infectious Diseases
E.C.Y. Toh, N.L. Huq, S.G. Dashper and E.C. Reynolds


Cysteine proteases are one of the largest groups of proteases and are involved in many important biological functions in all kingdoms of life. They are virulence factors of a range of eukaryotic, bacterial and viral pathogens and are involved in host invasion, pathogen replication and disruption of the host immune response. Their activity is regulated by a range of protease inhibitors. This review discusses the various families of cysteine protease inhibitors, their different modes of inhibition and their evolutionary relationships. These inhibitors as well as the recent discovery of propeptide and propeptide-like inhibitors provide insights into the structures that are important for particular inhibitory mechanisms, thus forming the foundation for the design of future therapeutics.


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Compacting Proteins: Pros and Cons of Osmolyte-Induced Folding
E.P. Melo, N. Estrela, C. Lopes, A.C. Matias, E. Tavares and V. Ochoa-Mendes

Biomedical applications of osmolytes, including stabilization of protein-based pharmaceutics, preservation of living biological material and potential therapeutic prescription in vivo, are intimately related to the fact that osmolytes favour the native structure of proteins. The shift towards the native structure is associated to the compaction of the protein by a non-specific mechanism. This compaction is observed mostly for the unfolded state but also for the transition state ensemble and even for the native state. In addition, more stable three-dimensional structures are more stabilized by osmolytes if the overall protein fold is the same indicating that point mutations and osmolytes should share a similar mechanism for protein stabilization. A synergistic effect to increase protein stability between accumulation of osmolytes and protein engineering strategies seems to have operated during evolution. However, the conformational pre-organization of the unfolded state (compaction) induced by osmolytes which increases the folding rate, might lead to the accumulation of off-folding pathway intermediates with non-native structure that delay folding. Also, osmolytes favor protein aggregation as an alternative way to shield protein surfaces from the solvent. The sometimes observed effect of osmolytes on the prevention of protein aggregation is apparent as they only decrease the accumulation of aggregation-competent partially unfolded states.


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Applications and Modifications of 1,2,3,4-Tetrahydroisoquinoline-3-Carboxylic Acid (Tic) in Peptides and Peptidomimetics Design and Discovery
Y. Zhang, H. Fang and W. Xu

Tic, short for 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, is a kind of unnatural α-amino acids. Due to its distinct geometrical conformation and biological activity, the structure of Tic, regarded as the surrogate of proline and the rigid analogue of phenylalanine or tyrosine, has been introduced into many compounds, which target diverse enzymes or receptors. The most successful example is that substituting the Tic residue for the proline residue of enalapril led to an approved drug quinapril. In this review, we will summarize the applications and modifications of Tic in peptides and peptidomimetics design and discovery, and hope to spark medicinal researchers' inspiration in the field of protein and peptide drug design and optimization.


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Erbin, a Negative Regulator in Diverse Signal Pathways
L. Dan, M. Shi, H. Duan, C. Han and N. Guo

Erbin belongs to the LAP protein family. Originally, Erbin was described as a Her2-interacting protein. Recent studies demonstrated that Erbin could inhibit the Ras-mediated activation of the mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB) and transforming growth factor β (TGF-β) signaling pathways. It suggests that Erbin may function as a signaling molecule. The functions of Erbin in determining cell polarity and cell adhesion have been well described. This review mainly focuses on the recent findings in regulation of signaling pathways by Erbin.