Others, more specific, focus on the estimation of the activity of stimulus-response signaling circuits from gene expression data (1113). Game L. Jia X. Shortly thereafter, two papers revealed a remarkable structural and functional similarity between the phosphorylated form of serine and glutamic acid. Salavert F. These are: exon_variant, intron_variant, synonymous_codon, coding_sequence_variant, non_synonymous_codon, splice_region_variant, splice_acceptor_variant, splice_donor_variant, stop_gained, stop_lost, 5_prime_UTR_variant, 3_prime_UTR_variant, 5KB_upstream_variant, 5KB_downstream_variant.Consequence types are taken from CellBase (19). Huber W. Haw R. Vidal-Puig A. Carbon atoms are shown in cyan; oxygen, in red; nitrogen, in blue; and phosphorous in gold. Spieth J. The bottom right of the figure show the symbols used to denote expressed and non-expressed genes, genes harboring deleterious mutations and the interactions that produce signal transduction. Signaling circuits are defined as the sub-pathways (within the pathways) that transmit signals from a receptor node, which receives the stimulus to an effector node that triggers the response. The substitution of serine or threonine for phosphomimetic aspartic or glutamic acid or non-phosphorylatable residues, such as alanine, will be discussed, along with other permutations, including natural analogs of oxidized methionine and cysteine. The mice that were phosphodeficient (Ala) in the two serine residues showed onset of disease pathogenesis from the mutant mhtt- as measured by neuropathological examination of brain tissue sections, as well as by various motor and psychological tests. Published by Oxford University Press on behalf of Nucleic Acids Research. Petryszak R. Even in the age of high-resolution mass spectrometry, site-directed mutagenesis will continue to be a powerful tool for studying and validation of signaling networks. Once the probabilities for each node in the circuit have been assigned for a particular tissue, a simple probabilistic product from the receptor node to the effector node, across all the connecting nodes in the pathway, can be used to model the probability of signal transmission (12,13). Alonso R. Hallstrom B.M. Post-translational modification of proteins offers another layer of complexity in the regulation of cellular processes. Sivertsson A. Post-translational modification (PTM), the chemical modification of a protein after its translation, represents an evolutionarily conserved mechanism of regulation of protein function. However, such relationships are difficult to find and often lack reproducibility (4,26). The first method lies at the level of the transcript. Medina I. This provided the first direct evidence for the structural mimicking of a phosphate group using site-directed mutagenesis. Kawashima M. Weiser J. Amino acid oxidation is a common mechanism for diversification of certain residues; and, like phosphorylation, there are both addition and removal effector proteins associated with the modification. In addition to the graphical output, each pathway displays a table which lists the affected circuits with relevant information, including receptor and effector proteins, the activation status and the particular cell functionality triggered by the circuit. For example, a mere phosphorylation event induces a large structural change in the bacterial receiver domain of the nitrogen regulatory protein C (NtrC) (Kern et al., 1999) (Fig. However, caution must always be taken in the interpretation of data obtained from studies using biomimetic constructs. A table summarizing the results obtained for all the selected pathways can also be downloaded. Node probabilities are computed as: (i) the product of their constituent protein probabilities, if the node is a protein complex or (ii) as the maximum of the values of the protein probabilities, if these are alternative (12,13). The most easily deciphered systems are those in which there is a large chemical difference between the modified and non-modified group and systems that are controlled by a unimodal adding or removing of an effector moiety, as in the prototypical case of phosphorylation (i.e., addition or removal of a phosphate group with a kinase or phosphatase, respectively). Fiorelli B. As PhD students, we found it difficult to access the research we needed, so we decided to create a new Open Access publisher that levels the playing field for scientists across the world. Gibbs R.A. Wray N.R.
The program can also be used in registered user mode. Then, standard variant calling format (VCF) input files, containing the variants detected in individuals, are scanned for variants in the protein coding genes that compose the pathways. Please check for further notifications by email. This third possibility is quite interesting because the study of mutations within a systems perspective allows discarding putative disease-causing genes harboring mutations with apparent deleterious consequences, that the robustness of the pathway turn into innocuous variants; (iv) the integration of both expression and mutation data in the model brings about another possibility, which is typically ignored by conventional models without data integration: deleterious mutations affecting genes that are not expressed in the tissue of interest are irrelevant for signaling in this particular tissue. Schema of the analysis of impact of mutations over signaling pathways. Alternate splicing of the same gene product can result in a variety of unique proteins with unique functions. Keays M. DeMaria A. Romualdi C. Chen X. In addition, a complete list of user-defined gene expression values can be provided through the button Custom for conditions not represented in the tissue databases used. Smaller cell size, increased protein synthesis, and a severe decrease of circulating insulin were among the phenotypic signatures of the phospho-deficient variant.
Sato Y. phosphorylation, sulfoxidation and nitrosylation). Output of a fictitious combination of gene expression and mutations in version of the Calcium signaling pathway modified for illustrating the examples. Burdett T.
aspartic acid than into any other residue, demonstrating evolution away from the switchable into permanent ON or OFF functions. Only a subset of consequence types is compatible with variation that affects protein coding genes.
The amount of unique proteins per unit RNA transcript has been dramatically amplified to be far more diverse than Central Dogma of protein expression would have suggested. Figure 2 represents different scenarios that can be found when complex signaling circuits are analyzed under a systems biology perspective and include: (i) signal deactivations, when the impaired proteins interrupts the signal flux in the receptor-effector signaling circuit in which they are included; (ii) signal activations, when the affected protein is a repressor that was short-circuiting the circuit; (iii) neutral effects, when a receptor-effector signaling circuit is internally redundant and the signal can reach the effector protein using an alternative unaffected branch. This largely reversible labelling offers the ability to tune and coordinate signalling networks on a timescale faster than is required for protein synthesis and proteolysis. As mentioned, PTMs that result in a significant size or charge difference from the unmodified states have been among the earliest developed. (Black and Mould, 1991) (Hoshi and Heinemann, 2001) A family of enzymes known as methionine sulfoxide reductases have been found competent to reduce the methionine sulfoxide back to a thioether, a necessary requirement for a signalling relay. Thank you for submitting a comment on this article. Goto S. Tan F. The result was an explosion in the usage of point mutations as surrogates for phosphorylated or phospho-defective forms of potential regulatory sites.
SIFT, PolyPhen and phastCons values are taken from CellBase (19) as well, through the VARIANT (23) tool (see database version annotations at https://github.com/opencb/cellbase/wiki/Data-Sources-and-Species). Note that there are structural similarities between cysteine and the non-modifiable isoleucine and between S-nitrosocysteine and arginine. Salavert F. The figure illustrates the possible effects due to the combination of gene expression and gene loss of function within the topology of a pathway. Liu L.et al. In another case, nitroso-cysteine modification was mimicked by substitution with asparagine in studies investigating the effect of nitrosylation on ATPase activity of the 90 kDa heat shock protein (HSP90). Medina I. While discussing how site-directed mutagenesis offers to researchers a tool to engineer a constitutively active OFF and ON forms of a protein, we will also provide examples of how PTM translates into a chemical phenotype through the regulation of enzyme activity or modulation of binding affinity to partners. (Retzlaff et al., 2009) (Scroggins and Neckers, 2009) In this study an NO-insensitive HSP90 was rendered sensitive to inactivation by NO treatment due to replacement of an alanine residue in the C-terminal domain with a cysteine, as this corresponding site is known to be a cysteine in all other HSP variants. Huang B. In another salient example, both phosphomimetic and phospho-deficient mutations were generated in a transgenic mouse model of Huntingtons disease - a neurodegenerative disorder characterized by motor impairments and various psychiatric symptoms. Recently, some methods based on signaling pathways aim to discover activation of sub-networks within them (810). Rosenbloom K.
2013 The Author(s). Representative post-translational modifications mimicked by natural point mutations using site-directed mutagenesis. Site-directed mutagenesis, a molecular biology technique used to introduce a point mutation into primary DNA sequence at a defined site, was first described by Michael Smith in 1978. Isostructural similarities between natural amino acids and post-translational modifications. It is believed that the integration of both types of data (27): gene activity (expression data) and gene functionality (affected or not by deleterious mutations) can be helpful for disease gene prioritization. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (. Probabilities of 1 (presence) or 0 (absence) are assigned to any of the proteins in the pathway according to the gene expression reported for the tissue of interest in the database selected for the analysis. Modern sequencing technologies produce increasingly detailed data on genomic variation. This chapter will highlight the use of site-directed mutagenesis for studying signal transduction networks. PATHiVAR can be found at: http://pathivar.babelomics.org. In the future we plan to include different signaling pathway descriptions coming from other repositories, such as REACTOME (31), and also allowing users to input their own pathway definitions. Tarraga J. The ultimate verification of the experimental models obtained in in vitroassays or even in cultured cells comes with experiments in living organisms. Jurman G.et al. The model is recalculated for the perturbed (mutated) system. It is instructive to understand the precise strengths and limitations of biomimetic approaches in order to extract the most meaningful data from experiments. Mutation of the engineered site to asparagine (HSP90 A577N) recapitulates NO treatment of the engineered cysteine mutant, in contrast to a control isoleucine mutant (HSP90 A577I), which serves as an unmodifiable mimick (shown in Fig 4).
Highlighted residues and the surface layer proximal to residue 55 in HupR were color-coded by atom type: carbon atoms are cyan, nitrogen atoms are blue, oxygen atoms are red, and phosphorous atoms are green (inhibitor compound). Xu J.
Garapati P.
Coulibaly I.
(Bottom) Surface representation of the wild-type and the phosphomimetic Asp55E variants of Hydrogen Uptake Protein Regulator (HupR). Sales G.
How? These results further suggested that the N-terminus of httmay be a target for future drug design to treat disease, even after the initializing mutation is present. Sjostedt E. PATHiVAR can be directly used in anonymous mode (Run item in the main menu), and therefore all the uploaded data and the results obtained (and not saved in the user's terminal) will be lost at the end of the session. Reduction of an active site cysteine-sulfinic acid is first accomplished through ATP-dependent phospho-deficient of the sulfinic acid residue, followed by attack of a neighboring cysteine from sulfiredoxin (Srx) enzyme on the sulfinic phosphory ester intermediate. PATHiVAR removes from the model those proteins harboring deleterious mutations (as defined by the user) that impairs its proper functionality and recalculates the probability of signal transmission across all the stimulus-response circuits of the pathways studied in the selected tissue again, obtaining thus the perturbed signaling pattern. Nevertheless, it serves as an instructive case in which it is acknowledged that a given PTM can have multiple roles or be required in multiple steps of a signalling cascade or pathway.
The second is through targeted post-translational modification of existing proteins and peptides to chemically tag them. For example, cysteine sulfinic acid differs from aspartic acid by a single-atom replacement of sulphur atom with a carbon atom. Oksvold P. For example, the carboxylic acid functionality of glutamic acid has differing fundamental chemical properties from a serine-phosphate group, including, but not limited to, access to a (-2) charge state (in the case of phosphate) and different acid dissociation constants. and consequently have no effect in the particular tissue of study. The upload option (Select VCF file option) of the form brings about the STUDIES workspace, where VCF data files reside, or where they can be uploaded from the local computer. The resulting effect of the combination of gene expression and gene product integrity, when interpreted over the system defined by topology of the pathways, can be diverse and often have unexpected consequences. Finally, the information on protein functionality is integrated in the model by removing all the proteins impaired by deleterious mutations. Hillier L.W. Gonzalez C.Y. The model uses known gene expression values, taken from two popular curated gene expression repositories (Human Protein Atlas (14) and Expression Atlas (15)), to derive individual probabilities of gene activation that are combined according to the signaling circuit wiring to infer what we consider the unperturbed pattern of signal transmission across all the selected pathways in the selected tissue. Price A.L.
Phosphomimetic and phospho-deficient mutations have been knocked-in as well, leading to new understanding of downstream events to protein modification in the context of a living organism. It provides a powerful tool for fast and reversible modification of protein structure, which effects dynamic changes in protein function, and ultimately translates into a cellular phenotype. Wu G. Furlanello C. This is due to the subtle spatial and charge density differences between methylated and non-methylated forms of an amino acid residue. Caudy M. None declared. This unstructuring has been shown to be important in the interaction with membrane contents, and may further alter protein specificity. In the Boolean model, gene expression is taken as a proxy of the presence of a protein in the pathway (8,9,12,13,18). The Boolean model used here is a simplification derived from the statistical model used in PATHiWAYS (12,13). Contact our London head office or media team here. Despite vast precedent for the utilization of amino acid surrogates and mimics of post-translational modifications in the literature, it must be remembered that the data and interpretation are only as robust as the chemical match of the surrogate moiety to the target. Dopazo J. Outside the coding regions this prediction can be extended using the phastCons (22) conservation score. Such methods should also make it possible to construct DNAs with specific modified biological functions M. Smith and his colleagues proposed in the paper. Kryvych N.et al. Hou M. Even with these limitations, it is no wonder the technique of site-directed mutagenesis has penetrated the field of signal transduction since the very conception of the technology. To date our community has made over 100 million downloads. Dopazo J. Gonzaga-Jauregui C. From a systems biology perspective (29), diseases can be interpreted as the failure of cellular functionalities represented by functional modules, such as pathways (2). Results are displayed in an advanced interactive visual framework, CellMaps (https://github.com/opencb/cell-maps/wik), which provides a graphical output in which aspect, colors and shapes of the components of the pathway can easily be reconfigured to produce camera-ready figures. Despite this, the single mutation has proven a valuable tool in the mimicking of phosphorylated residues. Biomimetic point mutations have been fundamental for studying some other means of protein modification including sulfoxidation, S-nitrosylation, tyrosine nitration, acetylation, methylation, etc. Oxidized forms of cysteine, including nitrosyl, sulfenic acid, and sulfinic acid variants, have been implicated in reversible signalling arrays (Reddie and Carroll, 2008), and some have been mimicked with the use of natural amino acids. A single residue modification from Asp54 (blue sticks) to the phosphorylated form (red sticks) results in major protein restructuring, including movement of -helix 4 (black arrows) away from the active site to generate a hydrophobic patch. Despite the obvious potential of pathways as conceptual tools to understand the effects of gene mutations over cell signaling, the lack of user-friendly applications for this purpose drastically limits the current application of these methods.
Subsequent options allow choosing the consequence types considered in the study and setting thresholds for the pathogenicity indexes. Ma L. Bejerano G. Hopfield J.J. The already significant chemical diversity of the amino acid pool is amplified profoundly when individual amino acids are condensed into peptide chains. Our team is growing all the time, so were always on the lookout for smart people who want to help us reshape the world of scientific publishing. The pathways to be analyzed are selected (Figure 1B). PATHiVar is available at: http://pathivar.babelomics.org. Present address: Rosa D. Hernansaiz-Ballesteros, Randall Division of Cell & Molecular Biophysics, King's College London, London, UK. This technique clearly demonstrated that lossof-phosphorylation of these two serine sites is a key signature of the pathogenesis in vivo. Clawson H.
can be helpful for finding disease genes (5), drug targets (6), new-generation mechanism-based biomarkers (7), etc. Structural coordinates were obtained from the Protein Databank (PDB code: 1FU0, 1PTF, 2JK1, 2VUH). The systems biology perspective, provided by the models of signaling circuits presented here, offers an optimal framework to locate recurrent functional failures that can be better related to diseases or complex traits than the original raw genomic measurement (gene expression or mutation) from which the models were derived. Ribbon representation of X-ray crystal structure of the Yeast HSP90 dimer; native Ala 577 (left) and engineered variants at position 577 (right) are highlighted in red. The user selects the tissue of interest (with the possibility of changing some gene expression values if necessary, through the Additional gene list box) or provides a complete list of user-defined gene expression through the button Custom that will be used for the model to derive the unperturbed system (Figure 1D). The quest to understand and control structure-function relationship has revealed that Nature is an exquisite chemist. Once the signalome has been modeled and the unperturbed signaling pattern in any tissue has been derived, the prediction of the effect of deleterious variants affecting to pathway proteins is straightforward. (A) signal deactivation: the gene GNA11 is expressed but harbors a deleterious mutation and the signal does not flux downstream; (B) signal activation: the repressor INH harbors a deleterious mutation and therefore cannot inhibit PLN and the signal flux, that would be interrupted here with a functional protein, is activated instead; (C) neutral effect: PLCG1 with a deleterious mutation does not transmit the signal, however, The signal is transmitted anyway from EGFR to both, ITPR1 and PRKCA, through the protein PLCD3, because the receptor-effector signaling circuit is internally redundant; (D) neutral effect: several examples show how mutations affect to genes that are not expressed in the tissue studied (CACNA1A, CACNA1I, RYR1, etc.) Providing a constitutively activated or deactivated form of the protein or removing entirely the potential for protein modification, it has also been instrumental in dissecting signal transduction networks. In the figure, blue background indicates gene expression, while gray background means no expression in the tissue studied. Allison D.B. Therefore, it is quite likely that different individuals sharing a disease do not show common mutations (or mutations in common genes), but rather have a common cell functionality affected.
Lupski J.R. (Yang et al., 1997) This technology has been used to investigate the role of individual amino acids in many biological processes and disease states, such as ASD (Autism Spectrum Disorder) (Bader et al., 2011), malignant hyperthermia (associated with heat stroke susceptibility) (Durham et al., 2008), and depression (Talbot et al., 2010), in the context of a living mammals. In a model wherein phosphorylation of Ser87 blocks membrane recruitment and fibril formation, it was shown that substitution of native Ser87 with alanine resulted in wild-type-like membrane association and fibril formation, while authentic phospho-Ser87, along with the Ser87E mutant, showed blunted formation of fibrils and poor membrane recruitment. 2 are examples of natural mimics of some well-studied post-translational modifications, highlighting structural similarities. As summarized in an excellent review by Wash and co-authors, (Walsh et al., 2005), Nature has devised two mechanisms of proteome diversification over the course of evolution. Li J. Minguez P. This phosphomimicking strategy has been used in the investigation of the mechanism of peroxiredoxin (Pxr) (Jonsson et al., 2009), an enzyme involved in the ATP-dependent reduction of cysteine sulfinic acid back to a thiol residue. The impact and damaging effect of non-synonymous variants depend on the type of amino acid change and can be predicted by computing SIFT (20) and PolyPhen (21) damage scores. (Schneider et al., 1988) It was suggested that a negative charge, and not a phospho-group per-se, was required to promote DNA replication. in the context of known functional modules. Shown in Fig. Disruptions in the signal flux can be easily attributed to particular deleterious mutations found in the VCF file. Uhlen M. Conventional analysis of genomic data seeks to relate gene expression (24) or mutations (25) to disease or complex phenotypes. Phosphorylation induces marked structural and surface-contour changes. The default choice is: non_synonymous_codon, stop_gained and stop_lost consequence types, with SIFT and PolyPhen thresholds of 0.05 and 0.95, respectively, which corresponds to the more obvious scenario of deleterious, loss-of-function variants. (Ruvinsky et al., 2005) In this model, all five potentially phosphorylatable serine residues in the putative region of rS6 were mutated to alanine (rpS6P/) to abolish the potential for their phosphorylation. It is probable that certain interactions, or classes of interactions, may be more stringent in which the electronic features of post-translationally modified residues are recognized and interpreted as signals. To our knowledge, there is no other similar tool available. Here we present a new web server, PATHiVAR, which can be used to easily infer mutations that are expected to have relevant consequences for cell functionality, because they affect genes belonging to signaling pathways. However, some genes might have peculiar expression values that could be not properly or accurately represented in the databases or present atypical expression behaviors in certain conditions. Although no citation or rationale was used for the mutant choices, these mimicking residues indeed recapitulated ATPase activity and chaperone activity of the NO-free and NO-bound forms of engineered HSP90 protein. The importance of a cautious eye when utilizing signalling mimics was recently made salient when a phosphometic serine to glutamic acid mutant recapitulated one aspect of a signalling cascade, but not another. Substitution of a cysteine residue with a serine residue offers an effective single-atom replacement of a sulphur atom with an oxygen atom and eliminates sulphur-based chemistry from the site, while minimizing steric differences.
Licensee IntechOpen. (Reizer et al., 1989) The crystal structure of unmodified and phospho-Ser46 would later be determined (Jia et al, 1994) (Audette et al., 2000), and an image of the electrostatic potential shows the large surface change that accompanies phosphorylation (Figure 3). Compound heterozygosity (having simultaneously two different recessive alleles at a particular locus) is supported. The differences between the unperturbed (D) and the perturbed (F) signal transduction maps are reported by PathiVar. Home > Books > Genetic Manipulation of DNA and Protein - Examples from Current Research, Submitted: May 7th, 2011 Published: February 5th, 2013, Total Chapter Downloads on intechopen.com. Here we show how a simple Boolean model, based on KEGG, one of the most popular descriptions of signaling pathways (30), can integrate gene activity (expression) and gene functionality (mutation) in a straightforward manner.
