scholarly journals Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes

2014 ◽  
Vol 2014 ◽  
pp. 1-16 ◽  
Author(s):  
Tatiana M. Grishaeva ◽  
Yuri F. Bogdanov
Keyword(s):  
Synaptonemal Complex ◽  
Protein Interactions ◽  
Phylogenetic Trees ◽  
Flowering Plants ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Lateral Element ◽  
Origin And Evolution ◽  
Eukaryotic Proteomes ◽  
Related Proteins

The problems of the origin and evolution of meiosis include the enigmatic variability of the synaptonemal complexes (SCs) which, being morphology similar, consist of different proteins in different eukaryotic phyla. Using bioinformatics methods, we monitored all available eukaryotic proteomes to find proteins similar to known SC proteins of model organisms. We found proteins similar to SC lateral element (LE) proteins and possessing the HORMA domain in the majority of the eukaryotic taxa and assume them the most ancient among all SC proteins. Vertebrate LE proteins SYCP2, SYCP3, and SC65 proved to have related proteins in many invertebrate taxa. Proteins of SC central space are most evolutionarily variable. It means that different protein-protein interactions can exist to connect LEs. Proteins similar to the known SC proteins were not found in Euglenophyta, Chrysophyta, Charophyta, Xanthophyta, Dinoflagellata, and primitive Coelomata. We conclude that different proteins whose common feature is the presence of domains with a certain conformation are involved in the formation of the SC in different eukaryotic phyla. This permits a targeted search for orthologs of the SC proteins using phylogenetic trees. Here we consider example of phylogenetic trees for protozoans, fungi, algae, mosses, and flowering plants.

scholarly journals An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 460
Author(s):  
Valentina Cipriani ◽  
Nikolas Pontikos ◽  
Gavin Arno ◽  
Panagiotis I. Sergouniotis ◽  
Eva Lenassi ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Protein Interactions ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Sequencing Data ◽  
Variant Prioritization ◽  
Real Patient ◽  
Human Phenotype ◽  
Support Tool ◽  
Variant Frequency

Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients’ sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein–protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients’ HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.

scholarly journals A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

2020 ◽  
Vol 117 (21) ◽  
pp. 11836-11842 ◽  
Author(s):  
Shayne D. Wierbowski ◽  
Tommy V. Vo ◽  
Pascal Falter-Braun ◽  
Timothy O. Jobe ◽  
Lars H. Kruse ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Massively Parallel ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Numerous Model ◽  
High Quality Protein ◽  
Protein Interactome ◽  
Wide Range ◽  
Dna Elements ◽  
General Tool

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we developPCR-mediatedLinkage of barcodedAdaptersTo nucleic acidElements forsequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome forOryza sativacovering 2,300 genes and constructing a high-quality protein–protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein–protein interactions in a wide range of organisms.

NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges

1998 ◽  
Vol 76 (2-3) ◽  
pp. 177-188 ◽  
Author(s):  
Jianxing Song ◽  
Feng Ni
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Experimental Approach ◽  
Structural Information ◽  
Peptide Ligands ◽  
Protein Protein Interactions ◽  
Binding Residues ◽  
Related Proteins ◽  
Binding Inhibitors

Using the design of bivalent and bridge-binding inhibitors of thrombin as an example, we review an NMR-based experimental approach for the design of functional mimetics of protein-protein interactions. The strategy includes: (i) identification of binding residues in peptide ligands by differential resonance perturbation, (ii) determination of protein-bound structures of peptide ligands by use of transferred NOEs, (iii) minimization of larger protein and peptide ligands on the basis of NMR structural information, and (iv) linkage of two weakly binding mimetics to produce an inhibitor with enhanced affinity and specificity. This approach can be especially effective for the design of potent and selective functional mimetics of protein-protein interactions because it is less likely that the surfaces of two related proteins or enzymes share two identical binding sites or regions.Key words: NMR, protein-protein interactions, functional mimetics, bridge-binding inhibitors, thrombin.

scholarly journals Comparative Proteomic Analysis of Paulownia fortunei Response to Phytoplasma Infection with Dimethyl Sulfate Treatment

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Zhen Wei ◽  
Zhe Wang ◽  
Xiaoyu Li ◽  
Zhenli Zhao ◽  
Minjie Deng ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Dimethyl Sulfate ◽  
Morphological Characteristics ◽  
Forest Tree ◽  
Protein Protein Interactions ◽  
Absolute Quantitation ◽  
Phytoplasma Infection ◽  
Paulownia Fortunei ◽  
Isobaric Tags ◽  
Related Proteins

Paulownia fortunei is a widely cultivated economic forest tree species that is susceptible to infection with phytoplasma, resulting in Paulownia witches’ broom (PaWB) disease. Diseased P. fortunei is characterized by stunted growth, witches’ broom, shortened internodes, and etiolated and smaller leaves. To understand the molecular mechanism of its pathogenesis, we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography coupled with tandem mass spectrometry approaches to study changes in the proteomes of healthy P. fortunei, PaWB-infected P. fortunei, and PaWB-infected P. fortunei treated with 15 mg·L−1 or 75 mg·L−1 dimethyl sulfate. We identified 2969 proteins and 104 and 32 differentially abundant proteins that were phytoplasma infection responsive and dimethyl sulfate responsive, respectively. Based on our analysis of the different proteomes, 27 PaWB-related proteins were identified. The protein-protein interactions of these 27 proteins were analyzed and classified into four groups (photosynthesis-related, energy-related, ribosome-related, and individual proteins). These PaWB-related proteins may help in developing a deeper understanding of how PaWB affects the morphological characteristics of P. fortunei and further establish the mechanisms involved in the response of P. fortunei to phytoplasma.

Site-specific recombination by φC31 integrase and other large serine recombinases

2010 ◽  
Vol 38 (2) ◽  
pp. 388-394 ◽  
Author(s):  
Margaret C.M. Smith ◽  
William R.A. Brown ◽  
Andrew R. McEwan ◽  
Paul A. Rowley
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Serine Recombinases ◽  
Tyrosine Recombinases ◽  
Dna Binding Sites ◽  
Attachment Sites ◽  
Φc31 Integrase ◽  
Related Proteins ◽  
Control Protein

Most temperate phages encode an integrase for integration and excision of the prophage. Integrases belong either to the λ Int family of tyrosine recombinases or to a subgroup of the serine recombinases, the large serine recombinases. Integration by purified serine integrases occurs efficiently in vitro in the presence of their cognate (~50 bp) phage and host attachment sites, attP and attB respectively. Serine integrases require an accessory protein, Xis, to promote excision, a reaction in which the products of the integration reaction, attL and attR, recombine to regenerate attP and attB. Unlike other directional recombinases, serine integrases are not controlled by proteins occupying accessory DNA-binding sites. Instead, it is thought that different integrase conformations, induced by binding to the DNA substrates, control protein–protein interactions, which in turn determine whether recombination proceeds. The present review brings together the evidence for this model derived from the studies on φC31 integrase, Bxb1 integrase and other related proteins.

scholarly journals NGPINT: A Next-generation protein-protein interaction software

2020 ◽  
Author(s):  
Sagnik Banerjee ◽  
Valeria Velásquez-Zapata ◽  
Gregory Fuerst ◽  
J. Mitch Elmore ◽  
Roger P. Wise
Keyword(s):  
Protein Interactions ◽  
Model Organisms ◽  
Cdna Libraries ◽  
Published Data ◽  
Data Sets ◽  
Next Generation ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Alternative Approach ◽  
Simulated Test

ABSTRACTMapping protein-protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to interrogate cDNA libraries represent an alternative approach that optimizes scale, cost, and effort. We present NGPINT, a robust and scalable software to identify all putative interactors of a protein using Y2H in batch culture. NGPINT combines diverse tools to align sequence reads to target genomes, reconstruct prey fragments and compute gene enrichment under reporter selection. Central to this pipeline is the identification of fusion reads containing sequences derived from both the Y2H expression plasmid and the cDNA of interest. To reduce false positives, these fusion reads are evaluated as to whether the cDNA fragment forms an in-frame translational fusion with the Y2H transcription factor. NGPINT successfully recognized 95% of interactions in simulated test runs. As proof of concept, NGPINT was tested using published data sets and recognized all validated interactions. NGPINT can be used in any organism with an available reference, thus facilitating the discovery of protein-protein interactions in non-model organisms.

scholarly journals Expanding Interactome Analyses beyond Model Eukaryotes

2021 ◽  
Author(s):  
Katherine James ◽  
Anil Wipat ◽  
Simon Cockell
Keyword(s):  
Genome Sequence ◽  
Protein Interactions ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Data Types ◽  
Interaction Prediction ◽  
Diverse Species ◽  
Eukaryotic Species

Interactome analyses have traditionally been applied to yeast, human and other model organisms due to the availability of protein-protein interactions data for these species. Recently these techniques have been applied to more diverse species using computational interaction prediction from genome sequence and other data types. This review describes the various types of computational interactome networks that can be created and how they have been used in diverse eukaryotic species, highlighting some of the key interactome studies in non-model organisms.

scholarly journals Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

2020 ◽  
Vol 37 (8) ◽  
pp. 2394-2413 ◽  
Author(s):  
Tao Shi ◽  
Razgar Seyed Rahmani ◽  
Paul F Gugger ◽  
Muhua Wang ◽  
Hui Li ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Flowering Plants ◽  
Expression Level ◽  
Small Scale ◽  
Whole Genome ◽  
Functional Constraints ◽  
Expression Divergence ◽  
Protein Protein Interactions ◽  
Methylation Patterns ◽  
The Impact

Abstract For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

The interaction of IQGAPs with calmodulin-like proteins

2011 ◽  
Vol 39 (2) ◽  
pp. 694-699 ◽  
Author(s):  
Sevvel Pathmanathan ◽  
Elaine Hamilton ◽  
Erwan Atcheson ◽  
David J. Timson
Keyword(s):  
Protein Interactions ◽  
Light Chain ◽  
Protein Protein Interactions ◽  
Iq Motif ◽  
Calcium Dependent ◽  
Essential Light Chain ◽  
Cellular Processes ◽  
Wide Range ◽  
Related Proteins ◽  
Do So

Since their identification over 15 years ago, the IQGAP (IQ-motif-containing GTPase-activating protein) family of proteins have been implicated in a wide range of cellular processes, including cytoskeletal reorganization, cell–cell adhesion, cytokinesis and apoptosis. These processes rely on protein–protein interactions, and understanding these (and how they influence one another) is critical in determining how the IQGAPs function. A key group of interactions is with calmodulin and the structurally related proteins myosin essential light chain and S100B. These interactions occur primarily through a series of IQ motifs, which are α-helical segments of the protein located towards the middle of the primary sequence. The three human IQGAP isoforms (IQGAP1, IQGAP2 and IQGAP3) all have four IQ motifs. However, these have different affinities for calmodulin, myosin light chain and S100B. Whereas all four IQ motifs of IQGAP1 interact with calmodulin in the presence of calcium, only the last two do so in the absence of calcium. IQ1 (the first IQ motif) interacts with the myosin essential light chain Mlc1sa and the first two undergo a calcium-dependent interaction with S100B. The significance of the interaction between Mlc1sa and IQGAP1 in mammals is unknown. However, a similar interaction involving the Saccharomyces cerevisiae IQGAP-like protein Iqg1p is involved in cytokinesis, leading to speculation that there may be a similar role in mammals.

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