MisPred: a resource for identification of erroneous protein sequences in public databases

Correct prediction of the structure of protein-coding genes of higher eukaryotes is still a difficult task; therefore, public databases are heavily contaminated with mispredicted sequences. The high rate of misprediction has serious consequences because it significantly affects the conclusions that may be drawn from genome-scale sequence analyses of eukaryotic genomes. Here we present the MisPred database and computational pipeline that provide efficient means for the identification of erroneous sequences in public databases. The MisPred database contains a collection of abnormal, incomplete and mispredicted protein sequences from 19 metazoan species identified as erroneous by MisPred quality control tools in the UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, NCBI/RefSeq and EnsEMBL databases. Major releases of the database are automatically generated and updated regularly. The database (http://www.mispred.com) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in a variety of formats

FixPred: a resource for correction of erroneous protein sequences.

Protein databases are heavily contaminated with erroneous (mispredicted, abnormal and incomplete) sequences and these erroneous data significantly distort the conclusions drawn from genome-scale protein sequence analyses. In our earlier work we described the MisPred resource that serves to identify erroneous sequences; here we present the FixPred computational pipeline that automatically corrects sequences identified by MisPred as erroneous. The current version of the associated FixPred database contains corrected UniProtKB/Swiss-Prot and NCBI/RefSeq sequences from Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Danio rerio, Fugu rubripes, Ciona intestinalis, Branchostoma floridae, Drosophila melanogaster and Caenorhabditis elegans; future releases of the FixPred database will include corrected sequences of additional Metazoan species. The FixPred computational pipeline and database (http://www.fixpred.com) are easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in a variety of formats. Database URL: http://www.fixpred.com

Exon-phase symmetry and intrinsic structural disorder promote modular evolution in the human genome

A key signature of module exchange in the genome is phase symmetry of exons, suggestive of exon shuffling events that occurred without disrupting translation reading frame. At the protein level, intrinsic structural disorder may be another key element because disordered regions often serve as functional elements that can be effectively integrated into a protein structure. Therefore, we asked whether exon-phase symmetry in the human genome and structural disorder in the human proteome are connected, signalling such evolutionary mechanisms in the assembly of multi-exon genes. We found an elevated level of structural disorder of regions encoded by symmetric exons and a preferred symmetry of exons encoding for mostly disordered regions (>70% predicted disorder). Alternatively spliced symmetric exons tend to correspond to the most disordered regions. The genes of mostly disordered proteins (>70% predicted disorder) tend to be assembled from symmetric exons, which often arise by internal tandem duplications. Preponderance of certain types of short motifs (e.g. SH3-binding motif) and domains (e.g. high-mobility group domains) suggests that certain disordered modules have been particularly effective in exon-shuffling events. Our observations suggest that structural disorder has facilitated modular assembly of complex genes in evolution of the human genome. © 2013 The Author(s)

K153R polymorphism in myostatin gene increases the rate of promyostatin activation by furin

Recent studies demonstrated an association between the K153R polymorphism in the myostatin gene with extreme longevity, lower muscle strength and obesity but the molecular basis of these associations has not been clarified. Here, we show that the K153R mutation significantly increases the rate of proteolysis of promyostatin by furin, but has no effect on the activity of the latent complex or the cleavage of the latent complex by bone morphogenetic protein 1 (BMP-1). The increased rate of activation of K153R mutant promyostatin may explain why this polymorphism is associated with obesity, lower muscle strength and extension of lifespan

Új, orvosbiológiai szempontból fontos moduláris fehérjék azonosítása, szerkezeti és funkcionális jellemzése = Identification and structure-function studies on novel medically important modular proteins

A gerincesekre jellemző moduláris fehérjék kitüntetett orvosbiológiai jelentősége miatt fontos ezeknek a fehérjéknek az azonosítása, funkciójuk tisztázása. 1.) Az általunk korábban azonosított WFIKKN1 és WFIKKN2 multidomén fehérjék közül a WFIKKN2 -ről ismert, hogy kötődik miosztatinhoz. SPR mérésekkel jellemeztük a fehérjék és doménjeik kölcsönhatását miosztatinnal. NMR spektroszkópiával meghatároztuk a WFIKKN1 második Kunitz típusú doménjének térszerkezetét. Az SPR mérések, a KU2 domén térszerkezete és a korábbi enzimkinetikai méréseink eredményei alapján valószinűnek tűnik, hogy a WFIKKN1 fehérje is egy TGF-beta családba tartozó fehérje aktivitásának szabályozásában játszik szerepet. 2.) Meghatároztuk a Wnt jelátvitelben részt vevő WIF-1 fehérje WIF doménjének térszerkezetét. A domén térszerkezetét az immunoglobulin domének szerkezetére emlékeztető 8 beta redő által alkotott szendvics szerkezet és két alfa helix jellemzi. Az NMR spektroszkópiai térszerkezet meghatározásokat Gottfried Otting munkacsoportjával együttműködésben végeztük. 3.) A bioinformatikai módszerekkel azonosított gének jelentős hányadáról bizonyosodik be, hogy megjósolt szerkezetük téves. Módszert dolgoztunk ki olyan fehérjék azonosítására, melyek szerkezete ellentmond alapvető fehérjeszerkezeti törvényszerűségeknek. A módszer alkalmas abnormális fehérjeformák azonosítására és lehetőséget nyújt a génpredikciós eljárások minőségellenőrzésére. Az elemzés menete a http://mispred.enzim.hu honlapon megtalálható. | 1.) Recently we have identified two novel proteins (WFIKKN1 and WFIKKN2) one of which (WFIKKN2) has been shown to bind to myostatin and inhibit myostatin activity. We have shown that - similarly to the homologous protein - WFIKKN1 also binds to myostatin and thus may also participate in the regulation of the activity of TGF-beta family members. 2.) In collaboration with the NMR group of Gottfried Otting we have determined the three-dimensional structure of the WIF domain of Wnt- Inhibitory-Factor-1. The fold consists of an eight-stranded beta-sandwich reminiscent of the immunoglobulin fold. 3.) The predicted structure of a significant proportion of the computationally predicted genes is incorrect, therefore we have developed tools for the identification of mispredicted genes. The rationale of this approach is that a gene is suspected to be mispredicted if some features of the encoded protein conflict with our current knowledge about proteins. With the help of this tool we have shown that a significant proportion of mRNAs produced by alternative splicing encode non-viable, aberrant proteins with no physiological role

Exon skipping-rich transcriptomes of animals reflect the significance of exon-shuffling in metazoan proteome evolution

Animals are known to have higher rates of exon skipping than other eukaryotes. In a recent study, Grau-Bove et al. (Genome Biology 19:135, 2018) have used RNA-seq data across 65 eukaryotic species to investigate when and how this high prevalence of exon skipping evolved. They have found that bilaterian Metazoa have significantly increased exon skipping frequencies compared to all other eukaryotic groups and that exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving events. The authors have hypothesized that the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes.Here we offer a different explanation for the higher frequency of frame-preserving exon skipping in Metzoa than in all other eukaryotes. In our view these observations reflect the fact that the majority of multidomain proteins unique to metazoa and indispensable for metazoan type multicellularity were assembled by exon-shuffling from symmetrical' modules (i.e. modules flanked by introns of the same phase), whereas this type of protein evolution played a minor role in other groups of eukaryotes, including plants. The higher frequency of symmetrical' exons in Metazoan genomes provides an explanation for the enrichment for frame-preserving events since skipping or inclusion of symmetrical' modules during alternative splicing does not result in a reading-frame shift

A humán agyi tripszin biológiai funkciójának felderítése: új stratégia = Searching for the biological function of human brain trypsin: new strategy

A primata specifikus szerin proteázt, a humán tripszin 4-et munkacsoportunk klónozta és expresszáltatta először heterológ rendszerben. Az aktív enzim kristályszerkezetét is mi határoztuk meg először. A humán tripszin 4 biológiai funkciójának felderítése volt a jelen pályázat célja. Tekintettel a fehérje primátákban való előfordulására a funkciót nem elsősorban az élettan, hanem a modern molekuláris biológia, enzimológia és sejtbiológia eszközeivel kutattuk. Végleges felderítésével ugyan adósak maradtunk, az elmúlt négy év kutatásai számos, a humán proteáz funkciójának tisztázásához támpontot nyújtó felfedezéshez vezettek. Ezek a jövetkezők: 1) Megállapítottuk, hogy a primata-specifikus tripszin 4 egyik, feltehetően biológiai szubsztrátja a mielin bázikus fehérje. 2) Post mortem emberi agy mintákból tripszinogén 4 B-izoformát izoláltunk és megállapítottuk, hogy a fehérje transzlációja egy CUG triplett által kódolt iniciátor leucinnal indul. Feltételeztük, hogy ez a mechanizmus a gén expresszió szabályozásának eszköze. 3) Felderítettük a humán tripszinogén 4 asztroglia sejten belüli transzportjának útját és aktivációjának lehetséges helyét. | For the first time human trypsin 4 was cloned and expressed in a heterologous system by our research team. The first crystal structure of this protease was also reported by our group. Exploration of the biological function of human trypsin 4 was the goal of our present grant proposal. Considering that this enzyme only occurs in Primates the biological function of trypsin 4 was studied by the means of modern molecular biology, enzymology and cell biology, rather than by those of physiology. Though we cannot unambiguosly define the biological function(s) of this protease yet, our last 4-year reserach led to several discoveries, which may provide a good basis for further exploring the physiological or pathological functions of human trypsin 4. These discoveries are as follows: 1) We provided indirect evidence that myelin basic protein (MBP) might be one of the biological substrates of human trypsin 4. 2) From samples of post mortem human brain for the first time we isolated and characterized Isoform B of trypsinogen 4 and established that the translation of human trypsinogen 4 can be initiated at a CUG codon with an N-terminal leucine residue. We proposed that this unconventional translation initiation may be a new mechanism to regulate gene expression. 3) The transport of human trypsinogen 4 was explored in astroglia cells, and the possible intracellular site of its activation was determined

A lucerna szimbiotikus nitrogénkötés kialakításában kulcsfontosságú szerepet játszó receptor fehérje molekuláris jellemzése = Molecular characterization of a receptor protein playing an essential role in symbiotic nitrogen fixation of alfalfa.

A pillangósvirágú növények egyedülálló szimbiotikus kapcsolatban állnak a rizóbium baktériumokkal, ami egy speciális növényi szerv, a gyökérgümő képződéséhez vezet, ahol a légköri nitrogénkötés történik. A növény-baktérium kapcsolat kölcsönös jelcserét indít be a gümőképződés fejlődési programban. Napjainkban több protein-kinázt azonosítottak, amelyek feltehetőleg a nodulációhoz vezető szignál transzdukcióban vesznek részt. A szignál kaszkád a Nod faktor felismerés és továbbítás (NORK rendszer) során vezet el a nodulációig. A NORK rendszer egyik eleme a NORK (NOdulation Reception Kinase) fehérje, amelyik több más kinázzal együttműködve juttatja el a jelet a Nod-faktor érzékelésétől a gümő képzéséig. Izoláltuk a NORK membrán fehérjét lucerna gyökér extraktumból. Két-dimenziós elektroforézissel elválasztottuk és immunoblotton azonosítottuk. Eredményeink alátámasztására, epitop jelzett NORK fehérje tranziens expresszióját igazoltuk dohánylevélben Agrobacterium tumefaciens infiltrálás segítségével. A NORK fehérje szerepének és funkciójának tisztázására a NORK rendszer más kináz fehérjéivel való kapcsolatát (LYK3, NFP) is vizsgáltuk fehérje-fehérje kapcsolatok kimutatásával. Az LRR1 típusú növényi receptor-szerű kinázok (RLK) filogenetikai analízise alapján arra következthetünk, hogy a NORK/SYMRK fehérje homológjai egy jól elkülönülő monofiletikus csoportot alkotnak az LRR1 RLK családon belül, és pillangósvirágú növényeken kívüli taxonokban is megtalálhatók. | Legume roots engage in a unique symbiotic relationship with rhizobia, in which special plant organs, the nodules, are formed and support nitrogen fixation. The plant-bacteria interactions involve the exchange of signals that trigger specific cellular and developmental programs in both. Recently several protein kinases have identified, which are participating in specialized signal transduction pathways that culminate in the induction of a transcriptional program of nodulation.The signal cascade leading to nodulation is part of the Nod-factor perception/ transduction system (the NORK system) active in legume roots. The identified NOdulation Receptor Kinase, NORK, is an integral component of the signalling pathway, in which the coordinated interaction of the components is needed for Nod-factor signal perception and transduction. Isolation of NORK from root extract of alfalfa, separation by 2D and detection on immunoblot were done. Epitop tagged NORK were transiently expressed in tobacco leaves by Agrobacterium tumefaciens infiltration. To justify interactions with other kinases in the NORK system (LYK3, NFP), we investigated the role and function of NORK by protein-protein interaction studies. Phylogenetic analysis of the LRR1-type plant receptor like kinases (RLK) revealed that homologues of the NORK/SYMRK protein constitute a single monophyletic clade within the LRR1 RLK family and members of this group exist in several non-legume plants

Duplication-divergence model of protein interaction network

We show that the protein-protein interaction networks can be surprisingly well described by a very simple evolution model of duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the probability to retain a duplicated link during divergence. When this parameter is large, the network growth is not self-averaging and an average vertex degree increases algebraically. The lack of self-averaging results in a great diversity of networks grown out of the same initial condition. For small values of the link retention probability, the growth is self-averaging, the average degree increases very slowly or tends to a constant, and a degree distribution has a power-law tail.Comment: 8 pages, 13 figure