Arabidopsis Yak1 protein (AtYak1) is a dual specificity protein kinase
KAUST DepartmentDesert Agriculture Initiative
Biological and Environmental Sciences and Engineering (BESE) Division
Online Publication Date2015-10-09
Print Publication Date2015-10-24
Permanent link to this recordhttp://hdl.handle.net/10754/579844
MetadataShow full item record
AbstractYak1 is a member of dual-specificity Tyr phosphorylation-regulated kinases (DYRKs) that are evolutionarily conserved. The downstream targets of Yak1 and their functions are largely unknown. Here, a homologous protein AtYAK1 was identified in Arabidopsis thaliana and the phosphoprotein profiles of the wild type and an atyak1 mutant were compared on two-dimensional gel following Pro-Q Diamond phosphoprotein gel staining. Annexin1, Annexin2 and RBD were phosphorylated at serine/ threonine residues by the AtYak1 kinase. Annexin1, Annexin2 and Annexin4 were also phosphorylated at tyrosine residues. Our study demonstrated that AtYak1 is a dual specificity protein kinase in Arabidopsis that may regulate the phosphorylation status of the annexin family proteins.
CitationArabidopsis Yak1 protein (AtYak1) is a dual specificity protein kinase 2015 FEBS Letters
- Plant dual-specificity tyrosine phosphorylation-regulated kinase optimizes light-regulated growth and development in Arabidopsis.
- Authors: Huang WY, Wu YC, Pu HY, Wang Y, Jang GJ, Wu SH
- Issue date: 2017 Sep
- Mutations of the AtYAK1 Kinase Suppress TOR Deficiency in Arabidopsis.
- Authors: Forzani C, Duarte GT, Van Leene J, Clément G, Huguet S, Paysant-Le-Roux C, Mercier R, De Jaeger G, Leprince AS, Meyer C
- Issue date: 2019 Jun 18
- Serine/threonine/tyrosine protein kinase from Arabidopsis thaliana is dependent on serine residues for its activity.
- Authors: Reddy MM, Rajasekharan R
- Issue date: 2007 Apr 1
- CDPKs are dual-specificity protein kinases and tyrosine autophosphorylation attenuates kinase activity.
- Authors: Oh MH, Wu X, Kim HS, Harper JF, Zielinski RE, Clouse SD, Huber SC
- Issue date: 2012 Nov 30
- Tyrosine phosphorylation of protein kinase complex BAK1/BIK1 mediates Arabidopsis innate immunity.
- Authors: Lin W, Li B, Lu D, Chen S, Zhu N, He P, Shan L
- Issue date: 2014 Mar 4
Showing items related by title, author, creator and subject.
ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrievalWang, Jim Jing-Yan; Gao, Xin; Wang, Quanquan; Li, Yongping (BMC Bioinformatics, Springer Nature, 2012-05-08) [Article]Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update the Protein Hierarchial Context Coherently in an iterative algorithm--ProDis-ContSHC.We test the performance of ProDis-ContSHC on two benchmark sets, i.e., the ASTRAL 1.73 database and the FSSP/DALI database. Experimental results demonstrate that plugging our supervised contextual dissimilarity measures into the retrieval systems significantly outperforms the context-free dissimilarity/similarity measures and other unsupervised contextual dissimilarity measures that do not use the class label information.Conclusions: Using the contextual proteins with their class labels in the database, we can improve the accuracy of the pairwise dissimilarity/similarity measures dramatically for the protein retrieval tasks. In this work, for the first time, we propose the idea of supervised contextual dissimilarity learning, resulting in the ProDis-ContSHC algorithm. Among different contextual dissimilarity learning approaches that can be used to compare a pair of proteins, ProDis-ContSHC provides the highest accuracy. Finally, ProDis-ContSHC compares favorably with other methods reported in the recent literature. 2012 Wang et al.; licensee BioMed Central Ltd.
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure predictionCui, Xuefeng; Lu, Zhiwu; wang, sheng; Wang, Jim Jing-Yan; Gao, Xin (Bioinformatics, Oxford University Press (OUP), 2016-06-15) [Article]Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.
Auxin efflux by PIN-FORMED proteins is activated by two different protein kinases, D6 PROTEIN KINASE and PINOIDZourelidou, Melina; Absmanner, Birgit; Weller, Benjamin; Barbosa, Inês CR; Willige, Björn C; Fastner, Astrid; Streit, Verena; Port, Sarah A; Colcombet, Jean; de la Fuente van Bentem, Sergio; Hirt, Heribert; Kuster, Bernhard; Schulze, Waltraud X; Hammes, Ulrich Z; Schwechheimer, Claus (eLife, eLife Sciences Publications, Ltd, 2014-06-19) [Article]The development and morphology of vascular plants is critically determined by synthesis and proper distribution of the phytohormone auxin. The directed cell-to-cell distribution of auxin is achieved through a system of auxin influx and efflux transporters. PIN-FORMED (PIN) proteins are proposed auxin efflux transporters, and auxin fluxes can seemingly be predicted based on the-in many cells-asymmetric plasma membrane distribution of PINs. Here, we show in a heterologous Xenopus oocyte system as well as in Arabidopsis thaliana inflorescence stems that PIN-mediated auxin transport is directly activated by D6 PROTEIN KINASE (D6PK) and PINOID (PID)/WAG kinases of the Arabidopsis AGCVIII kinase family. At the same time, we reveal that D6PKs and PID have differential phosphosite preferences. Our study suggests that PIN activation by protein kinases is a crucial component of auxin transport control that must be taken into account to understand auxin distribution within the plant.