KiPho: malaria parasite kinome and phosphatome portal

Abstract The Plasmodium kinases and phosphatases play an essential role in the regulation of substrate reversible-phosphorylation and overall cellular homeostasis. Reversible phosphorylation is one of the key post-translational modifications (PTMs) essential for parasite survival. Thus, a complete and comprehensive information of malarial kinases and phosphatases as a single web resource will not only aid in systematic and better understanding of the PTMs, but also facilitate efforts to look for novel drug targets for malaria. In the current work, we have developed KiPho, a comprehensive and one step web-based information resource for Plasmodium kinases and phosphatases. To develop KiPho, we have made use of search methods to retrieve, consolidate and integrate predicted as well as annotated information from several publically available web repositories. Additionally, we have incorporated relevant and manually curated data, which will be updated from time to time with the availability of new information. The KiPho (Malaria Parasite Kinome—Phosphatome) resource is freely available at http://bioinfo.icgeb.res.in/kipho.

[1]  Ruedi Aebersold,et al.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome , 2007, Nature Methods.

[2]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[3]  Edward W. Tate,et al.  Genome-wide Functional Analysis of Plasmodium Protein Phosphatases Reveals Key Regulators of Parasite Development and Differentiation , 2014, Cell host & microbe.

[4]  Livia Perfetto,et al.  HuPho: the human phosphatase portal , 2012, The FEBS journal.

[5]  Kara Dolinski,et al.  BioGRID: A Resource for Studying Biological Interactions in Yeast. , 2016, Cold Spring Harbor protocols.

[6]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[7]  Andrew F Neuwald,et al.  Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources. , 2005, Methods.

[8]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[9]  A. Andreeva,et al.  Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes , 2004, BMC Evolutionary Biology.

[10]  Li Li,et al.  PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished) , 2002, Nucleic Acids Res..

[11]  P Vincens,et al.  Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.

[12]  Xun Li,et al.  The human DEPhOsphorylation database DEPOD: a 2015 update , 2014, Nucleic Acids Res..

[13]  P. Kennelly,et al.  Protein phosphatases--a phylogenetic perspective. , 2001, Chemical reviews.

[14]  R. Ménard,et al.  Signalling in malaria parasites. The MALSIG consortium. , 2009, Parasite.

[15]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[16]  Yu Xue,et al.  EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases , 2013, Nucleic Acids Res..

[17]  A. Tobin,et al.  Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. , 2011, Nature communications.

[18]  L. Ranford-Cartwright,et al.  SIGNALLING IN MALARIA PARASITES , 2017 .

[19]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[20]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[21]  K. Wolstencroft,et al.  PhosphaBase: An ontology‐driven database resource for protein phosphatases , 2004, Proteins.

[22]  D. Gupta,et al.  Genome wide in silico analysis of Plasmodium falciparum phosphatome , 2014, BMC Genomics.

[23]  Christian J Stoeckert,et al.  Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. , 2006, Genome research.

[24]  S. Hanks,et al.  Genomic analysis of the eukaryotic protein kinase superfamily: a perspective , 2003, Genome Biology.

[25]  Joshua E Elias,et al.  The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. , 2011, Cell host & microbe.

[26]  Luciano Milanesi,et al.  Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity , 2005, BMC Bioinformatics.

[27]  Pauline Ward,et al.  Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote , 2004, BMC Genomics.