Antibody-Like Phosphorylation Sites. Theme for Studies of Cancer, Aging and Evolution

Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.

KinasePhos 3.0:Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites

The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus,UniProtKB,the GPS 5.0,and Phospho.ELM.In total,41,421 experimentally verified kinase-specific phosphorylation sites were identified.A total of 1380 unique kinases were identified,including 753 with existing classification information from KinBase and the remaining 627 annotated by building a phylogenetic tree.Based on this kinase classification,a total of 771 predictive models were built at the individual,family,and group levels,using at least 15 experimentally verified substrate sites in positive training datasets.The improved models demonstrated their effectiveness compared with other prediction tools.For example,the prediction of sites phosphorylated by the protein kinase B,casein kinase 2,and protein kinase A families had accuracies of 94.5%,92.5%,and 90.0%,respectively.The average prediction accuracy for all 771 models was 87.2%.For enhancing interpretability,the SHapley Additive exPlanations(SHAP)method was employed to assess feature importance.The web interface of KinasePhos 3.0 has been redesigned to provide comprehensive annotations of kinase-specific phosphorylation sites on multiple proteins.Additionally,considering the large scale of phosphoproteomic data,a downloadable prediction tool is available at https://awi.cuhk.edu.cn/KinasePhos/download.html or https://github.com/tom-209/KinasePhos-3.0-executable-file.

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins

In eukaryotes,protein phosphorylation is specifically catalyzed by numerous protein kinases(PKs),faithfully orchestrates various biological processes,and reversibly determines cellular dynamics and plasticity.Here we report an updated algorithm of Group-based Prediction System(GPS)5.0 to improve the performance for predicting kinase-specific phosphorylation sites(p-sites).Two novel methods,position weight determination(PWD)and scoring matrix optimization(SMO),were developed.Compared with other existing tools,GPS 5.0 exhibits a highly competitive accuracy.Besides serine/threonine or tyrosine kinases,GPS 5.0 also supports the prediction of dual-specificity kinase-specific p-sites.In the classical module of GPS 5.0,617 individual predictors were constructed for predicting p-sites of 479 human PKs.To extend the application of GPS5.0,a species-specific module was implemented to predict kinase-specific p-sites for 44,795 PKs in161 eukaryotes.The online service and local packages of GPS 5.0 are freely available for academic research at http://gps.biocuckoo.cn.

Molecular Basis and Regulation of Ammonium Transporter in Rice

Rice grows in flooded paddy fields and takes up ammonium as the preferred nitrogen （N） source. Ammonium uptake is facilitated by a family of integral membrane proteins known as ammonium transporters found in all domains of life. However, the molecular mechanism and functional characteristics of the ammonium transporters （AMT） in rice have not been determined in detail yet. In this review, we report a genome-wide search for AMT genes in rice, resulting in the increase of the number of potential AMT proteins to at least 12, including members of both the alpha and beta sub-groups. Analysis of the predicted protein sequences for the 12 OsAMT proteins identified many conserved phosphorylation sites in both the alpha and beta group members, which could potentially play a role in controlling the activity of the transporters. Present knowledge of the expression of rice AMT genes is also summarized in detail. Future studies should focus on the structural and functional characteristics of OsAMT proteins to provide insight into the mechanism of ammonium uptake and its regulation in rice. Such research could improve utilization and decrease wastage of N fertilizer in rice cultivation.

Characterization and Expression of Ammonium Transporter in Peach (Prunus persica) and Regulation Analysis in Response to External Ammonium Supply

As the preferred nitrogen(N)source,ammonium(NH_(4)^(+))contributes to plant growth and development and fruit quality.In plants,NH 4+uptake is facilitated by a family of NH_(4)^(+) transporters(AMT).However,the molecular mechanisms and functional characteristics of the AMT genes in peach have not been mentioned yet.In this present study,excess NH_(4)^(+) stress severely hindered shoot growth and root elongation,accompanied with reduced mineral accumulation,decreased leaf chlorophyll concentration,and stunned photosynthetic performance.In addition,we identified 14 putative AMT genes in peach(PpeAMT).Expression analysis showed that PpeAMT genes were differently expressed in peach leaves,stems and roots,and were distinctly regulated by external NH_(4)^(+) supplies.Putative cis-elements involved in abiotic stress adaption,Ca^(2+) response,light and circadian rhythms regulation,and seed development were observed in the promoters of the PpeAMT family genes.Phosphorylation analysis of residues within the C-terminal of PpeAMT proteins revealed many conserved phosphorylation residues in both the AMT1 and AMT2 subfamily members,which could potentially play roles in controlling the NH 4+transport activities.This study provides gene resources to study the biological function of AMT proteins in peach,and reveals molecular basis for NH_(4)^(+) uptake and N nutrition mechanisms of fruit trees.

FERONIA cytoplasmic domain:node of varied signal outputs

The receptor-like kinase(RLK)FERONIA(FER),located on the plasma membrane,belongs to the Catharanthus roseus RLK1-like kinase family(CrRLK1L)and participates in widespread biological processes in plants in a context-dependent fashion.Genetic studies in Arabidopsis illustrated the versatile roles that FER plays in fertilization,vegetative growth,defense and stress responses,cell-wall homeostasis,as well as protein synthesis.These studies also helped to identify genes and signal pathways involved in FER signal transduction.Despite increasingly larger numbers of studies discussing how FER senses its ligand,Rapid alkalinization factor(RALF)peptides,and further regulates downstream factors,few have shown the mechanisms of how FER mediates the specific regulation of downstream signals in context of the phosphorylation of its cytoplasmic domain.As understanding this would help in better understanding the diversity and complexity of FER function,this paper aims to review the roles of FER in regulating different signal outputs from the view of the role of its cytoplasmic domain.

Computational identification and analysis of neurodegenerative disease associated protein kinases in hominid genomes

Protein kinases play an important role in the incidence of neurodegenerative diseases.However their incidence in non-human primates is found to be very low.Small differences among the genomes might influence the disease susceptibilities.The present study deals with finding the genetic differences of protein kinases in humans and their three closest evolutionary partners chimpanzee,gorilla and orangutan for three neurodegenerative diseases namely,Alzheimer’s,Parkinson’s and Huntington’s diseases.In total 47 human protein kinases associated with three neurodegenerative diseases and their orthologs from other three nonhuman primates were identified and analyzed for any possible susceptibility factors in humans.Multiple sequence alignment and pairwise sequence alignment revealed that,18 human protein kinases including DYRK1A,RPS6KB1,and GRK6 contained significant indels and substitutions.Further phosphorylation site analysis revealed that eight kinases including MARK2 and LTK contained sites of phosphorylation exclusive to human genomes which could be particular candidates in determining disease susceptibility between human and non-human primates.Final pathway analysis of these eight kinases and their targets revealed that these kinases could have long range consequences in important signaling pathways which are associated with neurodegenerative diseases.

Structural biology study of human TNF receptor associated factor 4 TRAF domain

TRAF4 is a unique member of TRAF family,which is es-sential for innate immune response,nervous system and other systems.In addition to being an adaptor protein,TRAF4 was identifi ed as a regulator protein in recent studies.We have determined the crystal structure of TRAF domain of TRAF4(residues 292-466)at 2.60Åresolution by X-ray crystallography method.The trimericly assembled TRAF4 resembles a mushroom shape,containing a super helical“stalk”which is made of three right-handed intertwinedαhelixes and a C-terminal“cap”,which is divided at resi-due L302 as a boundary.Similar to other TRAFs,both intermolecular hydrophobic interaction in super helical“stalk”and hydrogen bonds in“cap”regions contribute directly to the formation of TRAF4 trimer.However,differ-ing from other TRAFs,there is an additional fl exible loop(residues 421-426),which contains a previously identifi ed phosphorylated site S426 exposing on the surface.This S426 was reported to be phosphorylated by IKKαwhich is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation.Therefore,the crystal structure of TRAF4-TRAF is valuable for under-standing its molecular basis for its special function and provides structural information for further studies.