PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Bel, Michiel Van; Silvestri, Francesca; Weitz, Eric; Kreft, Łukasz; Botzki, Alexander; Coppens, Frederik; Vandepoele, Klaas

doi:10.1093/nar/gkab1024

Cited by 155 publications

(127 citation statements)

References 29 publications

(32 reference statements)

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“…The ‘ Plant database ’ section includes an Update paper from the popular comparative genomics resource PLAZA ( 100 ) which reports a near-doubling of species covered and new and improved features throughout, including the API. The paper on BRAD ( 101 ), the dedicated Brassica database, reports a particular focus on synteny analysis tools and looks forward to accommodating the more diverse omics data and pangenome information now becoming available for the Family.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

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Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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“…To develop the phylogenetic tree, the orthologs of AtLLPs present in Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Amborella trichopoda, Arabidopsis lyrata, Brassica oleracea, Brassica rapa, Daucus carota, Solanum lycopersicum, Solanum tuberosum, Oryza sativa ssp. japonica, Zea mays, Triticum aestivum , and Populus trichocarpa were identified using PLAZA 5.0 [ 33 ]. Their peptide sequences were retrieved from NCBI and Phytozome [ 34 ].…”

Section: Methodsmentioning

confidence: 99%

In silico characterization, molecular phylogeny, and expression profiling of genes encoding legume lectin-like proteins under various abiotic stresses in Arabidopsis thaliana

et al. 2022

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Background Lectin receptor-like kinases (Lec-RLKs), a subfamily of RLKs, have been demonstrated to play an important role in signal transduction from cell wall to the plasma membrane during biotic stresses. Lec-RLKs include legume lectin-like proteins (LLPs), an important group of apoplastic proteins that are expressed in regenerating cell walls and play a role in immune-related responses. However, it is unclear whether LLPs have a function in abiotic stress mitigation and related signaling pathways. Therefore, in this study, we examined the possible role of LLPs in Arabidopsis thaliana (AtLLPs) under various abiotic stresses. Results The study was initiated by analyzing the chromosomal localization, gene structure, protein motif, peptide sequence, phylogeny, evolutionary divergence, and sub-cellular localization of AtLLPs. Furthermore, the expression profiling of these AtLLPs was performed using publicly accessible microarray datasets under various abiotic stresses, which indicated that all AtLLPs were differently expressed in both root and shoot tissues in response to abiotic stresses. The cis-regulatory elements (CREs) analysis in 500 bp promoter sequences of AtLLPs suggested the presence of multiple important CREs implicated for regulating abiotic stress responses, which was further supported by expressional correlation analysis between AtLLPs and their CREs cognate transcription factors (TFs). qRT-PCR analysis of these AtLLPs after 2, 6, and 12 h of cold, high light, oxidative (MV), UV-B, wound, and ozone stress revealed that all AtLLPs displayed differential expression patterns in most of the tested stresses, supporting their roles in abiotic stress response and signaling again. Out of these AtLLPs, AT1g53070 and AT5g03350 appeared to be important players. Furthermore, the mutant line of AT5g03350 exhibited higher levels of ROS than wild type plants till 12 h of exposure to high light, MV, UV-B, and wound, whereas its overexpression line exhibited comparatively lower levels of ROS, indicating a positive role of this gene in abiotic stress response in A. thaliana. Conclusions This study provides basic insights in the involvement of two important representative AtLLPs, AT1g53070 and AT5g03350, in abiotic stress response. However, further research is needed to determine the specific molecular mechanism of these AtLLPs in abiotic stress mitigation and related signaling pathways in A. thaliana.

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“…× ventrata (NvNpr), N. rafflesiana (NrNpr1 and NrNpr2), and N. ampullaria (NaNpr1 and NaNpr2). BLASTP analysis was also performed using Dicots Plaza 5.0 against the Arabidopsis thaliana genome sequence database (Van bel et al 2022). The conserved amino acids in neprosins were determined via a multiple sequence alignment (MSA) using neprosins and their BLASTP hits against NCBI nr and Dicots Plaza 5.0 Arabidopsis thaliana genome sequence database with Clustal Omega (Madeira et al 2019) and ConSurf (Ashkenazy et al 2016).…”

Section: Methodsmentioning

confidence: 99%

Neprosin belongs to a new family of glutamic peptidase based on in silico evidence

Ting

Baharin

Ramzi

et al. 2022

Preprint

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Neprosin is a novel prolyl endopeptidase (PEP) first discovered in the insectivorous tropical pitcher plants of Nepenthes species. Neprosin has two uncharacterized functional domains of neprosin activation peptide (PF14365) and neprosin domain (PF03080), which can be found in many uncharacterized plant proteases. A previous study has shown neprosin activity in hydrolyzing proline-rich gliadin, a gluten component that triggers celiac disease. In this study, an extensive in silico structure-function analysis of neprosins was conducted to investigate the catalytic mechanism of this protein family. Results from multiple sequence alignment and ConSurf showed neprosins lack the catalytic triad and motifs of common prolyl endopeptidase family S9. Protein models of neprosins from Nepenthes x ventrata (NvNpr) and N. rafflesiana (NrNpr1) were generated using four ab initio methods and comparatively assessed to get high-quality models. Structural alignment of neprosin models to experimental structures in the Protein Data Bank (PDB) found a high structural similarity to glutamic peptidases. Further investigations reveal more resemblances to glutamic peptidases with low optimum pH that activates the enzyme via autoproteolysis for maturation. Two highly conserved glutamic acid residues, which are stable according to molecular dynamics simulation, can be found at the substrate cleft and active site corresponding to a glutamic peptidase. Protein docking demonstrated that mature neprosins bind well with potent antigen αI-gliadin at the putative active cleft. Taken together, neprosins represent a new member of the glutamic peptidase family G3, with a putative catalytic dyad of two glutamic acids. This study illustrates a hypothetical enzymatic mechanism of the neprosin family and demonstrates the useful application of an accurate ab initio protein structure prediction in the structure-function study of a novel protein family.

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PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Cited by 155 publications

References 29 publications

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

In silico characterization, molecular phylogeny, and expression profiling of genes encoding legume lectin-like proteins under various abiotic stresses in Arabidopsis thaliana

Neprosin belongs to a new family of glutamic peptidase based on in silico evidence

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