Detecting sequence signals in targeting peptides using deep learning

Armenteros, José Juan Almagro; Salvatore, Marco; Emanuelsson, Olof; Winther, Ole; Heijne, Gunnar von; Elofsson, Arne; Nielsen, Henrik

doi:10.26508/lsa.201900429

Cited by 721 publications

(643 citation statements)

References 38 publications

Supporting

Mentioning

639

Contrasting

Order By: Relevance

“…We predicted the chloroplast transit peptide (cTP) of VC1 using TargetP online (version 2.0) 19 . An E. coli codon-optimized version of VC1 coding for an N-terminal His-tag and lacking the predicted cTP-coding region ( Supplementary File 7 ) was synthesized (GenScript) and cloned into expression vector pET22b(+) using restriction sites NdeI and HindIII.…”

Section: Methodsmentioning

confidence: 99%

VC1 catalyzes a key step in the biosynthesis of vicine from GTP in faba bean

Björnsdotter

Nadzieja

Chang

et al. 2020

Preprint

View full text Add to dashboard Cite

25Faba bean is a widely adapted and high-yielding legume cultivated for its protein-rich seeds 1 . 26 However, the seeds accumulate the anti-nutritional pyrimidine glucosides vicine and convicine, which 27 can cause haemolytic anaemia-favism-in the 400 million individuals genetically predisposed by a 28 deficiency in glucose-6-phosphate dehydrogenase 2 . Here, we identify the first enzyme associated with 29 vicine and convicine biosynthesis, which we name VC1. We show that VC1 co-locates with the major QTL 30 for vicine and convicine content and that the expression of VC1 correlates highly with vicine content 31 across tissues. We also show that low-vicine varieties express a version of VC1 carrying a small, frame-32 shift insertion, and that overexpression of wild-type VC1 leads to an increase in vicine levels. VC1 33 encodes a functional GTP cyclohydrolase II, an enzyme normally involved in riboflavin biosynthesis from 34 the purine GTP. Through feeding studies, we demonstrate that GTP is a precursor of vicine both in faba 35 bean and in the distantly related plant bitter gourd. Our results reveal an unexpected biosynthetic origin 36 for vicine and convicine and pave the way for the development of faba bean cultivars that are free from 37 these anti-nutrients, providing a safe and sustainable source of dietary protein. 38 39 Main Text 40 According to the UN's Intergovernmental Panel on Climate Change (IPCC), switching to a plant-based 41 diet can reduce carbon emissions, especially in the West 3 . The suggested change in diet will require a wider 42and more varied cultivation of locally adapted protein crops. On a worldwide basis, faba bean ( Fig. 1a) has 43 the highest yield of the legumes after soybean (1.92 Mg/ha in 2013-2017) 4 and the highest seed protein 44 content of the starch-containing legumes (29% dry-matter basis) 5 . Furthermore, faba bean is adapted to 45 cool climates such as Mediterranean winters and northern European summers, where soybean performs 46 poorly 6 . The main factor restricting faba bean cultivation and consumption is the presence of the anti-47 2, Supplementary File 6). Using seed coat cDNA and PCR primers able to distinguish between VC1 and vc1, 132

show abstract

Section: Methodsmentioning

confidence: 99%

VC1 catalyzes a key step in the biosynthesis of vicine from GTP in faba bean

Björnsdotter

Nadzieja

Chang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Similarities between PAC domain sequences have been calculated using either Blast2seq (https://blast.ncbi.nlm.nih.gov/Blast.cgi) or needle (http://www.bioinformatics.nl/cgi-bin/ emboss/needle). The sub-cellular localization of proteins has been predicted with TargetP-2.0 ( [45], http://www.cbs.dtu.dk/services/TargetP/) and the presence of β-sheets and/or α-helices using SABLE ( [46], http://sable.cchmc.org/) and NetSurfP ( [47], http://www.cbs.dtu.dk/services/NetSurfP/). The selected PAC domains starting at the Gly amino acid located three amino acids upstream of Cys 1 and ending at Cys 6 have been aligned using PROMALS3D ( [48], http://prodata.swmed.edu/ promals3d/promals3d.php) to take into account the prediction of α-sheets.…”

Section: Comparisons and Alignment Of Pac Domainsmentioning

confidence: 99%

The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage

Nguyen-Kim

Clemente

Laimer

et al. 2020

IJMS

View full text Add to dashboard Cite

Plant cell wall proteins play major roles during plant development and in response to environmental cues. A bioinformatic search for functional domains has allowed identifying the PAC domain (Proline-rich, Arabinogalactan proteins, conserved Cysteines) in several proteins (PDPs) identified in cell wall proteomes. This domain is assumed to interact with pectic polysaccharides and O-glycans and to contribute to non-covalent molecular scaffolds facilitating the remodeling of polysaccharidic networks during rapid cell expansion. In this work, the characteristics of the PAC domain are described in detail, including six conserved Cys residues, their spacing, and the predicted secondary structures. Modeling has been performed based on the crystal structure of a Plantago lanceolata PAC domain. The presence of β-sheets is assumed to ensure the correct folding of the PAC domain as a β-barrel with loop regions. We show that PDPs are present in early divergent organisms from the green lineage and in all land plants. PAC domains are associated with other types of domains: Histidine-rich, extensin, Proline-rich, or yet uncharacterized. The earliest divergent organisms having PDPs are Bryophytes. Like the complexity of the cell walls, the number and complexity of PDPs steadily increase during the evolution of the green lineage. The association of PAC domains with other domains suggests a neo-functionalization and different types of interactions with cell wall polymers

show abstract

“…FPP-derived Table 1. N-terminal sequences are omitted according to prediction by TargetP-2.0 [21] (http://www.cbs.dtu.dk/services/TargetP). Highly conserved regions are highlighted in gray.…”

Section: Trans-prenyltransferasesmentioning

confidence: 99%

Functional Gene Network of Prenyltransferases in Arabidopsis thaliana

Kopcsayová

Vranová

2019

Molecules

View full text Add to dashboard Cite

Prenyltransferases (PTs) are enzymes that catalyze prenyl chain elongation. Some are highly similar to each other at the amino acid level. Therefore, it is difficult to assign their function based solely on their sequence homology to functional orthologs. Other experiments, such as in vitro enzymatic assay, mutant analysis, and mutant complementation are necessary to assign their precise function. Moreover, subcellular localization can also influence the functionality of the enzymes within the pathway network, because different isoprenoid end products are synthesized in the cytosol, mitochondria, or plastids from prenyl diphosphate (prenyl-PP) substrates. In addition to in vivo functional experiments, in silico approaches, such as co-expression analysis, can provide information about the topology of PTs within the isoprenoid pathway network. There has been huge progress in the last few years in the characterization of individual Arabidopsis PTs, resulting in better understanding of their function and their topology within the isoprenoid pathway. Here, we summarize these findings and present the updated topological model of PTs in the Arabidopsis thaliana isoprenoid pathway.

show abstract

Detecting sequence signals in targeting peptides using deep learning

Cited by 721 publications

References 38 publications

VC1 catalyzes a key step in the biosynthesis of vicine from GTP in faba bean

VC1 catalyzes a key step in the biosynthesis of vicine from GTP in faba bean

The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage

Functional Gene Network of Prenyltransferases in Arabidopsis thaliana

Contact Info

Product

Resources

About