PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants

Gou, Xiangjian; Feng, Xuanjun; Shi, Haoran; Guo, Tingting; Xie, Rongqian; Liu, Yaxi; Wang, Qi; Yang, Banglie; Chen, Lixue; Lu, Yanli

doi:10.1111/pbi.13823

Cited by 13 publications

(8 citation statements)

References 87 publications

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“…In line with this, substitutions between B73 and mexicana were predicted to be neutral (http://www. ppved.org.cn/) (Figure S3b) (Gou et al, 2022). Therefore, the different effects of ZmDRO1 B73 and ZmDRO1 mex may be resulting from the transcriptional level.…”

Section: Resultsmentioning

confidence: 99%

“…Multiple sequence alignment of orthologous genes of DRO1 from 18 species showed that all four amino acid substitutions in ZmDRO1 between B73 and mexicana were not conserved (Figure S3 a). In line with this, substitutions between B73 and mexicana were predicted to be neutral ( http://www.ppved.org.cn/ ) (Figure S3 b) (Gou et al ., 2022 ). Therefore, the different effects of ZmDRO1 B73 and ZmDRO1 mex may be resulting from the transcriptional level.…”

Section: Resultsmentioning

confidence: 99%

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ABA‐inducible DEEPER ROOTING1 improves adaptation of maize to water deficiency

Feng

Li²,

Cai³

et al. 2022

Plant Biotechnology Journal

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Root architecture remodelling is critical for forage moisture in water-limited soil. DEEPER ROOTING 1 (DRO1) in Oryza, Arabidopsis, and Prunus has been reported to improve drought avoidance by promoting roots to grow downward and acquire water from deeper soil. In the present study, we found that ZmDRO1 responded more strongly to abscisic acid (ABA)/drought induction in Zea mays ssp. mexicana, an ancestral species of cultivated maize, than in B73. It was proposed that this is one of the reasons why Zea mays ssp. mexicana has a more noticeable change in the downward direction angle of the root and fewer biomass penalties under waterdeficient conditions. Thus, a robust, synthetic ABA/drought-inducible promoter was used to control the expression of ZmDRO1 B73 in Arabidopsis and cultivated maize for drought-resistant breeding. Interestingly, ABA-inducible ZmDRO1 promoted a larger downward root angle and improved grain yield by more than 40% under water-limited conditions. Collectively, these results revealed that different responses to ABA/drought induction of ZmDRO1 confer different drought avoidance abilities, and we demonstrated the application of ZmDRO1 via an ABAinducible strategy to alter the root architecture of modern maize to improve drought adaptation in the field.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

ABA‐inducible DEEPER ROOTING1 improves adaptation of maize to water deficiency

Feng

Li²,

Cai³

et al. 2022

Plant Biotechnology Journal

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“…Ala161 is present in all canonical HSP70 family members (DnaK-homologues) across bacteria, archaea, and eukaryotes, but varies in non-canonical HSP70- related gene families, such as bacterial HSCA/Cs and HSP110s. Two computational tools, PredictSNP (Bendl et al 2014) and PPVED (Gou et al 2022), both predicted a deleterious effect of an A to T substitution on protein function (Fig S7). Further, severe deleterious effects resulting from an A to T substitution within an alpha-helix of an Arabidopsis kinase have been reported (Piovesana et al 2023).…”

Section: Discussionmentioning

confidence: 99%

Design of anArabidopsis thalianareporter line to detect heat-sensing and signaling mutants

Guihur

Bourgine

Rebeaud

et al. 2023

Preprint

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Background: Global warming is a major challenge for plant survival and growth. Understanding the molecular mechanisms by which higher plants sense and adapt to upsurges in the ambient temperature, is essential for developing strategies to enhance plant tolerance to heat stress. Here, we designed a special heat-responsive Arabidopsis thaliana reporter line that allowed an in-depth investigation of the mechanisms underlying the accumulation of protective heat-shock proteins (HSPs) in response to high temperature. Methods: A transgenic Arabidopsis thaliana reporter line named "Heat-Inducible Bioluminescence And Toxicity" (HIBAT) was designed to express from a conditional heat-inducible promoter, a fusion gene encoding for nanoluciferase and D-amino acid oxidase, whose expression was found to be toxic only in the presence of D-valine. HIBAT seedlings were exposed to different heat treatments in presence or absence of D-valine and analyzed for survival rate, bioluminescence and HSP gene expression. Results: Whereas at 22C, HIBAT seedlings grew unaffected by D-valine, and all survived following iterative heat treatments without D-valine, 98% died following heat treatments on D-valine. The HSP17.3B promoter was highly specific to heat, as it remained unresponsive to various plant hormones, Flagellin, H2O2, osmotic stress and high salt. Confirming that HIBAT does not significantly differ from its Col-0 parent, RNAseq analysis of heat-treated seedlings showed a strong correlation between the two lines. Using HIBAT, a forward genetic screen revealed candidate loss-of-function mutants defective either at accumulating HSPs at high temperature or at repressing HSP accumulation at low, non-heat-shock temperatures. Conclusion: This study adds insights into the molecular mechanisms by which higher plants sense and adapt to rapid elevations of ambient temperatures. HIBAT was valuable tool to identify Arabidopsis mutants defective in the response to high temperature stress. Our findings open new avenues for future research on the regulation of HSP expression and understanding their role in the onset of plant acquired thermotolerance

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“…Finally, PROVEAN (PROtein Variant Effect ANalyzer) v1.1.5 [60], SIFT4G [61] and PPVED [62] predicted whether an amino acid substitution affected protein function.…”

Section: Gomentioning

confidence: 99%

A chromosome-level genome assembly ofSolanum chilense, a tomato wild relative associated with resistance to salinity and drought

Molitor,

Kurowski,

Fidalgo de Almeida

et al. 2023

Preprint

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Solanum chilenseis a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. In this study we generated a high-quality, chromosome-level,de novoassembly for theS. chilenseaccession LA1972 using a hybrid assembly strategy with ∼180 Gbp of Illumina short reads and ∼50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium® reads. The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ∼219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for ade novotranscriptome assembly. This chromosome-level, high-quality reference genome forS. chilenseaccession LA1972 will support future breeding efforts for more sustainable tomato production. Gene sequences related to drought and salt resistance were compared betweenS. chilenseandS. lycopersicumto identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1andethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.

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PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants

Cited by 13 publications

References 87 publications

ABA‐inducible DEEPER ROOTING1 improves adaptation of maize to water deficiency

ABA‐inducible DEEPER ROOTING1 improves adaptation of maize to water deficiency

Design of anArabidopsis thalianareporter line to detect heat-sensing and signaling mutants

A chromosome-level genome assembly ofSolanum chilense, a tomato wild relative associated with resistance to salinity and drought

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