Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Cruz, Edward R.; Nguyen, Hung Son; Nguyen, Tin; Wallace, Ian S.

doi:10.1111/tpj.14372

Cited by 42 publications

(26 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…PTMs modulate several biological processes, such as photosynthesis, stress tolerance, and plant immunity (Guerra et al, 2015;Grabsztunowicz et al, 2017;Yin et al, 2019). Major limitations in PTM studies include identifying the link between an individual PTM and its corresponding functions in plant growth and development; only a few of these links have been characterized to date (Cruz et al, 2019). CRISPR targeting of specific PTM sites can be used to generate mutations, with the resulting phenotypic variations providing insight into PTM function (Arsova et al, 2018).…”

Section: Targeting Posttranslational Modificationsmentioning

confidence: 99%

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

et al. 2021

View full text Add to dashboard Cite

The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.

show abstract

Section: Targeting Posttranslational Modificationsmentioning

confidence: 99%

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Recently, an Arabidopsis thaliana proteome database was released examining gene expression and [protein] across organs [144] and development [145], but no such resource has been developed for abiotic stress response, making comparing this work across plant species di cult. It is also possible post-translational modi cations play an important role in NCED3 activity, but none are well described at this time [146]. To the best of the author's knowledge, no other study examining transcript, protein, and metabolite concentrations has been performed that includes NCED3 and ABA at this time.…”

Section: Nced3 Protein Concentration Was Not Changed By Wdmentioning

confidence: 99%

Abscisic Acid Metabolism in Leaves and Roots of Four Vitis Species in Response to Water Deficit

Toups¹,

Cochetel²,

Galdamez³

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Abscisic acid is a phytohormone involved in water deficit response. Abscisic acid metabolism is regulated by biosynthesis, conjugation, and catabolism. NCED3 is the rate limiting step of abscisic acid biosynthesis and is a key contributor to plant water deficit responses. In this study NCED3 transcript accumulation and abscisic acid metabolism were further characterized as key water deficit responses in four Vitis species (Vitis vinifera (Cabernet Sauvignon), Vitis champinii (Ramsey), Vitis riparia (Riparia Gloire), and Vitis vinifera x Vitis girdiana (SC2)) under three levels of water deficit in leaves and roots. Results: The concentrations of abscisic acid and derivative metabolites increased with water deficit and was dependent upon the species. RNA-Seq and RT-qPCR data were consistent with the changes in abscisic acid metabolite concentrations; the corresponding transcript abundances substantiate NCED3 as a key gene in the water deficit response; however, NCED3 protein concentrations assayed in Western Blots were not affected. Major differences in abscisic acid metabolism at the gene, protein, and metabolite levels were detected between leaves and roots in these four species. NCED3 transcript abundance and abscisic acid concentration in drought-tolerant Ramsey increased earlier and more significantly than the other species during long-term, moderate to severe water deficits but were not stimulated as much by short-term, rapid dehydration. In drought-sensitive Riparia, NCED3 transcript abundance and abscisic acid metabolite concentrations increased to a lower extent than in Ramsey during moderate to severe water deficits, but short-term rapid dehydration induced a significantly higher abscisic acid concentration in Riparia than Ramsey. Conclusions: Grapevine species have distinct abscisic acid metabolism that depends highly on the severity and duration of stress and organ (leaves or roots). This study confirms that abscisic acid metabolism and NCED3 are part of a core water deficit response in Vitis species. Relative quantities of transcripts, proteins, abscisic acid and derivative metabolites were determined, but many aspects of abscisic acid metabolism and water deficit responses warrant additional investigation. This study provides a better understanding of how Vitis is adapted to dry environments, which may be exploited for future breeding programs.

show abstract

“…Post-translational protein modification plays a very important role in living organisms. It makes proteins more complex in structure, more complete in function, more precise in regulation and more specific in function (Cruz et al, 2019). Common post-translational modifications of proteins include ubiquitination, phosphorylation, glycosylation, methylation, acetylation and so on (Wang and Wang, 2019).…”

Section: Introductionmentioning

confidence: 99%

Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination

et al. 2020

View full text Add to dashboard Cite

Ubiquitylation is a form of post-translational modification of proteins that can alter localization, functionality, degradation, or transcriptional activity within a cell. E2 ubiquitin-conjugating enzyme (UBC) and E3 ubiquitin ligases are the primary determinants of substrate specificity in the context of ubiquitin conjugation. Multiubiquitination modifies target proteins for 26S proteasome degradation, while monoubiquitination controls protein activation and localization. At present, research on the monoubiquitination, especially histone monoubiquitination, has mostly focused on model plants with relatively few on crop species. In this study, we identified 91 UBC-like genes in soybean. The chromosomal localization, phylogenetic relationships, gene structures, and putative cis-acting elements were evaluated. Furthermore, the tissuespecific expression patterns of UBC Class I genes under drought stress were also investigated. Among Class I genes, GmUBC9 induction in response to drought stress was evident, and so this gene was selected for further analysis. GmUBC9 localized to the nucleus and endoplasmic reticulum. The overexpression of GmUBC9 in Arabidopsis led to enhanced tolerance for drought conditions across a range of stages of development, while overexpression in soybean hairy roots similarly led to improvements in tolerance for drought conditions, increased proline content, and reduced MDA content in soybean seedlings compared to wild type plants. HISTONE MONOUBIQUITINATION 2 (HUB2), an E3-like protein involved in histone H2B ubiquitylation (H2Bub1), was found to interact with GmUBC9 through Y2H analysis and BiFC assays in Arabidopsis and soybean. Under drought conditions, the level of H2Bub1 increased, and transcription of drought response genes was activated in GmUBC9 transgenic Arabidopsis and soybean. In addition, GmUBC9 transgenic Arabidopsis and soybean showed a late-flowering phenotype and

show abstract

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Cited by 42 publications

References 56 publications

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

Abscisic Acid Metabolism in Leaves and Roots of Four Vitis Species in Response to Water Deficit

Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination

Contact Info

Product

Resources

About