Article
Biochemical Research Methods
Inigo Saiz-Fernandez, Martin Cerny, Jan Skalak, Bretislav Brzobohaty
Summary: The study optimized a method for establishing split-root systems in young Arabidopsis thaliana seedlings, finding that partial de-rooting is less stressful and can be used in drought experiments. Additionally, the system allows for applying water-soluble compounds with minimal effects of rehydration.
Review
Plant Sciences
Julia Mergner, Bernhard Kuster
Summary: Proteins play essential roles in cellular processes, and studying protein expression, interactions, and modifications is crucial for understanding the molecular mechanisms underlying plant phenotypes. Mass spectrometry technology allows for the global identification and quantification of thousands of proteins, revealing dynamic changes in the plant proteome.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Plant Sciences
R. Glen Uhrig, Sira Echevarria-Zomeno, Pascal Schlapfer, Jonas Grossmann, Bernd Roschitzki, Niklas Koerber, Fabio Fiorani, Wilhelm Gruissem
Summary: The study reports the changes in the Arabidopsis leaf rosette proteome and phosphoproteome during the diurnal cycle, indicating proteins involved in nitrogen and hormone metabolism undergo simultaneous changes in protein abundance and phosphorylation status. The phosphoproteome at light-dark transitions reveals dynamic changes at phosphorylation sites.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Developmental Biology
Yingzhang Huang, Limeng Zhou, Chunhui Hou, Dianjing Guo
Summary: This study reveals the proteome landscape of Arabidopsis early embryogenesis through nanoproteomic analysis, and identifies gene enrichment related to ribosome biogenesis and auxin signaling. The positive correlation between mRNA and protein is confirmed by integrating RNA-sequencing data. This work provides valuable insights for further investigation into plant embryo development.
Article
Plant Sciences
Mohamed Ayash, Mohammad Abukhalaf, Domenika Thieme, Carsten Proksch, Mareike Heilmann, Martin Hartmut Schattat, Wolfgang Hoehenwarter
Summary: The plant nucleus, despite its importance in genetic information and gene expression, has been understudied. In this study, nuclear proteome fractions from Arabidopsis thaliana cells treated with two elicitors of plant immunity were analyzed. The research revealed potential nuclear protein import upon elicitation of immunity and changes in protein abundance in the nucleus related to plant immunity processes. Promiscuous ribosome assembly and the role of prohibitins and cytochrome C in plant immune responses were also highlighted.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Yanmei Chen, Yi Wang, Jun Yang, Wenbin Zhou, Shaojun Dai
Summary: This paper reviews recent breakthroughs and strategies in unraveling the diversity of the plant proteome, focusing on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. It also discusses PTM crosstalk, multiple PTMs temporally regulating protein life cycles, quantitative studies using MS to measure protein turnover rates, and future directions in the study of the plant proteome.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Myung-Shin Kim, Seung-Won Lee, Kibum Kim, Yerin Kim, Hyunjoo Hwang, Peter Hinterdorfer, Doil Choi, Kisung Ko
Summary: Transgenic plants are a promising strategy for producing valuable biotherapeutic proteins, but optimization of codon sequences and expression cassette elements is necessary. This study utilized single-cell RNA sequencing to analyze the expression pattern of a llama antibody in transgenic tobacco leaves, providing a foundation for selecting the best cell types or tissues for high production.
Editorial Material
Biochemistry & Molecular Biology
Mary E. Byrne
Summary: The variation in leaf shapes is determined by an evolutionary genetic pathway that modifies shape through regulating regional growth in the developing leaf.
Article
Plant Sciences
Amanda L. Smythers, Nikita Bhatnagar, Chien Ha, Parinita Majumdar, Evan W. McConnell, Boominathan Mohanasundaram, Leslie M. Hicks, Sona Pandey
Summary: This study investigates the role of reversible protein oxidation in plant stress response and identifies a complex network of reversible oxidations associated with ABA and G-protein signaling. The findings indicate that functional G-proteins are required to maintain intracellular redox homeostasis and fully execute plant stress responses.
Article
Biochemistry & Molecular Biology
Ana Jurado-Flores, Cecilia Gotor, Luis C. C. Romero
Summary: Hydrogen sulfide (H2S) functions as a signaling molecule in plants, bacteria, and mammals, regulating various physiological and pathological processes. This study investigated the regulation of protein persulfidation and found that the persulfidation profile of proteins in leaves changed under different growth conditions such as light regimen and carbon deprivation. Different proteins were found to be persulfidated between light and dark conditions, with pathways related to protein folding and processing being enriched in the dark and proteasome and ubiquitin-dependent processes being affected under light conditions. Carbon starvation led to a reduction in persulfidation of proteins involved in metabolic processes and sulfur assimilation.
Article
Biochemistry & Molecular Biology
Przemyslaw Kopec, Marta Hornyak, Jakub Pastuszak, Anna Szczerba, Marcin Rapacz, Jacek Waga, Agnieszka Plazek
Summary: Proteomic changes in common buckwheat under high temperature stress varied between accessions and their organs, with 15 heat-affected proteins common to both accessions. Indole-3-glycerol phosphate synthase was identified as a potential marker of heat sensitivity in buckwheat plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Ling Pan, Miroslav Berka, Martin Cerny, Jan Novak, Marketa Luklova, Bretislav Brzobohaty, Inigo Saiz-Fernandez
Summary: This study reveals the effects of cytokinin (CK) deficiency on the proteomic and metabolomic responses of flg22-triggered immunity. It shows that CK deficiency alters the plant defense response, particularly through the induction of callose deposition, upregulation of defense-related proteins, increased amino acid biosynthesis, and regulation of plant photosynthesis. The study also suggests that jasmonic acid (JA) may play an important role in the immune response of plants deficient in CKs.
Article
Plant Sciences
Bowen Chen, Changrong Li, Yingying Chen, Shengkan Chen, Yufei Xiao, Qi Wu, Lianxiang Zhong, Kaiyong Huang
Summary: The study identified proteins involved in early somatic embryogenesis (SE) of two Eucalyptus species, and highlighted potential regulatory networks related to high regeneration potential in Eucalyptus.
Article
Biochemistry & Molecular Biology
Xuemei Zhang, Bowen Tan, Zihan Cheng, Dan Zhu, Tingbo Jiang, Sixue Chen
Summary: The McHB7 gene in ice plant enhances the salt tolerance by regulating the changes in proteins and metabolites, resulting in increased photosynthesis efficiency and chlorophyll content. Additionally, McHB7 also modulates the expression of stress-related proteins to scavenge reactive oxygen species and enhance plant salt tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Brandon G. Roy, Stacy DeBlasio, Yong Yang, Theodore Thannhauser, Michelle Heck, Marc Fuchs
Summary: We investigated changes in the proteome and transcriptome of Nicotiana benthamiana plants infected by grapevine fanleaf virus (GFLV) with an emphasis on vein clearing symptom development. Comparative analyses of plants infected by wildtype GFLV strains and their mutant strains identified host biochemical pathways involved in viral symptom development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Editorial Material
Biochemistry & Molecular Biology
Setsuko Komatsu, Jesus V. Jorrin-Novo
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Bonoso San-Eufrasio, Ezequiel Dario Bigatton, Victor M. Guerrero-Sanchez, Palak Chaturvedi, Jesus V. Jorrin-Novo, Maria-Dolores Rey, Maria Angeles Castillejo
Summary: The study aimed to identify potential markers for drought tolerance in holm oak by analyzing proteins and derived peptides. A total of 30 proteins and 46 peptides related to redox, stress, synthesis, folding, degradation, and metabolism were identified in drought experiments on seedlings from four different provenances. Two proteins, subtilisin and chaperone GrpE protein, showed increased levels in three populations, making them promising markers for validation in future experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jose Valero-Galvan, Raquel Gonzalez-Fernandez, Jesus V. Jorrin-Novo
Summary: This study evaluated the nutritional composition of Quercus virginiana seeds and compared it with three Mediterranean Quercus species. The results showed that Quercus virginiana seeds had smaller size and weight but higher sugar and total lipid content. Additionally, Quercus coccifera seeds exhibited outstanding levels of phenolics and flavonoids and antioxidant activity.
Article
Multidisciplinary Sciences
Antonio Rafael Sanchez-Rodriguez, Maria-Dolores Rey, Hasna Nechate-Drif, Maria Angeles Castillejo, Jesus Jorrin-Novo, Jose Torrent, Maria Carmen del Campillo, Daniel Sacristan
Summary: The joint application of phosphorus and zinc promoted the translocation of these nutrients to grains, significantly increasing aboveground dry matter and grain zinc content in maize plants grown on Mediterranean soils. On the other hand, individual application of phosphorus or zinc might reduce aboveground dry matter and yield at harvest, leading to changes in grain quality-related proteins.
SCIENTIFIC REPORTS
(2021)
Review
Forestry
Monica Escandon, Maria Angeles Castillejo, Jesus V. Jorrin-Novo, Maria-Dolores Rey
Summary: The genus Quercus, comprising around 500 species of oak trees, is threatened by environmental cues of biotic or abiotic origin. Biotechnology plays a crucial role in proposing sustainable management and conservation strategies for forests, with a focus on exploiting natural diversity and selecting more resilient genotypes. Research on molecular mechanisms of stress tolerance and resistance, as well as the identification of related genes and metabolites, is being carried out using omics approaches integrated with physiological and morphological techniques.
Article
Plant Sciences
K. Crisostomo-Ayala, M. Hernandez de la Torre, M. A. Pedreno, J. A. Hernandez, C. Perez, E. Bustos, M. Sanchez-Olate, D. Rios
Summary: Aristotelia chilensis, a species endemic to Chile, showed the best photosynthetic performance in spring and summer with higher photosynthetically active radiation. Total phenol content and antioxidant activity were influenced by season and leaf type. Morphological adaptations were observed in apical leaves throughout the year.
BIOLOGIA PLANTARUM
(2021)
Article
Biochemistry & Molecular Biology
Karel Vives Hernandez, Jordi Moreno-Romero, Martha Hernandez de la Torre, Claudia Perez Manriquez, Darcy Rios Leal, Jaime F. Martinez-Garcia
Summary: The study compared the content of stevioside and rebaudioside A in two commonly used S. rebaudiana cultivars, Morita II and Criolla, finding significant differences between them. Enhanced expression of three genes involved in SG biosynthesis in Morita II may contribute to its higher accumulation of rebaudioside A. Light conditions can affect SG accumulation, with higher light intensity leading to increased expression of biosynthetic genes and higher levels of stevioside and rebaudioside A.
Article
Chemistry, Applied
Ariadna Lopez-Rodriguez, Martha Hernandez, Adrian Carrillo-Galvez, Jose Becerra, Victor Hernandez
Summary: Despite its worldwide relevance as an invasive plant, there are few studies on the allelopathic activity of Ulex europaeus (gorse). This study analyzed the allelochemical profile of gorse and its phytotoxic effects on Lactuca sativa germination. The results showed that the methanolic extract of gorse roots inhibited seed germination at a certain concentration. The presence of antimicrobial, antioxidant, and cytotoxic compounds in gorse could explain its superiority as an invader in the Chilean ecosystem.
NATURAL PRODUCT RESEARCH
(2023)
Article
Forestry
Marta Tienda-Parrilla, Cristina Lopez-Hidalgo, Victor M. Guerrero-Sanchez, Alvaro Infantes-Gonzalez, Rocio Valderrama-Fernandez, Maria-Angeles Castillejo, Jesus Jorrin-Novo, Maria-Dolores Rey
Summary: The effect and responses to drought stress were analyzed in Quercus ilex L. seedlings using a nontargeted metabolomic approach. Potential mechanisms and molecular markers of drought tolerance were identified, and putative bioactive compounds were characterized.
Article
Green & Sustainable Science & Technology
Sofiene B. M. Hammami, Sami Chaari, Narjes Baazaoui, Riadh Drira, Noureddine Drira, Karim Aounallah, Asma Maazoun, Zied Antar, Jesus V. Jorrin Novo, Taoufik Bettaieb, Hava F. Rapoport, Besma Sghaier-Hammami
Summary: The date palm, a tolerant fruit species to salt stress, shows the ability to exclude chloride ions and adjust biomass allocation according to stress levels. Both leaves and roots play important roles in this tolerance strategy.
Article
Plant Sciences
Manuel Salas-Moreno, Maria Angeles Castillejo, Erika Rodriguez-Cavallo, Jose Marrugo-Negrete, Dario Mendez-Cuadro, Jesus Jorrin-Novo
Summary: Changes in the proteome of P. fasciculatum leaves under different Cd stress conditions were identified, including proteins associated with carbohydrate and energy metabolism, photosynthesis, protein structure, transport and metabolism, antioxidant stress and defense, RNA and DNA processing, and signal transduction.
Article
Plant Sciences
Victor M. Guerrero-Sanchez, Cristina Lopez-Hidalgo, Maria-Dolores Rey, Maria Angeles Castillejo, Jesus Jorrin-Novo, Monica Escandon
Summary: The integrated analysis of different omic layers can provide new knowledge and validate regulatory mechanisms of gene expression. This study validated the application of this approach to non-model species and identified the key roles of protein homeostasis and transcriptional control in the early response to drought.
Review
Forestry
Noor Muhammad, Maria Angeles Castillejo, Maria-Dolores Rey, Jesus V. Jorrin-Novo
Summary: This article introduces the formation of broad-leaved evergreen forests by Quercus spp. in the Hindu Kush and Himalayan regions of Pakistan. Seven species of Quercus genus have been identified, but they have received little attention in terms of their economic value and bioactivity evaluation. Quercus spp. show promise for commercial applications, but are currently threatened by human activities and climate change. This review highlights the importance of these forgotten species and discusses various aspects of their distribution, morphology, traditional uses, phytochemical constituents, and threats. The lack of molecular studies on populations of these species in Pakistan is a critical gap that needs to be addressed for conservation and management strategies. Future research directions in molecular approaches for Quercus are also discussed.
Article
Agronomy
Jose G. Vazquez-Garcia, Joel Torra, Candelario Palma-Bautista, Fernando Bastida, Ricardo Alcantara-de la Cruz, Joao Portugal, Jesus V. Jorrin-Novo, Rafael De Prado
Summary: In recent decades, direct sowing in cereal agriculture in Spain has led to increased use of herbicides, such as glyphosate, and the emergence of weedy species from the genus Avena. This study taxonomically characterized different accessions of Avena fatua, Avena byzantina, and Avena sterilis and found that one A. fatua accession had evolved resistance to glyphosate. The study also revealed that A. byzantina and A. sterilis had low susceptibility to glyphosate and showed limited foliar uptake and movement of the herbicide. Enzyme activity and affinity measurements suggested that a non-target site mechanism may be involved in glyphosate susceptibility differences.
Review
Biochemical Research Methods
J. Jorrin Novo
Summary: This review presents the author's opinion on proteomics, its application to plant biology, and translation to biotechnology. Proteomics sheds light on plant biological processes and can be applied to areas such as food traceability and allergen detection. Researchers should validate and optimize proteomics data, avoiding blindly accepting results.
EXPERT REVIEW OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)
