Pub Date : 2025-08-15Epub Date: 2025-06-27DOI: 10.1016/j.jprot.2025.105486
Hanne De Rijcke , An Staes , Stefaan De Smet , Marc Heyndrickx , Sam Millet , Leander Meuris , Devos SImon , Kris Gevaert , Christof Van Poucke
In this study, we evaluated the effects of experimenter handling and batch effects on proteomic analyses of mucosal scrapings in pigs. We analyzed mucosal samples from twelve piglets that were fed two distinct diets. Mucosal samples were obtained from a 60 cm segment collected from the jejunum, which was divided into six equal segments. Scrapings were collected by two experimenters, who each handled three of the six segments per pig. Both experimenters were given the exact same instructions for performing the mucosal scrapings. Samples were then randomized and processed in two separate groups on different days to examine batch effects. Protein extraction and digestion was carried out using Midi S-Traps (ProtiFi) and peptides were analyzed by DIA-MS. Data processing and statistical analysis were performed using DIA-NN and RStudio. Our analyses revealed no significant experimenter effects, but we observed small batch effects across datasets. Our findings emphasize the importance of standardized protocols to minimize experimenter-induced variability and the necessity of correcting for batch effects during data analysis. Our study provides a framework for minimizing unwanted variability in future proteomic studies, ensuring more reliable and reproducible findings.
Significance
With this study, we aimed to contribute to the improvement of the reliability and reproducibility of proteomic analyses in intestinal mucosal research. By systematically evaluating the effects of experimenter handling and batch processing on mucosal scraping samples, the study highlights key sources of variability that can influence proteomic outcomes. While experimenter effects were minimal, the identification of batch effects underscores the necessity of standardized protocols and appropriate corrections during data analysis. These findings provide a framework for minimizing unwanted variability in future studies, ultimately enhancing the accuracy of proteomic data interpretation and advancing research in intestinal health and disease.
{"title":"Collecting and analysing pig mucosal scraping samples for mass spectrometry-based proteomics: A study on factors causing variation in proteomic data","authors":"Hanne De Rijcke , An Staes , Stefaan De Smet , Marc Heyndrickx , Sam Millet , Leander Meuris , Devos SImon , Kris Gevaert , Christof Van Poucke","doi":"10.1016/j.jprot.2025.105486","DOIUrl":"10.1016/j.jprot.2025.105486","url":null,"abstract":"<div><div>In this study, we evaluated the effects of experimenter handling and batch effects on proteomic analyses of mucosal scrapings in pigs. We analyzed mucosal samples from twelve piglets that were fed two distinct diets. Mucosal samples were obtained from a 60 cm segment collected from the jejunum, which was divided into six equal segments. Scrapings were collected by two experimenters, who each handled three of the six segments per pig. Both experimenters were given the exact same instructions for performing the mucosal scrapings. Samples were then randomized and processed in two separate groups on different days to examine batch effects. Protein extraction and digestion was carried out using Midi S-Traps (ProtiFi) and peptides were analyzed by DIA-MS. Data processing and statistical analysis were performed using DIA-NN and RStudio. Our analyses revealed no significant experimenter effects, but we observed small batch effects across datasets. Our findings emphasize the importance of standardized protocols to minimize experimenter-induced variability and the necessity of correcting for batch effects during data analysis. Our study provides a framework for minimizing unwanted variability in future proteomic studies, ensuring more reliable and reproducible findings.</div></div><div><h3>Significance</h3><div>With this study, we aimed to contribute to the improvement of the reliability and reproducibility of proteomic analyses in intestinal mucosal research. By systematically evaluating the effects of experimenter handling and batch processing on mucosal scraping samples, the study highlights key sources of variability that can influence proteomic outcomes. While experimenter effects were minimal, the identification of batch effects underscores the necessity of standardized protocols and appropriate corrections during data analysis. These findings provide a framework for minimizing unwanted variability in future studies, ultimately enhancing the accuracy of proteomic data interpretation and advancing research in intestinal health and disease.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105486"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144518894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-01DOI: 10.1016/j.jprot.2025.105467
Binjie Qi , Haifeng Dou , Wei Liu , E. Andrew Bennett , Huiyun Rao , Yimin Yang
Eggshells are significant cultural symbols linked to funeral customs and social development. Identifying their species is crucial in archaeological research. However, their small fragment size makes eggshells difficult to accurately identify using traditional methods. Recent mass spectrometry advances have significantly enhanced eggshell species identification in archaeological research, but their success remains limited. For example, Anser cygnoides and Anser anser eggshells cannot yet be reliably distinguished. This paleoproteomic study uses Zooarchaeology by Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry to identify by proteotyping the species of eggshells from the Xitou site in China. We established a series of peptide markers and amino acid variants to distinguish A. cygnoides from A. anser, and with this method attribute three Xitou eggshell specimens to the graylag goose. Carbon isotope analysis and shell thickness measurements were conducted to understand the domestication of the geese associated with these eggshells. The isotope results indicate that these geese primarily ate C3 plants, and shell thickness results suggest they were possibly domesticated. These findings firstly provide direct molecular evidence of possibly domesticated graylag geese in China and offer new insights into poultry domestication and cultural practices.
Significance
Combing ZooMS and LC-MS/MS analysis, we have identified novel peptide markers to distinguish the eggshells of swan goose (Anser cygnoides) from those of graylag goose (Anser anser). Using a series of ZooMS markers and amino acid variations, the eggshells from Xitou site (north China) were identified to be derived from graylag goose. Further eggshells thickness and isotope analysis show that these geese were likely domesticated and primarily fed on C3 plants, offering valuable insights into early geese farming and sustainable practices during the Western Zhou period. Furthermore, the discovery of eggs as burial items highlights the important role that geese played in ancient Chinese culture and rituals.
{"title":"Differentiating goose eggshells through proteomics: A case study from Xitou, North China","authors":"Binjie Qi , Haifeng Dou , Wei Liu , E. Andrew Bennett , Huiyun Rao , Yimin Yang","doi":"10.1016/j.jprot.2025.105467","DOIUrl":"10.1016/j.jprot.2025.105467","url":null,"abstract":"<div><div>Eggshells are significant cultural symbols linked to funeral customs and social development. Identifying their species is crucial in archaeological research. However, their small fragment size makes eggshells difficult to accurately identify using traditional methods. Recent mass spectrometry advances have significantly enhanced eggshell species identification in archaeological research, but their success remains limited. For example, <em>Anser cygnoides</em> and <em>Anser anser</em> eggshells cannot yet be reliably distinguished. This paleoproteomic study uses Zooarchaeology by Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry to identify by proteotyping the species of eggshells from the Xitou site in China. We established a series of peptide markers and amino acid variants to distinguish <em>A. cygnoides</em> from <em>A. anser</em>, and with this method attribute three Xitou eggshell specimens to the graylag goose. Carbon isotope analysis and shell thickness measurements were conducted to understand the domestication of the geese associated with these eggshells. The isotope results indicate that these geese primarily ate C<sub>3</sub> plants, and shell thickness results suggest they were possibly domesticated. These findings firstly provide direct molecular evidence of possibly domesticated graylag geese in China and offer new insights into poultry domestication and cultural practices.</div></div><div><h3>Significance</h3><div>Combing ZooMS and LC-MS/MS analysis, we have identified novel peptide markers to distinguish the eggshells of swan goose (<em>Anser cygnoides</em>) from those of graylag goose (<em>Anser anser</em>). Using a series of ZooMS markers and amino acid variations, the eggshells from Xitou site (north China) were identified to be derived from graylag goose. Further eggshells thickness and isotope analysis show that these geese were likely domesticated and primarily fed on C<sub>3</sub> plants, offering valuable insights into early geese farming and sustainable practices during the Western Zhou period. Furthermore, the discovery of eggs as burial items highlights the important role that geese played in ancient Chinese culture and rituals.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105467"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-19DOI: 10.1016/j.jprot.2025.105483
Rafael F. Castelli , Haroldo C. de Oliveira , Marlon D.M. Santos , Amanda C. Camillo-Andrade , Flavia C.G. Dos Reis , Paulo C. Carvalho , Marcio L. Rodrigues
In the fungus Cryptococcus neoformans, the aminophospholipid translocase 1 (Apt1) flippase plays roles in virulence, membrane architecture, and extracellular vesicle (EV) polysaccharide cargo. The effect of APT1 deletion on the fungal proteome is unknown, limiting the understanding of its functions in physiology. The APT gene family also includes APT2, whose functions in C. neoformans are virtually unknown. We investigated the impact of APT1 and APT2 deletion on EV formation in C. neoformans. The absence of Apt1, but not Apt2, led to a decreased concentration of the polysaccharide glucuronoxylomannan in EVs. We characterized the EV and cellular proteomes of C. neoformans mutants lacking APT1 and APT2, comparing them to the proteomes of wild-type (WT) cells. Paired comparisons revealed that WT and mutant EVs shared a significant part of their cargo but showed several strain-specific molecules and exhibited major differences in the abundance of various proteins. Conversely, the cellular proteomes of both mutants largely overlapped with WT (95.4 % shared proteins. Protein network analyses highlighted mutant-specific shifts: the apt1Δ/apt2Δ proteomes converged on secondary metabolite biosynthesis and RNA metabolism clusters, diverging from the predominance of translation in WT cells. These findings establish APT1 and APT2 as key regulators of EV composition in C. neoformans.
Significance
Our study reveals that the aminophospholipid translocase 1 (Apt1) and aminophospholipid translocase 2 (Apt2) play distinct roles in the physiology of Cryptococcus neoformans, particularly in the formation and composition of extracellular vesicles (EVs). By demonstrating that Apt1 deletion alters the proteomic landscape and reduces glucuronoxylomannan levels in EVs, while Apt2 deletion has no such effect, our findings provide critical insights into the functional divergence of these flippases. These insights underscore the potential of Apt1, but not necessarily Apt2, as therapeutic targets for developing novel antifungal strategies against this significant human pathogen.
{"title":"The flippases Apt1 and Apt2 differentially influence extracellular vesicle cargo and polysaccharide secretion in Cryptococcus neoformans","authors":"Rafael F. Castelli , Haroldo C. de Oliveira , Marlon D.M. Santos , Amanda C. Camillo-Andrade , Flavia C.G. Dos Reis , Paulo C. Carvalho , Marcio L. Rodrigues","doi":"10.1016/j.jprot.2025.105483","DOIUrl":"10.1016/j.jprot.2025.105483","url":null,"abstract":"<div><div>In the fungus <em>Cryptococcus neoformans</em>, the aminophospholipid translocase 1 (Apt1) flippase plays roles in virulence, membrane architecture, and extracellular vesicle (EV) polysaccharide cargo. The effect of <em>APT1</em> deletion on the fungal proteome is unknown, limiting the understanding of its functions in physiology. The <em>APT</em> gene family also includes <em>APT2</em>, whose functions in <em>C. neoformans</em> are virtually unknown. We investigated the impact of <em>APT1</em> and <em>APT2</em> deletion on EV formation in <em>C. neoformans</em>. The absence of Apt1, but not Apt2, led to a decreased concentration of the polysaccharide glucuronoxylomannan in EVs. We characterized the EV and cellular proteomes of <em>C. neoformans</em> mutants lacking <em>APT1</em> and <em>APT2</em>, comparing them to the proteomes of wild-type (WT) cells. Paired comparisons revealed that WT and mutant EVs shared a significant part of their cargo but showed several strain-specific molecules and exhibited major differences in the abundance of various proteins. Conversely, the cellular proteomes of both mutants largely overlapped with WT (95.4 % shared proteins. Protein network analyses highlighted mutant-specific shifts: the <em>apt1Δ/apt2Δ</em> proteomes converged on secondary metabolite biosynthesis and RNA metabolism clusters, diverging from the predominance of translation in WT cells. These findings establish <em>APT1</em> and <em>APT2</em> as key regulators of EV composition in <em>C. neoformans</em>.</div></div><div><h3>Significance</h3><div>Our study reveals that the aminophospholipid translocase 1 (Apt1) and aminophospholipid translocase 2 (Apt2) play distinct roles in the physiology of <em>Cryptococcus neoformans</em>, particularly in the formation and composition of extracellular vesicles (EVs). By demonstrating that Apt1 deletion alters the proteomic landscape and reduces glucuronoxylomannan levels in EVs, while Apt2 deletion has no such effect, our findings provide critical insights into the functional divergence of these flippases. These insights underscore the potential of Apt1, but not necessarily Apt2, as therapeutic targets for developing novel antifungal strategies against this significant human pathogen.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105483"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-03DOI: 10.1016/j.jprot.2025.105470
Julia Lautenbach , Qussai Abbas , Sarah Brajkovic , Tobias Sieberer , Michael Neumüller , Bernhard Kuster , Brigitte Poppenberger
Anthocyanins are colorful plant pigments with antioxidant properties, and a diet rich in these flavonoids bears health benefits. Therefore, a strong anthocyanin accumulation in edible plant parts is of significant interest, and in Malus domestica, the domesticated apple, certain red-fleshed apple varieties exhibit this trait. Enhanced anthocyanin accumulation in the flesh of apple fruits is attributed to the hyperactivation of the MYB transcription factor MdMYB10, which acts as a key regulator of anthocyanin biosynthesis by inducing the expression of multiple biosynthetic genes. While several studies have explored the underlying genetic mutations and resulting transcriptome changes, there is a lack of research on proteome alterations that cause the red-fleshed apple phenotype. To address this gap, a mass spectrometry-based proteomics approach was employed. Comparative proteomics identified differentially abundant proteins in young and mature fruits of the red-fleshed ‘Bay13645’ variety compared to the white-fleshed ‘Gala’. Whereas several MYB transcription factors were enriched during early fruit development, they were no longer among the hyper-abundant proteins in ripe fruits of the red-fleshed genotype. In contrast, anthocyanin biosynthetic enzymes were enriched more strongly in ripe fruits of the red-fleshed cultivar, supporting previous results which had indicated developmental stage-specific differences in the control of the pigmentation process. The proteomic approach also identified novel regulatory factors and enzymes that may contribute to the red-fleshed apple phenotype, including a BAHD acyltransferase, Mal d proteins, and transcription factors of diverse families, and their potential relevance for the exhibition of this trait is discussed.
Significance
This study offers insights into the molecular mechanisms driving anthocyanin accumulation in red-fleshed apples. Utilizing a mass spectrometry-based proteomics strategy, the study reveals proteome alterations during fruit development that underlie the red-fleshed phenotype in Malus domestica. Notably, key enzymes of anthocyanin biosynthesis were markedly upregulated, underscoring their role in the pigmentation of the apple fruit pulp. Importantly, the study also identifies previously uncharacterized proteins, including a BAHD acyltransferase and a suite of transcription factors, shedding new light on the regulatory network orchestrating anthocyanin accumulation. These findings significantly expand our understanding of metabolic pathways that contribute to fruit pigmentation and open promising avenues for targeted crop improvement.
{"title":"Unraveling the proteomic landscape of red-fleshed apples to identify regulators of anthocyanin accumulation","authors":"Julia Lautenbach , Qussai Abbas , Sarah Brajkovic , Tobias Sieberer , Michael Neumüller , Bernhard Kuster , Brigitte Poppenberger","doi":"10.1016/j.jprot.2025.105470","DOIUrl":"10.1016/j.jprot.2025.105470","url":null,"abstract":"<div><div>Anthocyanins are colorful plant pigments with antioxidant properties, and a diet rich in these flavonoids bears health benefits. Therefore, a strong anthocyanin accumulation in edible plant parts is of significant interest, and in <em>Malus domestica</em>, the domesticated apple, certain red-fleshed apple varieties exhibit this trait. Enhanced anthocyanin accumulation in the flesh of apple fruits is attributed to the hyperactivation of the MYB transcription factor MdMYB10, which acts as a key regulator of anthocyanin biosynthesis by inducing the expression of multiple biosynthetic genes. While several studies have explored the underlying genetic mutations and resulting transcriptome changes, there is a lack of research on proteome alterations that cause the red-fleshed apple phenotype. To address this gap, a mass spectrometry-based proteomics approach was employed. Comparative proteomics identified differentially abundant proteins in young and mature fruits of the red-fleshed ‘Bay13645’ variety compared to the white-fleshed ‘Gala’. Whereas several MYB transcription factors were enriched during early fruit development, they were no longer among the hyper-abundant proteins in ripe fruits of the red-fleshed genotype. In contrast, anthocyanin biosynthetic enzymes were enriched more strongly in ripe fruits of the red-fleshed cultivar, supporting previous results which had indicated developmental stage-specific differences in the control of the pigmentation process. The proteomic approach also identified novel regulatory factors and enzymes that may contribute to the red-fleshed apple phenotype, including a BAHD acyltransferase, Mal d proteins, and transcription factors of diverse families, and their potential relevance for the exhibition of this trait is discussed.</div></div><div><h3>Significance</h3><div>This study offers insights into the molecular mechanisms driving anthocyanin accumulation in red-fleshed apples. Utilizing a mass spectrometry-based proteomics strategy, the study reveals proteome alterations during fruit development that underlie the red-fleshed phenotype in <em>Malus domestica</em>. Notably, key enzymes of anthocyanin biosynthesis were markedly upregulated, underscoring their role in the pigmentation of the apple fruit pulp. Importantly, the study also identifies previously uncharacterized proteins, including a BAHD acyltransferase and a suite of transcription factors, shedding new light on the regulatory network orchestrating anthocyanin accumulation. These findings significantly expand our understanding of metabolic pathways that contribute to fruit pigmentation and open promising avenues for targeted crop improvement.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105470"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144221333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-03DOI: 10.1016/j.jprot.2025.105471
Zhao-qun Wu , Chao-nan Guan , Ye-Bo Yang , Yue-Xuan Zhang , Meng-Yu Gai , Shi-Yi Wang , Xiu-Xing Zhang , Yu-Wen Wang , Jing Xue , Bo-Hao Duan , Hai-Ling Yang
Populus tomentosa hybrid poplar 741 is a superior tree species in northern China. Due to its rapid growth, high productivity, and range of available genetic tools, it has always been a focus of forestry research. The perennial genetically modified Populus 741, exhibiting sustained overexpression of PtoCYCD3;3, consistently shows adaxial curvature and pronounced surface wrinkling. The curvature of leaves holds great significance for forestry production systems. Moderate leaf curling can optimize the angle of light reception, thereby enhancing the efficiency of light absorption and photosynthetic performance, shortening the wood maturation cycle, and improving economic feasibility. Protein phosphorylation modification is a major regulatory mechanism in the cell cycle process. To investigate these morphological changes, TMT quantitative proteomics and phosphoproteomics were performed on leaves of transgenic and wild-type plants. Among 6005 identified proteins, 648 showed increased abundance, whereas 386 were reduced. In phosphoproteomics, 68 proteins exhibited differential phosphorylation, with 31 increasing and 37 decreasing. Quantitative proteomics identified significant changes in protein abundance associated with photosynthesis, phytohormones, and cell proliferation. Notably, histone deacetylase 6 (HDA6), ANGUSTIFOLIA (AN), and cellulose synthase-like (CSL) proteins associated with leaf curling were significantly upregulated in transgenic poplar. Phosphoproteomics revealed enrichment of proteins such as HERK1, DGK, OST1, and BIG, which are involved in brassinosteroid (BR), abscisic acid (ABA), and other phytohormone signaling pathways. These analyses demonstrated the impact of exogenous gene PtoCYCD3;3 integration on photosynthetic pathways, hormone signaling, and cell proliferation, highlighting its role in modulating leaf morphogenesis in perennial Populus 741.
Significance
Current assessments of the effects of exogenously introduced genes in Populus species are largely limited to short-term studies in annual or semiannual genetically modified specimens. In this study, we collected mature leaves from both perennial wild-type and transgenic 741 poplar trees and conducted comprehensive proteomic and phosphoproteomic analyses. The results not only revealed alterations in the abundance of multiple proteins associated with leaf curling but also elucidated key plant hormones and signaling pathways involved in leaf morphogenesis. These findings complement the signaling network involved in leaf morphogenesis and provide a novel perspective for studying perennial transgenic plants.
{"title":"Identification of crucial genes sustaining the curled leaf phenotype in perennial transgenic poplar via advanced proteomic and phosphoproteomic analyses","authors":"Zhao-qun Wu , Chao-nan Guan , Ye-Bo Yang , Yue-Xuan Zhang , Meng-Yu Gai , Shi-Yi Wang , Xiu-Xing Zhang , Yu-Wen Wang , Jing Xue , Bo-Hao Duan , Hai-Ling Yang","doi":"10.1016/j.jprot.2025.105471","DOIUrl":"10.1016/j.jprot.2025.105471","url":null,"abstract":"<div><div><em>Populus tomentosa</em> hybrid poplar <em>741</em> is a superior tree species in northern China. Due to its rapid growth, high productivity, and range of available genetic tools, it has always been a focus of forestry research. The perennial genetically modified <em>Populus 741</em>, exhibiting sustained overexpression of <em>PtoCYCD3;3</em>, consistently shows adaxial curvature and pronounced surface wrinkling. The curvature of leaves holds great significance for forestry production systems. Moderate leaf curling can optimize the angle of light reception, thereby enhancing the efficiency of light absorption and photosynthetic performance, shortening the wood maturation cycle, and improving economic feasibility. Protein phosphorylation modification is a major regulatory mechanism in the cell cycle process. To investigate these morphological changes, TMT quantitative proteomics and phosphoproteomics were performed on leaves of transgenic and wild-type plants. Among 6005 identified proteins, 648 showed increased abundance, whereas 386 were reduced. In phosphoproteomics, 68 proteins exhibited differential phosphorylation, with 31 increasing and 37 decreasing. Quantitative proteomics identified significant changes in protein abundance associated with photosynthesis, phytohormones, and cell proliferation. Notably, histone deacetylase 6 (HDA6), ANGUSTIFOLIA (AN), and cellulose synthase-like (CSL) proteins associated with leaf curling were significantly upregulated in transgenic poplar. Phosphoproteomics revealed enrichment of proteins such as HERK1, DGK, OST1, and BIG, which are involved in brassinosteroid (BR), abscisic acid (ABA), and other phytohormone signaling pathways. These analyses demonstrated the impact of exogenous gene <em>PtoCYCD3;3</em> integration on photosynthetic pathways, hormone signaling, and cell proliferation, highlighting its role in modulating leaf morphogenesis in perennial <em>Populus 741</em>.</div></div><div><h3>Significance</h3><div>Current assessments of the effects of exogenously introduced genes in <em>Populus</em> species are largely limited to short-term studies in annual or semiannual genetically modified specimens. In this study, we collected mature leaves from both perennial wild-type and transgenic <em>741</em> poplar trees and conducted comprehensive proteomic and phosphoproteomic analyses. The results not only revealed alterations in the abundance of multiple proteins associated with leaf curling but also elucidated key plant hormones and signaling pathways involved in leaf morphogenesis. These findings complement the signaling network involved in leaf morphogenesis and provide a novel perspective for studying perennial transgenic plants.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105471"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-06DOI: 10.1016/j.jprot.2025.105479
Qinghua Xing , Xinyi Tao , Qingping Hu , XiaoMeng Guo , Yingjie Zhang , Xinwei Mao , Haisheng Wang , Jun Li , Baisuo Zhao
N. thermophilus is the first true anaerobic halophilic alkalithermophile. It employs a unique dual mechanism for hypersaline adaptation, utilizing both “compatible solutes” and “salt in” strategies. However, the molecular mechanisms underlying its responses to alkaline pH and thermal stress remain poorly characterized. An iTRAQ-based quantitative proteomics analysis revealed that N. thermophilus used a cross and unique adaptation strategies to three individual extreme stresses. This study fills gaps by elucidating previously unexplored alkaline-specific regulatory processes. It also provides the first comprehensive analysis of its thermal adaptation mechanisms. In response to high-salt and alkaline stress, the organism shifts its metabolism toward glycolysis and pyruvate-derived acetate synthesis, helping to meet increased ATP demands. Heat shock proteins are up-regulated during both alkaline and thermal adaptations, reflecting the “No free lunch” principle. Alkaline pH uniquely induces DNA repair proteins and S-adenosylmethionine biosynthesis enzymes, promoting genomic stability in proton-deficient environments. Besides, the compact genome and the positive correlation between GC content with growth temperature may be also a lineage-specific thermal adaptation of the halophilic and alkalithermophilic order Natranaerobiales. These findings illuminate the layered adaptation strategies that help address cross-stress challenges. Meanwhile, stress-specific reconfigurations enhance flexibility for survival in individual extremes. This work provides novel insights into the survival mechanisms of polyextremophiles, as well as advancing their potential biotechnological applications.
Significance
Halophilic alkalithermophile N. thermophilus exemplify life's capacity to thrive in environments where multiple physicochemical extremes intersect. However, the mechanisms underlying alkaline adaptation remain inadequately characterized, and our understanding of thermal adaptation is limited to genomic analyses. This study addresses critical gaps by disentangling the responses to hypersaline, alkalinity, and thermal stress, thereby elucidating how N. thermophilus organizes its survival strategies. This research reveals that N. thermophilus employs a strategy that combines conserved cross-stress mechanisms with unique stress adaptations to cope with the three distinct extreme stresses of high salinity, alkalinity, and temperature. By identifying the molecular modules through which these mechanisms operate, this research sets the stage for future applications in synthetic biology, particularly in the design of extremophile chassis for bioprocessing under multi-extreme conditions. These insights not only enhance our understanding of polyextremophiles but also pave the way for innovative biotechnological solutions.
{"title":"Cross and unique stress adaptation strategies of the polyextremophile Natranaerobius thermophilus to individual high salt, alkaline pH, and elevated temperature","authors":"Qinghua Xing , Xinyi Tao , Qingping Hu , XiaoMeng Guo , Yingjie Zhang , Xinwei Mao , Haisheng Wang , Jun Li , Baisuo Zhao","doi":"10.1016/j.jprot.2025.105479","DOIUrl":"10.1016/j.jprot.2025.105479","url":null,"abstract":"<div><div><em>N. thermophilus</em> is the first true anaerobic halophilic alkalithermophile. It employs a unique dual mechanism for hypersaline adaptation, utilizing both “compatible solutes” and “salt in” strategies. However, the molecular mechanisms underlying its responses to alkaline pH and thermal stress remain poorly characterized. An iTRAQ-based quantitative proteomics analysis revealed that <em>N. thermophilus</em> used a cross and unique adaptation strategies to three individual extreme stresses. This study fills gaps by elucidating previously unexplored alkaline-specific regulatory processes. It also provides the first comprehensive analysis of its thermal adaptation mechanisms. In response to high-salt and alkaline stress, the organism shifts its metabolism toward glycolysis and pyruvate-derived acetate synthesis, helping to meet increased ATP demands. Heat shock proteins are up-regulated during both alkaline and thermal adaptations, reflecting the “No free lunch” principle. Alkaline pH uniquely induces DNA repair proteins and S-adenosylmethionine biosynthesis enzymes, promoting genomic stability in proton-deficient environments. Besides, the compact genome and the positive correlation between GC content with growth temperature may be also a lineage-specific thermal adaptation of the halophilic and alkalithermophilic order <em>Natranaerobiales</em>. These findings illuminate the layered adaptation strategies that help address cross-stress challenges. Meanwhile, stress-specific reconfigurations enhance flexibility for survival in individual extremes. This work provides novel insights into the survival mechanisms of polyextremophiles, as well as advancing their potential biotechnological applications.</div></div><div><h3>Significance</h3><div>Halophilic alkalithermophile <em>N. thermophilus</em> exemplify life's capacity to thrive in environments where multiple physicochemical extremes intersect. However, the mechanisms underlying alkaline adaptation remain inadequately characterized, and our understanding of thermal adaptation is limited to genomic analyses. This study addresses critical gaps by disentangling the responses to hypersaline, alkalinity, and thermal stress, thereby elucidating how <em>N. thermophilus</em> organizes its survival strategies. This research reveals that <em>N. thermophilus</em> employs a strategy that combines conserved cross-stress mechanisms with unique stress adaptations to cope with the three distinct extreme stresses of high salinity, alkalinity, and temperature. By identifying the molecular modules through which these mechanisms operate, this research sets the stage for future applications in synthetic biology, particularly in the design of extremophile chassis for bioprocessing under multi-extreme conditions. These insights not only enhance our understanding of polyextremophiles but also pave the way for innovative biotechnological solutions.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105479"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144243163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-05-30DOI: 10.1016/j.jprot.2025.105468
Sandrine Reymond , Lyssia Gruaz , Domitille Schvartz , Anna Penalba , Joan Montaner , Jean-Charles Sanchez
Managing acute stroke is challenging and requires the differentiation of stroke subtypes while excluding stroke mimics. Understanding the biological processes underlying the different stroke subtypes could help improve acute stroke care and patient outcomes. Plasma-derived extracellular vesicles (EVs) have emerged as promising tools for investigating these processes through their unique cargo.
Therefore, we aimed at exploring the protein content of plasma-derived EVs in a cohort composed of patients with hemorrhagic stroke (n = 10), ischemic stroke with large-vessel occlusion (LVO) (n = 10) and without LVO (n = 10), transient ischemic attack (n = 10), stroke mimics (n = 10) and healthy controls (n = 10). EVs were isolated by size exclusion chromatography from 150 μL of plasma. Characterization was performed by transmission electron microscopy, western blotting and nanoparticle tracking analysis, and confirmed an efficient EV enrichment. Proteomics analysis was conducted using data-independent acquisition mass spectrometry and a supervised partial least squares discriminant analysis (PLS-DA) model was applied on proteomics data.
The PLS-DA model successfully distinguished healthy controls, severe stroke subtypes (LVO ischemic and hemorrhagic stroke), and non LVO ischemic stroke, identifying key proteins influencing these patterns. These findings suggest that EVs and their protein cargo may play a role in critical processes like inflammation and coagulation in acute stroke pathology.
{"title":"Proteomic analysis of plasma-derived extracellular vesicles: Insights into acute stroke pathophysiology","authors":"Sandrine Reymond , Lyssia Gruaz , Domitille Schvartz , Anna Penalba , Joan Montaner , Jean-Charles Sanchez","doi":"10.1016/j.jprot.2025.105468","DOIUrl":"10.1016/j.jprot.2025.105468","url":null,"abstract":"<div><div>Managing acute stroke is challenging and requires the differentiation of stroke subtypes while excluding stroke mimics. Understanding the biological processes underlying the different stroke subtypes could help improve acute stroke care and patient outcomes. Plasma-derived extracellular vesicles (EVs) have emerged as promising tools for investigating these processes through their unique cargo.</div><div>Therefore, we aimed at exploring the protein content of plasma-derived EVs in a cohort composed of patients with hemorrhagic stroke (<em>n</em> = 10), ischemic stroke with large-vessel occlusion (LVO) (<em>n</em> = 10) and without LVO (n = 10), transient ischemic attack (n = 10), stroke mimics (n = 10) and healthy controls (n = 10). EVs were isolated by size exclusion chromatography from 150 μL of plasma. Characterization was performed by transmission electron microscopy, western blotting and nanoparticle tracking analysis, and confirmed an efficient EV enrichment. Proteomics analysis was conducted using data-independent acquisition mass spectrometry and a supervised partial least squares discriminant analysis (PLS-DA) model was applied on proteomics data.</div><div>The PLS-DA model successfully distinguished healthy controls, severe stroke subtypes (LVO ischemic and hemorrhagic stroke), and non LVO ischemic stroke, identifying key proteins influencing these patterns. These findings suggest that EVs and their protein cargo may play a role in critical processes like inflammation and coagulation in acute stroke pathology.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105468"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144195458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-15Epub Date: 2025-06-16DOI: 10.1016/j.jprot.2025.105482
Jessica Guedes , Leticia Szadai , Nicole Woldmar , Ágnes Judit Jánosi , Klára Koroncziová , Blanka Míra Lengyel , Bella Kelemen , Eszter Boltas , Rolland Gyulai , Elisabet Wieslander , Krzysztof Pawłowski , Peter Horvatovich , Lazaro Betancourt , A. Marcell Szasz , Zoltan Vereb , Peter Horvath , Henriett Oskolás , Roger Appelqvist , Johan Malm , Gyorgy Marko-Varga , Jeovanis Gil
Melanoma remains the most aggressive form of skin cancer, characterized by high metastatic potential, genetic heterogeneity, and resistance to conventional therapies. The Melanoma MEGA-Study is a multi-center initiative designed to address these clinical challenges by integrating advanced proteogenomic profiling, clinical metadata, with AI-driven digital pathology and machine learning analytics, aiming to enhance personalized treatment strategies and improve patient outcomes. Between 2013 and 2022, a cohort of 1653 melanoma patients each contributed a primary tumor sample, with 361 providing 819 metastatic tumor samples. Clinical data collection for this cohort continued until May 2023. Comprehensive analyses using high-resolution mass spectrometry, optimized workflows for formalin-fixed paraffin-embedded tissues, and advanced digital pathology platforms enabled precise mapping of the tumor microenvironment, identification of metabolic reprogramming, and characterization of immune evasion signatures. The European Cancer Moonshot Lund Center's MEGA-Study, under the academic umbrella of Lund and Szeged universities, marks a significant advancement in its collaborative efforts with the National Institutes of Health (NIH) under the Cancer Moonshot partnership. This initiative exemplifies the center's dedication to pioneering cancer research and underscores the strength of its international collaborations.
Significance
The significance of this study lies in its pioneering integration of high-resolution proteomics, AI-driven digital pathology, and comprehensive clinical annotation to unravel the complex molecular landscape of melanoma. By leveraging a robust, population-based cohort of 1653 patients, including extensive analyses of both primary and metastatic tumor specimens, our approach provides unprecedented insights into the proteogenomic alterations that underpin tumor progression, immune evasion, and therapeutic resistance. The preliminary application of advanced mass spectrometry techniques to formalin-fixed paraffin-embedded tissues, combined with state-of-the-art digital pathology and machine learning, has enabled the identification of novel protein biomarkers and metabolic signatures that hold promise for refining patient stratification and informing personalized treatment strategies. This integrative framework not only deepens our understanding of melanoma biology but also establishes a scalable model for precision oncology that can be extended to other complex malignancies. Ultimately, our findings have the potential to transform clinical practice by facilitating earlier risk stratification, improving prognostication, and guiding the development of targeted therapeutic interventions for this highly aggressive cancer.
{"title":"The melanoma MEGA-study: Integrating proteogenomics, digital pathology, and AI-analytics for precision oncology","authors":"Jessica Guedes , Leticia Szadai , Nicole Woldmar , Ágnes Judit Jánosi , Klára Koroncziová , Blanka Míra Lengyel , Bella Kelemen , Eszter Boltas , Rolland Gyulai , Elisabet Wieslander , Krzysztof Pawłowski , Peter Horvatovich , Lazaro Betancourt , A. Marcell Szasz , Zoltan Vereb , Peter Horvath , Henriett Oskolás , Roger Appelqvist , Johan Malm , Gyorgy Marko-Varga , Jeovanis Gil","doi":"10.1016/j.jprot.2025.105482","DOIUrl":"10.1016/j.jprot.2025.105482","url":null,"abstract":"<div><div>Melanoma remains the most aggressive form of skin cancer, characterized by high metastatic potential, genetic heterogeneity, and resistance to conventional therapies. The Melanoma MEGA-Study is a multi-center initiative designed to address these clinical challenges by integrating advanced proteogenomic profiling, clinical metadata, with AI-driven digital pathology and machine learning analytics, aiming to enhance personalized treatment strategies and improve patient outcomes. Between 2013 and 2022, a cohort of 1653 melanoma patients each contributed a primary tumor sample, with 361 providing 819 metastatic tumor samples. Clinical data collection for this cohort continued until May 2023. Comprehensive analyses using high-resolution mass spectrometry, optimized workflows for formalin-fixed paraffin-embedded tissues, and advanced digital pathology platforms enabled precise mapping of the tumor microenvironment, identification of metabolic reprogramming, and characterization of immune evasion signatures. The European Cancer Moonshot Lund Center's MEGA-Study, under the academic umbrella of Lund and Szeged universities, marks a significant advancement in its collaborative efforts with the National Institutes of Health (NIH) under the Cancer Moonshot partnership. This initiative exemplifies the center's dedication to pioneering cancer research and underscores the strength of its international collaborations.</div></div><div><h3>Significance</h3><div>The significance of this study lies in its pioneering integration of high-resolution proteomics, AI-driven digital pathology, and comprehensive clinical annotation to unravel the complex molecular landscape of melanoma. By leveraging a robust, population-based cohort of 1653 patients, including extensive analyses of both primary and metastatic tumor specimens, our approach provides unprecedented insights into the proteogenomic alterations that underpin tumor progression, immune evasion, and therapeutic resistance. The preliminary application of advanced mass spectrometry techniques to formalin-fixed paraffin-embedded tissues, combined with state-of-the-art digital pathology and machine learning, has enabled the identification of novel protein biomarkers and metabolic signatures that hold promise for refining patient stratification and informing personalized treatment strategies. This integrative framework not only deepens our understanding of melanoma biology but also establishes a scalable model for precision oncology that can be extended to other complex malignancies. Ultimately, our findings have the potential to transform clinical practice by facilitating earlier risk stratification, improving prognostication, and guiding the development of targeted therapeutic interventions for this highly aggressive cancer.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"319 ","pages":"Article 105482"},"PeriodicalIF":2.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-30Epub Date: 2025-05-11DOI: 10.1016/j.jprot.2025.105455
Maximilian Wolf , Julian Lange , Dirk Benndorf , Lina Welz , Susanna Nikolaus , Laura Katharina Siever , Florian Tran , Kay Schallert , Patrick Hellwig , Stefan Schreiber , Matthias Gunzer , Philip Rosenstiel , Udo Reichl , Timon Adolph , Almina Jukic , Konrad Aden , Robert Heyer
The gut microbiome is an important contributor to the development and the course of inflammatory bowel disease (IBD). While changes in the gut microbiome composition were observed in response to IBD therapy using biologics, studies elucidating human and microbial proteins and pathways in dependence on therapy success are sparse. Fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine the clinical response and remission. Fecal metaproteomes of remitting patients (n = 12) and of non-remitting patients (n = 12) were compared before treatment and changes within both groups were assessed over sampling time to identify functional changes and potential human and microbial biomarkers. The abundance of proteins associated with neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients. There were changes in pathways of microbial metabolism in samples from patients with remission after therapy, including an increased butyrate fermentation. Distinct changes of proteins related to gut inflammation and gut microbiome metabolism showed whether IBD remission was achieved or not. This suggests that metaproteomics could be a useful tool for monitoring remission in IBD therapies.
Significance
IBD is rising in incidence, especially in newly industrialized countries, and the microbiome is an important contributor to its pathogenesis. Despite manifold therapeutical options, achieving remission is often ineffective, and choosing new alternative drugs remains often empirical. Therefore, efficient tools for monitoring therapeutic response and assessing the effectiveness of drugs in specific patients are mandatory. In the present study, we show that the use of metaproteomics is a promising avenue to address these challenges. We observed the amelioration of inflammation and restoration of a healthy microbiome in remitting patients in contrast to non-remitting patients. Therefore, metaproteomics is a valuable tool for monitoring the therapy success in IBD.
{"title":"Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease","authors":"Maximilian Wolf , Julian Lange , Dirk Benndorf , Lina Welz , Susanna Nikolaus , Laura Katharina Siever , Florian Tran , Kay Schallert , Patrick Hellwig , Stefan Schreiber , Matthias Gunzer , Philip Rosenstiel , Udo Reichl , Timon Adolph , Almina Jukic , Konrad Aden , Robert Heyer","doi":"10.1016/j.jprot.2025.105455","DOIUrl":"10.1016/j.jprot.2025.105455","url":null,"abstract":"<div><div>The gut microbiome is an important contributor to the development and the course of inflammatory bowel disease (IBD). While changes in the gut microbiome composition were observed in response to IBD therapy using biologics, studies elucidating human and microbial proteins and pathways in dependence on therapy success are sparse. Fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine the clinical response and remission. Fecal metaproteomes of remitting patients (<em>n</em> = 12) and of non-remitting patients (n = 12) were compared before treatment and changes within both groups were assessed over sampling time to identify functional changes and potential human and microbial biomarkers. The abundance of proteins associated with neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients. There were changes in pathways of microbial metabolism in samples from patients with remission after therapy, including an increased butyrate fermentation. Distinct changes of proteins related to gut inflammation and gut microbiome metabolism showed whether IBD remission was achieved or not. This suggests that metaproteomics could be a useful tool for monitoring remission in IBD therapies.</div></div><div><h3>Significance</h3><div>IBD is rising in incidence, especially in newly industrialized countries, and the microbiome is an important contributor to its pathogenesis. Despite manifold therapeutical options, achieving remission is often ineffective, and choosing new alternative drugs remains often empirical. Therefore, efficient tools for monitoring therapeutic response and assessing the effectiveness of drugs in specific patients are mandatory. In the present study, we show that the use of metaproteomics is a promising avenue to address these challenges. We observed the amelioration of inflammation and restoration of a healthy microbiome in remitting patients in contrast to non-remitting patients. Therefore, metaproteomics is a valuable tool for monitoring the therapy success in IBD.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105455"},"PeriodicalIF":2.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-30Epub Date: 2025-05-18DOI: 10.1016/j.jprot.2025.105457
Vasti T. Juárez-González , Eduardo Luján-Soto , Paola I. Aguirre de la Cruz , Mayra Aquino-Luna , Jorge Herrera-Díaz , Brenda A. López-Ruiz , Tzvetanka D. Dinkova
Maize somatic embryogenesis process depends on explant characteristics and genotype. The relationship between explant developmental timing and embryogenic potential of derived tissues is still poorly understood. The present work explored the adjustments of transcriptomes and proteomes from explants with contrasting embryogenic potential – immature and mature zygotic embryos from the Tuxpeño VS-535 genotype – during callus induction. Differentially accumulated transcripts and proteins were represented by oxidation/reduction, stress response, and metabolic process adjustments during the dedifferentiation of both explants. However, the explant with high embryogenic potential and derived callus displayed more significant enrichment in cell proliferation and plant hormone signal transduction pathways. Between the differentially accumulated proteins, it is of notice a significantly higher enrichment of catabolic and anoxia processes in non-embryogenic as opposed to anabolic and oxidation-reduction processes in the embryogenic callus induction. Transcription factors such as Auxin Response Factors (ARFs), signal transduction (Homeobox; HB), and embryogenesis-related AP2-EREB mRNAs characterized the immature embryos. Activator and repressor ARFs substantially differed at the early stages of callus induction between immature and mature embryo explants. The overall analysis of these findings helps to understand the molecular basis of gene expression regulation during callus dedifferentiation and auxin responses from maize explants with contrasting embryogenic potential.
Significance
This work contributes with overall transcript and protein patterns during the callus induction phase of Mexican landrace Tuxpeño VS-535 maize somatic embryogenesis from immature and mature embryos. Using comparisons between explants, between each explant and the induced callus, and between callus, differential biological process enrichment at transcript and protein levels for the embryogenic callus induction indicated key roles for cell proliferation, hormone signaling and biosynthetic processes for embryogenic callus induction. Furthermore, a battery of TF family enriched in the immature embryo, including several auxin response factors support the differential gene expression reprogramming during dedifferentiation from explants with contrasting embryogenic potential in maize somatic embryogenesis.
{"title":"Differential gene expression networks and auxin responses during maize callus induction from explant tissues with contrasting embryogenic potential","authors":"Vasti T. Juárez-González , Eduardo Luján-Soto , Paola I. Aguirre de la Cruz , Mayra Aquino-Luna , Jorge Herrera-Díaz , Brenda A. López-Ruiz , Tzvetanka D. Dinkova","doi":"10.1016/j.jprot.2025.105457","DOIUrl":"10.1016/j.jprot.2025.105457","url":null,"abstract":"<div><div>Maize somatic embryogenesis process depends on explant characteristics and genotype. The relationship between explant developmental timing and embryogenic potential of derived tissues is still poorly understood. The present work explored the adjustments of transcriptomes and proteomes from explants with contrasting embryogenic potential – immature and mature zygotic embryos from the Tuxpeño VS-535 genotype – during callus induction. Differentially accumulated transcripts and proteins were represented by oxidation/reduction, stress response, and metabolic process adjustments during the dedifferentiation of both explants. However, the explant with high embryogenic potential and derived callus displayed more significant enrichment in cell proliferation and plant hormone signal transduction pathways. Between the differentially accumulated proteins, it is of notice a significantly higher enrichment of catabolic and anoxia processes in non-embryogenic as opposed to anabolic and oxidation-reduction processes in the embryogenic callus induction. Transcription factors such as Auxin Response Factors (ARFs), signal transduction (Homeobox; HB), and embryogenesis-related AP2-EREB mRNAs characterized the immature embryos. Activator and repressor ARFs substantially differed at the early stages of callus induction between immature and mature embryo explants. The overall analysis of these findings helps to understand the molecular basis of gene expression regulation during callus dedifferentiation and auxin responses from maize explants with contrasting embryogenic potential.</div></div><div><h3>Significance</h3><div>This work contributes with overall transcript and protein patterns during the callus induction phase of Mexican landrace Tuxpeño VS-535 maize somatic embryogenesis from immature and mature embryos. Using comparisons between explants, between each explant and the induced callus, and between callus, differential biological process enrichment at transcript and protein levels for the embryogenic callus induction indicated key roles for cell proliferation, hormone signaling and biosynthetic processes for embryogenic callus induction. Furthermore, a battery of TF family enriched in the immature embryo, including several auxin response factors support the differential gene expression reprogramming during dedifferentiation from explants with contrasting embryogenic potential in maize somatic embryogenesis.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105457"},"PeriodicalIF":2.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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