Review
Biochemistry & Molecular Biology
Delara Akhter, Yuchan Zhang, Jianping Hu, Ronghui Pan
Summary: Protein ubiquitination plays a crucial role in regulating diverse cellular processes in eukaryotic organisms, including growth, development, and stress response. Despite its importance, the mechanisms underlying protein ubiquitination in peroxisomes, especially in plants, are poorly understood. This review provides a comprehensive summary of the current knowledge on the involvement of protein ubiquitination in peroxisome biology, focusing on plants.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Review
Plant Sciences
Su Yin Phua, Barbara De Smet, Claire Remacle, Kai Xun Chan, Frank Van Breusegem
Summary: The evolution of photosynthesis in plants has been crucial but has also led to challenges in the form of reactive oxygen species (ROS) production. Multiple forms of ROS are generated in various plant cell compartments, requiring a sophisticated network of ROS detoxification and signaling tailored to individual organelles to safeguard the cell as a whole.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Youssef Khalil, Sara Carrino, Fujun Lin, Anna Ferlin, Heena V. Lad, Francesca Mazzacuva, Sara Falcone, Natalie Rivers, Gareth Banks, Danilo Concas, Carlos Aguilar, Andrew R. Haynes, Andy Blease, Thomas Nicol, Raya Al-Shawi, Wendy Heywood, Paul Potter, Kevin Mills, Daniel P. Gale, Peter T. Clayton
Summary: This study demonstrates the powerful insight brought by proteomic and metabolomic profiling of Hacl1(-/-) mice in better understanding disease mechanism in fatty acid alpha-oxidation disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Tina A. Schrader, Ruth E. Carmichael, Markus Islinger, Joseph L. Costello, Christian Hacker, Nina A. Bonekamp, Jochen H. Weishaupt, Peter M. Andersen, Michael Schrader
Summary: This study reveals a novel pathway for peroxisome division and identifies the role of FIS1 in peroxisome division.
JOURNAL OF CELL SCIENCE
(2022)
Review
Cell Biology
Francesca Di Cara, Stephane Savary, Werner J. Kovacs, Peter Kim, Richard A. Rachubinski
Summary: Peroxisomes are essential metabolic organelles involved in lipid metabolism and immune regulation. Lipid metabolites of peroxisomes, such as PUFAs, play a crucial role in immune modulation. Peroxisomal redox metabolism and beta-oxidation control immune signaling and cell development. The association between peroxisome dysfunction and inflammatory diseases has sparked research on targeting peroxisomes for therapeutic intervention in immune disorders, inflammation, and cancer.
TRENDS IN CELL BIOLOGY
(2023)
Review
Neurosciences
Stephanie Vrijsen, Celine Vrancx, Mara Del Vecchio, Johannes V. Swinnen, Patrizia Agostinis, Joris Winderickx, Peter Vangheluwe, Wim Annaert
Summary: Neurodegenerative diseases are characterized by early abnormalities in endolysosomes, mitochondria, endoplasmic reticulum, and lipid metabolism. Dysregulation of inter-organellar communication through membrane contact sites (MCSs) plays a crucial role in these diseases, especially in the communication between the endoplasmic reticulum and mitochondria. Other MCSs, such as those involving endolysosomes and lipid droplets, are also emerging as important contributors to disrupted inter-organellar homeostasis in neurodegenerative diseases.
FRONTIERS IN NEUROSCIENCE
(2022)
Review
Cell Biology
Ruth E. Carmichael, Markus Islinger, Michael Schrader
Summary: Peroxisomes are dynamic organelles that can adjust their morphology and metabolic functions according to cellular needs. Their multiplication involves the coordination of several proteins, and defects in these proteins can lead to abnormal cellular dynamics and neurological defects.
Article
Plant Sciences
Ting Zhang, Ya-Nan Li, Xue Li, Wangliu Gu, Emily Kolojane Moeketsi, Ruiwen Zhou, Xiaobo Zheng, Zhengguang Zhang, Haifeng Zhang
Summary: The study identified MoPCS60 as a key peroxisomal-CoA synthetase involved in fatty acid beta-oxidation and pathogenicity in rice blast fungi. MoPCS60 was highly expressed during the conidial and early infectious stages and was induced under oleate treatment.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Multidisciplinary
Xin Zhao, Zhangjiang He, Yifei Gao, Yanze Kan, Yufei Jiao, Yunxia Liu, Shuaishuai Huang, Zhibing Luo, Yongjun Zhang
Summary: In the insect fungal pathogen, Beauveria bassiana, BbSre1 regulates oxidative stress response, peroxisome division, and redox homeostasis. Gene disruption inhibits peroxisome division, affects redox homeostasis, and impairs lipid/fatty acid metabolism and sterol biosynthesis. These findings broaden our understanding of the role of Sre1 in regulating oxidative stress and lipid metabolism.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Cell Biology
Archna Ravi, Lavinia Palamiuc, Brooke M. Emerling
Summary: While organelles are individual compartments with specialized functions, inter-organelle communication is essential for cellular homeostasis. This communication is mediated by phospholipids on organelle membranes, particularly phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PI-4,5-P-2). This review focuses on the role of non-canonical Type II PIPKs in generating PI-4,5-P-2 and their impact on organelle crosstalk, cellular health, and human diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Plant Sciences
Jana Vasilev, Ann-Kathrin Mix, Thomas Heimerl, Uwe G. Maier, Daniel Moog
Summary: Peroxisomes play important roles in metabolic processes in eukaryotic cells, such as detoxification of reactive oxygen species and degradation of fatty acids. Recent studies have found the presence of peroxisomes in cryptophytes and other chromalveolates. This study investigated the subcellular localization of candidate proteins in a diatom and found that peroxisomes in cryptophytes are involved in various metabolic processes, but not in the beta-oxidation of fatty acids.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Genetics & Heredity
Nayan Moni Deori, Shirisha Nagotu
Summary: Peroxisomes are dynamic organelles involved in various cellular functions, and their biogenesis and inter-organelle contacts are regulated by two protein families, Pex11 and Pex30.
Article
Biochemistry & Molecular Biology
Lars Kuerschner, Philipp Leyendecker, Kristina Klizaite, Maria Fiedler, Jennifer Saam, Christoph Thiele
Summary: In this study, new tracers were introduced to study fatty acid beta-oxidation and metabolic intermediates. The findings revealed differences in metabolic handling of fatty acids of different chain length and identified a salvage pathway when mitochondrial beta-oxidation was hindered.
JOURNAL OF LIPID RESEARCH
(2022)
Article
Microbiology
Sotirios Vasileiadis, Chiara Perruchon, Benjamin Scheer, Lorenz Adrian, Nicole Steinbach, Marco Trevisan, Patricia Plaza-Bolanos, Ana Aguera, Antonis Chatzinotas, Dimitrios G. Karpouzas
Summary: This study confirms the key role of Sphingomonas in the degradation of thiabendazole and identifies potential microbial interactions governing consortium functioning. Specifically, Sphingomonas transforms thiabendazole into terminal compounds through specific pathways and exhibits strong interactions with Hydrogenophaga.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Andrea Cillingova, Renata Toth, Anna Mojakova, Igor Zeman, Romana Vrzonova, Barbara Sivakova, Peter Barath, Martina Nebohacova, Zuzana Klepcova, Filip Brazdovic, Hana Lichancova, Viktoria Hodorova, Brona Brejova, Tomas Vinar, Sofia Mutalova, Veronika Vozarikova, Giacomo Mutti, Lubomir Tomaska, Atilla Gacser, Toni Gabaldon, Jozef Nosek
Summary: Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. In this study, the yeast Candida parapsilosis was investigated and it was found that the genes involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is regulated by transcriptional activators. It was also proposed that bicarbonate ions resulting from decarboxylation of hydroxybenzoates contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes.
Article
Multidisciplinary Sciences
Wei Ma, Xueying Guan, Jie Li, Ronghui Pan, Luyao Wang, Fengjun Liu, Hongyu Ma, Shuijin Zhu, Jin Hu, Yong-Ling Ruan, Xiaoya Chen, Tianzhen Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Plant Sciences
Yuying Fu, Zhihao Zhang, Jun Liu, Min Chen, Ronghui Pan, Weimin Hu, Yajing Guan, Jin Hu
JOURNAL OF PLANT GROWTH REGULATION
(2020)
Article
Plant Sciences
Zhan Li, Huimin Liu, Zehong Ding, Jiapei Yan, Huiyun Yu, Ronghui Pan, Jin Hu, Yajing Guan, Jian Hua
Article
Chemistry, Applied
Yue Gao, Shanshan Pan, Genyuan Guo, Qingqing Gu, Ronghui Pan, Yajing Guan, Jin Hu
PROGRESS IN ORGANIC COATINGS
(2020)
Article
Agriculture, Multidisciplinary
Mohamed S. Sheteiwy, Hongbo Shao, Weicong Qi, Paul Daly, Anket Sharma, Hiba Shaghaleh, Yousef Alhaj Hamoud, Mohamed A. El-Esawi, Ronghui Pan, Qun Wan, Haiying Lu
Summary: The study indicates that the application of 60 μmol/L jasmonic acid (JA) through seed priming and foliar application can effectively improve water status, photosynthetic performance, chlorophyll content, antioxidant activity, and hormonal levels in soybean plants under salinity stress, ultimately enhancing plant growth and providing tolerance against excessive soil salinity.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Biochemistry & Molecular Biology
Ruonan Xu, Ronghui Pan, Yuchan Zhang, Yanlei Feng, Ujjal Kumar Nath, Yinbo Gan, Chunhai Shi, Delara Akhter
Summary: Purple-colored leaves in plants play important biological functions and can be potential sources of phenotypic markers in breeding. Transcriptional profiling helps to identify mechanisms of leaf pigmentation in crop plants. This study identified differentially expressed genes regulating purple leaf color in genetically unlike rice genotypes, showing enrichment in metabolic processes and phenylpropanoid biosynthesis. Key genes associated with anthocyanin biosynthesis and regulatory genes were up-regulated in purple mutant leaves, providing valuable insights for further research on molecular mechanisms of anthocyanin biosynthesis in rice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Yanxiang Lin, Pan Li, Yuchan Zhang, Delara Akhter, Ronghui Pan, Zhixi Fu, Mingqing Huang, Xiaobo Li, Yanlei Feng
Summary: Our study assembled and analyzed 22 new mitogenomes and 12 new plastomes in the Convolvulaceae family. We found variations in both the plastid and mitochondrial genomes of these plants that were rarely observed in other angiosperms. Dodders, in particular, showed gene and intron losses, duplications, structural variations, and insertions of foreign DNAs. The phylogeny reconstructed by plastid protein coding sequences confirmed the previous relationships of the tribes. The mitogenome in Cuscuta japonica was significantly larger and integrated massive DNAs from other species, while other dodders maintained small-sized mitogenomes, revealing diverse evolutionary strategies. Mutations unique to plants were found in the mitochondrial gene ccmFc, which has undergone gene fission and splicing shift. Our findings provide valuable insights into the evolution of Convolvulaceae and plant parasitism.
Article
Plant Sciences
Yanlei Feng, Xiaoguo Xiang, Delara Akhter, Ronghui Pan, Zhixi Fu, Xiaohua Jin
Summary: This study decoded the mitochondrial genomes of Fagales, revealing their dynamic and mosaic characteristics, potentially influenced by independent and unequal transfers of third-party DNA.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Qianwen Deng, He Li, Yanlei Feng, Ruonan Xu, Weiran Li, Rui Zhu, Delara Akhter, Xingxing Shen, Jianping Hu, Hangjin Jiang, Ronghui Pan
Summary: This study performed a large-scale and in-depth analysis of the peroxisome targeting signal 1 (PTS1) domain in plants, identifying and validating low-frequency PTS1 tripeptides and revealing enhancing and inhibiting sequence patterns upstream of the tripeptide. The study also showed that nonpolar and acidic residues have strong enhancing and inhibiting effects on peroxisome targeting, and that positive charges alone do not have the anticipated enhancing effect. The findings significantly advance our knowledge of the PTS1 domain in plants and potentially other eukaryotic species.
Article
Biochemistry & Molecular Biology
Yang Li, Zhiguo Liu, Chao Liu, Zheyi Shi, Lan Pang, Chuzhen Chen, Yun Chen, Ronghui Pan, Wenwu Zhou, Xue-Xin Chen, Antonis Rokas, Jianhua Huang, Xing-Xing Shen
Summary: Horizontal gene transfer (HGT) is a significant evolutionary force that plays a crucial role in insect adaptation. In this study, we systematically analyzed 218 high-quality insect genomes and identified 1,410 genes acquired through HGT from non-metazoan donors. Lepidopterans had the highest number of HGT-acquired genes. Genes with introns showed higher expression levels, suggesting the involvement of intron gains in HGT adaptation. Additionally, we successfully edited a prevalent but previously unreported HGT-acquired gene in diamondback moths, which was found to affect courtship behavior.
Review
Biochemistry & Molecular Biology
Delara Akhter, Yuchan Zhang, Jianping Hu, Ronghui Pan
Summary: Protein ubiquitination plays a crucial role in regulating diverse cellular processes in eukaryotic organisms, including growth, development, and stress response. Despite its importance, the mechanisms underlying protein ubiquitination in peroxisomes, especially in plants, are poorly understood. This review provides a comprehensive summary of the current knowledge on the involvement of protein ubiquitination in peroxisome biology, focusing on plants.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Computer Science, Hardware & Architecture
Haigang Zhang, Ronghui Pan, Fengjun Chang, Liming He, Zhongming Dong, Jinfeng Yang
Summary: In current industrial production, defective products have become a bottleneck for enterprises to improve product quality. Artificial detection is inferior to machine vision based detection in terms of speed, accuracy, and stability. However, data-driven based supervised recognition algorithms often fail in the presence of unknown defects. This paper proposes a detection model, called Zero-DD, for surface defects of industrial products with zero samples, which achieves high-precision detection by being sensitive to unknown defects.
COMPUTERS & ELECTRICAL ENGINEERING
(2023)
Article
Computer Science, Artificial Intelligence
Haigang Zhang, Dong Wang, Zhibin Chen, Ronghui Pan
Summary: Visual inspection of appearance defects on industrial products is a research hotspot, but deep learning faces challenges due to lack of samples and class imbalance. Transfer learning is a good solution, but cross-dataset bias is a problem. In this study, an adaptive industrial defect detection model is proposed based on model-agnostic meta-learning (MAML) and Siamese network, with added coordinate attention mechanism.
PEERJ COMPUTER SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Canhong Gao, Mohamed S. Sheteiwy, Jiajun Han, Zhaorong Dong, Ronghui Pan, Yajing Guan, Yousef Alhaj Hamoud, Jin Hu
PLANT SIGNALING & BEHAVIOR
(2020)