Article
Plant Sciences
Aigerim Soltabayeva, Aizat Bekturova, Assylay Kurmanbayeva, Dinara Oshanova, Zhadyrassyn Nurbekova, Sudhakar Srivastava, Dominic Standing, Moshe Sagi
Summary: The study investigated the role of degraded purine metabolites in plant responses to wounding or UV-C stress using Arabidopsis mutants. Disruption of purine degradation pathway led to increased senescence, cell death, and oxidative stress indicators in the mutant compared to the wild-type plants. After UV-C stress, ureides were remobilized to support young leaf growth, while after wounding, they remained in the wounded middle leaves to act as antioxidants or healing agents. UV-C radiation and wounding triggered purine degradation in old and damaged leaves, resulting in ureide accumulation and premature leaf senescence when purine degradation is impaired.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Yi-Hsin Chung, Ting-Chieh Chen, Wen-Ju Yang, Soon-Ziet Chen, Jia-Ming Chang, Wei-Yu Hsieh, Ming-Hsiun Hsieh
Summary: Plants and bacteria have different pathways for synthesizing vitamin B1. Through genetic engineering, introducing bacterial vitamin B1 synthesis genes into plants can enhance the production of vitamin B1.
Article
Plant Sciences
A. V. Murtuzova, E. V. Tyutereva, O. V. Voitsekhovskaja
Summary: SnRK1 is a major activator of catabolic processes in plants, including autophagy, during stress responses. It acts as a sensor of cell energy status and may also participate in regulating photosynthesis. In Arabidopsis, overexpression of the SnRK1 catalytic subunit KIN10 led to altered chloroplast photochemical activity under both optimal conditions and salinity stress, while inhibition of SnRK1 activity resulted in a lack of response to salinity at the level of chloroplast photochemistry.
RUSSIAN JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Plant Sciences
Sunetra Sen, Sridev Mohapatra
Summary: The study reveals that the plant growth-promoting rhizobacterium Pseudomonas putida GAP-P45 tightly regulates polyamine metabolism in water-stressed Arabidopsis thaliana, impacting both biosynthesis and catabolism of polyamines. The inoculation of GAP-P45 led to the upregulation of polyamine catabolic genes and increased activity of copper amine oxidase, indicating enhanced putrescine turnover in water-stressed plants. Additionally, the accumulation of GABA was differentially impacted under these conditions, suggesting a complex interplay of polyamine metabolism under water stress.
JOURNAL OF PLANT GROWTH REGULATION
(2022)
Article
Plant Sciences
Corentin Dourmap, Anne Marmagne, Sandrine Lebreton, Gilles Clement, Anne Guivarc'h, Arnould Savoure, Celine Masclaux-Daubresse
Summary: This study investigated the phenotypes of Arabidopsis plants with mutations in the p5cdh gene and found that these mutants had lower seed yield and produced lighter seeds, indicating defects in stem-to-seed resource allocation. Furthermore, under high nitrate supply, the defects in carbon, nitrogen, and biomass allocation to seeds in p5cdh mutants were significantly amplified. Interestingly, these defects were not observed in the prodh1 prodh2 double-mutant. This study highlights the essential role of P5CDH in the carbon and nitrogen remobilization for seed development in Arabidopsis.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Rui Li, Ya Yang, Hanping Cao, Xiang Peng, Qin Yu, Linshen He, Ji Chen, Lien Xiang, Wanhong Liu
Summary: Heavy metal pollution in the soil poses a serious threat to both crop growth and human health. In this study, a new metallothionein encoding gene, NtMT2F, was cloned from Cd-hyperaccumulator tobacco and expressed in E. coli and A. thaliana to examine its biological function. The results showed that NtMT2F effectively enhanced resistance to heavy metal stress, particularly Cd, in both E. coli and transgenic A. thaliana. The findings suggest that NtMT2F could be a promising protein candidate for phytoremediation of heavy metal-contaminated environments.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Andrew D. Mathis, Ryan M. Otto, Kimberly A. Reynolds
Summary: This study presents a generalizable approach to quantify the relationship between growth rate and titrated changes in gene expression level using CRISPRi. A compounding mutational strategy is effective for generating a monotonic relationship between mutation number and growth rate effect. Molecular barcoding is implemented to detect and correct for mutations that escape CRISPRi targeting machinery, revealing deleterious growth rate effects overlooked by standard methods.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Ben Vezina, Louise M. Judd, Fiona K. McDougall, Wayne S. J. Boardman, Michelle L. Power, Jane Hawkey, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres
Summary: The study identified the dynamics of Klebsiella pneumoniae strain transmission clusters within grey-headed flying fox colonies, including both intra- and inter-colony transmission, and highlighted gene flow between human clinical and flying fox isolates. Additionally, inter-species horizontal plasmid transmission was observed. The metabolic models generated showed no distinction in metabolic capabilities, instead being consistent with population structure and lineage.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Agronomy
Ye Ai, Jiabao Chen, Yinglong Chen, Xiaoqian Wang, Ning Wang, Wenyuan Liang, Xinbo Sun, Yuehui Chao, Liebao Han
Summary: This study reports the complete mitochondrial genome of P. pratensis for the first time, revealing its basic structure, gene content, and codon usage bias. Comparison with other related plants shows that P. pratensis has greater genetic variation and rearrangement in its mitochondrial genome. These findings provide an important foundation for further genetic research on bluegrass.
Article
Biochemistry & Molecular Biology
Michael J. Currie, Lavanyaa Manjunath, Christopher R. Horne, Phillip M. Rendle, Ramaswamy Subramanian, Rosmarie Friemann, Antony J. Fairbanks, Andrew C. Muscroft-Taylor, Rachel A. North, Renwick C. J. Dobson
Summary: The study found that the enzyme NanE may use a novel substrate-assisted proton displacement mechanism for catalysis, by re-evaluating the central role of Glu180 and the catalytic lysine, and identifying several active-site residues related to the mechanism. This discovery could be helpful in developing inhibitors for the enzyme or producing biocatalysts capable of changing the stereochemistry of molecules through enzyme engineering.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Plant Sciences
Yao Zheng, Cecile Cabassa-Hourton, Holger Eubel, Guillaume Chevreux, Laurent Lignieres, Emilie Crilat, Hans-Peter Braun, Sandrine Lebreton, Arnould Savoure
Summary: This study reveals evidence of physical proximity and interactions among ProDH, P5CDH, and OAT in the mitochondria of Arabidopsis during dark-induced leaf senescence, suggesting the formation of a complex during P5C metabolism.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Joshua A. M. Kaste, Yair Shachar-Hill
Summary: The study demonstrates that integrating relative gene expression levels into metabolic flux predictions improves the accuracy of the predictions in a multi-tissue system.
Editorial Material
Biochemistry & Molecular Biology
Deirdre H. Mclachlan
Summary: Long-distance wound signalling in plants involves systemic propagation of calcium waves, and a new study proposes a mechanism whereby pressure changes trigger this response.
Article
Biochemistry & Molecular Biology
Joseph A. Edwards, Usha Bishnoi Saran, Jason Bonnette, Alice MacQueen, Jun Yin, Tu Uyen Nguyen, Jeremy Schmutz, Jane Grimwood, Len A. Pennacchio, Chris Daum, Tijana Glavina del Rio, Felix B. Fritschi, David B. Lowry, Thomas E. Juenger
Summary: A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition. This study characterized the root microbiota of switchgrass in its native range and found that field location is the primary determinant of microbiome composition. They also identified loci impacting the abundance of microbial strains and found a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota.
Review
Plant Sciences
Claus-Peter Witte, Marco Herde
Article
Biochemistry & Molecular Biology
Mingjia Chen, Claus-Peter Witte
Article
Biochemistry & Molecular Biology
Guido Durian, Mastoureh Sedaghatmehr, Lilian P. Matallana-Ramirez, Silke M. Schilling, Sieke Schaepe, Tiziana Guerra, Marco Herde, Claus-Peter Witte, Bernd Mueller-Roeber, Waltraud X. Schulze, Salma Balazadeh, Tina Romeis
Article
Plant Sciences
Markus Niehaus, Henryk Straube, Patrick Kuenzler, Nils Rugen, Jan Hegermann, Patrick Giavalisco, Holger Eubel, Claus-Peter Witte, Marco Herde
Article
Biochemistry & Molecular Biology
Sang-Hoon Kim, Claus-Peter Witte, Sangkee Rhee
Summary: RNA modifications can regulate RNA stability and translation efficiency. Pseudouridine is a prevalent RNA modification and its degradation pathway in Arabidopsis was recently characterized. AtPUKI, a pseudouridine kinase, has unique nucleoside binding sites and conformational changes that contribute to its high catalytic efficiency for pseudouridine over uridine.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Henryk Straube, Claus-Peter Witte, Marco Herde
Summary: This review focuses on the analysis of nucleotides in plants, highlighting the recent advances and challenges in this field. Liquid chromatography coupled to mass spectrometry has been instrumental in advancing our understanding of nucleotide metabolism in plants. The complexity of the metabolite matrix in plants suggests that the methods developed for nucleotide analysis in plants may also be applicable to other organisms.
Article
Multidisciplinary Sciences
Katharina J. Heinemann, Sun-Young Yang, Henryk Straube, Nieves Medina-Escobar, Marina Varbanova-Herde, Marco Herde, Sangkee Rhee, Claus-Peter Witte
Summary: The study focuses on the dephosphorylation of XMP in plant cells and identifies an XMP phosphatase in Arabidopsis with specificity to XMP. The researchers demonstrate that XMPP initiates the catabolism of adenylate-derived nucleotides in vivo, while guanylates enter catabolism through a different pathway. The crystal structure and mutational analysis of XMPP provide insights into its high substrate specificity and efficient catalysis of the small XMP pool in vivo.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Luisa Voss, Katharina J. Heinemann, Marco Herde, Nieves Medina-Escobar, Claus-Peter Witte
Summary: Tropical legumes export fixed nitrogen in the form of ureides, which involves the synthesis of several enzymes and transitions between infected and uninfected cells.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Henryk Straube, Jannis Straube, Jannis Rinne, Lisa Fischer, Markus Niehaus, Claus-Peter Witte, Marco Herde
Summary: In plants, inosine is selectively introduced in some tRNAs through enzymatic action, but not in other RNA or DNA molecules. However, our findings indicate that Arabidopsis thaliana's RNA and DNA contain (deoxy)inosine, which likely arises from non-enzymatic adenosine deamination in nucleic acids and the incorporation of (deoxy)inosine triphosphate during nucleic acid synthesis. Through various approaches, including biochemical analyses, LC-MS, and RNA-Seq, we characterized a conserved plant enzyme called inosine triphosphate pyrophosphatase (ITPA) and investigated the sources of deaminated purine nucleotides in plants.
Article
Biochemistry & Molecular Biology
Xiaoguang Chen, Sang-Hoon Kim, Sangkee Rhee, Claus-Peter Witte
Summary: The Arabidopsis enzyme PNK1 is involved in inosine salvage and regulation of purine and pyrimidine metabolism. PNK1 mutation leads to increased purine nucleotide catabolism, over-accumulation of uridine and UTP, and growth depression. Cold stress causes purine nucleotide accumulation, but is not controlled by PNK1.
Article
Biochemistry & Molecular Biology
Wenlei Wang, Huijie Liu, Feifei Wang, Xiaoye Liu, Yu Sun, Jie Zhao, Changhua Zhu, Lijun Gan, Jinping Yu, Claus-Peter Witte, Mingjia Chen
Summary: This study reveals the occurrence of N4-acetylation of cytidine in plant RNA and identifies two N-ACETYLTRANSFERASEs FOR CYTIDINE IN RNA (ACYR1 and ACYR2) that are essential for plant development. Mutations in these genes result in defects in leaf and embryo development due to reduced acetylation and destabilization of the TOUGH transcript. These findings highlight the critical role of N4-acetylation of cytidine in plant development.
Article
Biochemistry & Molecular Biology
Markus Niehaus, Henryk Straube, Andre Specht, Chiara Baccolini, Claus-Peter Witte, Marco Herde
Summary: This study comprehensively analyzes the thymidylate metabolism during seed germination and seedling establishment in Arabidopsis. It reveals the important role of organelle thymidine salvage in thymidylate pool formation and the compensatory effect of cytosolic thymidylate synthesis in seedlings. The study also discovers a novel function of an organelle enzyme in removing noncanonical nucleotide triphosphates.
Article
Biotechnology & Applied Microbiology
Jannis Rinne, Claus-Peter Witte, Marco Herde
Summary: The study describes the establishment of the knockout marker gene MAR1 for selection of CRISPR/Cas9-edited Arabidopsis seedlings and tomato explants in tissue culture. Mutations of MAR1 induced by the CRISPR system confer kanamycin-resistance to Arabidopsis plants and tomato tissues. Co-selection of a mutation in a second target gene at higher frequency has been observed for the first time in plants, indicating the potential utility of this technique for selecting edited plants.
FRONTIERS IN GENOME EDITING
(2021)
Article
Biochemistry & Molecular Biology
Henryk Straube, Markus Niehaus, Sarah Zwittian, Claus-Peter Witte, Marco Herde
Summary: A new method was developed to detect and quantify low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants with high sensitivity and robustness. The study revealed the intricate interconnection between deoxyribonucleotide metabolism and ribonucleoside catabolism, as well as the correlation between nucleotide ratios and genomic contents across different plant species. The findings demonstrate the potential of this method in providing valuable insights into plant nucleotide metabolism.
Meeting Abstract
Biophysics
Pyeoung-Ann Kang, Juntaek Oh, Haehee Lee, Claus-Peter Witte, Sangkee Rhee
BIOPHYSICAL JOURNAL
(2020)
