Article
Plant Sciences
Peter N. Karssemeijer, Kris A. de Kreek, Rieta Gols, Mikhaela Neequaye, Michael Reichelt, Jonathan Gershenzon, Joop J. A. van Loon, Marcel Dicke
Summary: Plants face both aboveground and belowground attackers, and the response of Brussels sprouts' primary roots to root herbivory by cabbage root fly larvae was studied, along with aboveground herbivory by cabbage aphids or diamondback moth caterpillars. The study found that root herbivory leads to major transcriptomic rearrangement, modulated by aboveground feeding caterpillars. Knocking out aliphatic glucosinolate biosynthesis enhanced the performance of the specialist root herbivore, suggesting a downregulation of an effective defense by the herbivore. These findings contribute to understanding how plants cope with root herbivory and may aid in developing sustainable solutions for controlling devastating root pests.
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.
Article
Biology
Charlotte Seydel, Julia Biener, Vladimir Brodsky, Svenja Eberlein, Thomas Naegele
Summary: This study suggests that Fourier polynomials can be used to predict plant responses in varied environmental conditions and quantify and analyze metabolism and its reaction towards environmental fluctuations.
COMMUNICATIONS BIOLOGY
(2022)
Review
Plant Sciences
Takuya Yoshida, Alisdair R. Fernie
Summary: Phytohormones are crucial in regulating plant growth, development, and stress responses globally. They play important roles in the transcriptional regulation of stress-responsive genes and metabolic adjustment. The balance between growth promotion and stress resistance is maintained through the coordinated action of phytohormones.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Anastasia Kitashova, Vladimir Brodsky, Palak Chaturvedi, Iro Pierides, Arindam Ghatak, Wolfram Weckwerth, Thomas Naegele
Summary: A plant's genome encodes the proteins necessary for metabolism, and its interactions with the environment affect its growth, development, and adaptation to adverse conditions. Despite advances in genome sequencing technologies, predicting metabolic phenotypes from genotype x environment interactions remains incomplete. Understanding the dependence and expression of molecular organization levels in growth conditions is a current challenge.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Ze-Hua Guo, Shiu-Cheung Lung, Mohd Fadhli Hamdan, Mee-Len Chye
Summary: Lipids play diverse biological functions, including signal transduction, cellular membrane biogenesis, and carbon storage. Fatty acids are synthesized in the plastids and then transported to the endoplasmic reticulum for further acylation to form triacylglycerols or incorporation into phosphatidylcholine. Acyl-CoA-binding proteins (ACBPs) play a crucial role in lipid transfer and maintaining intracellular acyl-CoA pools, while other proteins such as lipid transfer proteins and annexins are also important in lipid binding.
PROGRESS IN LIPID RESEARCH
(2022)
Review
Microbiology
A. M. Pirttila, V. Brusila, J. J. Koskimaki, P. R. Wali, A. L. Ruotsalainen, M. Mutanen, A. M. Markkola
Summary: Prokaryotic and eukaryotic microbial symbiotic communities exist across different kingdoms, extending the host genome and aiding adaptation to changing environments. Plants and insects carry a variety of microbes on their surfaces, internally, and even within cells, with the insect gut being a selective environment. Despite their high dependence and frequent interaction, it remains uncertain how much plants and insects exchange and modify each other's microbiomes. This review focuses on herbivores that feed on plants in forest ecosystems, discussing the plant microbiome, overlap with insect microbial communities, and the effects of microbiome exchange on each host's fitness.
Article
Multidisciplinary Sciences
Kun-Hsiang Liu, Menghong Liu, Ziwei Lin, Zi-Fu Wang, Binqing Chen, Cong Liu, Aping Guo, Mineko Konishi, Shuichi Yanagisawa, Gerhard Wagner, Jen Sheen
Summary: Nitrate is a crucial nutrient and signaling molecule for plant growth. This study identified NLP7 as the primary nitrate sensor in plants, which regulates metabolic and growth responses upon nitrate perception. The use of a fluorescent split biosensor allowed visualization of single-cell nitrate dynamics in planta. Further analyses revealed that NLP7's nitrate sensor domain resembles that of a bacterial nitrate sensor, NreA.
Article
Plant Sciences
Mei Luo, Bin Li, Georg Jander, Shaoqun Zhou
Summary: Non-volatile metabolites play a crucial role in plant-insect interactions, serving as both nutrients and defensive compounds. Functional genetics studies have identified receptors targeting plant non-volatile metabolites in insects, while the understanding of plant receptors for insect-derived molecules is limited. Insect feeding induces changes in plant specialized metabolism, but the effects on core metabolism vary among species. Furthermore, non-volatile metabolites can facilitate tripartite communication in plant communities through direct root-to-root communication and interactions with parasitic plants, mycorrhizae, and the rhizosphere microbiome.
Article
Chemistry, Multidisciplinary
Ling Chuang, Shenyu Liu, Jakob Franke
Summary: A biosynthetic pathway for the modification of already cyclized tirucallane triterpenoids in Sapindales plants is discovered, in which a cytochrome P450 monooxygenase and two isomerases control the bifurcation between different plant triterpenoid classes. These enzymes are crucial for the biotechnological production of various triterpenoids.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Avinash Sreedasyam, Christopher Plott, Md Shakhawat Hossain, John T. Lovell, Jane Grimwood, Jerry W. Jenkins, Christopher Daum, Kerrie Barry, Joseph Carlson, Shengqiang Shu, Jeremy Phillips, Mojgan Amirebrahimi, Matthew Zane, Mei Wang, David Goodstein, Fabian B. Haas, Manuel Hiss, Pierre-Francois Perroud, Sara S. Jawdy, Yongil Yang, Rongbin Hu, Jenifer Johnson, Janette Kropat, Sean D. Gallaher, Anna Lipzen, Eugene Shakirov, Xiaoyu Weng, Ivone Torres-Jerez, Brock Weers, Daniel Conde, Marilia R. Pappas, Lifeng Liu, Andrew Muchlinski, Hui Jiang, Christine Shyu, Pu Huang, Jose Sebastian, Carol Laiben, Alyssa Medlin, Sankalpi Carey, Alyssa A. Carrell, Jin-Gui Chen, Mariano Perales, Kankshita Swaminathan, Isabel Allona, Dario Grattapaglia, Elizabeth A. Cooper, Dorothea Tholl, John P. Vogel, David J. Weston, Xiaohan Yang, Thomas P. Brutnell, Elizabeth A. Kellogg, Ivan Baxter, Michael Udvardi, Yuhong Tang, Todd C. Mockler, Thomas E. Juenger, John Mullet, Stefan A. Rensing, Gerald A. Tuskan, Sabeeha S. Merchant, Gary Stacey, Jeremy Schmutz
Summary: Gene functional descriptions are important for identifying candidate genes involved in trait variation, and plant responses to environmental cues can provide molecular targets for plant improvement. However, many genes across the plant phylogeny lack functional annotations. The Joint Genome Institute (JGI) Plant Gene Atlas is a valuable resource that integrates transcript abundance data from 18 diverse species to identify expression profiles and discover previously undocumented gene functions. The Gene Atlas is accessible through the JGI Plant Gene Atlas and Phytozome websites, allowing users to access differential gene expression, track orthologs, and visualize gene ontology and pathway enrichments.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Pratap Adinath Divekar, Srinivasa Narayana, Bhupendra Adinath Divekar, Rajeev Kumar, Basana Gowda Gadratagi, Aishwarya Ray, Achuit Kumar Singh, Vijaya Rani, Vikas Singh, Akhilesh Kumar Singh, Amit Kumar, Rudra Pratap Singh, Radhe Shyam Meena, Tusar Kanti Behera
Summary: Plants have evolved adaptive strategies to defend against herbivores by synthesizing plant secondary metabolites (PSMs). PSMs play important roles in detecting and responding to herbivore attacks, and have limited adaptability to insects. They cause direct toxicity to pests and indirectly protect plants by attracting herbivore natural enemies. Understanding the molecular regulation of PSM biosynthesis can contribute to improving plant tolerance to herbivores.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Benjamad Khonkhaeng, Metha Wanapat, Sawitree Wongtangtintharn, Kampanat Phesatcha, Chanadol Supapong, Chanon Suntara, Chalermpon Yuangklang, Kraisit Vasupen, Jiravan Khotsakdee, Pin Chanjula, Pongsatorn Gunun, Nirawan Gunun, Anusorn Cherdthong
Summary: This study found that combining Gryllus bimaculatus with Sesbania grandiflora can improve protein utilization, in vitro digestibility, propionate concentration, and cumulative gas production.
Review
Plant Sciences
Shaoqun Zhou, Georg Jander
Summary: Plant-derived volatile organic compounds play key roles in interactions with insect herbivores, acting as toxic or deterrent agents, signal molecules, and priming signals for plant tissues. The functions of VOC blends are strongly influenced by environmental conditions and specific plant-insect interactions. The complexity of plant-insect chemical communication via VOCs is enriched by the sophisticated molecular perception mechanisms of insects, which influence insect behavior in ways that are not fully understood.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Bethany M. Moore, Yun Sun Lee, Peipei Wang, Christina Azodi, Erich Grotewold, Shin-Han Shiu
Summary: The modeling and experimental validation of transcriptional response to wounding and jasmonic acid identified temporal cis-regulatory codes and new regulatory sequences important for wound response. The study provides a global predictive model for wound response and highlights the significance of regulatory factors and open chromatin regions in different types of wound response.
Article
Biochemical Research Methods
Adrian J. Jervis, Pablo Carbonell, Sandra Taylor, Rehana Sung, Mark S. Dunstan, Christopher J. Robinson, Rainer Breitling, Eriko Takano, Nigel S. Scrutton
ACS SYNTHETIC BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Zaigham Shahzad, Ross Eaglesfield, Craig Carr, Anna Amtmann
NATURE COMMUNICATIONS
(2020)
Article
Biology
Luke Kemp, Laura Adam, Christian R. Boehm, Rainer Breitling, Rocco Casagrande, Malcolm Dando, Appolinaire Djikeng, Nicholas G. Evans, Richard Hammond, Kelly Hills, Lauren A. Holt, Todd Kuiken, Alemka Markotic, Piers Millett, Johnathan A. Napier, Cassidy Nelson, Sean S. Oheigeartaigh, Anne Osbourn, Megan J. Palmer, Nicola J. Patron, Edward Perello, Wibool Piyawattanametha, Vanessa Restrepo-Schild, Clarissa Rios-Rojas, Catherine Rhodes, Anna Roessing, Deborah Scott, Philip Shapira, Christopher Simuntala, Robert D. J. Smith, Lalitha S. Sundaram, Eriko Takano, Gwyn Uttmark, Bonnie C. Wintle, Nadia B. Zahra, William J. Sutherland
Article
Biochemical Research Methods
Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
PLOS COMPUTATIONAL BIOLOGY
(2020)
Review
Biotechnology & Applied Microbiology
Dominic R. Whittall, Katherine Baker, Rainer Breitling, Eriko Takano
Summary: Spider silk is known for its impressive mechanical properties, but farming spiders for silk is impractical. Research focuses on producing recombinant spider silk proteins in more feasible hosts, with the goal of developing a highly efficient and cost-effective production system. Genes encoding these proteins have been successfully expressed in various host platforms, showing potential for large-scale production.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Katsuaki Nitta, Rainer Breitling, Eriko Takano, Sastia P. Putri, Eiichiro Fukusaki
Summary: The study focused on absolute quantification of intracellular and extracellular metabolites of Streptomyces coelicolor M1146 in different growth phases and under different mutations. Results showed significant impact of mutations on key metabolites, providing insights into changes in secondary metabolite precursors before and after phosphate depletion.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2021)
Article
Multidisciplinary Sciences
Ross Eaglesfield, Mary Ann Madsen, Suparna Sanyal, Julien Reboud, Anna Amtmann
Summary: The N-terminal hydrophobic domain of the model protein proteorhodopsin (PR) plays a critical role in recruiting ribosomes to the membrane and facilitating its insertion, offering a possible explanation for efficient membrane protein biogenesis in a pre-translocon era. Additionally, artificially attaching ribosomes to the membrane can restore the insertion of N-terminally truncated PR.
Article
Engineering, Biomedical
A. D. Roberts, D. R. Whittall, R. Breitling, E. Takano, J. J. Blaker, S. Hay, N. S. Scrutton
Summary: This study examines the use of human serum albumin (HSA) as a binder for simulated Lunar and Martian regolith to produce extraterrestrial regolith biocomposites (ERBs). These HSA-based ERBs display high compressive strengths, can potentially be 3D-printed, and represent an intriguing avenue for extraterrestrial construction using human-derived feedstocks.
MATERIALS TODAY BIO
(2021)
Review
Biochemistry & Molecular Biology
Jack A. Connolly, William R. Harcombe, Michael J. Smanski, Linda L. Kinkel, Eriko Takano, Rainer Breitling
Summary: Microbiomes consisting of diverse communities of organisms from across kingdoms can significantly impact plant growth and health through intercellular signals. Utilizing these signals to engineer microbiomes for beneficial interactions with crops represents a significant opportunity in advancing microbiome engineering. Achieving an optimized microbiome through the selection of synergistic consortia and genetic engineering of signal pathways is crucial for this goal.
NATURAL PRODUCT REPORTS
(2022)
Article
Plant Sciences
Gil Eshel, Nick Duppen, Guannan Wang, Dong-Ha Oh, Yana Kazachkova, Pawel Herzyk, Anna Amtmann, Michal Gordon, Vered Chalifa-Caspi, Michelle Arland Oscar, Shirli Bar-David, Amy Marshall-Colon, Maheshi Dassanayake, Simon Barak
Summary: This study investigates the genetic adaptations of the heat-tolerant Brassicaceae species Anastatica hierochuntica to desert environments. By comparing the responses to heat stress in the transcriptomes of A. hierochuntica and Arabidopsis thaliana, the research identifies extremophyte adaptations. The study finds that A. hierochuntica exhibits similar transcriptome adjustments to heat as A. thaliana, but with a lower basal expression and higher heat-induced expression. Positively selected genes in A. hierochuntica are associated with stomatal opening, nutrient acquisition, UV-B induced DNA repair, and its unique photoperiod-insensitive, early-flowering phenotype. The study suggests that the evolution of a flexible transcriptome allows plants to quickly respond to extreme temperature fluctuations, while positive selection of stress tolerance and early flowering genes facilitates an opportunistic desert lifestyle.
Article
Biochemical Research Methods
Erik K. R. Hanko, Tariq A. Joosab Noor Mahomed, Ruth A. Stoney, Rainer Breitling
Summary: TFBMiner is a tool that identifies putative metabolite-responsive transcription factor-based biosensors (TFBs) through data mining and analysis. It utilizes a heuristic rule-based gene organization model to identify gene clusters involved in the catabolism of user-defined molecules and their associated transcriptional regulators, providing wet-lab scientists with a ranked list of candidates. The pipeline was validated by identifying known sensors and discovering a biosensor for S-mandelic acid.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Mary Ann Madsen, Stefan Semerdzhiev, Jordan D. Twigg, Claire Moss, Charles D. Bavington, Anna Amtmann
Summary: Microorganisms produce diverse extracellular polymeric substances (EPS), which have a wide range of industrial applications. Cyanobacterial EPS are particularly versatile with complex structures. However, understanding the genetic makeup and regulation of EPS biosynthetic pathways in cyanobacteria is limited. This study measured the effect of changing culture media on EPS production and composition in Synechocystis sp. PCC 6803, and integrated this information with transcriptomic data. The analysis revealed a Wzy-dependent biosynthetic pathway and a protective role for xylose-rich EPS.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Plant Sciences
Jake Harris, Anna Amtmann, Jurriaan Ton
Summary: Priming is a plant's ability to remember environmental stress and improve their response to recurring stress. Epigenetic modifications in DNA and histone proteins may carry short-term and long-term memory or mediate transgenerational effects in plants. New experimental tools allow scientists to manipulate epigenetic modifications in specific locations of the genome, enabling them to study the causality between these modifications and gene expression under stress. Combining site-directed epigenetic manipulation with specific promoters creates opportunities for studying and engineering spatiotemporal patterns of priming.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Plant Sciences
Giorgio Perrella, Carlo Fasano, Naomi A. Donald, Loretta Daddiego, Weiwei Fang, Damiano Martignago, Craig Carr, Lucio Conti, Pawel Herzyk, Anna Amtmann
Summary: Early responses of plants to environmental stress factors can prevent damage, but may delay growth and development in fluctuating conditions. The study shows that HDC1 regulates stress responsiveness in Arabidopsis seedlings by attenuating transcriptome re-programming and inhibiting the induction of two genes (LEA and MAF5) under salt stress. This finding reveals the molecular mechanism of HDC1 in tuning stress responsiveness in plants.
Article
Biology
Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
COMMUNICATIONS BIOLOGY
(2019)
