Correction
Plant Sciences
O. Batistic, R. Waadt, L. Steinhorst, K. Held, J. Kudla
Summary: The ribosome stalling at AUG-stop sequences plays a critical role in regulating the expression of NIP5;1 in Arabidopsis thaliana in response to boron conditions, with boric acid triggering this process. Through ribosome profiling analysis, hundreds of translationally regulated genes functioning in various biological processes were identified, with a particular emphasis on the role of uORFs. The presence of minimum uORFs (AUG-stops) suggests these elements play a global role in responding to boron, as evidenced by the increased ribosome occupancy of stop codons under high-boron conditions.
Article
Engineering, Environmental
Yinan Zhang, Gang Sa, Ying Zhang, Siyuan Hou, Xia Wu, Nan Zhao, Yuhong Zhang, Shurong Deng, Chen Deng, Jiayin Deng, Huilong Zhang, Jun Yao, Yanli Zhang, Rui Zhao, Shaoliang Chen
Summary: Phytoremediation shows promise in remediating heavy metal-polluted soil and water. By studying a cadmium-hypersensitive plant, researchers identified a gene that facilitates cadmium enrichment, which could be a target for improving phytoremediation through genetic engineering.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Jie Pan, Huairen Zhang, Zhenping Zhan, Ting Zhao, Danhua Jiang
Summary: Seed germination is a complex process involving extensive changes in metabolism, gene expression, and cellular identity. This study examines the dynamics and function of histone H3 lysine 27 trimethylation (H3K27me3) during germination in Arabidopsis. The results suggest that H3K27me3 reprogramming occurs with a delay compared to transcriptomic changes and that H3K27 demethylation, mediated by RELATIVE OF EARLY FLOWERING 6 (REF6), is necessary for robust germination and the activation of hormone-related and expansin-coding genes.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Plant Sciences
Roisin C. McGarry, Harmanpreet Kaur, Yen-Tung Lin, Guadalupe Lopez Puc, Leor Eshed Williams, Esther van der Knaap, Brian G. Ayre
Summary: Modifying gene expression in cotton plants through the CLV-WUS regulatory network can alter the balance between cellular differentiation and stem cell proliferation, thereby affecting fruit size and crop value.
Article
Biochemistry & Molecular Biology
Jaroslav Fulnecek, Eva Klimentova, Albert Cairo, Sona Valuchova Bukovcakova, Panagiotis Alexiou, Zbynek Prokop, Karel Riha
Summary: The C-terminal SAP domain of Ku70 is involved in the initial phases of Ku-DNA interaction but not the sliding process. Ku lacking the SAP domain can still function in classical NHEJ and telomere maintenance.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Vida Strancar, Katarina P. van Midden, Daniel Krahn, Kyoko Morimoto, Marko Novinec, Christiane Funk, Simon Stael, Christopher J. Schofield, Marina Klemencic, Renier A. L. van der Hoorn
Summary: This study developed activity-based probes for the three main types of Metacaspases and demonstrated the essential role of calcium in the activation process. The findings suggest the formation of active, unprocessed intermediates upon calcium binding before precursor protein maturation.
Article
Biochemistry & Molecular Biology
Anting Zhu, Mengmeng Liu, Zhitao Tian, Wei Liu, Xin Hu, Min Ao, Jingqi Jia, Taotao Shi, Hongbo Liu, Dongqin Li, Hailiang Mao, Handong Su, Wenhao Yan, Qiang Li, Caixia Lan, Alisdair R. Fernie, Wei Chen
Summary: This study investigated the relationship between metabolite modification and gene function in wheat. By profiling metabolic fragment enrichment in wheat leaves, the researchers identified 1,483 quantified metabolites that can be modified in an enzyme-catalyzed manner. Through genome-wide association studies, they were able to efficiently mine candidate genes associated with these metabolites. In further functional studies, a flavonoid pathway specific to Triticeae crops and its underlying metabolic gene cluster were elucidated. The researchers also reconstructed this pathway in rice using the major effect gene from the cluster. This study provides valuable insights into the genetic architecture of wheat and has implications for crop improvement.
Article
Biochemistry & Molecular Biology
Yingying Xing, Ning Xu, Deepak D. Bhandari, Dmitry Lapin, Xinhua Sun, Xuming Luo, Yeqiong Wang, Jidong Cao, Hongbin Wang, Gitta Coaker, Jane E. Parker, Jun Liu
Summary: The pathogen targets the plant iron sensor protein BRUTUS through the effector protein AvrRps4 to facilitate iron uptake and pathogen proliferation in Arabidopsis thaliana. AvrRps4 inhibits the degradation of iron regulatory proteins and enhances the accumulation of immune proteins, contributing to immune responses mediated by RPS4/EDS1.
Article
Plant Sciences
Rui Wang, Anna A. Dobritsa
Summary: In this study, the Arabidopsis mutant tex2 was characterized, showing that the TEX2 gene plays a crucial role in exine development when expressed in the tapetum. Loss of TEX2 leads to abnormal primexine formation and failure of correct sporopollenin assembly. Additionally, tex2 tapetum accumulates metabolic inclusions related to sporopollenin polyketide biosynthesis, providing a potential tool for studying genetic relationships between genes involved in exine formation.
Article
Plant Sciences
Ayako Nishizawa-Yokoi, Ritsuko Motoyama, Tsuyoshi Tanaka, Akiko Mori, Keiko Iida, Seiichi Toki
Summary: Land plants have developed defense systems, including DNA damage response (DDR) and DNA repair systems, to protect themselves. In rice, the transcription factor OsSOG1 plays a crucial role in controlling DDR and DNA repair and has differences compared to Arabidopsis.
Article
Multidisciplinary Sciences
Dana J. Somers, David B. Kushner, Alexandria R. Mckinnis, Dzejlana Mehmedovic, Rachel S. Flame, Thomas M. Arnold
Summary: Cruciferous plants produce sulforaphane (SFN) which acts as an inhibitor of histone deacetylases (HDACs). Consuming SFN can alter enzyme activities, DNA-histone binding, and gene expression in mammals within minutes. This study demonstrates that SFN can also inhibit HDAC enzymes in insects, leading to slower development in a dose-dependent manner. However, specialist feeder insects like Trichoplusia ni are not negatively affected by SFN, suggesting a potential co-evolutionary adaptation. These findings suggest that plant-derived HDAC inhibitors serve as epigenetic weapons against herbivores.
Article
Plant Sciences
Ayako N. Sakamoto, Tomoaki Sakamoto, Yuichiro Yokota, Mika Teranishi, Kaoru O. Yoshiyama, Seisuke Kimura
Summary: The study on SOG1 in Physcomitrella patens revealed that PpSOG1a and PpSOG1b work redundantly in DNA damage responses, indicating the establishment of plant-specific DNA repair systems before the evolution of vascular plants.
Review
Plant Sciences
Michelle Roenspies, Patrick Schindele, Holger Puchta
Summary: The powerful CRISPR/Cas system has revolutionized plant breeding by enabling precise genome manipulation, moving beyond simply knocking in or out single genes to inducing targeted chromosomal rearrangements. This technique has the potential to transform plant breeding by altering genetic linkages between traits and overcoming natural obstacles to breeding processes like inversions. Recent breakthroughs in chromosome engineering in plants suggest potential applications in shaping plant chromosomes based on breeding needs.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Leonie Hacker, Niklas Capdeville, Laura Feller, Janina Enderle-Kukla, Annika Dorn, Holger Puchta
Summary: WSS1A is crucial for repair of DNA-protein crosslinks in plants; Loss of WSS1A leads to reduced rDNA repeats and chromosomal fragmentation; WSS1A is involved in suppressing DSB formation or in DSB repair itself, especially in the absence of other factors from the RTR complex.
Article
Biochemistry & Molecular Biology
Leonie Hacker, Annika Dorn, Janina Enderle, Holger Puchta
Summary: The research reveals that Arabidopsis thaliana has two main repair pathways for TOP2cc, mediated by TDP2 and WSS1A, while MUS81 plays a major role in global DPC repair. Additionally, TDP1 and TDP2 function in TOP1cc repair, preventing erroneous pathways.
Article
Biochemical Research Methods
Michelle Ronspies, Patrick Schindele, Rebecca Wetzel, Holger Puchta
Summary: The rise of CRISPR-Cas system enables the induction of double-strand breaks at desired target sites in the genome. In plant somatic cells, double-strand breaks are repaired through an error-prone pathway leading to mutations. Recent study successfully achieved chromosomal rearrangements in Arabidopsis by combining efficient SaCas9 with an egg-cell-specific promoter. The chromosome-engineering protocol used Agrobacterium-mediated transformation to introduce SaCas9 and guide RNAs into Arabidopsis, and the generation of homozygous lines requires approximately 1 year.
Editorial Material
Plant Sciences
Holger Puchta, Jiming Jiang, Kan Wang, Yunde Zhao
Article
Multidisciplinary Sciences
Angelina Schindele, Fabienne Gehrke, Carla Schmidt, Sarah Roehrig, Annika Dorn, Holger Puchta
Summary: CRISPR/Cas is mainly used for mutagenesis, but this study shows that induction of cell death can be achieved using the SaCas9 nuclease, referred to as CRISPR-Kill, for tissue engineering. By replacing the promoter, organogenesis can be blocked and specific traits can be targeted, such as eliminating petals and reducing lateral root numbers and length. CRISPR-Kill may have implications not only for controlling development but also altering biochemical properties of plants.
NATURE COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Niklas Capdeville, Patrick Schindele, Holger Puchta
Summary: Since their first adaptation for plant genome editing, CRISPR-Cas system nucleases and tools have revolutionized the field, enabling precise induction of predefined modifications and the generation of more efficient base editors. Prime editors have also been optimized for plant applications, allowing accurate substitutions, insertions, and deletions. Recent progress in chromosome restructuring allows not only genetic linkages and breakage, but also promoter swapping.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Patrick Schindele, Laura Merker, Tom Schreiber, Anja Prange, Alain Tissier, Holger Puchta
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Eva Dvorak Tomastikova, Klara Prochazkova, Fen Yang, Jitka Jemelkova, Andreas Finke, Annika Dorn, Mahmoud Said, Holger Puchta, Ales Pecinka
Summary: DNA-protein cross-links (DPCs) are highly toxic DNA lesions that block DNA replication and transcription. Arabidopsis has three pathways to repair DPCs: endonucleolytic cleavage, proteolytic degradation, and cleavage of phosphodiester bonds. The SMC5/6 complex is identified as an important factor in plant DPC repair through a genetic screen.
Article
Plant Sciences
Fabienne Gehrke, Paola Ruiz-Duarte, Angelina Schindele, Sebastian Wolf, Holger Puchta
Summary: The application of the CRISPR/Cas system as a biotechnological tool for genome editing has revolutionized plant biology. Recently, the repertoire was expanded by CRISPR-Kill, enabling CRISPR/Cas-mediated tissue engineering through genome elimination by tissue-specific expression. This new system not only provides spatial control by tissue-specific expression but also allows temporal control of CRISPR-mediated cell death in Arabidopsis thaliana.
Article
Biotechnology & Applied Microbiology
Janine Pietralla, Niklas Capdeville, Patrick Schindele, Holger Puchta
Summary: ErCas12a is a nuclease derived from Eubacterium rectale with potential applications in plant genome engineering. Optimized through protein engineering, an improved variant named imErCas12a showed significantly enhanced gene editing efficiency in comparison to the wild-type enzyme. This economically attractive alternative demonstrated strong editing efficiencies at lower temperatures and enabled editing of previously inaccessible targets without off-site activity.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Review
Plant Sciences
Holger Puchta, Andreas Houben
Summary: Spontaneous chromosomal rearrangements (CRs) play a vital role in speciation, genome evolution and crop domestication. Chromosome engineering, through methods such as chromosomal translocations, inversion reversions, and construction of minichromosomes, has the potential to modify genetic linkage groups, change the number of chromosomes, and establish genetic isolation, thus aiding breeding and plant biotechnology.
Article
Plant Sciences
Michelle Roenspies, Carla Schmidt, Patrick Schindele, Michal Lieberman-Lazarovich, Andreas Houben, Holger Puchta
Summary: This study demonstrates the suppression of meiotic recombination through chromosome restructuring, inducing a heritable inversion and discovering that genetic exchange mainly occurs at telomeric ends.
Article
Plant Sciences
Michelle Roenspies, Holger Puchta
Summary: A major challenge in plant breeding is the establishment or breakage of genetic linkages through random meiotic recombination. This problem can be addressed by utilizing CRISPR-Cas-mediated chromosome engineering. Researchers found that by inverting a segment of chromosome 2 in Arabidopsis thaliana, they were able to effectively suppress genetic crossovers in that region.
Article
Plant Sciences
Fabienne Gehrke, Angelina Schindele, Holger Puchta
Summary: Heritable plant chromosome engineering can be achieved in somatic cells using CRISPR/Cas to induce nonhomologous double-strand break repair pathways. This technology allows for large-scale restructuring of plant chromosomes, including duplications, inversions, and translocations. The use of nonhomologous end joining pathways in somatic cells facilitates efficient chromosomal rearrangements. This breakthrough has the potential to revolutionize plant breeding.
