Article
Plant Sciences
Selin Buelbuel, Yasuhito Sakuraba, Mastoureh Sedaghatmehr, Mutsumi Watanabe, Rainer Hoefgen, Salma Balazadeh, Bernd Mueller-Roeber
Summary: BBX14 is a negative regulator of nitrogen starvation-induced leaf senescence and is directly regulated by PIF4 and MYB44. It directly regulates the transcription of EIN3, which is involved in nitrogen signaling and leaf senescence.
Article
Plant Sciences
Wenbo Shan, Michaela Kubova, Terezie Mandakova, Martin A. Lysak
Summary: The nuclear organization in Arabidopsis thaliana, characterized by nucleolus-associated telomere clustering, is found to be universal in small-genome crucifer species but varies in large-genome species. This suggests that genomic properties rather than phylogenetic position play a significant role in determining interphase nuclear organization in crucifer genomes, where factors such as nuclear genome size and chromosome compartmentalization influence chromosome organization.
Article
Plant Sciences
Dawid Bielewicz, Jakub Dolata, Mateusz Bajczyk, Lukasz Szewc, Tomasz Gulanicz, Susheel S. Bhat, Anna Karlik, Monika Jozwiak, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Summary: HYL1, also known as DRB1, is a double-stranded RNA-binding protein involved in miRNA processing in plants. It was found to have a novel function in the transcription of MIR genes, affecting the distribution of RNA polymerase II and interacting with various transcription factors. Additionally, HYL1 was found to impact the expression of many other genes, particularly those involved in plastid organization.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Monika Zakrzewska-Placzek, Anna Golisz-Mocydlarz, Michal Krzyszton, Justyna Piotrowska, Malgorzata Lichocka, Joanna Kufel
Summary: This study demonstrates the involvement of AtNOL12 in rRNA biogenesis and its correlation with stress response in plants. The absence of AtNOL12 alters the expression of ribosomal protein and ribosome biogenesis genes, potentially impacting ribosome function.
Article
Plant Sciences
Craig S. S. Pikaard, Chinmayi Chandrasekhara, Anastasia McKinlay, Ramya Enganti, Dalen Fultz
Summary: Nucleolus organizer regions (NORs) are chromosomal loci where rRNA genes are clustered. NORs have been found to exhibit morphological differences in interspecific hybrids, which correlate with differences in rRNA gene transcription, known as nucleolar dominance. Studies have shown that nucleolar dominance is a result of selective rRNA gene silencing, involving chromatin modifications, and can occur in pure species as well as hybrids. Recent evidence suggests that silencing depends on the NOR location rather than the gene sequence.
Article
Plant Sciences
Zhenzhen Han, Jinyu Wang, Xinxin Wang, Xijia Zhang, Yanbo Cheng, Zhandong Cai, Hai Nian, Qibin Ma
Summary: In this study, the functional characterization of GmWRKY21 gene in soybean was investigated, and it was found that it promotes tolerance to aluminum stress. This finding is important for understanding the plant's response to stress and improving crop resilience.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Dario Paolo, Lisa Rotasperti, Arp Schnittger, Simona Masiero, Lucia Colombo, Chiara Mizzotti
Summary: Seed size is controlled by complex molecular networks in Arabidopsis, with the MADS-domain transcription factor SEEDSTICK playing a key role in regulating it. STK acts as a maternal activator of growth in the earlier phases of seed development by positively regulating cell cycle progression via activating the expression of E2Fa.
Article
Plant Sciences
Lei Gu, Xuanxuan Chen, Yunyan Hou, Heyan Wang, Hongcheng Wang, Bin Zhu, Xuye Du
Summary: In this study, a maize WRKY transcription factor gene, ZmWRKY70, was cloned and found to be accumulated under submergence stress in maize seedlings. ZmWRKY70 was localized in the nucleus and had transcriptional activation activity. Overexpression of ZmWRKY70 in Arabidopsis and maize increased the tolerance to submergence stress by upregulating the expression of key genes involved in anaerobic respiration. ZmWRKY70 enhanced the expression of ZmERF148 by binding to its promoter region. These findings suggest that ZmWRKY70 plays a significant role in submergence stress tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Anastasia McKinlay, Dalen Fultz, Feng Wang, Craig S. Pikaard
Summary: This paper presents a simple method for achieving greater than tenfold enrichment of Arabidopsis thaliana 45S rRNA gene sequences among ultra-long sequencing reads, providing a new approach for locating missing regions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Oscar J. Pundel, Liisa M. Blowes, John T. Connelly
Summary: Adhesive cues from the extracellular matrix (ECM) transmit mechanical forces through the cytoskeleton to specify the size and shape of the nucleus. This study finds that limited adhesion promotes nucleolar fusion, reduces nuclear volume, and condenses heterochromatin. Nucleolar remodeling impacts ribogenesis and protein synthesis, and is associated with specific transcriptional changes in ribogenesis genes.
Article
Plant Sciences
Beata Siemiatkowska, Matteo Chiara, Bhaskara G. Badiger, Matteo Riboni, Francesca D'Avila, Daniele Braga, Mohamed Abd Allah Salem, Damiano Martignago, Sara Colanero, Massimo Galbiati, Patrick Giavalisco, Chiara Tonelli, Thomas E. Juenger, Lucio Conti
Summary: Transcriptional reprogramming prior to morphological and physiological acclimation is crucial in drought stress responses, with the phytohormone abscisic acid (ABA) being the key signal regulating gene expression. GIGANTEA (GI) is identified as a key regulator of ABA-regulated transcriptional and physiological responses, controlling oscillations in ABA signals through DNA binding or function of different classes of transcription factors (TFs). GI plays a role in establishing a phase of reduced ABA sensitivity and related physiological responses by interacting with TFs at target regions.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Jessica A. S. Barros, Joao Henrique F. Cavalcanti, Karla G. Pimentel, David B. Medeiros, Jose C. F. Silva, Jorge A. Condori-Apfata, Taly Lapidot-Cohen, Yariv Brotman, Adriano Nunes-Nesi, Alisdair R. Fernie, Tamar Avin-Wittenberg, Wagner L. Araujo
Summary: This study investigated the metabolic adjustments in plants under carbon starvation and the role of the transcription factor WRKY45. The results showed that overexpression of WRKY45 leads to early senescence and altered amino acid metabolism, and is associated with dysregulation of mitochondrial signaling and activation of alternative respiration.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Hongjie Wang, Cheng Li, Lidan Wang, Hongying Zhong, Xin Xu, Yanbo Cheng, Hai Nian, Wenhua Liu, Pei Chen, Aixia Zhang, Qibin Ma
Summary: In this study, the GmABR1 gene from soybean was investigated for its aluminum tolerance. The results showed that GmABR1 gene was constitutively expressed in root tip, stem, and leaf tissues, and its transcript increased significantly under aluminum stress. GmABR1 may regulate plant resistance to aluminum stress through genes related to aluminum stress response and ABA response pathways.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Timothy O. Jobe, Qi Yu, Felix Hauser, Qingqing Xie, Yuan Meng, Tim Maassen, Stanislav Kopriva, Julian I. Schroeder
Summary: The SLIM1 transcription factor plays a crucial role in arsenic-induced gene expression and tolerance mechanisms. Mutant alleles in SLIM1 exhibit higher sensitivity to arsenic than cadmium, leading to increased oxidative stress and impaired sulfur assimilation. Enhanced arsenic accumulation in roots of slim1 mutants suggests altered redox status as a possible cause for their severe arsenic sensitivity.
Article
Plant Sciences
Yi-Chen Lee, Pei-Ting Tsai, Xun-Xian Huang, Huang-Lung Tsai
Summary: BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family members are plant-specific GAGA-motif binding factors (GAFs) controlling multiple developmental processes of growth and propagation. This study reveals the importance of BPCs in regulating growth and development by forming a meticulous repressor network. These findings provide insights into the molecular mechanisms controlling plant growth and development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Klara Konecna, Pavla Polanska Sovakova, Karin Antekova, Jiri Fajkus, Miloslava Fojtova
Summary: The study found that exposure to the hypomethylation drug zebularine resulted in shorter telomeres in Arabidopsis plants, with progressive changes across generations, high inter-individual variability, and diverse responses among different ecotypes. Shortening of telomeres corresponded to the transcriptional activation of transposable elements (TEs), indicating a correlated response to zebularine treatment. Changes in telomere lengths and TE transcript levels were not always associated with cytosine hypomethylation, suggesting an independent regulatory mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Petr Fajkus, Vratislav Peska, Jiri Fajkus, Eva Sykorova
Summary: This study examined the presence and functional status of TERT variants in allotetraploid Nicotiana species of diverse evolutionary ages, as well as in other diploid and polyploid plant species. Results showed various patterns of retention or loss of parental TERT variants and divergence in their functions, with all identified TERT variants confirmed to be expressed. Synteny analyses revealed the conservation and translocation of TERT genes in representative plant genomes, with translocation becoming fixed in target loci in various diploid and polyploid species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Ivana Goffova, Jiri Fajkus
Summary: Genes encoding ribosomal RNA (rDNA) are crucial for cell survival and are sensitive to factors causing genomic instability. Their repetitive nature makes them susceptible to inappropriate recombination events, leading to unstable rDNA copy numbers. The review summarizes the structure and organization of rDNA, its role in sensing genome changes, and its relationship to aging, as well as recent findings on factors involved in chromatin assembly and DNA repair for maintaining rDNA stability in plant models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Martin Lycka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jiri Fajkus, Miloslava Fojtova
Summary: This study introduces a new online toolset called WALTER for the rapid, reproducible, and user-friendly analysis of telomere length data and statistical evaluation, representing a major upgrade in TRF scan image processing.
BMC BIOINFORMATICS
(2021)
Article
Plant Sciences
Thomas Eekhout, Martina Dvorackova, Jose Antonio Pedroza Garcia, Martina Nespor Dadejova, Pooneh Kalhorzadeh, Hilde Van den Daele, Ilse Vercauteren, Jiri Fajkus, Lieven De Veylder
Summary: The inactivation of FAS1 gene results in the activation of ATM and SOG1-mediated G2/M arrest, rendering ATR and WEE1 redundant as checkpoint regulators. Knocking out SOG1 in fast plants restores replication stress sensitivity.
Article
Cell Biology
Michal Franek, Agata Kilar, Petr Fojtik, Marie Olsinova, Ales Benda, Vladimir Rotrekl, Martina Dvorackova, Jiri Fajkus
Summary: The analysis of histone variants and epigenetic marks is mainly conducted through genome-wide approaches, such as ChIP-seq, to study the chromatin organization. Extending chromatin and DNA fibers allows for the study of individual DNA repeats in their specific chromosomal context, providing valuable insights into the epigenetic organization of genomes. It is essential to use optimized fiber extension protocols and super-resolution microscopy for reproducible data and accurate evaluation of histone modifications.
JOURNAL OF CELL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Petr Fajkus, Agata Kilar, Andrew D. L. Nelson, Marcela Hola, Vratislav Peska, Ivana Goffova, Miloslava Fojtova, Dagmar Zachova, Jana Fulneckova, Jiri Fajkus
Summary: The study characterized the evolution of telomerase RNA (TR) in early diverging Viridiplantae and other Diaphoretickes lineages through identifying conserved upstream sequence elements and TR template regions. The results demonstrated deep conservation of TR motifs across different species, highlighting the common origin and evolutionary transitions in telomere repeats.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Vratislav Peska, Petr Fajkus, Michal Bubenik, Vaclav Brazda, Natalia Bohalova, Vojtech Dvoracek, Jiri Fajkus, Sonia Garcia
Summary: Telomerase RNA (TR) plays a crucial role in telomere DNA synthesis and assembly, but its sequence diversity poses challenges in characterizing it. Long telomere units and corresponding TRs were found in certain fungal species. The presence of variable lengths in the annealing sequence of the template region suggests that species with the same telomere sequence may have different TR templates.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Rekha Agrawal, Mohan Sharma, Nidhi Dwivedi, Sourobh Maji, Pallabi Thakur, Alim Junaid, Jiri Fajkus, Ashverya Laxmi, Jitendra K. Thakur
Summary: This study reveals the role of the Mediator complex as an integrator of jasmonate (JA) and auxin signaling pathways during thermomorphogenesis in Arabidopsis. Warm temperature induces the expression of JA signaling genes and promotes the accumulation of the JA signaling receptor COI1 and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9. The Mediator complex, specifically the mediator subunit MED17, occupies the promoters of thermosensory genes and facilitates enrichment of H3K4me3, which is dependent on the bHLH transcription factor PIF4.
Article
Biochemistry & Molecular Biology
Petr Fajkus, Matej Adamik, Andrew D. L. Nelson, Agata M. Kilar, Michal Franek, Michal Bubenik, Radmila Capkova Frydrychova, Alena Votavova, Eva Sykorova, Jiri Fajkus, Vratislav Peska
Summary: Unlike the catalytic subunit of telomerase, the RNA subunit (TR) shows significant differences in size, sequence and biogenesis across eukaryotes. Previous views assumed a common origin of TRs transcribed with RNA polymerase II in Opisthokonta and Trypanosomida, and TRs transcribed with RNA polymerase III in TSAR and Archaeplastida. However, new findings from studying Hymenoptera TRs challenge this assumption and suggest an evolutionary switch in TR type and biogenesis that is associated with the divergence of Arthropods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Klara Prikrylova Konecna, Agata Kilar, Petra Kovacikova, Jiri Fajkus, Eva Sykorova, Miloslava Fojtova
Summary: This study investigates the interaction between ARM and telomerase and explores the cellular functions of ARM. The results show that ARM is involved in crucial cellular processes and has a dominant effect. Additionally, ARM is implicated in circadian rhythms and responses to drugs and stimuli.
Article
Engineering, Environmental
Martin Lycka, Milos Bartak, Ondrej Helia, Stanislav Kopriva, Dana Moravcova, Josef Hajek, Lukas Fojt, Richard Cmelik, Jiri Fajkus, Miloslava Fojtova
Summary: Hydroponic experiments were conducted to investigate the effects of prolonged sulfate limitation and Cd exposure on Arabidopsis thaliana and Nicotiana tabacum. Both species showed adverse effects on morphology, photosynthetic and biochemical parameters, and nutritional status under low sulfate treatments and Cd stress. The responses to low sulfate supply, Cd exposure, or a combination of both factors were species-specific, and Cd exposure had opposing effects on the levels of certain elements in the roots.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Plant Sciences
Eva Dvorak Tomastikova, Fen Yang, Kristina Mlynarova, Said Hafidh, Sarka Schorova, Alzbeta Kusova, Marketa Pernisova, Tereza Prerovska, Bozena Klodova, David Honys, Jiri Fajkus, Ales Pecinka, Petra Prochazkova Schrumpfova
Summary: RUVBL1 and RUVBL2 are crucial for the proper development of male and female gametophytes in Arabidopsis. Mutations in these genes result in abnormal embryo sac structure and nuclear numbers. The expression of these proteins is observed in pollen grains, embryo sac, and tapetum cells, playing important roles in reproductive development.
Article
Plant Sciences
Michal Zavodnik, Petr Fajkus, Michal Franek, David Kopecky, Sonia Garcia, Steven Dodsworth, Andres Orejuela, Agata Kilar, Jiri Ptacek, Martin Matl, Anna Hyskova, Jiri Fajkus, Vratislav Peska
Summary: Telomerase, telomeric DNA, and associated proteins form a complex and conserved mechanism that maintains genome integrity by protecting chromosome ends. Evolutionary changes in telomere maintenance have given rise to species with unusual telomeric DNA sequences and telomerase components. Telomerase RNA (TR) plays a central role in telomere maintenance, and mutations in TR can disrupt telomere DNA synthesis and recognition by telomere proteins. Through bioinformatic and experimental analyses, this study investigates the evolutionary changes in TR that underlie telomere transitions in plants, and identifies telomere transitions corresponding to TR paralogs with diverse template regions.
Article
Cell Biology
Gianluca Teano, Lorenzo Concia, Lea Wolff, Leopold Carron, Ivona Biocanin, Katerina Adamusova, Miloslava Fojtova, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Chris Bowler, Celia Baroux, Alessandra Carbone, Aline Probst, Petra Prochazkova Schrumpfova, Jiri Fajkus, Simon Amiard, Stefan Grob, Clara Bourbousse, Fredy Barneche
Summary: A study in Arabidopsis reveals the role of linker histone H1 in nucleosome organization and its functional interactions with chromatin factors. It shows that H1 contributes to chromatin condensation and H3K27me3 deposition at Polycomb Repressive Complex 2 (PRC2) target genes, while selectively preventing H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins. This study provides insights into the mechanistic framework of how H1 safeguards nucleus architecture.