Article
Multidisciplinary Sciences
Shukun Luo, Bruna G. Coutinho, Prikshat Dadhwal, Yasuhiro Oda, Jiahong Ren, Amy L. Schaefer, E. Peter Greenberg, Caroline S. Harwood, Liang Tong
Summary: Some plant-associated proteobacteria have LuxR family transcription factors known as PipR subfamily members that play important roles in interactions with plant hosts and bacterial virulence of plants. The ethanolamine derivative, HEHEAA, was identified as an effective effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas GM79. Crystallization of a HEHEAA-responsive SBP revealed the molecular basis of PipR system responses to plant factors, showing that different PipR-associated SBPs bind different effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
Summary: The study analyzed the expression dynamics of thousands of genes with inducible promoters, revealing the impact of RNA polymerase and LacI repressor binding site strengths on gene expression. By fitting a statistical mechanics model, properties of theoretically optimal inducible promoters were accurately modeled. Through the examination of three alternative promoter architectures, the study showed how repositioning binding sites within promoters influences the combinatorial effects observed between promoter elements.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Keziah M. Omenge, Florian Ruempler, Subha Suvetha Kathalingam, Alexandra C. U. Furch, Guenter Theissen
Summary: Research has shown that different phytoplasma effector proteins have varying effects on host plants depending on the timing and manner of induction, all interfering with flower development and shoot branching. This suggests functional redundancy among these effector proteins, but also subtle differences that have important implications for plant branching patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Horticulture
Taghleb Al-Deeb, Mohammad Abo Gamar, Najib El-Assi, Hmoud Al-Debei, Rabea Al-Sayaydeh, Ayed M. Al-Abdallat
Summary: The study identified an orthologous gene of the DWARF AND DELAYED FLOWERING (DDF) members in Arabidopsis, SlDDF2, in tomato plants and observed its clear induction in response to ABA treatment, cold, salinity, and drought stresses. Transgenic lines with stress-inducible overexpression of SlDDF2 showed growth retardation phenotypes and higher chlorophyll content under stress conditions. Compared to wild-type plants, the transgenic lines exhibited enhanced tolerance to different abiotic stresses including water deficit, salinity, and cold.
Article
Biochemistry & Molecular Biology
Paola Pellanda, Mattia Dalsass, Marco Filipuzzi, Alessia Loffreda, Alessandro Verrecchia, Virginia Castillo Cano, Hugo Thabussot, Mirko Doni, Marco J. Morelli, Laura Soucek, Theresia Kress, Davide Mazza, Marina Mapelli, Marie-Eve Beaulieu, Bruno Amati, Arianna Sabo
Summary: Eukaryotic transcription factors have both specific DNA sequence motif recognition and non-specific DNA-binding activity. Non-specific DNA binding is essential for engaging with genomic regulatory regions, while sequence recognition contributes to transcriptional activation by stabilizing Myc onto DNA and unexpectedly promoting its transcriptional activity. The seemingly pervasive genome interaction profiles detected by ChIP-seq actually encompass diverse DNA-binding modes driving defined, sequence-dependent transcriptional responses.
Article
Plant Sciences
Yugo Kitazawa, Nozomu Iwabuchi, Kensaku Maejima, Oki Matsumoto, Masato Suzuki, Juri Matsuyama, Hiroaki Koinuma, Kenro Oshima, Shigetou Namba, Yasuyuki Yamaji
Summary: To gain a deeper understanding of protein function, it is crucial to identify its physical interactions with its target. Through random mutagenesis using error-prone PCR, we comprehensively studied the interface residues between phyllogen and MTF. Two novel residues were identified, which enhanced the affinity of phyllogen to MTF through mutations. These residues, along with other known interaction-involved residues, are clustered on the surface of the protein structure of phyllogen, suggesting their involvement in the interaction. In silico structural prediction using ColabFold revealed that phyllogen interacts with the K domain of MTF through the putative interface. Our study contributes to the understanding of the interaction mechanisms between phyllogen and MTF.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Jacqueline M. Dresch, Regan D. Conrad, Daniel Klonaros, Robert A. Drewell
Summary: This study examines the sequence variation of core promoter elements in Drosophila melanogaster and reveals the importance of considering detailed sequence composition features for accurate bioinformatic predictions.
Article
Plant Sciences
Yushun Zhang, Qiong Chen, Guanlin Zhu, Dechun Zhang, Weihong Liang
Summary: In this study, it was found that the C-terminal of the chromatin-remodeling factor CHR721 with a non-canonical PIP-box is essential for interacting with OsPCNA in rice, indicating that CHR721 and OsPCNA may play a critical role in DNA damage repair.
Article
Medicine, Research & Experimental
Ilkka Liikanen, Colette Lauhan, Sara Quon, Kyla Omilusik, Anthony T. Phan, Laura Barcelo Bartroli, Amir Ferry, John Goulding, Joyce Chen, James P. Scott-Browne, Jason T. Yustein, Nicole E. Scharping, Deborah A. Witherden, Ananda W. Goldrath
Summary: Adoptive T cell therapies show great promise in cancer treatment, but face challenges. Promoting CD8(+) T cell adaptation to tissue residency can enhance tumor-infiltrating lymphocyte function. Research has found that deleting the HIF negative regulator VHL can induce T cell differentiation into Trm-like TILs, increasing anti-tumor activity.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Review
Agronomy
Ahamed Khan, Noohi Nasim, Baveesh Pudhuvai, Bhupendra Koul, Santosh Kumar Upadhyay, Lini Sethi, Nrisingha Dey
Summary: This review discusses the application of synthetic promoters in plants to overcome the limitations of native promoters in terms of size, distribution, and induction, which ultimately leads to insufficient transcriptional activity. It emphasizes the basic structure and function of the promoter, with a focus on the role of Cis-elements in gene expression regulation. The importance of synthetic promoters in the field of plant biology is highlighted, along with information on two major approaches: conventional methods and advancements in gene editing technology. The efficiency of synthetic promoters and the expression level of transgenes are crucial for successful plant genetic manipulation, making the development of synthetic promoters highly promising for genetic engineering-mediated crop improvement.
Article
Plant Sciences
Himanshu Tak, Sanjana Negi, Thumballi R. Ganapathi
Summary: Increasing crop productivity is crucial for global food supply, and closing stomata plays a key role in pathogen resistance and drought tolerance. Novel research has uncovered insights into stomatal closure networks that can enhance crop endurance.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biochemistry & Molecular Biology
Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky, Tatiana V. Tatarinova
Summary: This study utilized computational approaches to predict genome-wide TSS in four conifer species, laying the groundwork for future research on gene regulatory regions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Masato Suzuki, Yugo Kitazawa, Nozomu Iwabuchi, Kensaku Maejima, Juri Matsuyama, Oki Matsumoto, Kenro Oshima, Shigetou Namba, Yasuyuki Yamaji
Summary: This study discovered a novel mechanism determining the degradation specificity of phyllogens through detailed analysis of a rice yellow dwarf phytoplasma homologue, and elucidated that phyllogen target specificity is regulated by both the MTF-binding ability and RAD23 recruitment ability of the MTF/phyllogen complex.
MOLECULAR PLANT PATHOLOGY
(2023)
Article
Plant Sciences
Jennifer P. C. To, Ian W. Davis, Matthew S. Marengo, Aabid Shariff, Catherine Baublite, Keith Decker, Rafaelo M. Galvao, Zhihuan Gao, Olivia Haragutchi, Jee W. Jung, Hong Li, Brent O'Brien, Anagha Sant, Tedd D. Elich
Summary: New expression elements were computationally generated for effective transgene expression in crops, showing precise initiation of transcripts, effective splicing of introns, and predictable processing of transcript ends. These elements have the potential to optimize gene expression in future plant biotechnology traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Zhi-Qin Liu, Lan-Ping Shi, Sheng Yang, Shan-Shan Qiu, Xiao-Ling Ma, Jin-Sen Cai, De-Yi Guan, Zong-Hua Wang, Shui-Lin He
Summary: The study reveals that the DWE element in the promoter of CaWRKY40 is critical for responses to Ralstonia solanacearum inoculation or heat stress, with preferential binding by CaWRKY40 and regulation by CaWRKY58 and CaWRKY27. Additionally, the presence of DWE in orthologous promoters of other WRKY40 genes indicates a conserved response mechanism to pathogen infection or heat stress mediated by WRKY40 binding to DWE.
MOLECULAR PLANT PATHOLOGY
(2021)