Article
Biochemistry & Molecular Biology
Jin-Ping Zou, Qiu-Feng Zhao, Ting Yang, Yi-Fen Shang, Golam Jalal Ahammed, Jie Zhou
Summary: The tomato E3 ubiquitin ligase RING1 interacts with COP9 Signalosome Subunit 4 (CSN4) and positively regulates JA-dependent basal defense against root-knot nematodes (RKNs).
Article
Biochemistry & Molecular Biology
Hongqin Zhang, Tianqing Yan, Ailing Zhong, Lin Guo, Renquan Lu
Summary: The upregulation of COPS5 is associated with platinum resistance in epithelial ovarian cancer (EOC), and its overexpression is correlated with shorter survival. Inhibition of COPS5 reduces EOC cell proliferation, migration, and sensitivity to platinum.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Florian Heigwer, Christian Scheeder, Josephine Bageritz, Schayan Yousefian, Benedikt Rauscher, Christina Laufer, Sergi Beneyto-Calabuig, Maja Christina Funk, Vera Peters, Maria Boulougouri, Jana Bilanovic, Thilo Miersch, Barbara Schmitt, Claudia Blass, Fillip Port, Michael Boutros
Summary: This article reports a study that utilizes synthetic genetic interaction and cell morphology data to investigate gene function. They used machine learning to assign functions to genes in 47 modules and identified an interaction between Cdk2 and the Cop9 signalosome complex. These data provide a genome-scale resource for uncovering the mechanisms underlying genetic interactions and their plasticity at the single-cell level.
Article
Multidisciplinary Sciences
Yunpeng Huang, Zhihui Wan, Yinglu Tang, Junxuan Xu, Bretton Laboret, Sree Nallamothu, Chenyu Yang, Boxiang Liu, Rongze Olivia Lu, Bingwei Lu, Juan Feng, Jing Cao, Susan Hayflick, Zhihao Wu, Bing Zhou
Summary: PKAN and PD are two distinct diseases with overlapping pathophysiology. The pathogenic genes PANK2 and PINK1 interact with each other. This study reveals that Fbl (the homolog of PANK2) can rescue PINK1 deficiency by regulating CoA metabolism and mitophagy, providing a potential intervention strategy for PD treatment.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Maria G. Fuzesi-Levi, Gili Ben-Nissan, Dina Listov, Yael Fridmann Sirkis, Zvi Hayouka, Sarel Fleishman, Michal Sharon
Summary: Protein degradation is an essential mechanism for reshaping the proteome in response to stimuli. Cullin-RING ligases (CRLs) are the largest E3 ubiquitin ligase family targeting proteins for degradation. Dysregulation of the CRL family is associated with cancer, making it an attractive target for therapeutic intervention. CSNAP, the smallest subunit of the COP9 signalosome complex (CSN), has been identified as a potential target for CSN inhibition. The results of this study demonstrate that a 16 amino acid peptide derived from CSNAP can displace the subunit from the CSN complex, attenuating its activity and suggesting a new therapeutic avenue.
LIFE SCIENCE ALLIANCE
(2023)
Article
Oncology
Natalia Martinez, Teresa Gragera, Maria Pilar de Lucas, Ana Belen Camara, Alicia Ballester, Berta Anta, Alberto Fernandez-Medarde, Tania Lopez-Briones, Judith Ortega, Daniel Pena-Jimenez, Antonio Barbachano, Ana Montero-Calle, Victor Cordero, Rodrigo Barderas, Teresa Iglesias, Monica Yunta, Jose Luis Oliva, Alberto Munoz, Eugenio Santos, Natasha Zarich, Jose M. Rojas-Cabaneros
Summary: Spry2 is a molecular modulator of tyrosine kinase receptor signaling pathways with cancer-type-specific effects. It undergoes phosphorylation in response to growth factor stimulation. The expression of Spry2 is distinctly altered in various types of cancer.
Article
Biochemistry & Molecular Biology
Hassan Hayek, Lauriane Gross, Aurelie Janvier, Laure Schaeffer, Franck Martin, Gilbert Eriani, Christine Allmang
Summary: Eukaryotic translation initiation factor 3 (eIF3) selectively recruits and controls the expression of various cellular mRNAs, including histone mRNAs. It mediates translation of H4 mRNA by binding to a specific stem-loop structure, as well as interacting with other histone mRNAs with distinct patterns. Depletion of eIF3 in vivo reduces histone mRNA binding and modulates histone neosynthesis, suggesting that eIF3 acts as a regulator of histone translation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Avijit Mallick, Shane K. B. Taylor, Sakshi Mehta, Bhagwati P. Gupta
Summary: The Axin family of proteins plays a crucial role in controlling various cellular processes and providing specificity to signaling pathways. This study focused on the Caenorhabditis elegans Axin homolog pry-1 and its interacting gene picd-1. The findings showed that picd-1 is involved in stress response and lifespan maintenance, and its expression overlaps with pry-1 in multiple tissues. Furthermore, pry-1 and picd-1 inhibit the activity of CRTC-1, a transcriptional coactivator promoting longevity. This study highlights the importance of picd-1 in mediating pry-1 function and suggests a potential role for Cabin-1 domain-containing protein in Axin signaling in other systems.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Janet K. Jang, Amy C. Gladstein, Arunika Das, Joanatta G. Shapiro, Zachary L. Sisco, Kim S. McKim
Summary: The study highlights the critical role of PP2A in maintaining spindle assembly and sister chromatid cohesion in Drosophila oocytes, showing an interplay with Aurora B activity.
JOURNAL OF CELL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Wen-Qi Huo, Zhi-Qiang Zhang, Zhong-Ying Ren, Jun-Jie Zhao, Cheng-Xiang Song, Xing-Xing Wang, Xiao-Yu Pei, Yan-Gai Liu, Kun-Lun He, Fei Zhang, Xin-Yang Li, Wei Li, Dai-Gang Yang, Xiong-Feng Ma
Summary: An improved and comprehensive meta-QTL analysis was conducted on 487 disease resistant QTLs from 31 studies in the last two decades. A consensus linkage map with genetic overall length of 3006.59 cM containing 8650 markers was constructed. A total of 28 Meta-QTLs (MQTLs) were discovered, among which nine MQTLs were identified as related to resistance to multiple diseases. Candidate genes were predicted based on public transcriptome data and enriched in pathways related to disease resistance. This study provides a new basis for marker-assisted selection of high disease resistance in cotton breeding.
Article
Multidisciplinary Sciences
Mohammad Jafar Tanin, Dinesh Kumar Saini, Karansher Singh Sandhu, Neeraj Pal, Santosh Gudi, Jyoti Chaudhary, Achla Sharma
Summary: In this study, a meta-analysis and genome-wide association studies were used to identify multiple abiotic stress tolerance loci and related genes in wheat. The findings provide valuable information for fine mapping, gene cloning, and marker-assisted breeding for multiple abiotic stress tolerances in wheat.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Elisabeth A. Marnik, Miguel V. Almeida, P. Giselle Cipriani, George Chung, Edoardo Caspani, Emil Karaulanov, Hin Hark Gan, John Zinno, Ida J. Isolehto, Fridolin Kielisch, Falk Butter, Catherine S. Sharp, Roisin M. Flanagan, Frederic X. Bonnet, Fabio Piano, Rene F. Ketting, Kristin C. Gunsalus, Dustin L. Updike
Summary: LOTUS and Tudor domain containing proteins play critical roles in germline development, helping to localize Vasa helicase and facilitate piRNA-mediated transposon silencing. In Caenorhabditis elegans, a new protein called LOTR-1 has been identified, which contains both LOTUS and Tudor domains. It colocalizes with Z-granule helicase ZNFX-1 and is involved in positioning small RNA amplification mechanisms at the 3' ends of RNA templates.
Article
Gastroenterology & Hepatology
Zhiyan Ruan, Minhua Liang, Ling Shang, Manxiang Lai, Xiangliang Deng, Xinguo Su
Summary: This study investigated the effect of Shikonin on immune evasion in pancreatic cancer by inhibiting PD-L1 glycosylation and activating the NF-KB/STAT3 and NF-kappa B/CSN5 signaling pathways. Shikonin was shown to block immune evasion in PC by lowering the expression of key proteins involved in immune evasion. These findings suggest important potential therapeutic implications for the treatment of pancreatic cancer.
Article
Agronomy
T. D. Vuong, H. Sonah, G. Patil, C. Meinhardt, M. Usovsky, K. S. Kim, F. Belzile, Z. Li, R. Robbins, J. G. Shannon, H. T. Nguyen
Summary: Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes in one soybean accession, providing comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping.
THEORETICAL AND APPLIED GENETICS
(2021)
Retraction
Reproductive Biology
Ding Zhu, Xueshuang Huang, Fang Liang, Lijing Zhao
Summary: The article has been retracted, please refer to the Retraction Notice for more details.
JOURNAL OF OVARIAN RESEARCH
(2021)
Article
Plant Sciences
Alin Finkelshtein, Hala Khamesa, Luu Anh Tuan, Manely Rabanim, Daniel A. Chamovitz
Summary: The hydrolysis product of indole-3-methylglucosinolate, indole-3-carbinol (I3C), is toxic to herbivorous insects and pathogens, while extensively studied in mammals for its properties in cancer prevention and treatment. A novel Arabidopsis mutant, ICT1, has been identified to be tolerant to I3C, with the tolerance mechanism involving the S30 ribosomal protein. The tolerance is specific to I3C and maintained the antagonistic action of I3C on auxin signaling through an auxin-independent mechanism.
Article
Biochemistry & Molecular Biology
Ashim Paul, Guru KrishnaKumar Viswanathan, Adi Huber, Elad Arad, Hamutal Engel, Raz Jelinek, Ehud Gazit, Daniel Segal
Summary: The dopamine-based hybrid molecule NQDA effectively inhibits the aggregation of key tau-derived amyloidogenic fragments PHF6 and PHF6*, as well as full-length tau protein, in in vitro experiments. It disassembles preformed fibrils and demonstrates significant binding efficiency with tau fibrils through entropic and enthalpic processes. NQDA shows comparable or lower IC50 values for inhibiting fibril formation compared to other amyloid inhibitors, suggesting its potential as a scaffold for developing therapeutics for Alzheimer's disease and other tauopathies.
Article
Multidisciplinary Sciences
Moshe Katz, Suraj Subramaniam, Orna Chomsky-Hecht, Vladimir Tsemakhovich, Veit Flockerzi, Enno Klussmann, Joel A. Hirsch, Sharon Weiss, Nathan Dascal
Summary: CaV1.2 channels play a crucial role in regulating cardiac muscle contraction, with 0-AR increasing contraction by enhancing calcium influx through these channels via PKA activation. A recent study identified Rad as essential for PKA regulation of CaV1.2, revealing two distinct pathways of PKA modulation of CaV1.2: Rad dependent and Rad independent.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Amit Kumar Singh, Shanmuhapreya Dhanapal, Alin Finkelshtein, Daniel A. Chamovitz
Summary: The study revealed the role of CSN5A in regulating the resetting of transcriptional memory genes and H3K4me3 after recurrent heat stress in plants. CSN5A is important for histone methylation and transcriptional stress memory following recurrent heat stress.
Article
Biochemistry & Molecular Biology
Tamar Neumann, Tamir Tuller
Summary: This study developed a predictive model of small subunit (SSU) density based on TCP-seq data and analyzed the effect of transcript features on SSU scanning dynamics. The results showed that the AUG context indeed affects the movement of the SSU, strong folding may cause the detachment of the SSU from the mRNA, and several novel sequence motifs can affect the SSU scan.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Itamar Menuhin-Gruman, Matan Arbel, Niv Amitay, Karin Sionov, Doron Naki, Itai Katzir, Omer Edgar, Shaked Bergman, Tamir Tuller
Summary: Modern synthetic biology relies on stable genetic constructs, but maintenance requires cell energy and natural selection can lead to loss of construct functionality. The ESO software tool automates the design of evolutionarily stable constructs while considering host organism characteristics to balance stability and gene expression.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Shai Shefer, Mario Lebendiker, Alin Finkelshtein, Daniel A. Chamovitz, Alexander Golberg
Summary: This study demonstrates that ulvan crude extract extracted from seaweed can serve as a biostimulant for terrestrial plants, specifically promoting the growth of Arabidopsis thaliana. Ulvan's stimulative effects are dependent on dosage and light intensity. The use of ulvan as a biostimulant could potentially reduce the use of harmful agrochemicals, mitigate their negative environmental impacts, and improve crop yields, thus contributing to global food security.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biology
Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller
Summary: The development of computational biology methodologies has provided a comprehensive understanding of the complexity of microbiomes and their impact on the environment. However, current microbiome engineering techniques neglect the interactions between genetic information and bacterial populations. In this study, a generic computational method was developed to automatically tune gene expression in microbiomes based on user preferences. The method has been validated through computational and experimental tools.
Article
Biotechnology & Applied Microbiology
Arup Panda, Tamir Tuller
Summary: The environment may impact the codon and amino acid choice of microbial communities, and samples from similar environmental niches show similar codon and amino acid distribution compared to samples from other habitats. Factors like GC content, functional or taxonomic abundance cannot fully explain the trends observed at the codon or amino acid level, implying a direct environmental influence on them.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Biotechnology & Applied Microbiology
Matan Arbel-Groissman, Itamar Menuhin-Gruman, Doron Naki, Shaked Bergman, Tamir Tuller
Summary: Evolutionary stability of synthetic constructs made of heterologous genes is a major challenge in synthetic biology, and the available tools to address this challenge are discussed in this review.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Immunology
Orit Malka, Ravit Malishev, Marina Bersudsky, Manikandan Rajendran, Mathumathi Krishnamohan, Jakeer Shaik, Daniel A. Chamovitz, Evgeni Tikhonov, Eliya Sultan, Omry Koren, Ron N. Apte, Benyamin Rosental, Elena Voronov, Raz Jelinek
Summary: Probiotic fermented yeast produces small molecules, tryptophol acetate and tyrosol acetate, which can inhibit hyperinflammation. These molecules were found to reduce pro-inflammatory cytokines and reactive oxygen species, while maintaining core immune functions. The anti-inflammatory effects were mediated through the downregulation of signaling pathways and NF-kB inhibition. This study highlights the potential therapeutic avenues for severe inflammation.
JOURNAL OF INNATE IMMUNITY
(2023)
Article
Immunology
Orit Malka, Ravit Malishev, Marina Bersudsky, Manikandan Rajendran, Mathumathi Krishnamohan, Jakeer Shaik, Daniel A. Chamovitz, Evgeni Tikhonov, Eliya Sultan, Omry Koren, Ron N. Apte, Benyamin Rosental, Elena Voronov, Raz Jelinek
Summary: The small-molecule metabolites tryptophol acetate and tyrosol acetate secreted by the probiotic yeast Kluyveromyces marxianus inhibit hyperinflammation by reducing the levels of proinflammatory cytokines and reactive oxygen species. The anti-inflammatory effects are mediated through the downregulation of TLR4, IL-1R, and TNFR signaling pathways and increased A20 expression.
JOURNAL OF INNATE IMMUNITY
(2023)
Article
Multidisciplinary Sciences
Rami Katz, Elad Attias, Tamir Tuller, Michael Margaliot
Summary: Research has shown that mRNAs compete for shared resources during translation, which can significantly impact the global dynamics of translation in the cell when resources are scarce. By modeling this competition using a network approach, it was found that adding a new mRNA has a complex effect on total protein production, with diminishing marginal utility as the number of mRNAs increases, leading to saturation of total protein production rate to a limiting value.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biochemistry & Molecular Biology
Stav Carmel Ezra, Tamir Tuller
Summary: This study investigates the translation initiation process in chloroplasts and develops computational models to understand and model translation regulation. The folding energy of rRNA and mRNA is found to correlate with codon usage and protein levels. Additionally, the presence of various structural elements in chloroplast transcripts is reported.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Satabdee Mohapatra, Guru Krishna Kumar Viswanathan, Lukas Wettstein, Elad Arad, Ashim Paul, Vijay Kumar, Raz Jelinek, Jan Munch, Daniel Segal
Summary: Human semen contains amyloidogenic peptides that can enhance HIV-1 infection. Vitamin C has a concentration-dependent effect on the formation of amyloid fibrils derived from PAP(248-286). Low molar ratios of vitamin C promote fibril formation while high molar ratios inhibit it.
RSC CHEMICAL BIOLOGY
(2021)