Article
Plant Sciences
Liyao Su, Tian Zhang, Bin Yang, Tianyu Dong, Xiaoyu Liu, Yibo Bai, Hui Liu, Jingsong Xiong, Yan Zhong, Zong-Ming (Max) Cheng
Summary: This study analyzed the evolutionary history, expansion and contraction patterns, and changes in interaction relationships of TIR1/AFB and AUX/IAA genes. The results showed that gene duplication and whole-genome duplication contributed to the expansion of the AUX/IAA gene family, while TIR1/AFB gene duplicates were lost after whole-genome duplication. Additionally, specific interactions and gene expression patterns were found to contribute to the functional diversification of TIR1/AFB and AUX/IAA.
Article
Horticulture
Yutong Zhao, Qing Wang, Dan Guan, Haiqing Yang, Jianwei Wu, Yueping Liu
Summary: Fruit softening is an important characteristic of peach fruit ripening. The role of TIR1 in the softening process of peach fruits has been little studied. In this study, low concentrations of exogenous NAA treatment resulted in reduced hardness of isolated peach fruits. The treatment also decreased the transcription levels of PpPG, Pp-β-GAL, and PpACS1 genes related to cell wall softening and ethylene synthesis.
Article
Multidisciplinary Sciences
Bin Huang, Yuxin Qi, Xueshuang Huang, Peng Yang
Summary: In this study, 23 Aux/IAA genes were identified in the genome of Salvia miltiorrhiza (S. miltiorrhiza) using bioinformatics methods. These genes were classified into typical IAA and atypical IAA based on their domain structure. The expression of these genes was found to be regulated by various hormones and environmental factors, in addition to auxins. The findings lay a solid foundation for further understanding the function of the Aux/IAA gene family and hold promising prospects for improving the genetics of S. miltiorrhiza and its associated species.
Review
Biochemistry & Molecular Biology
Anastasiia I. Petushkova, Lyudmila V. Savvateeva, Andrey A. Zamyatnin
Summary: Papain-like cysteine proteases are widely expressed enzymes that regulate protein turnover in lysosomes. Recent discoveries have shown that these proteases also have specific functions in different organelles and extracellular environments. Human cysteine cathepsins are the most studied proteases in this family and are involved in both physiological and pathological processes. The specificity of each protease to its substrates is determined by the structure of the binding cleft and the amino acid motifs in this region.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Yi Zhang, Yong-ping Xu, Ju-kui Nie, Hong Chen, Genji Qin, Bo Wang, Xiao-Dong Su
Summary: The crystal structures of TCP domains in complex with different dsDNA reveal their unique DNA-binding motif and three-site recognition mode. The TCP domains show broad specificity for DNA sequences even shorter than the consensus binding sites, adding complexity to the regulatory network of plant TCP transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
David Akopian, Colleen A. McGourty, Michael Rape
Summary: Cuilin-RING E3 ligases (CRLs) are essential ubiquitylation enzymes and the formation of CRL complexes is a tightly regulated process, with co-adaptors playing an important role in CRL assembly.
Article
Biology
Yasmin ElMaghloob, Begona Sot, Michael J. McIlwraith, Esther Garcia, Tamas Yelland, Shehab Ismail
Summary: The study demonstrates that BART acts as a bona fide co-GEF for ARL3, interacting with ARL3 and ARL13B to efficiently activate ARL3 and maintain its active state. This finding contributes to a better understanding of the role of ARL3 in regulating ciliary function.
Article
Multidisciplinary Sciences
Kristine F. R. Pobre-Piza, Melissa J. Mann, Ashley R. Flory, Linda M. Hendershot
Summary: The co-chaperones BiP, ERdj4, ERdj5, and GRP170 associate with aggregation-prone peptides. In this study, the impact of Interstitial Lung Disease (ILD)-associated mutants of surfactant protein C (SP-C) on protein maturation is investigated. The authors demonstrate that the ILD mutants disrupt di-sulfide bond formation and expose aggregation-prone peptides, leading to binding with ERdj4, ERdj5, and GRP170. Furthermore, the destabilized mutant BRICHOS domain affects the insertion of its transmembrane (TM) region in the ER membrane. This study provides insights into chaperone specificity, the recognition of aggregation-prone regions, and the consequences of disease-associated mutants on protein folding.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Tianxiao Ma, Adrian Jan Grzedowski, Thomas Doneux, Dan Bizzotto
Summary: In this study, a novel approach combining electrochemical and optical methods was used to investigate the properties of molecular monolayer interfaces, with a focus on detecting DNA hybridization. The results showed that the fluorescence intensity of the surface can be controlled by redox electrochemistry, and it depends on factors such as the potential controlling the oxidation state of the redox tag, the surface density of DNA, the composition ratio of the labeled and unlabeled DNA strands, and the local environment. The electrochemical-fluorescence measurements demonstrated improved detection of hybridized DNA compared to traditional electrochemical measurements, and the method also provided insights into the spatial heterogeneity of electron-transfer kinetics and the influence of the local interfacial environment.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Dan Bizzotto, Tianxiao Ma, Adrian Jan Grzedowski, Thomas Doneux
Summary: This study introduces a method that uses redox electrochemistry to control surface-based fluorescence intensity for detecting DNA hybridization and studying the uniformity of the surface response. By introducing fluorescent dyes and redox tags on single-strand DNA, significant changes in fluorescence intensity were observed. Comparing electrochemical-fluorescence measurements to electrochemical measurements showed improved performance in detecting hybridized DNA.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Daniel G. Droege, Timothy C. Johnstone
Summary: We have described a small-molecule platform that serves as an antidote for CO poisoning. This platform exhibits key properties such as CO binding and prevention of inactive oxo-bridged dimers. Our experiments demonstrate that the platform can rescue CO-poisoned red blood cells and restore their function.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sindhiya Sridharan, Santhosh Kumar Nagarajan, Kathirvel Venugopal, G. Devanand Venkatasubbu
Summary: This study investigates the impact of graphene and graphene oxide on the ALK5-lumican interaction. Results suggest that graphene oxide enhances the binding energy in holoenzyme (GO) while graphene reduces it in holoenzyme (G). The study provides insights for potential use of lumican and graphene oxide as a targeted/nano drug delivery system for wound healing in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Ophelie Lautier, Arianna Penzo, Jerome O. Rouviere, Guillaume Chevreux, Louis Collet, Isabelle Loiodice, Angela Taddei, Frederic Devaux, Martine A. Collart, Benoit Palancade
Summary: The research reveals that the formation of the nuclear pore complex involves co-translational events in the cytoplasm and nucleus. Different NPC subunits establish binary interactions during translation. Localized translation ensures the proper delivery of proteins to the pore and the nucleus.
Article
Biochemistry & Molecular Biology
Xinchen Lv, Xiaolin Zeng, Hongmiao Hu, Lixian Chen, Fan Zhang, Rui Liu, Yue Liu, Xuelin Zhou, Changshi Wang, Zhe Wu, Chanhong Kim, Yuehui He, Jiamu Du
Summary: Research shows that CONSTANS (CO) is a master transcription factor in triggering the floral transition in plants and is closely related to the regulation of the FLOWERING LOCUS T (FT) gene. CO binds to NUCLEAR FACTOR-YB/YC and forms a high affinity and specificity for the FT promoter through multivalent binding, regulating the transition of floral period.
Article
Multidisciplinary Sciences
Micaela Trexler, Michelle Brusatori, Gregory Auner
Summary: Influenza virus mutates rapidly and traditional tools are not suitable for rapidly mutating pathogens like Influenza virus. Developing a novel capture coating using sialic acid as a binding receptor may provide a potential platform for future diagnostic and interrogation of viable Influenza virus.
Article
Biochemistry & Molecular Biology
Mussa Quareshy, Justyna Prusinska, Martin Kieffer, Kosuke Fukui, Alonso J. Pardal, Silke Lehmann, Patrick Schafer, Charo I. del Genio, Stefan Kepinski, Kenichiro Hayashi, Andrew Marsh, Richard M. Napier
ACS CHEMICAL BIOLOGY
(2018)
Editorial Material
Plant Sciences
Marta Del Bianco, Stefan Kepinski
JOURNAL OF EXPERIMENTAL BOTANY
(2018)
Article
Multidisciplinary Sciences
Thomas Vain, Sara Raggi, Noel Ferro, Deepak Kumar Barange, Martin Kieffer, Qian Ma, Siamsa M. Doyle, Mattias Thelander, Barbora Parizkova, Ondrej Novak, Alexandre Ismail, Per-Anders Enquist, Adeline Rigal, Malgorzata Langowska, Sigurd Ramans Harborough, Yi Zhang, Karin Ljung, Judy Callis, Fredrik Almqvist, Stefan Kepinski, Mark Estelle, Laurens Pauwels, Stephanie Robert
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Plant Sciences
Akihiro Oochi, Jakub Hajny, Kosuke Fukui, Yukio Nakao, Michelle Gallei, Mussa Quareshy, Koji Takahashi, Toshinori Kinoshita, Sigurd Ramans Harborough, Stefan Kepinski, Hiroyuki Kasahara, Richard Napier, Jiri Friml, Ken-ichiro Hayashi
Article
Genetics & Heredity
Oluwaseyi Shorinola, Ryan Kaye, Guy Golan, Zvi Peleg, Stefan Kepinski, Cristobal Uauy
G3-GENES GENOMES GENETICS
(2019)
Review
Plant Sciences
Rakesh Kumar, Manish K. Pandey, Suruchi Roychoudhry, Harsh Nayyar, Stefan Kepinski, Rajeev K. Varshney
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Biology
Andre Kuhn, Sigurd Ramans Harborough, Heather M. McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiri Frim, Stefan Kepinski, Lars Ostergaard
Article
Plant Sciences
Natalie Henkhaus, Madelaine Bartlett, David Gang, Rebecca Grumet, Ingrid Jordon-Thaden, Argelia Lorence, Eric Lyons, Samantha Miller, Seth Murray, Andrew Nelson, Chelsea Specht, Brett Tyler, Thomas Wentworth, David Ackerly, David Baltensperger, Philip Benfey, James Birchler, Sreekala Chellamma, Roslyn Crowder, Michael Donoghue, Jose Pablo Dundore-Arias, Jacqueline Fletcher, Valerie Fraser, Kelly Gillespie, Lonnie Guralnick, Elizabeth Haswell, Mitchell Hunter, Shawn Kaeppler, Stefan Kepinski, Fay-Wei Li, Sally Mackenzie, Lucinda McDade, Ya Min, Jennifer Nemhauser, Brian Pearson, Peter Petracek, Katie Rogers, Ann Sakai, Delanie Sickler, Crispin Taylor, Laura Wayne, Ole Wendroth, Felipe Zapata, David Stern
Article
Plant Sciences
Barbora Parizkova, Asta Zukauskaite, Thomas Vain, Peter Grones, Sara Raggi, Martin F. Kubes, Martin Kieffer, Siamsa M. Doyle, Miroslav Strnad, Stefan Kepinski, Richard Napier, Karel Dolezal, Stephanie Robert, Ondrej Novak
Summary: This study introduces a sensitive and non-invasive method by incorporating a fluorophore into auxin molecules, enabling direct visualization of auxin distribution in plants. Utilizing multidisciplinary approaches such as genetics, chemical biology, and imaging techniques, the research provides insights into the important role of auxin in plant development.
Editorial Material
Plant Sciences
Marta Del Bianco, Stefan Kepinski
Article
Cell Biology
Suruchi Roychoudhry, Stefan Kepinski
Summary: Root system architecture is crucial for plants' below-ground resource capture and adaptation. The plant hormone auxin plays a key role in various aspects of root development, from cellular to whole-root-system level. This review focuses on the multiple gene signaling networks regulated by auxin biosynthesis, conjugation, and transport, which contribute to primary and lateral root development in Arabidopsis. The spatiotemporal regulation of auxin distribution controls transitions between cell division, cell growth, and differentiation, as well as the production of lateral roots. The effects of auxin and its signaling and transport pathways on the control of lateral root gravitropic setpoint angle (GSA), which determines the overall shape of the root system, are also summarized. Additionally, the modulation of auxin biosynthesis, transport, and canonical auxin signaling pathway by environmental conditions and their impact on root developmental plasticity are discussed.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Plant Sciences
Eshan Sharma, Akanksha Bhatnagar, Avantika Bhaskar, Susmita M. Majee, Martin Kieffer, Stefan Kepinski, Paramjit Khurana, Jitendra P. Khurana
Summary: The rice FB protein-coding gene OsFBX257 is differentially expressed under drought conditions and other abiotic stresses. It plays a significant role in modulating root architecture and improving drought stress tolerance in rice. OsFBX257 is a potential breeding target for alleviating drought stress-induced damage in rice.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Suruchi Roychoudhry, Katelyn Sageman-Furnas, Chris Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, Martina De Angelis, Heather L. Goodman, Nicola Capstaff, James P. B. Lloyd, Jack Mullen, Roger Hangarter, Jiri Friml, Stefan Kepinski
Summary: Lateral roots grow at non-vertical angles with respect to gravity through the regulation of hormone distribution and transport.
Article
Food Science & Technology
Stewart A. Jennings, Andrew J. Challinor, Pete Smith, Jennie I. Macdiarmid, Edward Pope, Sarah Chapman, Catherine Bradshaw, Heather Clark, Sylvia Vetter, Nuala Fitton, Richard King, Sithembile Mwamakamba, Tshilidzi Madzivhandila, Ian Mashingaidze, Christian Chomba, Masiye Nawiko, Bonani Nyhodo, Ndumiso Mazibuko, Precious Yeki, Pamela Kuwali, Alfred Kambwiri, Vivian Kazi, Agatha Kiama, Abel Songole, Helen Coskeran, Claire Quinn, Susannah Sallu, Andrew Dougill, Stephen Whitfield, Bill Kunin, Nalishebo Meebelo, Andrew Jamali, Dhaquirs Kantande, Prosper Makundi, Winfred Mbungu, Frank Kayula, Sue Walker, Sibongile Zimba, Joseph Hubert Galani Yamdeu, Ndashe Kapulu, Marcelo Valadares Galdos, Samuel Eze, Hemant G. Tripathi, Steven M. Sait, Stefan Kepinski, Emmanuel Likoya, Henry Greathead, Harriet Elizabeth Smith, Marcelin Tonye Mahop, Helen Harwatt, Maliha Muzammil, Graham Horgan, Tim Benton
Summary: The article introduces a novel integrated assessment framework called iFEED, which combines models with in-country knowledge and expert academic judgement to explore climate-smart and nutrition-secure food system futures. The framework was applied in Malawi, South Africa, Tanzania, and Zambia. The iFEED process involves participatory scenario workshops, integrated modeling of climate change and food production, and workshops with academic experts to incorporate in-country expertise and generate country-level recommendations. iFEED provides comprehensive reporting of model results and uncertainty, considers climate change mitigation and adaptation measures, and quantifies future population-level nutrition security.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2022)