@article{xiao_protein_2025,
	title = {The protein kinases {KIPK} and {KIPK}-{LIKE1} suppress overbending during negative hypocotyl gravitropic growth in {Arabidopsis}},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf056},
	doi = {10.1093/plcell/koaf056},
	abstract = {Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).},
	number = {4},
	urldate = {2025-04-25},
	journal = {The Plant Cell},
	author = {Xiao, Yao and Zourelidou, Melina and Bassukas, Alkistis E Lanassa and Weller, Benjamin and Janacek, Dorina P and Šimura, Jan and Ljung, Karin and Hammes, Ulrich Z and Li, Jia and Schwechheimer, Claus},
	month = apr,
	year = {2025},
	pages = {koaf056},
}

Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).

@article{aydin_probing_2025,
	title = {Probing substrate water access through the {O1} channel of {Photosystem} {II} by single site mutations and membrane inlet mass spectrometry},
	volume = {163},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-025-01147-4},
	doi = {10.1007/s11120-025-01147-4},
	abstract = {Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.},
	language = {en},
	number = {3},
	urldate = {2025-04-25},
	journal = {Photosynthesis Research},
	author = {Aydin, A. Orkun and de Lichtenberg, Casper and Liang, Feiyan and Forsman, Jack and Graça, André T. and Chernev, Petko and Zhu, Shaochun and Mateus, André and Magnuson, Ann and Cheah, Mun Hon and Schröder, Wolfgang P. and Ho, Felix and Lindblad, Peter and Debus, Richard J. and Mamedov, Fikret and Messinger, Johannes},
	month = apr,
	year = {2025},
	keywords = {CP43-V410, D1-E329, O1 channel, Oxygen evolving complex, Photosystem II, Substrate water exchange, Synechocystis sp. PCC 6803, Water delivery, Water oxidation, Water wheel},
	pages = {28},
}

Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	number = {4},
	urldate = {2025-04-22},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = apr,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem, cell wall, grafting, regeneration, stress, wounding, xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{bogacz_x-ray_2025,
	title = {X-ray {Absorption} {Spectroscopy} of {Dilute} {Metalloenzymes} at {X}-ray {Free}-{Electron} {Lasers} in a {Shot}-by-{Shot} {Mode}},
	volume = {16},
	url = {https://doi.org/10.1021/acs.jpclett.5c00399},
	doi = {10.1021/acs.jpclett.5c00399},
	abstract = {X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.},
	number = {15},
	urldate = {2025-04-22},
	journal = {The Journal of Physical Chemistry Letters},
	author = {Bogacz, Isabel and Szilagyi, Erzsi and Makita, Hiroki and Simon, Philipp S. and Zhang, Miao and Doyle, Margaret D. and Chatterjee, Kuntal and Kretzschmar, Moritz and Chernev, Petko and Croy, Nicholas and Cheah, Mun-Hon and Dasgupta, Medhanjali and Nangca, Isabela and Fransson, Thomas and Bhowmick, Asmit and Brewster, Aaron S. and Sauter, Nicholas K. and Owada, Shigeki and Tono, Kensuke and Zerdane, Serhane and Oggenfuss, Alexander and Babich, Danylo and Sander, Mathias and Mankowsky, Roman and Lemke, Henrik T. and Gee, Leland B. and Sato, Takahiro and Kroll, Thomas and Messinger, Johannes and Alonso-Mori, Roberto and Bergmann, Uwe and Sokaras, Dimosthenis and Yachandra, Vittal K. and Kern, Jan and Yano, Junko},
	month = apr,
	year = {2025},
	note = {Publisher: American Chemical Society},
	pages = {3778--3787},
}

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

@article{nair_elf3_2025,
	title = {{ELF3} coordinates temperature and photoperiodic control of seasonal growth in hybrid aspen},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225001903},
	doi = {10.1016/j.cub.2025.02.027},
	abstract = {Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.},
	number = {7},
	urldate = {2025-04-11},
	journal = {Current Biology},
	author = {Nair, Aswin and Maurya, Jay P. and Pandey, Shashank K. and Singh, Rajesh Kumar and Miskolczi, Pal C. and Aryal, Bibek and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2025},
	keywords = {EARLY FLOWERING 3(ELF3), FLOWERING LOCUS T (FT), growth cessation, hybrid aspen, perennial trees, seasonal growth},
	pages = {1484--1494.e2},
}

Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.