Biology subjects

Li, J.-X.

Publications and source records attributed to Li, J.-X..

6 recordsLinked to original sources

bioRxiv2026

Architecture and Energy Transfer of the Bacterial Photosynthetic Unit

In phototrophic organisms, pigment-protein membrane complexes are densely packed to form photosynthetic units (PSUs) that capture solar energy and convert it into chemical energy. Although the structures of many individual photosynthetic complexes have been resolved, how they are arranged and interact with others within photosynthetic membranes to enable efficient excitation energy transfer (EET) remains poorly understood. Here, we report cryo-electron microscopy structures of PSU supercomplex assemblies from the phototrophic a-proteobacterium Rhodovulum viride, including an RC-LH1 core associated with one or two peripheral LH2 complexes and a curved LH2 tetramer. These membrane-derived assemblies define the relative positions and orientations of neighboring photosynthetic complexes and place their pigment arrays in proximity across antenna-antenna and antenna-core interfaces. Structure-based simulations identify potential EET pathways within the PSU assemblies and reveal rapid energy transfer across both LH2-LH2 and LH2-LH1 interfaces. Collectively, these findings provide insights into the assembly and structural modularity of bacterial PSUs and elucidate how the lateral organization of membrane protein complexes facilitates efficient energy transfer. This work extends structural studies of bacterial photosynthesis from individual complexes to their native higher-order assembly, providing a framework for understanding how photosynthetic supercomplex organization shapes energy migration and for guiding the design of artificial photosynthesis.

biochemistry↗

bioRxiv2026

J-domain proteins stimulate PKL-mediated chromatin compaction at H3K4-hypomethylated genomic loci

Chromatin accessibility varies widely across distinct genomic regions in eukaryotes, yet the mechanisms governing these differential patterns remain poorly understood. Here, we identify a subfamily of functionally redundant J-domain proteins (JDPs) that assemble into a protein complex with PICKLE (PKL), an evolutionarily conserved CHD3-type chromatin remodeler, in Arabidopsis thaliana. JDPs are required not only for maintaining PKL protein stability but also for stimulating its nucleosome remodeling and ATPase activities. A previously uncharacterized histone-binding domain (HBD) within JDPs specifically recognizes the N-terminal tail of histone H3 when the H3K4me3 modification is absent. This interaction enhances PKL-mediated nucleosome sliding and ATPase activities in vitro, and promotes PKL-dependent chromatin compaction at H3K4me3-depleted genomic loci in vivo. The PKL-JDP complex drives chromatin compaction to repress developmentally regulated genes, thereby governing key developmental phase transitions, including the embryo-to-seedling transition and flowering. Collectively, these findings uncover a distinct mechanism by which the absence of H3K4me3 is sensed to initiate regional chromatin compaction, repress developmentally regulated genes, and facilitate key developmental transitions.

plant biology↗

bioRxiv2025

Individual differences in behavioral effects of xylazine and opioid-xylazine mixtures in male rats

RationaleRecent work in animals suggests xylazine neither enhances the rewarding effects nor intake of fentanyl. Anecdotal evidence from people who use drugs indicates some individuals prefer fentanyl adulterated with xylazine. Systematic examination of pharmacological interactions between xylazine and opioids is needed to understand the disparate findings between preclinical studies and human reports. ObjectivesThis study examined behavioral interactions between xylazine and opioids in rats to investigate the pharmacology underlying an emerging trend in drug use. MethodsThe sedative, hypothermic, subjective, and respiratory effects of xylazine and opioid-xylazine mixtures were examined in male rats. Locomotor activity was measured in an open field, and body temperature changes were measured with a rectal probe. Rats were trained to discriminate 0.04 mg/kg fentanyl, 0.02 mg/kg fentanyl, or 1.5 mg/kg xylazine from saline and were probed with fentanyl, xylazine, or both to observe whether the drug(s) generalized with the training dose. Whole body plethysmography was used to assess the effects of xylazine on respiration. ResultsXylazine depressed locomotor activity and core body temperature, but considerable variability between subjects was observed. In some subjects, xylazine fully substituted for fentanyl, and prolonged the subjective effects of fentanyl. Doses of 1 and 1.78 mg/kg xylazine only partially generalized to the training dose of 1.5 mg/kg xylazine. Xylazine exacerbated the respiratory depressant effects of opioids, and atipamezole reversed the xylazine enhancement of morphine-induced respiratory depression. ConclusionsIndividual differences were observed in multiple behavioral measures following xylazine administration and may recapitulate the divisiveness of xylazine reported in people who use drugs.

pharmacology and toxicology↗

bioRxiv2025

Structural basis for the RC-LH1 supercomplex of Dinoroseobacter shibae for anaerobic anoxygenic photosynthesis

Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, the architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present the 2.4-[A] cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 {beta}-subunits, each containing two spheroidenones per {beta}-heterodimer--a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, accounting for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown protein-LRC (Light-Respiratory Connector), which structurally bridges the RC and LH1 components and exhibits homology to NADH oxidoreductase subunit E, suggesting a functional coupling between photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.

biochemistry↗

bioRxiv2024

Wounding perception by jasmonate-mediated JAZ condensation in plants

Wounding is a common stress experienced by plants, resulting in a quick elicitation of jasmonates (JAs). The widely accepted mechanism of COI1-JAZ coreceptor posits that COI1 directly interacts with the active ligand of JAs, whereas JAZs facilitate to trap the ligand in the binding pocket. Here we show that the multiple JAZs of Arabidopsis undergo phase separation in response to wounding. Taking JAZ1 as an example, we found it is an independent sensor of JA-Ile, the active ligand in most plants. Under basal condition, dispersed JAZ1 interacts with MYC2 to inhibit downstream gene expressions. Upon wounding, JAZ1 binds to JA-Ile and forms condensates, reducing its affinity with MYC2 and tending to recruit COI1 as well as other proteasome related components for quick degradation, thereby accelerating signaling output. Our investigation unveils the underlying mechanism by which JAZ1 regulates swift signaling transduction via phase separation upon the direct perception of JA-Ile.

plant biology↗

bioRxiv2020

A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2

Mutations and transient conformational movements of receptor binding domain (RBD) that make neutralizing epitopes momentarily unavailable, present immune escape routes to SARS-CoV-2. To mitigate viral escape, we developed a cocktail of neutralizing antibodies (NAbs) targeting epitopes located on different domains of spike (S) protein. Screening of a library of monoclonal antibodies generated from peripheral blood mononuclear cells of COVID-19 convalescent patients yielded potent NAbs, targeting N-terminal domain (NTD) and RBD domain of S, effective at nM concentrations. Remarkably, combination of RBD-targeting NAbs and NTD-binding NAb, FC05, dramatically enhanced the neutralization potency in cell-based assays and animal model. Results of competitive SPR assays and cryo-EM structures of Fabs bound to S unveil determinants of immunogenicity. Combinations of immunogens, identified in NTD and RBD of S, when immunized in rabbits elicited potent protective immune responses against SARS-CoV-2. These results provide a proof-of-concept for neutralization-based immunogen design targeting SARS-CoV-2 NTD and RBD. One sentence summaryImmunogens identified in the NTD and RBD of the SARS-CoV-2 spike protein using a cocktail of non-competing NAbs when injected in rabbits elicited a potent protective immune response against SARS-CoV-2.

microbiology↗