Biology subjects

Lin, S.

Publications and source records attributed to Lin, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Discovery and binding site identification of a single-stranded DNA-binding protein that interacts with double-stranded DNA

Scientists have conducted in-depth studies on single-stranded DNA (ssDNA) binding and protein interaction network of single-stranded DNA binding proteins (SSBs). SSBs are widely present in cells from lower prokaryotes to higher mammals and are important proteins for ssDNA protection. In-depth studies in recent years have revealed a wide range of interactions between SSBs and other proteins. Studies have shown that in addition to playing the role of ssDNA protector, SSBs are also important members of biochemical pathways such as DNA replication and recombination. In this study, a single-stranded DNA binding protein SSF encoded by E. coli F plasmid with highly conserved N-terminal region was demonstrated to have ssDNA binding ability similar to E. coli SSB through gel migration experiments. At the same time, the dsDNA binding ability of SSF was also demonstrated, and the dissociation constant of this interaction (in the range of microliters) was determined by Micro-scale Thermophoresis (MST). Through the above experiments, a previously unreported SSB with dsDNA binding ability was revealed, and the region interacting with dsDNA was determined to be the C-terminal unstructured region. This study lays a foundation for further understanding of the mechanism of bacterial conjugation conducted by F plasmid, as well as the potential dsDNA binding ability and biological significance of other SSBs.

biochemistry↗

bioRxiv2024

Genome sequencing of 'Fuji' apple clonal varieties reveals evolutionary history and genetic mechanism of the spur-type morphology

Somatic variations arising during asexual reproduction can lead to the emergence of bud sports exhibiting advantageous traits, forming the basis for bud sport breeding in perennial plants. Here, we report a near-complete, fully phased genome assembly of Fuji apple, enabling comprehensive identification of somatic variants across 74 clonally propagated Fuji varieties. Phylogenetic analysis of Fuji sport varieties indicates that the emergence of spur-type and early maturation traits results from multiple independent formation events. A number of putative functional somatic variants are identified, including one spur-type specific deletion located in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in the spur-type varieties compared to the standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases the plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the 80-year cloning history of Fuji and provides valuable candidate causative mutations for apple breeding.

plant biology↗

bioRxiv2024

Urea amidolyase as the enzyme for urea utilization in algae: functional display in Chlamydomonas reinhardtii and evolution in algae

Urea is a crucial nitrogen nutrient source for algae with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but the urea amidolyase (UAD) system, albeit known to exist, has hardly been studied. Here, the phylogenetic distribution, expression patterns, and functional roles of UAD system are examined, which comprises subunits DUR1, DUR2, and DUR3. We find a widespread occurrence of UAD, spanning four major phytoplankton lineages, and potentially independent evolution of URE and lineage-specific loss. Besides, a stronger regulation of UAD by environmental nitrogen concentrations compared to URE is uncovered in both global ocean and local dinoflagellate-dominant bloom events. CRISPR-based mutation in Chlamydomonas reinhardtii shows that subunit DUR2 is essential for urea utilization. DUR2 inactivation led to completely growth restriction and upregulation of DUR1 and DUR3A, suggesting its functional interaction with them. In contrast, DUR3B inactivation only partially halted urea uptake and cell growth but significantly reduced gene expression across the entire UAD system. These findings not only reveal the crucial role of DUR2 in urea utilization in C. reinhardtii and potentially in many other algae, but also suggest DUR2 to be a more suitable indicator of urea utilization than urease, and underscore the importance to consider both URE and UAD enzyme systems when urea utilization by algae is assessed.

ecology↗

bioRxiv2024

Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance

The neuromuscular junction (NMJ) is the synapse formed between motor neurons and skeletal muscle fibers. Its stability relies on the continued expression of genes in a subset of myonuclei, called NMJ myonuclei. Here, we use single-nuclei RNA-sequencing (snRNA-seq) to identify numerous undescribed NMJ-specific transcripts. To elucidate how the NMJ transcriptome is regulated, we also performed snRNA-seq on sciatic nerve transected, botulinum toxin injected and Musk knockout muscles. These data show that NMJ gene expression is not only driven by agrin-Lrp4/MuSK signaling, but is also affected by electrical activity and trophic factors other than agrin. By selecting three previously undescribed NMJ genes Etv4, Lrtm1 and Pdzrn4, we further characterize novel contributors to NMJ stability and function. AAV-mediated overexpression and AAV-CRISPR/Cas9-mediated knockout show that Etv4 is sufficient to upregulate expression of [~]50% of the NMJ genes in non-synaptic myonuclei, while muscle-specific knockout of Pdzrn4 induces NMJ fragmentation. Further investigation of Pdzrn4 revealed that it localizes to the Golgi apparatus and interacts with MuSK protein. Collectively, our data provide a rich resource of NMJ transcripts, highlight the importance of ETS transcription factors at the NMJ and suggest a novel pathway for NMJ post-translational modifications.

molecular biology↗

bioRxiv2024

Mycelium as a scaffold for biomineralized engineered living materials

Engineered living materials (ELMs) are garnering considerable attention as a promising alternative to traditional building materials because of their potentially lower carbon footprint and additional functionalities conferred by living cells. However, biomineralized ELMs designed for load-bearing purposes are limited in their current design and usage for several reasons, including (1) low microbial viability and (2) limited control of specimen internal microarchitecture. We created third generation biomineralized ELMs from fungal mycelium scaffolds that were mineralized either by the fungus itself or by ureolytic bacteria. Both self-mineralized (i.e. fungally-mineralized) and bacterially-mineralized scaffolds retained high microbial viability for at least four weeks in room temperature or accelerated dehydration storage conditions, without the addition of protectants against desiccation. The microscale modulus of calcium carbonate varied with the different biomineralized scaffold conditions, and moduli were largest and stiffest for bacterial biomineralization of fungal mycelium. As an example of how mycelium scaffolds can enable the design of complex internal geometries of biomineralized materials, osteonal-bone mimetic architectures were patterned from mycelium and mineralized using ureolytic bacteria. These results demonstrate the potential for mycelium scaffolds to enable new frontiers in the design of biomineralized ELMs with improved viability and structural complexity. Progress and PotentialBiomineralized engineered living materials (ELMs) offer new approaches for increasing the sustainability of building materials and processes. However, the design and usage of biomineralized ELMs is constrained by several important limitations, including low microbial viability and limited ability to control internal microarchitecture. Fungal mycelium scaffolds, biomineralized by either fungi or bacteria, achieve much higher viability of ureolytic microorganisms than what has been reported for biomineralized ELMs. Further, mycelium scaffolds permit the manufacturing of complex architectures, such as inspired by the structure of osteonal bone. Mycelium scaffolds have the potential to enable new frontiers in the design and use of biomineralized ELMs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/592484v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@338d98org.highwire.dtl.DTLVardef@94f956org.highwire.dtl.DTLVardef@7d8ed6org.highwire.dtl.DTLVardef@12cb61e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Identification and Expression Analysis of CDPK Family in Eriobotrya japonica, reveals EjCDPK25 in Response to Freezing Stress in Fruitlets.

The fruitlets of loquat (Eriobotrya japonica Lindl.) are susceptible to freezing injury due to their developmental cycle encountering winter. Freezing stress severely damages the fruitlets, resulting in loss of fruit yield and quality. Studies have shown that Ca2+, as a second messenger, is involved in signal transduction in loquat fruitlets under freezing stress. However, the mechanism of downstream calcium signal transduction in loquat fruitlets under freezing stress is currently unclear. Calcium-depend protein kinase (CDPK) as the most particular calcium sensor family in plants, play an important role in multiple stress signal transduction including freezing. In this study, we identified the loquat CDPK family on a genome-wide scale. A total of 34 EjCDPK genes were identified and studied for basic structural and phylogenetic features. EjCDPKs can be divided into four subgroups phylogenetically. The patterns of exon-intron and protein motif are highly conserved among the subgroups. Collinearity analysis identified several segmental duplicate events in EjCDPK family. RNA-seq based transcription analysis indicated that partial of EjCDPKs differently expressed in response to freezing stress with tissue-specific. Moreover, we preformed correlation analysis between expression value and trait data of loquat fruitlet under freezing stress by weighted co-expression gene network. After that, EjCDPK25 was selected as the candidate because of its potential freezing stress response function. Protein kinase related GO terms were enriched in EjCDPK25 co-expression genes, and then QPCR was performed to examine the target genes expression pattern. In addition, EjCDPK25 was cloned to construct overexpression vector to obtain transgenic Arabidopsis plants. Transgenic and wild-type Arabidopsis were suffered freezing stress treatments (-5{degrees}C). The results showed that the survival rate of EjCDPK25 overexpressing transgenic Arabidopsis was significantly higher than WT. In summary, this study identified loquat CDPK family firstly, and our data provide significant insights into the evolution and function of loquat CDPKs. Above all, a freezing stress response gene EjCDPK25 was verified can increase the resistance of freezing stress in Arabidopsis.

plant biology↗

bioRxiv2024

Post-transcriptional regulatory pre-complex assembly drives timely cell-state transitions during differentiation

Complexes that control mRNA stability and translation promote timely cell-state transitions during differentiation by ensuring appropriate expression patterns of key developmental regulators. The Drosophila RNA-binding protein Brain tumor (Brat) promotes degradation of target transcripts during the maternal-to-zygotic transition in syncytial embryos and in uncommitted intermediate neural progenitors (immature INPs). We identified Ubiquitin-specific protease 5 (Usp5) as a Brat interactor essential for the degradation of Brat target mRNAs in both cell types. Usp5 promotes Brat-dedadenylase pre-complex assembly in mitotic neural stem cells (neuroblasts) by bridging Brat and the scaffolding components of deadenylase complexes lacking their catalytic subunits. The adaptor protein Miranda binds the RNA-binding domain of Brat, limiting its ability to bind target mRNAs in mitotic neuroblasts. Cortical displacement of Miranda activates Brat-mediated mRNA decay in immature INPs. We propose that the assembly of an enzymatically inactive and RNA-binding-deficient pre-complex poises mRNA degradation machineries for rapid activation driving timely developmental transitions.

developmental biology↗

bioRxiv2024

Interneuron FGF13 regulates seizure susceptibility via a sodium channel-independent mechanism

Developmental and Epileptic Encephalopathies (DEEs), a class of devastating neurological disorders characterized by recurrent seizures and exacerbated by disruptions to excitatory/inhibitory balance in the brain, are commonly caused by mutations in ion channels. Disruption of, or variants in, FGF13 were implicated as causal for a set of DEEs, but the underlying mechanisms were clouded because FGF13 is expressed in both excitatory and inhibitory neurons, FGF13 undergoes extensive alternative splicing producing multiple isoforms with distinct functions, and the overall roles of FGF13 in neurons are incompletely cataloged. To overcome these challenges, we generated a set of novel cell type-specific conditional knockout mice. Interneuron-targeted deletion of Fgf13 led to perinatal mortality associated with extensive seizures and impaired the hippocampal inhibitory/excitatory balance while excitatory neuron-targeted deletion of Fgf13 caused no detectable seizures and no survival deficits. While best studied as a voltage-gated sodium channel (Nav) regulator, we observed no effect of Fgf13 ablation in interneurons on Navs but rather a marked reduction in K+ channel currents. Re-expressing different Fgf13 splice isoforms could partially rescue deficits in interneuron excitability and restore K+ channel current amplitude. These results enhance our understanding of the molecular mechanisms that drive the pathogenesis of Fgf13-related seizures and expand our understanding of FGF13 functions in different neuron subsets.

neuroscience↗

bioRxiv2024

Bioinformatics Copilot 1.0: A Large Language Model-powered Software for the Analysis of Transcriptomic Data

The field of single-cell transcriptomics has been producing extensive datasets, advancing our understanding of cellular functions in various tissues, and empowering diagnosis, prognosis, and drug development. However, parsing through this data has been a monumental task, often stretching weeks to months. This bottleneck arises due to the sheer volume of data generated--ranging from hundreds of gigabytes to tens of terabytes--that demands extensive time for analysis. Moreover, the data analysis involves an intricate series of steps utilizing various software packages, creating a steep learning curve for biologists. Additionally, the iterative nature of data analysis in this domain necessitates a deep biological insight to formulate relevant questions, conduct analysis, interpret results, and refine hypotheses. This iterative loop has required close collaboration between biologists and bioinformaticians, which is hampered by protracted communication cycles. To address these challenges, we present a large language model-powered software, Bioinformatics Copilot 1.0. It allows users to analyze data through an intuitive natural language interface, without requiring proficiency in programming languages such as Python or R. It is engineered for cross-platform functionality, with support for Mac, Windows, and Linux. Importantly, it facilitates local data analysis, ensuring adherence to stringent data management regulations that govern the use of patient samples in medical and research institutions. We anticipate that this tool will expedite the data analysis workflow in numerous research endeavors, thereby accelerating advancements in the biomedical sciences.

bioinformatics↗

bioRxiv2024

A robust platform for BaEVRless-lentiviral synthesis and primary natural killer cell transduction

Lentiviral vectors are invaluable tools for genetic modification in human cells for research, biotechnological and clinical applications. However, certain cell types, such as primary human natural killer (NK) cells, present challenges in lentiviral transduction. Overcoming this limitation requires specific pseudotype modifications. BaEVRless-pseudotyped lentivirus (BaEVRless-LV) has shown promise in efficiently transducing human NK cells, B cells, and hematopoietic stem cells (HSCs). BaEVRless, a modified envelope protein derived from Baboon endogenous retrovirus, targets ASCT receptors in human cells. While effective for several immune cell types, BaEVRless-LV production in standard HEK293T cells is challenging. During lentiviral synthesis, BaEVRless protein induces hyper cell fusion, leading to rapid HEK293T cell death and reduced BaEVRless-LV titers. To solve this problem, we used CRISPR genome editing to knockout (KO) the ASCT2 gene in HEK293T cells, thereby abolishing BaEVRless-induced cell fusion. Using the ASCT2-KO cells and an optimized viral production protocol, we efficiently packaged high titers of BaEVRless-LV encoding various transgenes, including turbogfp, chimeric antigen receptor (CAR), and a pooled CRISPR sgRNA library. Our robust BaEVRless-LV synthesis platform is readily adaptable for manufacturing cell therapeutics and enables advanced research techniques such as CRISPR genetic screens in primary NK cells.

immunology↗

bioRxiv2024

Multi-omics Identify Serotonin Transporter as a Promising Therapeutic Target for Essential Tremor

Essential tremor (ET) stands as one of the most prevalent cerebellar movement disorders. However, effective treatment remains elusive, largely due to a limited understanding of its molecular pathology. Harmaline-induced tremor in mouse is a well-established animal model for ET, while with enigmatic mechanism. The aim of this study was to get insight into the molecular intricacies underlying cerebellar dysfunction in harmaline-induced tremor. Combining LC-MS/MS and RNA-Seq analysis, we delved into the variation of the cerebellum between harmaline-induced tremor and the control ones. This comprehensive investigation revealed a profile of this mouse model from mRNA and protein level, highlighting 5194 correlated coding molecules, with 19 proving to be significant. Further KEGG enrichment analysis identified cerebellar serotonin transporter (SERT) as the key molecule in harmaline-induced tremor. The implications of this transcriptomic and proteomic exploration underscore the potential therapeutic value of targeting SERT as a novel treatment approach for ET. In general, our study unveils crucial insights that could pave the way for molecular target identification and effective therapeutic interventions for ET.

neuroscience↗

bioRxiv2024

Muscle fiber Myc is dispensable for muscle growth and forced expression severely perturbs homeostasis

The oncogenic transcription factor Myc stimulates many growth processes including cell cycle progression and ribosome biogenesis. Myc expression is low in adult skeletal muscle, but is upregulated upon growth stimuli. Furthermore, muscle fiber Myc overexpression recapitulates many aspects of growth-related gene expression, suggesting Myc may mediate pro-growth responses to anabolic stimuli, such as exercise. Here, we tested this hypothesis by examining mouse models in which Myc was specifically eliminated or overexpressed in skeletal muscle fibers or muscle stem cells (MuSC). While muscle fiber Myc expression increased during muscle growth and Myc expression in MuSCs was required for successful muscle regeneration, muscle fiber Myc expression was dispensable for post-natal, mechanical overload or PKB/Akt-induced muscle growth in mice. Similarly, constitutive Myc expression did not promote skeletal muscle hypertrophy, but instead impaired muscle fiber structure and function within days. These data question the role of Myc in skeletal muscle growth.

physiology↗

bioRxiv2024

An injury-induced tissue niche shaped by mesenchymal plasticity coordinates the regenerative and disease response in the lung

Severe lung injury causes basal stem cells to migrate and outcompete alveolar stem cells resulting in dysplastic repair and a loss of gas exchange function. This "stem cell collision" is part of a multistep process that is now revealed to generate an injury-induced tissue niche (iTCH) containing Keratin 5+ epithelial cells and plastic Pdgfra+ mesenchymal cells. Temporal and spatial single cell analysis reveals that iTCHs are governed by mesenchymal proliferation and Notch signaling, which suppresses Wnt and Fgf signaling in iTCHs. Conversely, loss of Notch in iTCHs rewires alveolar signaling patterns to promote euplastic regeneration and gas exchange. The signaling patterns of iTCHs can differentially phenotype fibrotic from degenerative human lung diseases, through apposing flows of FGF and WNT signaling. These data reveal the emergence of an injury and disease associated iTCH in the lung and the ability of using iTCH specific signaling patterns to discriminate human lung disease phenotypes.

cell biology↗

bioRxiv2024

Psychological stress disturbs bone metabolism via miR-335-3p/Fos signaling in osteoclast

It has been well-validated that chronic psychological stress leads to bone loss, but the underlying mechanism remains unclarified. In this study, we established and analyzed the chronic unpredictable mild stress (CUMS) mice to investigate the miRNA-related pathogenic mechanism involved in psychological stress induced osteoporosis. Our result found that these CUMS mice exhibited osteoporosis phenotype that mainly attributed to the abnormal activities of osteoclasts. Subsequently, miRNA sequencing and other analysis showed that miR-335-3p, which is normally highly expressed in the brain, was significantly down-regulated in the nucleus ambiguous (NAC), serum, and bone of the CUMS mice. Additionally, in vitro studies detected that miR-335-3p is important for osteoclast differentiation, with its direct targeting site in FOS. Further studies demonstrated FOS was upregulated in CUMS osteoclast, and the inhibition of FOS suppressed the accelerated osteoclastic differentiation, as well as the expression of osteoclastic genes, such as Nfatc1, Acp5, Mmp9, in miR-335-3p restrained osteoclasts. In conclusion, this work indicated that psychological stress may down-regulate the miR-335-3p expression, which resulted in the accumulation of FOS and the up-regulation of NFACT1 signaling pathway in osteoclasts, leading to its accelerated differentiation and abnormal activity. These results decipher a previously unrecognized paradigm that miRNA can act as a link between psychological stress and bone metabolism. Impact statementmiR-335-3p, which targets FOS and inhibits its activation of NFATC1 signaling, is an important regulator for osteoclast function and responsible for the psychological stress induced osteoporosis

neuroscience↗

bioRxiv2024

UBA1-CDK16: A Sex-Specific Chimeric RNA and Its Role in Immune Sexual Dimorphism

RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identified UBA1-CDK16, a female-specific chimeric transcript. Intriguingly, both parental genes, are expressed in males and females. Mechanistically, UBA1-CDK16 is produced by cis-splicing between the two adjacent X-linked genes, originating from the inactive X chromosome. A female-specific chromatin loop, formed between the junction sites, facilitates the alternative splicing of its readthrough precursor. This unique chimeric transcript exhibits evolutionary conservation, evolving to be female-specific from non-human primates to humans. Furthermore, our investigation reveals that UBA1-CDK16 is enriched in the myeloid lineage and plays a regulatory role in myeloid differentiation. Notably, female COVID-19 patients who tested negative for this chimeric transcript displayed higher counts of neutrophils, highlighting its potential role in disease pathogenesis. These findings support the notion that chimeric RNAs represent a new repertoire of transcripts that can be regulated independently from the parental genes, and a new class of RNA variance with potential implications in sexual dimorphism and immune responses.

genomics↗

bioRxiv2024

Comparative genomics illuminates adaptive evolution of DVNP with lifestyle and with loss of histone H1 in dinoflagellates

About ten years ago dinoflagellate/viral nucleoprotein (DVNP) was discovered in dinoflagellates, an ecologically important and evolutionarily enigmatic group of aquatic protists. Apparently acquired from a viral origin, the appearance of DVNP coincided with the loss of nucleosome, a rare event in eukaryote evolution. Despite the potential importance of DVNP as the substitute of histones, its evolutionary trajectory and adaptive significance remain elusive. Here, we conducted comparative analyses using existing dinoflagellate genomes and transcriptomes from 26 species ranging from ancestral to later-diverging lineages to investigate the pattern of sequence and structural divergence. Results showed that the functional domestication of DVNP in ancestral dinoflagellates coincided with the loss of histone H1, while subsequent DVNP differentiation was accompanied by the yet another genomic innovation: acquisition of bacterial-originated histone-like protein. Furthermore, our data split DVNP into two major groups: the core DVNP that resembles histone H1 and shows consistently high levels of expression and the non-core DVNP with higher sequence variability and showing lower yet variable levels of expression. In addition, we observed a trend in DVNP evolution tracing that in lifestyle differentiation. This work offers insights into the adaptive evolution of DVNP, laying the foundation for further inquiries of evolutionary drivers and functional innovation of DVNP to enhance our understanding of dinoflagellate evolution and ecological success.

microbiology↗

bioRxiv2024

Rapid QC-MS - Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control

Consistently collecting high-quality liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) data is a time-consuming hurdle for untargeted workflows. Analytical controls such as internal and biological standards are commonly included in high throughput workflows, helping researchers recognize low integrity specimens regardless of their biological source. However, evaluating these standards as data are collected has remained a considerable bottleneck - in both person-hours and accuracy. Here we present Rapid QC-MS, an automated, interactive dashboard for assessing LC-MS/MS data quality. Minutes after a new data file is written, a browser-viewable dashboard is updated with quality control results spanning multiple performance dimensions such as instrument sensitivity, in-run retention time shifts, and mass accuracy drift. Rapid QC-MS provides interactive visualizations that help users recognize acute deviations in these performance metrics, as well as gradual drifts over periods of hours, days, months, or years. Rapid QC-MS is open-source, simple to install, and highly configurable. By integrating open-source python libraries and widely used MS analysis software, it can adapt to any LC-MS/MS workflow. Rapid QC-MS runs locally and offers optional remote quality control by syncing with Google Drive. Furthermore, Rapid QC-MS can operate in a semi-autonomous fashion, alerting users to specimens with potentially poor analytical integrity via frequently used messaging applications. Rapid QC-MS offers a fast, straightforward approach to help users collect high-quality untargeted LC-MS/MS data by eliminating many of the most time-consuming steps in manual data curation. Download for free: https://github.com/czbiohub-sf/Rapid-QC-MS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/578059v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@50d2b1org.highwire.dtl.DTLVardef@388373org.highwire.dtl.DTLVardef@3e31b5org.highwire.dtl.DTLVardef@1316c74_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Root-specific secondary metabolism at the single-cell level: a case study of theanine metabolism and regulation in the roots of tea plants (Camellia sinensis)

Root-synthesized secondary metabolites are critical quality-conferring compounds of foods, plant-derived medicines, and beverages. However, information at a single-cell level on root-specific secondary metabolism remains largely unexplored. L-theanine, an important quality component of tea, is primarily synthesized in roots, from which it is then transported to new shoots of tea plant. In this study, we present a single-cell RNA sequencing (scRNA-seq)-derived map for the tea plant root, which enabled cell-type-specific analysis of glutamate and ethylamine (two precursors of theanine biosynthesis) metabolism, and theanine biosynthesis, storage, and transport. Our findings support a model in which the theanine biosynthesis pathway occurs via multicellular compartmentation and does not require high co-expression levels of transcription factors and their target genes within the same cell cluster. This study provides novel insights into theanine metabolism and regulation, at the single-cell level, and offers an example for studying root-specific secondary metabolism in other plant systems.

plant biology↗