Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 433 records · Page 24Linked to original sources

bioRxiv2024

Enhancing Agrobacterium-Mediated Soybean Transformation Efficiency with an Auxiliary Solution

Soybean provides oil, protein, and biofuel. Efficient transformation systems are vital for advancing soybean research. Currently, Agrobacterium rhizogenes-mediated transformation is the predominant method for facilitating rapid transformation, producing transgenic hairy roots. However, the limitations of soybean transformation technology primarily originate from its low efficiency and genotype dependency, leaving significant room for improvement in the development more universally applicable and efficient methods. In this study, we explored the enhancement of soybean transformation efficiency through the generation and validation of three reporter vectors (ZsGreen, TdTomato, and Ruby) and the strategic use of Agrobacterium Auxiliary Solution (AAS) containing Silwet L-77 and hormone mixtures. Our findings demonstate that the incorporation of hormone mixtures and Silwet L-77 into AAS significantly improves hairy root transformation rates. Specifically, the combination of hormone mixtures with Silwet L-77 substantially increased both total root and cotyledon transformation efficiencies compared to the control. We also assessed the impact of vector size on transformation efficiency, observing a notable decrease in efficiency with larger vectors such as the Ruby cassette compared to smaller markers like GFP and RFP. Furthermore, our study examined the effects of AAS on the co-transformation rate of two separate vectors, revealing a slight but significant reduction in efficiency compared to single vector transformations. Additionally, we evaluated the role of AAS in enhancing soybean hypocotyl transformation rates in composite soybean plants across various varieties. The results consistently showed an increase in both positive roots and explant efficiencies with the addition of AAS, indicating its broad applicability and effectiveness in soybean transformation. However, significant varietal differences in transformation rates were observed, particularly between "Forrest" and other varieties such as "Williams 82" and "Dongnong 50". In summary, our research emphasizes the significant role of auxiliary agents and vector size in optimizing soybean transformation techniques, providing valuable insights for future advancements in soybean genetic modification and biotechnological research.

plant biology↗

bioRxiv2024

Cure or Curse? Simulation Indicates that Microbes Proliferate under Disinfection Measures in the Space Station

The long-term stay on the space station requirement poses a knotty issue about the stable hardware and reliable guarantee of astronauts health. Despite regular cleaning with wipes, microbes still proliferate in the space station. This study distilled three key factors--low-dose ionizing radiation, dilution and quaternary ammonium compound from the scenario. Species abundance and differential metabolites were applied to test their sole/combined influences on the three-simple-species microbial community succession. Mechanisms were built in mathematical models to generate the structural and behavior similarity. Results showed that LDIR, dilution and QAC, solely or jointly, could contribute to microbial proliferation. The synergy of disturbances might convert them from harmful factors to rewarding ones (e.g. the transformation of QAC into nutrients under LDIR), leading to this "Ecological Surprise". These results shed light on mechanisms driving microbial community succession in the space station and highlight the need for tailored biocontrol strategies in the specific environment.

ecology↗

bioRxiv2024

A high-continuity and annotated reference genome of allotetraploid Siberian wildrye (Elymus sibiricus L., Poaceae: Triticeae)

Elymus sibiricus L. (Siberian wildrye, Es), a species belonging to the wheat tribe, is extensively employed as forage and for the reclamation of degraded grasslands within the Qinghai-Tibet Plateau (QTP). This study provides a high-quality reference genome assembly for the allotetraploid Es, which is composed of 14 pseudomolecules with the total genome size of 6.57 Gb. Our finding suggest that large-scale bursts of retrotransposons are critical for the genome expansion of Es. We discovered a translocation event between the Es4H and Es6H chromosomes with a low frequency of combination. Phylogenetic analyses of 90 Es accessions and 25 diploid accessions representing proposed ancestors from various habitats revealed the existence of four distinct populations. We further provided support for the hypothesis that the QTP is the center of origin and genetic diversity for Es. Collectively, our study offers valuable insights into the evolution of Es, as well as providing genomic resources for genetic enhancement in the Elymus genus and wheat tribe.

genomics↗

bioRxiv2024

Improved vascularized lymph node transfer by periodic injection of hyaluronidase in a rodent model

BackgroundVascularized lymph node transfer (VLNT) is an advanced surgical approach for secondary lymphedema (SLE) treatment, but tissue fibrosis around the lymph node flap (VLNF) inhibiting lymphangiogenesis is the biggest challenge undermining its therapeutic efficacy. Hyaluronidase (HLD), which is an enzyme that breaks down hyaluronic acid, may have the efficacy of reducing fibrosis and increasing the chance of lymphangiogenesis in the injury site. Materials and methods52 Sprague-Dawley rats with VLNF were divided into a group injected periodically with HLD and a control group and followed up. A follow-up study was performed for 13 weeks starting 1 week after model formation was examined. The limb volume and dermal backflow pattern were observed to evaluate the degree of lymphedema. The real-time ICG fluorescence intensity changes were measured to evaluate the degree of lymphatic drainage to the flap. Lastly, the number of regenerative lymphatic vessels and the degree of fibrosis were investigated. ResultsIn the group injected with HLD periodically (VLNF+HLD group), swelling reduction and dermal backflow pattern recovery occurred rapidly in the 3rd week of follow-up compared to the only VLNF group. Moreover, the efficiency of lymphatic drainage into the flap was also improved in the VLNF+HLD group. They significantly had more newly formed lymphatic vessels along with a decrease in collagen fiber decomposition in the tissue around the VLNF by up to 26%. ConclusionThese encouraging results pave the way for developing a combination strategy for SLE treatment involving HLD and VLNT. Furthermore, this finding may guide future research on the development of new drugs that could enhance the efficacy of VLNT surgery for SLE patients. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/586511v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@12b4c7forg.highwire.dtl.DTLVardef@1ab4538org.highwire.dtl.DTLVardef@14d93adorg.highwire.dtl.DTLVardef@1a6b87_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Jumbo phages possess independent synthesis and utilization systems of NAD+

Jumbo phages, phages with genomes >200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how do jumbo phages complete their life cycle remain largely undefined. In this study, we assembled 668 high-quality jumbo phage genomes from over 15 TB of intestinal metagenomic data from 955 samples of five animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for synthesis of NAD+ by the salvage pathway or Preiss-Handler pathway, referred as NAD-jumbo phage. Besides synthesis genes of NAD+, these NAD-jumbo phages also encode at least 15 types of NAD+-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD+ but also redirect NAD+ metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earths ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater. In summary, this study expands our understanding of the diversity and survival strategies of phages, and in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation.

microbiology↗

bioRxiv2024

The microtubule regulator EFA-6 forms spatially restricted cortical foci dependent on its intrinsically disordered region and interactions with tubulins

Microtubules (MTs) are dynamic components of the cytoskeleton and play essential roles in morphogenesis and maintenance of tissue and cell integrity. Despite recent advances in understanding MT ultrastructure, organization, and growth control, how cells regulate MT organization at the cell cortex remains poorly understood. The EFA-6/EFA6 proteins are recently identified membrane-associated proteins that inhibit cortical MT dynamics. Here, combining visualization of endogenously tagged C. elegans EFA-6 with genetic screening, we uncovered tubulin-dependent regulation of EFA-6 patterning. In the mature epidermal epithelium, EFA-6 forms punctate foci in specific regions of the apical cortex, dependent on its intrinsically disordered region (IDR). We further show the EFA-6 IDR is sufficient to form biomolecular condensates in vitro. In screens for mutants with altered GFP::EFA-6 localization, we identified a novel gain-of-function (gf) mutation in an -tubulin tba-1 that induces ectopic EFA-6 foci in multiple cell types. tba-1(gf) animals exhibit temperature-sensitive embryonic lethality, which is partially suppressed by efa-6(lf), indicating the interaction between tubulins and EFA-6 is important for normal development. TBA-1(gf) shows reduced incorporation into filamentous MTs but has otherwise mild effects on cellular MT organization. The ability of TBA-1(gf) to trigger ectopic EFA-6 foci formation requires {beta}-tubulin TBB-2 and the chaperon EVL-20/Arl2. The tba-1(gf)-induced EFA-6 foci display slower turnover, contain the MT-associated protein TAC-1/TACC, and require the EFA-6 MTED. Our results reveal a novel crosstalk between cellular tubulins and cortical MT regulators in vivo. HighlightsO_LIThe MT regulator EFA-6 forms spatially restricted punctate cortical foci C_LIO_LIThe EFA-6 N-terminal intrinsically disordered region (IDR) is essential for the formation of cortical foci in vivo and is sufficient for droplet formation in vitro C_LIO_LITubulins regulate formation of EFA-6 foci via the EFA-6 MT elimination domain C_LIO_LIEFA-6 foci induced by altered tubulin heterodimer function display reduced turnover and recruit TAC-1/TACC C_LI

cell biology↗

bioRxiv2024

MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants

SummaryMassively parallel reporter assay (MPRA) is an important technology to evaluate the impact of genetic variants on gene regulation. Here, we present MPRAVarDB, an online database and web server, for exploring regulatory effects of genetic variants. MPRAVarDB harbors 18 MPRA experiments designed to assess the regulatory effects of genetic variants associated with GWAS loci, eQTLs and various genomic features, resulting in a total of 242,818 variants tested across more than 30 cell lines and 30 human diseases or traits. MPRAVarDB empowers the query of MPRA variants by genomic region, disease and cell line or by any combination of these query terms. Notably, MPRAVarDB offers a suite of pretrained machine learning models tailored to the specific disease and cell line, facilitating the genome-wide prediction of regulatory variants. MPRAVarDB is friendly to use, and users only need a few clicks to receive query and prediction results. Availabilityhttps://mpravardb.rc.ufl.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

Redefining the Game: MVAE-DFDPnet's Low-Dimensional Embeddings for Superior Drug-Protein Interaction Predictions

Precisely predicting drug-protein interactions (DPIs) is pivotal for drug discovery and advancing precision medicine. A significant challenge in this domain is the high-dimensional and heterogeneous data characterizing drug and protein attributes, along with their intricate interactions. In our study, we introduce a novel deep learning architecture: the Multi-view Variational Auto-Encoder embedded within a cascade Deep Forest (MVAE-DFDPnet). This framework adeptly learns ultra-low-dimensional embedding for drugs and proteins. Notably, our t-SNE analysis reveals that two-dimensional embedding can clearly define clusters corresponding to diverse drug classes and protein families. These ultra-low-dimensional embedding likely contribute to the enhanced robustness and generalizability of our MVAE-DFDPnet. Impressively, our model surpasses current leading methods on benchmark datasets, functioning in significantly reduced dimensional spaces. The models resilience is further evidenced by its sustained accuracy in predicting interactions involving novel drugs, proteins, and drug classes. Additionally, we have corroborated several newly identified DPIs with experimental evidence from the scientific literature. The code used to generate and analyze these results can be accessed from https://github.com/Macau-LYXia/MVAE-DFDPnet-V2.

bioinformatics↗

bioRxiv2024

3D live imaging and phenotyping of the subcellular cytotoxicity in cancer immunotherapy using event-triggered Bessel oblique plane microscopy

Clarification of the cytotoxic function of T cells is crucial for understanding human immune responses and immunotherapy procedures. Here, we report an event-triggered Bessel oblique plane microscopy (EBOPM) platform capable of smart 3D live imaging and phenotyping of chimeric antigen receptor (CAR)-modified T-cell cytotoxicity in cancer immunotherapy; the EBOPM platform has the following characteristics: an isotropic subcellular resolution of 320 nm, large-scale scouting over 400 interacting cell pairs, long-term observation across 5 hours, and quantitative analysis of the Terabyte-scale 3D, multichannel, time-lapse image datasets. Using this advanced microscopy platform, several key subcellular events in CAR-T cells were captured and comprehensively analyzed; these events included the instantaneous formation of immune synapses and the sustained changes in the microtubing morphology. Furthermore, we identified the actin retrograde flow speed, the actin depletion coefficient, the microtubule polarization and the contact area of the CAR-T/target cell conjugates as essential parameters strongly correlated with CAR-T-cell cytotoxic function. Our approach will be useful for establishing criteria for quantifying T-cell function in individual patients for all T-cell-based immunotherapies.

immunology↗

bioRxiv2024

How do Large Language Models understand Genes and Cells

Researching genes and their interactions is crucial for deciphering the fundamental laws of biological activity, advancing disease treatment, drug discovery and so on. Large language Models (LLMs), with their profound text comprehension and generation capabilities, have made significant strides across various natural science fields. However, their application in cell biology remains notably scarce. To alleviate this issue, in this paper, we selects seven mainstream LLMs and evaluates their performance across a range of problem scenarios. Our findings indicate that LLMs possess a certain level of understanding of genes and cells, and hold potential for solving real-world problems. Moreover, we have improved the current method of textual representation of cells, enhancing the LLMs ability to tackle cell annotation tasks. We encourage cell biology researchers to leverage LLMs for problem-solving while also being mindful of some challenges associated with their use. We release our code and data at https://github.com/epang-ucas/Evaluate_LLMs_to_Genes. CCS ConceptsApplied computing [->] Recognition of genes and regulatory elements; Bioinformatics; Computational genomics; Computational transcriptomics. ACM Reference FormatChen Fang, Yidong Wang, Yunze Song, Qingqing Long, Wang Lu, Linghui Chen, Pengfei Wang, Guihai Feng, Yuanchun Zhou, and Xin Li. 2024. How do Large Language Models understand Genes and Cells. 1, 1 (March 2024), 14 pages. https://doi.org/10.1145/nnnnnnn.nnnnnnn

bioinformatics↗

bioRxiv2024

GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects

With development of the single cell RNA-seq technologies, large numbers of cells can now be routinely sequenced by different platforms. This requires us to choose an efficient integration tool to merge those cells, and computational simulators to help benchmark and assess the performance of these tools. Although existing single cell RNA-seq simulators can simulate library size, biological and batch effects separately, they currently do not capture associations among these three factors. Here we present GLMsim, the first single cell RNA-seq simulator to simultaneously capture the library size, biology and unwanted variation and their associations via a generalized linear model, and to simulate data resembling the original experimental data in these respects. GLMsim is capable of quantitatively benchmarking different single cell integration methods, and assessing their abilities to retain biology and remove library size and batch effects.

bioinformatics↗

bioRxiv2024

Protein Retrieval via Integrative Molecular Ensembles (PRIME) through extended similarity indices

Molecular dynamics (MD) simulations are ideally suited to describe conformational ensembles of biomolecules such as proteins and nucleic acids. Microsecond-long simulations are now routine, facilitated by the emergence of graphical processing units. Processing such ensembles on the basis of statistical mechanics can bring insights about different biologically relevant states, their representative structures, states, and even dynamics between states. Clustering, which groups objects based on structural similarity, is typically used to process ensembles, leading to different states, their populations, and the identification of representative structures. For some purposes, such as in protein structure prediction, we are interested in identifying the representative structure that is more similar to the native state of the protein. The traditional pipeline combines hierarchical clustering for clustering and selecting the cluster centroid as representative of the cluster. However, even when the first cluster represents the native basin, the centroid can be several angstroms away in RMSD from the native state - and many other structures inside this cluster could be better choices of representative structures, reducing the need for protein structure refinement. In this study, we developed a module--Protein Retrieval via Integrative Molecular Ensemble (PRIME), that consists of tools to determine the most prevalent states in an ensemble using extended continuous similarity. PRIME is integrated with our Molecular Dynamics Analysis with N -ary Clustering Ensembles (MDANCE) package and can be used as a post-processing tool for arbitrary clustering algorithms, compatible with several MD suites. PRIME was validated with ensembles of different protein and protein complex systems for their ability to reliably identify the most native-like state, which we compare to their experimental structure, and to the traditional approach. Systems were chosen to represent different degrees of difficulty such as folding processes and binding which require large conformational changes. PRIME predictions produced structures that when aligned to the experimental structure were better superposed (lower RMSD). A further benefit of PRIME is its linear scaling - rather than the traditional O(N 2) traditionally associated to comparisons of elements in a set.

biophysics↗

bioRxiv2024

BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer

Bromodomain and extra-terminal domain (BET) proteins, which function partly through MYC, are critical epigenetic readers and emerging therapeutic targets in cancer. Whether and how BET inhibition simultaneously induces metabolic remodeling remains unclear. Here we find that even transient BET inhibition by JQ-1 and other pan-BET inhibitors blunts liver cancer cell proliferation and tumor growth. BET inhibition decreases glycolytic gene expression but enhances mitochondrial glucose and glutamine oxidative metabolism revealed by metabolomics and isotope labeling analysis. Specifically, BET inhibition downregulates miR-30a to upregulate glutamate dehydrogenase 1 (GDH1) independent of MYC, which produces -ketoglutarate for mitochondrial oxidative phosphorylation (OXPHOS). Targeting GDH1 or OXPHOS is synthetic lethal to BET inhibiton, and combined BET and OXPHOS inhibition therapeutically prevents liver tumor growth in vitro and in vivo. Together, we uncover an important epigenetic-metabolic crosstalk whereby BET inhibition induces MYC- independent and GDH1-dependendent glutamine metabolic remodeling that can be exploited for innovative combination therapy of liver cancer.

cancer biology↗

bioRxiv2024

Estrogen regulation and functional role of FGFR4 in estrogen receptor positive breast cancer

BackgroundResistance to endocrine therapy is a major challenge of managing estrogen receptor positive (ER+) breast cancer. We previously reported frequent overexpression of FGFR4 in endocrine resistant cell lines and breast cancers that recurred and metastasized following endocrine therapy, suggesting FGFR4 as a potential driver of endocrine resistance. In this study, we investigated the role of FGFR4 in mediating endocrine resistance and explored the therapeutic potential of targeting FGFR4 in advanced breast cancer. MethodsA gene expression signature of FGFR4 activity was examined in ER+ breast cancer pre- and post-neoadjuvant endocrine therapy and the association between FGFR4 expression and patient survival was examined. A correlation analysis was used to uncover potential regulators of FGFR4 overexpression. To investigate if FGFR4 is necessary to drive endocrine resistance, we tested response to FGFR4 inhibition in long term estrogen deprived (LTED) cells and their paired parental cells. Doxycycline inducible FGFR4 overexpression and knockdown cell models were generated to examine if FGFR4 was sufficient to confer endocrine resistance. Finally, we examined response to FGFR4 monotherapy or combination therapy with fulvestrant in breast cancer cell lines to explore the potential of FGFR4 targeted therapy for advanced breast cancer and assessed the importance of PAM50 subtype in response to FGFR4 inhibition. ResultsA FGFR4 activity gene signature was significantly upregulated post neoadjuvant aromatase inhibitor treatment, and high FGFR4 expression predicted poorer survival in patients with ER+ breast cancer. Gene expression association analysis using TCGA, METABRIC and SCAN-B datasets uncovered ER as the most significant gene negatively correlated with FGFR4 expression. ER negatively regulates FGFR4 expression at both the mRNA and protein level across multiple ER+ breast cancer cell lines. Despite robust overexpression of FGFR4, LTED cells did not show enhanced responses to FGFR4 inhibition compared to parental cells. Similarly, FGFR4 overexpression, knockdown or hotspot mutations did not significantly alter response to endocrine treatment in ER+ cell lines, nor did FGFR4 and fulvestrant combination treatment show synergistic effects. The HER2-like subtype of breast cancer showed elevated expression of FGFR4 and an increased response to FGFR4 inhibition relative to other breast cancer subtypes. ConclusionsDespite ER-mediated upregulation of FGFR4 post endocrine therapy, our study does not support a general role of FGFR4 in mediating endocrine resistance in ER+ breast cancer. Our data suggests that specific genomic backgrounds such as HER2 expression may be required for FGFR4 function in breast cancer and should be further explored.

cancer biology↗

bioRxiv2024

Nine high-quality Anas genomes provide new insights into Anas evolution and domestication

The evolutionary origin and genetic architecture of domestic animals are becoming more tractable as the availability of more domestic species genomes. Evolutionary studies of wild and domestic organisms have yielded many fascinating discoveries, while the stories behind the species diversity of Anas or the domestication of duck were largely unknown. Here, we assembled eight chromosome-level Anas genomes. Together with our recently available Pekin duck genome, we investigated Anas phylogeny, genetic differentiation, and gene flow. Extensive phylogenetic inconsistencies were observed in Anas genomes, particularly two phylogeny conflicts between autosome and Z-chromosome. However, the Z chromosome was less impacted by introgression and more suitable to elucidate phylogenetic relationships than autosomes. From the Z-chromosome perspective, we found that the speciation of Anas platyrhynchos and Anas zonorhyncha accompanied with female-biased gene flow, and remodeled duck domestication history. Moreover, we constructed an Anas pan-genome and identified several differentiated SVs between domestic and wild ducks. These SVs might act as repressors/enhancers to regulate their neighboring genes (i.e., GHR and FER), which represented the promising "domestication genes". Additionally, Anas genomes were found being presented LTR retrotransposon bursts, which might largely contribute to functional shifts of genes involved in duck domestication (i.e., MITF and IGF2BP1). This study opens a new window to unravel avian speciation and domestication from Z chromosome.

genomics↗

bioRxiv2024

A brain-to-text framework of decoding natural tonal sentences

Speech brain-computer interfaces (BCIs) directly translate brain activity into speech sound and text, yet decoding tonal languages like Mandarin Chinese poses a significant, unexplored challenge. Despite successful cases in non-tonal languages, the complexities of Mandarin, with its distinct syllabic structures and pivotal lexical information conveyed through tonal nuances, present challenges in BCI decoding. Here we designed a brain-to-text framework to decode Mandarin tonal sentences from invasive neural recordings. Our modular approach dissects speech onset, base syllables, and lexical tones, integrating them with contextual information through Bayesian likelihood and the Viterbi decoder. The results demonstrate accurate tone and syllable decoding under variances in continuous naturalistic speech production, surpassing previous intracranial Mandarin tonal syllable decoders in decoding accuracy. We also verified the robustness of our decoding framework and showed that the model hyperparameters can be generalized across participants of varied gender, age, education backgrounds, pronunciation behaviors, and coverage of electrodes. Our pilot study shed lights on the feasibility of more generalizable brain-to-text decoding of natural tonal sentences from patients with high heterogeneities.

neuroscience↗

bioRxiv2024

N-acetyltransferase 10-mediated mRNA N4-acetylation is Essential for the Translational Regulation During Oocyte Meiotic Maturation in Mice

Mammalian oocyte maturation is driven by the strict translational regulation of maternal mRNAs stored in the cytoplasm. However, the function and mechanism of post-transcriptional chemical modifications, especially the newly identified N4-acetylcytidine (ac4C) modification catalyzed by N-acetyltransferase 10 (NAT10), are unknown. In this study, we developed a low-input ac4C sequencing technology, ac4C LACE-seq, and mapped 8241 ac4C peaks at the whole-transcriptome level using 50 mouse oocytes at the germinal vesicle stage. We profiled the mRNA landscapes of NAT10-interactions and ac4C modifications. The NAT10-interacted and ac4C-modified transcripts are associated with high translation efficiency in oocytes. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. ac4C LACE-seq results indicated that Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors, such as MSY2, ZAR1, BTG4, and cyclin B1, which regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes showed decreased mRNA translation efficiency during meiotic maturation, partially due to the direct inhibition of ac4C sites on specific transcripts. In summary, we developed a low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in the precise regulation of oocyte meiotic maturation by enhancing translation efficiency.

developmental biology↗

bioRxiv2024

Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase

Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable to coordinate cupric ion draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a [~]31 kb DNA region, consisting of 19 open reading frames that encode five non-ribosomal peptide synthetase (ChmHIJLO), one modular polyketide synthases (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.

biochemistry↗