Biology subjects

Deng, Z.

Publications and source records attributed to Deng, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum

Sorghum bicolor is a C4 plant with the characteristics of high stress tolerance, which may be conferred partly by the underlying epigenetic mechanism unique to sorghum. In this study, we revealed some epigenomic features in sorghum that have never been reported before. The long H3K27me3 regions clustered in four areas, which we defined as H3K27me3 islands, were identified in sorghum. H3K36me3 plays some role in inhibiting the deposition of both H3K27me3 and H2A.Z, which may serve as partial motivation for the removal of H3K27me3 and H2A.Z in leaf and root. All the 7 histone marks are involved in the regulation of tissue-specific genes, especially the specific expression of C4 genes in leaf and peroxidase (POD) encoding genes in root, which are involved in the photosynthesis in leaf and lignin synthesis in root, respectively. These marks except H3K36me3 and H3K27me3 also engage in the regulation of stress genes in response to PEG treatment. However, we found that differential enrichment of histone marks on many tissue-specific genes was observed only between leaf and root but hardly in response to PEG treatment, although expression of these genes changed after PEG treatment.

plant biology↗

bioRxiv2023

Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants

Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains mysterious. Here, we report that gravistimulation by reorientation triggers the Mitogen-Activated Protein Kinase (MAPK) signaling-mediated phosphorylation of LAZY proteins, the key regulators of gravitropism accumulated more on the lower side of the plasma membrane in columella cells in regular growth Arabidopsis. Phosphorylation of LAZY increases its interaction with several TOC proteins on the surface of amyloplasts, facilitating the translocation of LAZY proteins from the plasma membrane to the amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle movement-triggered molecular polarity formation.

plant biology↗

bioRxiv2023

Retrieved Sequence Augmentation for Protein Representation Learning

The advancement of protein representation learning has been significantly influenced by the remarkable progress in language models. Accordingly, protein language models perform inference from individual sequences, thereby limiting their capacity to incorporate evolutionary knowledge present in sequence variations. Existing solutions, which rely on Multiple Sequence Alignments (MSA), suffer from substantial computational overhead and suboptimal generalization performance for de novo proteins. In light of these problems, we introduce a novel paradigm called Retrieved Sequence Augmentation (RSA) that enhances protein representation learning without necessitating additional alignment or preprocessing. RSA associates query protein sequences with a collection of structurally or functionally similar sequences in the database and integrates them for subsequent predictions. We demonstrate that protein language models benefit from retrieval enhancement in both structural and property prediction tasks, achieving a 5% improvement over MSA Transformer on average while being 373 times faster. Furthermore, our model exhibits superior transferability to new protein domains and outperforms MSA Transformer in de novo protein prediction. This study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available at https://github.com/HKUNLP/RSA.

bioinformatics↗

bioRxiv2023

Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance

Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% - 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following homology-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.

cancer biology↗

bioRxiv2023

Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase

An under-explored target for SARS-CoV-2 is non-structural protein 14 (Nsp14), a crucial enzyme for viral replication that catalyzes the methylation of N7-guanosine of the viral RNA at 5'-end; this enables the virus to evade the host immune response by mimicking the eukaryotic post-transcriptional modification mechanism. We sought new inhibitors of the S-adenosyl methionine (SAM)-dependent methyltransferase (MTase) activity of Nsp14 with three large library docking strategies. First, up to 1.1 billion make-on-demand ("tangible") lead-like molecules were docked against the enzymes SAM site, seeking reversible inhibitors. On de novo synthesis and testing, three inhibitors emerged with IC50 values ranging from 6 to 43 M, each with novel chemotypes. Structure-guided optimization and in vitro characterization supported their non-covalent mechanism. In a second strategy, docking a library of 16 million tangible fragments revealed nine new inhibitors with IC50 values ranging from 12 to 341 M and ligand efficiencies from 0.29 to 0.42. In a third strategy, a newly created library of 25 million tangible, virtual electrophiles were docked to covalently modify Cys387 in the SAM binding site. Seven inhibitors emerged with IC50 values ranging from 3.2 to 39 M, the most potent being a reversible aldehyde. Initial optimization of a second series yielded a 7 M acrylamide inhibitor. Three inhibitors characteristic of the new series were tested for selectivity against 30 human protein and RNA MTases, with one showing partial selectivity and one showing high selectivity. Overall, 32 inhibitors encompassing eleven chemotypes had IC50 values <50 M and 5 inhibitors in four chemotypes had IC50 values <10 M. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing multiple starting points for optimizing towards antiviral activity.

biophysics↗

bioRxiv2023

Benchmark and optimization of AlphaFold structures based virtual screening strategy

Recent advancements in artificial intelligence such as AlphaFold, have enabled more accurate prediction of protein three-dimensional structure from amino acid sequences. This has attracted significant attention, especially for the application of AlphaFold in drug discovery. However, how to take full advantage of AlphaFold to assist with virtual screening remains elusive. We evaluate the AlphaFold structures of 51 selected targets from the DUD-E database in virtual screening. Our analyses show that the virtual screening performance of about 35% of the AlphaFold structures is equivalent to that of DUD-E structures, and about 25% of the AlphaFold structures yield better results than the DUD-E structures. Remarkably, AlphaFold structures produce slightly better results than the Apo structures. Moreover, we develop a new consensus scoring method based on Z-score standardization and exponential function, which shows improved screening performance compared to traditional scoring methods. By implementing a multi-stage virtual screening process and the new consensus scoring method, we are able to improve the speed of virtual screening by about nine times without compromising the enrichment factor. Overall, our results provide insights into the potential use of AlphaFold in drug discovery and highlight the value of consensus scoring and multi-stage virtual screening.

bioinformatics↗

bioRxiv2022

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity

The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as are molecular adaptations facilitating cross-biome transitions. Here, we conduct large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,276 MAGs). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. Distinct brackish basins co-hosted numerous species despite differences in salinity and geographic distance, the latter having stronger intra-species population structuring effects. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed towards the brackish biome. Transitions were accompanied by changes in isoelectric point distribution and amino acid composition of inferred proteomes, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content result in species-level separation between aquatic biomes.

microbiology↗

bioRxiv2022

Comparative genomic analyses of Lactococcus garvieae isolated from bovine mastitis in China

Lactococcus garvieae is an emerging zoonotic pathogen, but there are few reports regarding bovine mastitis. The recent prevalence of L. garvieae poses an increasing disease threat and global public health risk. A total of 39 L. garvieae isolates were obtained from 2899 bovine clinical mastitis milk samples in 6 provinces of China from 2017 to 2021. Five clonal complexes were determined from 32 MLST types of L. garvieae; ST46 was the predominant sequence type and 13 novel MLST types were identified. All isolates were resistant to chloramphenicol and clindamycin, but susceptible to penicillin, ampicillin, amoxicillin-clavulanic acid, imipenem, ceftiofur, enrofloxacin, and marbofloxacin. Based on genomic analyses, L. garvieae had 6310 genes, including 1015, 3641 and 1654 core, accessory and unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, Glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase and NADH oxidase. Most isolates had lsaD and mdtA AMR genes. Based on COG results, the functions of defense, transcription and replication, recombination and repair were enhanced in unique genes, whereas functions of translation, ribosomal structure and biogenesis were enhanced in core genes. The KEGG functional categories enriched in unique genes included human disease and membrane transport, whereas COG functional categories enriched in core genes included energy metabolism, nucleotide metabolism and translation. No gene was significantly associated with host specificity. In addition, core genome SNPs analysis suggested potential host adaptation of some isolates in several sequence types. Therefore, this study characterized L. garvieae isolated from mastitis and assessed host adaptation of L. garvieae to various hosts. IMPORTANCEThis study provides important insights on bovine mastitis key topic pathogen Lactococcus garvieae, which constitutes mastitis concerns. However, comprehensive genomic analyses of L. garvieae from dairy farms have not been performed. This study gives a detailed and comprehensive novel feature in L. garvieae, an important but poorly characterized bacterium, recovered in the past 5 years in 6 Chinese provinces. We documented diverse contributory genetic processes, including predominant sequence type ST46 and 13 novel MLST types. L. garvieae had 6310 genes, including 1015, 3641 and 1654 core, accessory and unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, Glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase and NADH oxidase, and resistant to chloramphenicol and clindamycin. Most isolates had lsaD and mdtA antimicrobial resistance genes. No gene was significantly associated with host specificity. This is the first absolute quantification of L. garvieae isolated from mastitis and identified host adaptation of L. garvieae to various hosts.

microbiology↗

bioRxiv2022

Structural mechanism of leaflet-specific phospholipid modulation of a pentameric ligand-gated ion channel

Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To elucidate the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open conformation. The structure shows a bound phospholipid in an outer leaflet site, and conformational changes in the phospholipid binding site unique to the open state. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the open state of a pLGIC by specific, state-dependent binding to this site.

biophysics↗

bioRxiv2022

A Modular Chemoenzymatic Approach to C14-Functionalized Steroids

C14-functionalized steroids belong to a unique class of steroids with important biological activities. However, the lack of efficient methods to access C14-functionalized steroids impede related steroidal drug discovery. Herein we report a modular chemoenzymatic approach to access diversified C14-functionalized steroids. We first identified a novel C14-hydroxylase (CYP14A) from Cochliobolus lunatus with high catalytic efficiency and substrate promiscuity. Protein engineering of CYP14A generated three variants I111A, M115K and V124A that greatly improved the C14-hydroxy regioselectivity. Based on this efficient biocatalytic method, a range of C14-OH steroids with C17 side chain were prepared in good yields, which was then transformed into {Delta}14 olefins through a facile elimination. The newly formed {Delta}14 olefin served as a versatile handle to install diversified functional groups (e.g. epoxide, {beta}-OH, F, Cl and N3) at C14 position through hydrofunctionalization. Furthermore, the synthetic utility of this powerful chemoenzymatic methodology was demonstrated by performing a 7-step semisynthesis of periplogenin and the diversity-oriented synthesis of cardenolide (+)-digitoxigenin and its three diastereomers in a concise manner.

biochemistry↗

bioRxiv2022

A common mechanism of temperature-sensing in thermoTRP channels

Detecting temperature is crucial for the survival of living organisms. Though the thermo transient receptor potential (thermoTRP) channels, such as TRPV1 or TRPM8, have been identified as prototypic heat or cold sensors, respectively, how they detect temperature remains elusive. Here we first identified groups of clustered residues in these channels that undergo burial/exposure conformational rearrangements during temperature activation by analyzing available protein structures or hydroxyl radical footprinting-mass spectroscopy (HRF-MS). By systematically perturbing water-protein interactions at these residues, we found that the temperature sensitivity in these channels were modulated in accordance with the sidechain hydrophobicity. The changes in energy associated with changes in water-protein interactions were sufficient for thermo activation. Therefore, our study has established that the water-protein interactions as a common mechanism underlying temperature sensing in TRPM8 and TRPV1.

biophysics↗

bioRxiv2022

Temporal and Spatial Resolution of a Protein Quake that Activates Hydrogen Tunneling in Soybean Lipoxygenase

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen deuterium exchange experiments to detect a radiating cone of aliphatic side chains that extends from the iron active site of SLO to the protein-solvent interface. Employing eight variants of SLO, nanosecond fluorescence Stokes shifts have been measured using a probe appended to the identified surface loop. We report a remarkable identity of the enthalpies of activation for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within the identified thermal network. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, these new data implicate a thermally initiated, cooperative protein quake as the source of the activation of SLO. These findings indicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis.

biophysics↗

bioRxiv2022

An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging

Fluorescent in situ hybridization (FISH) can provide spatial information about DNA/RNA targets in fixed cells and tissues. However, the workflows of multiplexed FISH-based imaging that use sequential rounds of hybridization quickly become laborious as the number of rounds increases because of liquid handling demands. Here, we present an open-source and low-cost fluidics system that is purpose built for automating the workflows of sequential FISH-based imaging. Our system features a fluidics module with 16 addressable channels in which flow is positive pressure-driven and switched on/off by solenoid valves in order to transfer FISH reagents to the sample. Our system also includes a controller with a main printed circuit board that can control up to 120 solenoid valves and allows users to control the fluidics module via serial communication. We demonstrate the automatic and robust fluid exchange with this system by targeting the alpha satellite repeat in HeLa cell with 14 rounds of sequential hybridization and imaging. We anticipate that this simple and flexible system will be of utility to researchers performing multiplexed in situ assays in a range of experimental systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/485524v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@19812f6org.highwire.dtl.DTLVardef@104e5b5org.highwire.dtl.DTLVardef@84d1acorg.highwire.dtl.DTLVardef@1e19d87_HPS_FORMAT_FIGEXP M_FIG C_FIG Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@12d112forg.highwire.dtl.DTLVardef@1c3515forg.highwire.dtl.DTLVardef@135ce2org.highwire.dtl.DTLVardef@13709e1org.highwire.dtl.DTLVardef@69bf82_HPS_FORMAT_FIGEXP M_TBL C_TBL

bioengineering↗

bioRxiv2022

Editing the CsDMR6 Gene in Citrus Results in Resistance to the Bacterial Disease Citrus Canker

Citrus is one of the most important fruit crops in the world. Citrus production worldwide faces challenges from devastating bacterial diseases, including citrus canker caused by Xanthomonas citri ssp. citri (Xcc). Improving citrus resistance to citrus canker and other major bacterial diseases has been a top priority in citrus biotechnology. Disabling disease susceptibility genes has emerged as a novel, promising approach to engineering disease resistance. The bottleneck for applying such an approach has been the identification of proper disease susceptibility-related genes in citrus. Here we show the first successful case of editing the CsDMR6 gene in citrus and obtaining strong resistance to citrus canker in six mutants in two citrus cultivars, Duncan grapefruit and Carrizo citrange. Multiple types of deletions and insertions were induced in CsDMR6, resulting in frameshift of its coding region and presumably loss of gene function. The mutation frequency in most of the mutants reached 71.8% to 98.9%. The mutants showed 71.2% to 99.8% reduction in citrus canker lesion and greater than 99.7% or 2.45 to 4.95 Log10 unit reduction in Xcc bacterial cell population. Mutants also accumulated more salicylic acid and expressed much higher levels of the NPR1 gene than the wildtype with or without Xcc inoculation, which suggests potential resistance to other diseases in these mutants. The guide RNAs for targeting CsDMR6 were selected from highly conserved regions and have 100% nucleotide identity with DMR6 homologs in important citrus species; these guide RNAs are expected to work in other important citrus species and cultivars.

plant biology↗

bioRxiv2022

An evolutionarily conserved mechanism for control the translation of long proteins

Plants have evolved sophisticated mechanisms to regulate gene expression to activate immune responses against pathogen infections. However, how the translation system contributes to plant immunity is largely unknown. The evolutionarily conserved thiolation modification of tRNA ensures efficient decoding during translation. Here we show that tRNA thiolation is required for plant immunity in Arabidopsis. We identify a cgb Arabidopsis mutant, which is hyper-susceptible to the pathogen Pseudomonas syringae. CGB encodes ROL5, a homolog of yeast NCS6 required for tRNA thiolation. ROL5 physically interacts with CTU2, a homolog of yeast NCS2. Mutations in either ROL5 or CTU2 result in loss of tRNA thiolation. Further analyses reveal that both transcriptional reprogramming and translational reprogramming during immune responses are compromised in cgb. Notably, the translation of the salicylic acid receptor NPR1 is reduced in cgb, resulting in reduced salicylic acid signaling. Our study not only reveals a new regulatory mechanism for plant immunity but also uncovers a new biological function of tRNA thiolation.

biochemistry↗

bioRxiv2022

A chromosome-level phased Citrus sinensis genome facilitates understanding Huanglongbing tolerance mechanisms at the allelic level in an irradiation induced mutant

Sweet orange (SWO) originated from introgressive hybridization of pummelo and mandarin resulting in a highly heterozygous genome. Here, we assembled a chromosome-level phased Valencia SWO (DVS) genome with [~]98.5% completeness, high accuracy (QV=50.6), and the highest annotation BUSCO completeness (99.2%) thus far in citrus. DVS harbors a high level of allelic variances and enables study of allelic somatic structural mutations and corresponding allelic expression alteration in two SWO mutants, one with high Huanglongbing tolerance (T19) and one more sensitive (T78). In T78, a large deletion on the pummelo-origin chr8 causes regional allelic expression absence. In T19, seven upregulated genes are located at one terminal of a translocated segment, including three genes related to heat shock protein (HSP) regulation. Furthermore, 68 of 133 HSPs are significantly upregulated in T19, which may be related to its enhanced HLB tolerance by preventing phloem necrosis. The DVS will advance allelic level studies in citrus.

plant biology↗

bioRxiv2022

Functional and evolutionary significance of unknown genes from uncultivated taxa

Most microbes on our planet remain uncultured and poorly studied. Recent efforts to catalog their genetic diversity have revealed that a significant fraction of the observed microbial genes are functional and evolutionary untraceable, lacking homologs in reference databases. Despite their potential biological value, these apparently unrelated orphan genes from uncultivated taxa have been routinely discarded in metagenomics surveys. Here, we analyzed a global multi-habitat dataset covering 151,697 medium and high-quality metagenome assembled genomes (MAGs), 5,969 single-amplified genomes (SAGs), and 19,642 reference genomes, and identified 413,335 highly curated novel protein families under strong purifying selection out of previously considered orphan genes. These new protein families, representing a three-fold increase over the total number of prokaryotic orthologous groups described to date, spread out across the prokaryote phylogeny, can span multiple habitats, and are notably overrepresented in recently discovered taxa. By genomic context analysis, we pinpointed thousands of unknown protein families to phylogenetically conserved operons linked to energy production, xenobiotic metabolism and microbial resistance. Most remarkably, we found 980 previously neglected protein families that can accurately distinguish entire uncultivated phyla, classes, and orders, likely representing synapomorphic traits that fostered their divergence. The systematic curation and evolutionary analysis of the unique genetic repertoire of uncultivated taxa opens new avenues for understanding the biology and ecological roles of poorly explored lineages at a global scale.

microbiology↗

bioRxiv2021

The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for their organoleptic and nutraceutical properties of the juice. Herein we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively. The analysis of the long terminal repeat (LTR) allowed the identification of 1921 regions on the primary and 1911 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in-silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of C. sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome. In parallel, total RNA was extracted from fruit, flower, leaf and root enabling the detection of 38,205 and 37,753 predicted transcripts on primary and alternative assemblies respectively. Among those, the highest and lowest number of tissue-specific transcripts were detected in flower (2.73% and 2.71% in primary and alternative assemblies respectively) and leaf (0.7% and 0.68%) while gene ontology analysis enables a more precise characterization of the expressed genes based on their function. The availability of a reference genome is an important prerequisite both for the set-up of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.

genomics↗