Biology subjects

Xiang, Y.

Publications and source records attributed to Xiang, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Divergent Minimum Inhibitory Concentrations of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [≥]8 g/mL) compared to CAM (77.4% resistant at [≥]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant--particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗

bioRxiv2025

A class of COPI adaptors regulates processing of transmembrane receptors by reinforcing their Golgi retention

Many transmembrane (TM) receptors undergo essential post-translational modification in the Golgi prior to their delivery to the plasma membrane. Whether and how the passage and accompanied modification of these receptors across the Golgi is controlled remains unclear. Here, we show that leptin receptor overlapping transcript (LEPROT) and LEPROT-like 1 (LEPROTL1) regulate receptor activation by securing their sufficient Golgi retention. LEPROTs localize to cis and medial Golgi in a COPI-dependent manner. Deletion of LEPROTs in cells causes expedited release of receptors transiting through the Golgi, and leakage of some Golgi-enriched proteins into the endomembrane compartments. LEPROTs interact directly with COPI coats and simultaneously engage a variety of integral membrane proteins with relatively long TM domains at acidic pH. Loss of LEPROTs dysregulates receptor activity, including that of EGFR and TFRC, due to defective modification. Collectively, LEPROTs serve as a class of COPI adaptors for TM receptors, ensuring adequate preparation, which is vital for subsequent action on the plasma membrane.

cell biology↗

bioRxiv2025

Structural and Functional Studies of Rabbit SAMD9 Reveal a Distinct tRNase Module That Underlies the Antiviral Activity

Human SAMD9 and SAMD9L (collectively SAMD9/9L) are large cytoplasmic proteins with antiviral and antiproliferative activities, recently shown to regulate protein synthesis by specifically cleaving phenylalanine tRNA (tRNAPhe). The enzymatic activity of human SAMD9 (hSAMD9) resides within its N-terminal tRNase domain, which depends on three essential basic residues for tRNA binding and biological activity. While these residues are highly conserved across mammalian SAMD9/9L, lagomorph SAMD9 orthologs uniquely harbor a charge-reversal acidic residue at one of three sites, a change known to inactivate hSAMD9/9L. Here, we show that despite this variation, rabbit SAMD9 (rSAMD9) potently restricts vaccinia virus replication and specifically reduces tRNAPhe levels, mirroring hSAMD9. However, unlike hSAMD9, rSAMD9s minimal tRNase module extends beyond the homologous tRNase domain (amino acid 158-389) to include the SIR2 region. Additional basic residues, one unique to rSAMD9, were also found to be important for its antiviral activity. The crystal structure of rSAMD9158-389 closely resembles hSAMD9156-385, though with difference in loop conformations. These findings demonstrate that lagomorph SAMD9 preserves core tRNA-targeting and antiviral functions despite a key residue variation and the need for an extended tRNase module. AUTHOR SUMMARYSterile Alpha Motif Domain-containing 9 (SAMD9) and its paralog SAMD9-like (SAMD9L) are antiviral factors and tumor suppressors. Gain of function (GoF) mutations of SAMD9/9L, however, cause a spectrum of human diseases with immunological or/and neurological presentations. We recently identified the effector domain of SAMD9/9L as a previously unrecognized tRNase, a function critical for both their normal physiological roles and the pathogenic effects of by patient-derived mutations. We also identified three basic residues within the tRNase domain that are highly conserved across mammalian SAMD9/9L as key to its enzymatic and biological activities. However, lagomorph SAMD9 orthologs uniquely harbor a negatively charged acidic residue at one of three sites. Through extensive structural and functional analyses, here we demonstrate that rabbit SAMD9 (rSAMD9) retains both tRNA- cleaving and antiviral activities, despite notable differences in its tRNase module- including a unique basic residue specific to rSAMD9 and a larger domain architecture extending beyond the conserved tRNase core. These data highlight both the evolutionary conservation of tRNase activity in mammalian SAMD9/9L and the flexibility of the tRNase module within the protein family.

biochemistry↗

bioRxiv2025

Identification of Novel Mutations Causing Clofazimine Resistance in Mycobacterium intracellulare

Clofazimine (CFZ) is a promising repurposed drug for treating Mycobacterium avium-intracellulare complex pulmonary disease (MAC-PD), but its resistance mechanisms in M. intracellulare remain poorly understood. In this study, we generated 36 CFZ-resistant M. intracellulare mutants in vitro and identified various mutations in the marR gene (WP_009952290.1) in 61% of resistant mutants through whole-genome sequencing. Mutations were identified in additional genes encoding flavin-dependent oxidoreductase (ssuD, C67A), membrane lipoprotein (lppI, C207 deletion), glucose-methanol-choline oxidoreductase (G157 deletion), MASE1 domain-containing protein (C62G), and PPE family protein (222C deletion). Gene complementation experiments demonstrated that introducing the wild-type marR in CFZ-resistant strains (L72 and L74) with marR mutations reduced CFZ minimum inhibitory concentrations (MICs) from 1 g/mL to the susceptible baseline (0.25 g/mL), confirming its critical role in CFZ resistance. Notably, the M. intracellulare MarR lacks homology to M. tuberculosis MarR family protein Rv0678 (MmpR) whose mutations are involved in CFZ and bedaquiline (BDQ) resistance and is flanked by non-efflux pump genes (dhmA and doxX), and unlike M. tuberculosis, its mutation does not cause bedaquiline cross-resistance, indicating a different MarR and distinct regulatory mechanism for CFZ resistance in M. intracellulare. This work highlights marR as a key determinant of CFZ resistance in M. intracellulare and underscores the need for further mechanistic studies with implications for clinical diagnostics and therapeutic strategies.

microbiology↗

bioRxiv2025

Emergence of a New ST617 Hypervirulent Klebsiella pneumoniaewith ESBL+ and Strong Biofilm Forming Ability in China

The increasing infections caused by hypervirulent Klebsiella pneumoniae (hvKP) resistant to carbapenem, broad-spectrum {beta}-lactam and colistin has posed great challenges to global public health. However, the typing and detailed molecular features of the multi-drug resistant hvKP remain to be improved. Here, we characterized a broad-spectrum {beta}-lactam-resistant K. pneumoniae ST617 isolate that has not been previously reported to cause severe disease in China. We obtained the whole-genome sequence of one K. pneumoniae ST617 isolate--HZ7--from a patient with bile duct infection. Phylogenetic reconstruction was performed to investigate the possible host evolutionary origin of HZ7, and the virulence property was studied in comparison with the nearest ST617 neighbours--YZ strains isolated from patient blood infections. Our studies indicated that the HZ7 is an ESBL+ Kp that is likely evolved from environmental or animal-derived sources. Importantly, the virulence assay showed that HZ7 was highly virulent and compared with the well known hvKP strain--NTUH-K2044 and the highly virulent clinical strain ST11-K64--HZ54--isolated from a patient with severe pneumonia. In addition, HZ7 showed strong biofilm formation ability. Whole-genome sequencing analysis identified seven potential virulence genes in HZ7: kp7_000748, kp7_002156, kp7_002157, kp7_002158, kp7_002159, kp7_003103, kp7_003104, which are absent in K. pneumoniae patient isolates from Yangzhou and the environmental samples. Finally, transcriptomic analysis of HZ7 identified six genes--wcaJ, fimA, mrkH, pgaA, ugd, and gndA that are associated with biofilm formation. Given its high virulence likely associated with the seven unique genes acquired via horizontal transfer and strong biofilm forming ability, this strain should be closely monitored to prevent wider spread in the clinic.

microbiology↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

Small Molecule Modulators of TOX protein to Re-invigorate T cell Activity

The TOX protein (thymocyte selection-associated high mobility group box) is a critical transcription factor implicated in both T acute lymphoblastic leukemia (T-ALL) and CD8+ T cell exhaustion. Gene perturbation studies suggest that inhibiting TOX may have therapeutic implications for both leukemia and T cell exhaustion. However, due to its complex molecular mechanisms and intrinsically disordered structure, TOX has not been effectively targeted by small molecules to date. In this study, we used small molecule microarray (SMM) screening and biochemical assays to identify a series of TOX protein-protein interaction (PPI) inhibitors. We identified KI-TOX-A3 as a TOX protein binder and potent TOX PPI inhibitor. In T-ALL, KI-TOX-A3 revealed selective cytotoxicity and proteosome-dependent TOX degradation. In CD8+ T cells, KI-TOX-A3 potently reversed T cell exhaustion by decreasing surface inhibitory receptors, increasing expression of effector cytokines, and enhancing cancer cell killing activity. We also demonstrate the utility of KI-TOX-A3 to probe potential epigenetic regulatory mechanisms of TOX via KAT7 acetylation in T cells.

biochemistry↗

bioRxiv2025

Enhanced epigenetic modulation via mRNA-encapsulated lipid nanoparticles enables targeted anti-inflammatory control

Temporal transcriptional modulation of immune-related genes offers powerful therapeutic potential for treating inflammatory diseases. Here, we introduce an enhanced zinc finger (ZF)-based transcriptional repressor delivered via lipid nanoparticles for controlling immune signaling pathways in vivo. By targeting Myd88, an essential adaptor molecule involved in immunity, our system demonstrates therapeutic efficacy against septicemia in C57BL/6J mice and improves repeated AAV administration by reducing antibody responses. This epigenetic engineering approach provides a platform for safe and efficient immunomodulation applicable across diseases caused by imbalanced inflammatory responses.

immunology↗

bioRxiv2025

Repurposing AZD-5991 for inhibiting growth and biofilm formation of Staphylococcus aureus by disrupting the cell membrane and targeting FabI.

Staphylococcus aureus infections have already become a major threat to public health worldwide. Drug resistance and biofilm formation are two critical factors that significantly affect the efficacy of the antimicrobial treatment of S. aureus infections using conventional antibiotics. Therefore, the discovery of novel antimicrobial agents with potent antibacterial and antibiofilm activity has become a hotspot in recent years. Here, we first demonstrated the remarkable inhibitory activity of AZD-5991, a selective Mcl-1 inhibitor, against S. aureus. The MIC50 and MIC90 of AZD-5991 against S. aureus were 12.5 M, and AZD-5991 significantly inhibited the growth of S. aureus at a subinhibitory concentration of 1/2 x MIC. Besides, AZD-5991 displayed bactericidal activity and a robust capacity for inhibiting biofilm formation against S. aureus with very low drug toxicity against host cell lines. Our data demonstrated the disruption of S.aureus cell integrity by AZD-5991 through membrane permeability assays and the ingredients of the bacterial phospholipids could neutralize the antibacterial activity of AZD-5991. Moreover, whole-genome sequencing and proteomic analysis were also applied to gain insights into the possible impact of AZD-5991 on the fatty metabolism of S. aureus. Furthermore, the antibacterial activity of AZD-5991 was significantly elevated by exogenous fatty acids linoleic acid (C18:2 {Delta} 9,12) and arachidonic acid (C20:4 {Delta} 5,8,11,14). Lastly, the biolayer interferometry assay supported the direct interaction of AZD-5991 with FabI, a necessary protein related closely to bacterial growth and fatty acid metabolism. Conclusively, this study suggests that AZD-5991 could inhibit the planktonic growth and biofilm formation of S. aureus by disrupting the cell membrane and targeting FabI. AZD-5991 might be a promising new antibiotic candidate for the antimicrobial treatment of S. aureus infections resistant to traditional clinical drugs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/638150v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@658444org.highwire.dtl.DTLVardef@cea949org.highwire.dtl.DTLVardef@1cc003dorg.highwire.dtl.DTLVardef@23de22_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Clinical and Taxonomic Characterization of a Novel Urinary Tract Pathogen Providencia lanzhouensis

BackgroundThe genus Providencia includes species of ecological and clinical significance, with some acting as opportunistic pathogens in hospital-acquired infections such as urinary tract infection (UTI). However, overlapping phenotypic traits and genetic similarities pose challenges for accurate species characterization. This study exemplifies this challenge by identifying a novel Providencia isolate through genomic analysis. ResultsIn this study, strain PAZ2 was isolated from the urine sample of a hospitalized patient in Lanzhou, Gansu Province, China. Initial mass spectrometry analysis identified the strain as Providencia alcalifaciens. It exhibits a resistance profile against antibiotics including ampicillin, tetracycline, tigecycline, polymyxin B, colistin, trimethoprim-sulfamethoxazole, and ciprofloxacin. However, whole-genome sequence analysis indicated that this strain is a novel species with an average nucleotide identity (ANI) values ranging from 79.92% to 94.73% and digital DNA-DNA hybridization (dDDH) values between 21.2% and 57.6% when compared with all known Providencia species. Furthermore, strain PAZ2 exhibited unique biochemical properties that differentiated it from all previously described species within the genus. ConclusionsGenomic and biochemical evidence supports PAZ2 as a novel Providencia species, which we named Providencia lanzhouensis sp. nov. This finding enhances the taxonomy of Providencia and underscores its clinical relevance, notably in UTIs and other nosocomial infections. Accurate identification is crucial for guiding effective treatment and preventing misdiagnosis. Further studies should investigate its pathogenicity, antimicrobial resistance, and epidemiology to inform infection control measures.

microbiology↗

bioRxiv2024

C-Reactive Protein Drives Potent Clearance of Blood Bacteria in the Liver by Activating the Complement System

Plasma C-reactive protein (CRP) is widely used as a biomarker for bacterial infections due to its massive induction during infections, however, the precise function of CRP in bacterial infections remains undefined. Here we show that CRP enables Kupffer cells (liver macrophages) to capture and eliminate a wide range of encapsulated bacteria from the bloodstream of mice and thereby provides rapid and effective immunity. Mechanistically, CRP binds to the structurally diverse capsular polysaccharides of major Gram-positive and -negative pathogens, and thereby activates complement C3 at the bacterial surface. The C3-opsonized microbes are in turn captured by C3 receptors on the surface of Kupffer cells, and eliminated in the liver sinusoids. Since CRP principally shares the functional features of antibodies in pathogen recognition/execution, CRP-based defense combines the broad spectrum of the innate immunity with the swiftness, potency and specificity of the adaptive immunity, which helps explain massive rise of CRP during systemic bacterial infections.

immunology↗

bioRxiv2024

The Fusarium graminearum effector protease FgTPP1 suppresses immune responses and facilitates Fusarium Head Blight Disease

Most plant pathogens secrete effector proteins to circumvent host immune responses, thereby promoting pathogen virulence. One such pathogen is the fungus Fusarium graminearum, which causes Fusarium Head Blight (FHB) disease on wheat and barley. Transcriptomic analyses revealed that F. graminearum expresses many candidate effector proteins during early phases of the infection process, some of which are annotated as proteases. However, the contributions of these proteases to virulence remains poorly defined. Here, we characterize a F. graminearum endopeptidase, FgTPP1 (FGSG_11164), that is highly upregulated during wheat spikelet infection and is secreted from fungal cells. To elucidate the potential role of FgTPP1 in F. graminearum virulence, we generated FgTPP1 deletion mutants ({Delta}Fgtpp1) and performed FHB infection assays. While the number of completely bleached spikes infected by F. graminearum wild-type reached 50% of total infected spikes, the number of fully bleached spikes infected by{Delta} Fgtpp1 mutants was 25%, suggesting FgTPP1 contributes to fungal virulence. Transient expression of green fluorescent protein (GFP)-tagged FgTPP1 revealed that FgTPP1 localizes, in part, to chloroplasts and attenuates chitin-mediated activation of mitogen-activated protein kinase (MAPK) signaling, reactive oxygen species production, and cell death induced by an autoactive disease resistance protein when expressed in planta. Notably, the FgTPP1 protein is conserved across the Ascomycota phylum, making it a core effector among ascomycete plant pathogens. These properties make FgTPP1 an ideal candidate for decoy substrate engineering, with the goal of engineering resistance to FHB, and likely other crop diseases caused by ascomycete fungi.

plant biology↗

bioRxiv2024

MiRNA-21-5p and MiRNA-125-5p Serve as Biomarkers for Diagnosis and Prognosis of Gastric Cancer

BackgroundGastric cancer is one of the most common diseases worldwide. MicroRNAs (miRNAs) are small non-coding RNAs, typically 19-25 nucleotides in length, which represent potential targets for therapeutic intervention. Methods and ResultsIn this study, we performed a data mining analysis for gastric cancer (GC) by integrating differentially expressed genes obtained from the Gene Expression Omnibus (GEO) database with data from The Cancer Genome Atlas (TCGA) database. We compared the expression levels of miRNA-125-5p and miRNA-21-5p in cancer cells and GES-1 cells. Our analysis revealed up-regulation of these two miRNAs in both GEO and TCGA datasets, which was further validated by quantitative polymerase chain reaction (qPCR). Additionally, survival analysis, risk score analysis, and downstream analyses, including functional enrichment analysis, target gene prediction, and protein-protein interaction analysis, were conducted. ConclusionThe expression levels of miRNA-125-5p and miRNA-21-5p are upregulated in gastric cancer cells, which contribute to the diagnosis of gastric cancer and serve as novel biomarkers.

molecular biology↗

bioRxiv2024

A unique mechanism of snRNP core assembly

The assembly of spliceosomal snRNP cores involves seven Sm proteins (D1/D2/F/E/G/D3/B) forming a ring around each snRNA and typically requires several essential assembly chaperones, particularly the SMN-Gemins complex implicated in spinal muscular atrophy (SMA). Strikingly, in budding yeast, snRNP core assembly only involves Brr1, a nonessential homolog of Gemin2. To unravel this enigma, we systematically investigated snRNP core assembly in budding yeast using biochemical and genetic approaches. We discovered two distinct pathways in budding yeast: chaperone-mediated and direct. The chaperone-mediated pathway involves two proteins, Brr1 and a novel protein, Lot5, but is inefficient. Lot5 binds D1/D2/F/E/G to form a heterohexameric ring (6S). Brr1 binds D1/D2/F/E/G and 6S but cannot displace Lot5 to facilitate assembly. Disruption of both BRR1 and LOT5 genes caused mild growth retardation, but LOT5 overexpression substantially impeded growth. The direct pathway uniquely involves F/E/G as a trimer and a stable D1/D2/F/E/G intermediate complex, explaining the non-essentiality of assembly chaperones. These findings unveil a unique assembly mechanism of snRNP cores, illuminate the evolution of assembly chaperones, and suggest avenues for studying SMA pathophysiology.

molecular biology↗

bioRxiv2024

Genomic evolution reshapes cell type diversification in the amniote brain

Over 320 million years of evolution, amniotes have developed complex brains and cognition through largely unexplored genetic and gene expression mechanisms. We created a comprehensive single-cell atlas of over 1.3 million cells from the telencephalon and cerebellum of turtles, zebra finches, pigeons, mice, and macaques, employing single-cell resolution spatial transcriptomics to validate gene expression patterns across species. Our study revealed significant species-specific variations in cell types, highlighting their conservation and diversification in evolution. We found pronounced differences in telencephalon excitatory neurons (EX) and cerebellar cell types between birds and mammals. Birds predominantly express SLC17A6 in EX, whereas mammals expressed SLC17A7 in neocortex and SLC17A6 elsewhere, possibly due to loss of SLC17A7 function loss in birds. Additionally, we identified a novel bird-specific Purkinje cell subtype (SVIL+), implicating the LSD11/KDM1A pathway in learning and circadian rhythms, and related numerous positively selected genes in birds, suggesting an evolutionary optimization of cerebellar functions for ecological and behavioral adaptation. Our findings elucidate the complex interplay between genetic evolution and environmental adaptation, underscoring the role of genetic diversification in the development of specialized cell types across amniotes.

evolutionary biology↗

bioRxiv2024

Mealtime alters daily rhythm in nuclear O-GlcNAcome to regulate hepatic gene expression

The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observe daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF) using label-free global O-GlcNAc proteomics. Additional site-specific O-GlcNAc analysis by tandem mass tag mass spectrometry further supports temporal differences in O-GlcNAcylation by revealing day-night differences. Proteins involved in gene expression are enriched among rhythmically O-GlcNAcylated proteins, suggesting rhythmic O-GlcNAcylation may directly regulate the daily rhythmicity of the hepatic transcriptome. We show that rhythmic O-GlcNAcylation can also indirectly modulate the hepatic transcriptome by interacting with phosphorylation. Several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. Specifically, we show that O-GlcNAcylation occurs at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse significantly alters O-GlcNAcylation rhythm. Whereas global O-GlcNAcylation analysis indicates dampening of global O-GlcNAcylation rhythm in mice fed under DRF, site-specific analysis reveals differential responses of O-GlcNAc sites when timing of food intake is altered. Notably, a substantial number of O-GlcNAcylation sites exhibit inverted day-night profiles when mice are subjected to DRF. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm may contribute to the disruption in liver transcriptomic rhythm previously observed in DRF condition. In summary, our results provide new mechanistic insights into metabolic regulation of daily hepatic transcriptomic rhythm via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.

physiology↗

bioRxiv2024

Isolation and characterization of three lytic podo-bacteriophages with two receptor recognition modules against multidrug-resistant Klebsiella pneumoniae

The multidrug-resistant nosocomial pathogen Klebsiella pneumoniae is considered as one of the major threats to public health. Recent studies showed that bacteriophages could be used as an alternative to antibiotics for treating infections caused by multidrug-resistant K. pneumoniae. Here we isolated and characterized three lytic bacteriophages Kp7, Kp9 and Kp11 of K. pneumoniae. Transmission electron microscopy analysis showed that all three phages have an isometric head of approximately 60 nm in diameter and a short noncontractile tail. Host specificity, one-step growth curve, tolerance to pH and temperature changes were characterized for Kp7, Kp9, and Kp11. Mass-spectrum and bioinformatical analysis identified two different types of tail fibers in each phage. The tail fiber proteins gp52 of Kp7, gp43 of Kp9 and gp46 of Kp11 are homologous and have robust enzymatic activity in digesting purified serotype K2 capsule of K. pneumoniae. However, tail fiber proteins gp51 of Kp7, gp42 of Kp9 and gp45 of Kp11 have diverse sequences and show weak or no enzyme activity in digesting purified serotype K2 capsule. Genetic knockout and biochemical assays indicated that the capsule is essential for the infection of Kp7, Kp9 and Kp11. Spot tests showed that 15 clinical isolates of drug-resistant K. pneumoniae with the serotype K2 capsule can all be infected by Kp7, Kp9 and Kp11 but with different susceptibility. Further mechanistic studies showed that transcriptional inhibition at the early stage of phage infection determines the susceptibility of different K. pneumoniae isolates.

microbiology↗

bioRxiv2024

Targeted Degradation of CDK9 Potently Disrupts the MYC Transcriptional Network

Cyclin-dependent kinase 9 (CDK9) coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release states. It is an important co-factor for transcription factors, such as MYC, that drive aberrant cell proliferation when their expression is deregulated. CDK9 modulation offers an approach for attenuating dysregulation in such transcriptional programs. As a result, numerous drug development campaigns to inhibit CDK9 kinase activity have been pursued. More recently, targeted degradation has emerged as an attractive approach. However, comprehensive evaluation of degradation versus inhibition is still critically needed to assess the biological contexts in which degradation might offer superior therapeutic benefits. We validated that CDK9 inhibition triggers a compensatory mechanism that dampens its effect on MYC expression and found that this feedback mechanism was absent when the kinase is degraded. Importantly, CDK9 degradation is more effective than its inhibition for disrupting MYC transcriptional regulatory circuitry likely through the abrogation of both enzymatic and scaffolding functions of CDK9. Highlights- KI-CDK9d-32 is a highly potent and selective CDK9 degrader. - KI-CDK9d-32 leads to rapid downregulation of MYC protein and mRNA transcripts levels. - KI-CDK9d-32 represses canonical MYC pathways and leads to a destabilization of nucleolar homeostasis. - Multidrug resistance ABCB1 gene emerged as the strongest resistance marker for the CDK9 PROTAC degrader.

cancer biology↗