Biology subjects

Kang, X.

Publications and source records attributed to Kang, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Dynamic Localization of Leukemia Stem Cells via CXCL12 Regulates Leukemia Progression

The processes that govern leukemia progression and remission are poorly understood. Our research reveals that the CXCL12 gradient, traditionally associated with LSC quiescence and survival, critically determines LSC localization and associated behavior. Specifically, CXCL12 guides LSCs to either the quiescent niche in the metaphysis, characterized by N-cadherin-expressing mesenchymal stromal cells (N-cad+ MSCs), or the proliferative niche in the central marrow (CM), marked by sinusoidal endothelial cells and associated stromal cells. We identified that the CXCL12 gradient is finely regulated by the interplay between dipeptidyl peptidase 4 (DPP4) on LSCs and glypican-3 (GPC3) on N-cad+ MSCs. DPP4 deactivates CXCL12, while GPC3 inhibits DPP4, resulting in a higher CXCL12 concentration in the metaphysis and a lower concentration in the CM. This differential gradient facilitates leukemia progression by promoting LSC quiescence and survival in the metaphysis versus relative proliferation and apoptosis in the CM. Depletion of Dpp4 from LSCs or Cxcl12 from N-cad+ MSCs disrupts this gradient, mobilizing LSCs from the metaphysis to the CM and significantly hindering leukemia development. Our findings redefine the role of CXCL12 in LSC behavior and provide a clearer understanding of leukemia progression. This novel insight highlights the potential for targeted therapeutic strategies that disrupt the CXCL12 gradient to treat minimal residual LSCs, offering a promising path toward a lasting cure for acute myeloid leukemia (AML).

cancer biology↗

bioRxiv2024

THE NEURONAL ARCHITECTURE OF AUTONOMIC DYSREFLEXIA

Autonomic dysreflexia is a life-threatening medical condition characterized by episodes of uncontrolled hypertension that occur in response to sensory stimuli after spinal cord injury (SCI)1-7. The fragmented understanding of the mechanisms underlying autonomic dysreflexia hampers the development of therapeutic strategies to manage this condition, leaving people with SCI at daily risk of heart attack and stroke8-18. Here, we expose the complete de novo neuronal architecture that develops after SCI and causes autonomic dysreflexia. In parallel, we uncover a competing, yet overlapping neuronal architecture activated by epidural electrical stimulation of the spinal cord that safely regulates blood pressure after SCI. The discovery that these adversarial neuronal architectures converge onto a single neuronal subpopulation provided a blueprint for the design of a mechanism-based intervention that reversed autonomic dysreflexia in mice, rats, and humans with SCI. These results establish a path for the effective treatment of autonomic dysreflexia in people with SCI.

neuroscience↗

bioRxiv2024

High glucose treatment induced nuclei aggregation of microvascular endothelial cells via foxo1a-klf2a pathway

BACKGROUNDHyperglycemia is a major contributor to endothelial dysfunction and blood vessel damage, leading to severe diabetic microvascular complications. Despite the growing body of research on the underlying mechanisms of endothelial cell dysfunction, the available drugs based on current knowledge fall short of effectively alleviating these complications. Therefore, our endeavor to explore novel insights into the cellular and molecular mechanisms of endothelial dysfunction is crucial for the field. METHODSIn this study, we carried out a high-resolution imaging and time-lapse imaging analysis of the behavior of endothelial cells in Tg(kdrl:ras-mCherry::fli1a:nEGFP) zebrafish embryos upon high glucose treatment. Genetic manipulation and chemical biology approaches were utilized to analyze the underlying mechanism of high-glucose-induced nuclei aggregation and aberrant migration of zebrafish endothelial cells and cultured human endothelial cells. Bioinformatical analysis of single-cell RNA sequencing data and molecular biological techniques to identify the target genes of Foxo1a. RESULTSIn this study, we observed that the high glucose treatment resulted in nuclei aggregation of endothelial cells in zebrafish intersegmental vessels (ISVs). Additionally, the aberrant migration of microvascular endothelial cells in high glucose-treated embryos, which might be a cause of nuclei aggregation, was discovered. High glucose-induced aggregation of vascular endothelial nuclei via foxo1a downregulation in zebrafish embryos. Then, we revealed that high glucose resulted in the downregulation of foxo1a expression and increased the expression of its direct downstream effector, klf2a, through which the aberrant migration and aggregation of vascular endothelial nuclei were caused. CONCLUSIONSHigh glucose treatment caused the nuclei of endothelial cells to aggregate in vivo, which resembles the crowded nuclei of endothelial cells in microaneurysms. High glucose suppresses foxo1a expression and increases the expression of its downstream effector, klf2a, thereby causing the aberrant migration and aggregation of vascular endothelial nuclei. Our findings provide a novel insight into the mechanism of microvascular complications in hyperglycemia.

cell biology↗

bioRxiv2024

Comparative Metagenomics Provide Mechanistic Insights into the Biodegradation of the Non-hydrolysable Plastic Polyvinyl Chloride in Gut Microbiota of Insect Larvae

Using microbiomes to mitigate global plastic pollution is of paramount importance. Insect microbiomes have garnered emerging interest for their ability to biodegrade non-hydrolysable plastic polymers. The larvae of Spodoptera frugiperda, a globally prevalent migratory crop pest, are accidentally discovered to consume polyvinyl chloride (PVC) plastic films, highlighting the role of their gut microbiome. Following the migration of S. frugiperd in China, this study displays a comprehensive geographical profile of its larval gut microbiota and a significant shift after PVC feeding. Using comparative metagenomics we revealed the functional redundancy within the larval gut microbiomes of two distinct insects after PVC ingestion, we discovered a surprisingly potent PVC-dechlorinating activity of an NADH peroxidase (6.48 mg/L chlorine produced in 96 hours with NADH as a cofactor) encoded by Enterococcus casseliflavus EMBL-3. These findings open a new avenue for understanding plastic biodegradation mechanism and enable the development of biotechnologies to mitigate global plastic pollution.

microbiology↗

bioRxiv2023

HyLight: Strain aware assembly of low coverage metagenomes

Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of a microbial community at strain level poses major methodical challenges, because relative frequencies of individual strains match the rate of sequencing errors, which hampers the identification of their characteristic genetic variants. While next-generation sequencing (NGS) reads are too short to span complex repetitive regions, the considerably longer third-generation sequencing (TGS) reads are affected by larger sequencing error rates or are just significantly more expensive. Suppressing TGS coverage to limit costs implies losses in terms of the accuracy of the assemblies. Therefore, existing approaches have remained fragmentary: all approaches presented so far agree on losses in strain awareness, accuracy, possibly excessive costs of the assemblies, or combinations thereof. We present HyLight as, to the best of our knowledge, the first metagenome assembly approach that is not affected by any of the aforementioned drawbacks. In experiments, we demonstrate that HyLight assemblies are strain-aware, contiguous, contain little errors, and because operating on low coverage TGS data of the cheap kind, come at drastically reduced costs. HyLight implements hybrid assembly, which exploits the complementarity of TGS and NGS data. For unifying the two types of data, HyLight utilizes strain resolved overlap graphs (OG), which support the accurate reconstruction of the individual members of microbial communities at strain level: HyLight outperforms existing approaches in terms of strain identity preserving sequence by on average 25.53% (across all experiments / data sets: first quartile: 21.53%, median: 26.81%, third quartile: 31.98%), achieving near-complete strain awareness on many data sets. In summary, HyLight appears to implement the first protocol that delivers assemblies that are strain-aware, contiguous and accurate in combination.

bioinformatics↗

bioRxiv2023

pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding

Profiling the binding of T cell receptors (TCRs) of T cells to antigenic peptides presented by MHC proteins is one of the most important unsolved problems in modern immunology. Experimental methods to probe TCR-antigen interactions are slow, labor-intensive, costly, and yield moderate throughput. To address this problem, we developed pMTnet-omni, an Artificial Intelligence (AI) system based on hybrid protein sequence and structure information, to predict the pairing of TCRs of {beta} T cells with peptide-MHC complexes (pMHCs). pMTnet-omni is capable of handling peptides presented by both class I and II pMHCs, and capable of handling both human and mouse TCR-pMHC pairs, through information sharing enabled this hybrid design. pMTnet-omni achieves a high overall Area Under the Curve of Receiver Operator Characteristics (AUROC) of 0.888, which surpasses competing tools by a large margin. We showed that pMTnet-omni can distinguish binding affinity of TCRs with similar sequences. Across a range of datasets from various biological contexts, pMTnet-omni characterized the longitudinal evolution and spatial heterogeneity of TCR-pMHC interactions and their functional impact. We successfully developed a biomarker based on pMTnet-omni for predicting immune-related adverse events of immune checkpoint inhibitor (ICI) treatment in a cohort of 57 ICI-treated patients. pMTnet-omni represents a major advance towards developing a clinically usable AI system for TCR-pMHC pairing prediction that can aid the design and implementation of TCR-based immunotherapeutics.

immunology↗

bioRxiv2023

Mapping Chromatin Occupancy of Ppp1r1b-lncRNA Genome-Wide Using Chromatin Isolation by RNA Purification (ChIRP)-seq

Long non-coding RNA (lncRNA) mediated transcriptional regulation is increasingly recognized as an important gene regulatory mechanism during development and disease. LncRNAs are emerging as critical regulators of chromatin state; yet the nature and the extent of their interactions with chromatin remain to be fully revealed. We have previously identified Ppp1r1b-lncRNA as an essential epigenetic regulator of myogenic differentiation in cardiac and skeletal myocytes in mice and humans. We further demonstrated that Ppp1r1b-lncRNA function is mediated by the interaction with the chromatin-modifying complex polycomb repressive complex 2 (PRC2) at the promoter of myogenic differentiation transcription factors, TBX5 and MyoD1. Herein, we employed an unbiased chromatin isolation by RNA purification (ChIRP) and high throughput sequencing to map the repertoire of Ppp1r1b-lncRNA chromatin occupancy genome-wide in the mouse muscle myoblast cell line. We uncovered a total of 99732 true peaks corresponding to Ppp1r1b-lncRNA binding sites at high confidence (P-value < 1e-5 and enrichment score [≥] 10). The Ppp1r1b-lncRNA-binding sites averaged 558 bp in length and were distributed widely within the coding and non-coding regions of the genome. Approximately 46% of these true peaks were mapped to gene elements, of which 1180 were mapped to experimentally validated promoter sequences. Importantly, the promoter-mapped binding sites were enriched in myogenic transcription factors and heart development while exhibiting focal interactions with known motifs of proximal promoters and transcription initiation by RNA polII, including TATA, transcription initiator, CCAAT-box, and GC-box, supporting Ppp1r1b-lncRNA role in transcription initiation of myogenic regulators. Remarkably, nearly 40% of Ppp1r1b-lncRNA-binding sites mapped to gene introns, were enriched with the Homeobox family of transcription factors, and exhibited TA-rich motif sequences, suggesting potential motif specific Ppp1r1b-lncRNA-bound introns. Lastly, more than 136521enhancer sequences were detected in Ppp1r1b-lncRNA-occupancy sites at high confidence. Among these enhancers,12% exhibited cell type/tissue-specific enrichment in fetal heart and muscles. Together, our findings provide further insights into the genome-wide Ppp1r1b-lncRNA: Chromatin interactome that may potentially dictate its function in myogenic differentiation and potentially other cellular and biological processes.

genomics↗

bioRxiv2023

GABRD promotes the progression of breast cancer through CDK1-dependent cell cycle regulation

PurposeY-aminobutyric acid (GABA) is an important inhibitory amino acid neurotransmitter that exerts its biological function by binding to GABA receptors, which not only play an important role in neuromodulation, but also involved in regulating the development of tumors. Gamma-aminobutyric acid type A receptor subunit delta (GABRD) encodes the {delta} subunit of GABAA receptor, its impact on breast cancer has not been clearly studied. This study is aiming to reveal the relationship between GABRD and breast cancer development. MethodsWe performed a tissue microarray to quantify GABRD expression levels in tumor tissue and paracarcinoma tissue. The regulation of GABRD in the proliferation, migration, and apoptosis of breast cancer was examined by a loss-of-function study. A GeneChip microarray was used to probe GABRD for potential downstream molecules. The interaction between GABRD and CDK1 was verified by a set of functional tests and rescue experiments as well as coimmunoprecipitation. ResultsGABRD was expressed at significantly higher levels in tumor tissues and was associated with advanced tumor progression. Silencing GABRD resulted in a significant decrease in proliferation and migration and an increase in apoptosis of breast cancer. GABRD regulated the cell cycle by directly interacting with CDK1, which was identified as an important downstream target. ConclusionGABRD is the breast cancer-related gene and highlights the importance of the GABRD-CDK1 axis in regulating breast cancer proliferation, which provides potential for the development of novel therapeutics.

cancer biology↗

bioRxiv2023

TMELand: An end-to-end pipeline for quantification and visualization of Waddington's epigenetic landscape based on gene regulatory network

Waddingtons epigenetic landscape is a framework depicting the processes of cell differentiation and reprogramming under the control of a gene regulatory network (GRN). Traditional model-driven methods for landscape quantification focus on the Boolean network or differential equation-based models of GRN, which need sophisticated prior knowledge and hence hamper their practical applications. To resolve this problem, we combine data-driven methods for inferring GRNs from gene expression data with model-driven approach to the landscape mapping. Specifically, we build an end-to-end pipeline to link data-driven and model-driven methods and develop a software tool named TMELand for GRN inference, visualizing Waddingtons epigenetic landscape, and calculating state transition paths between attractors to uncover the intrinsic mechanism of cellular transition dynamics. By integrating GRN inference from real transcriptomic data with landscape modeling, TMELand can facilitate studies of computational systems biology, such as predicting cellular states and visualizing the dynamical trends of cell fate determination and transition dynamics from single-cell transcriptomic data. The source code of TMELand, a user manual, and model files of case studies can be downloaded freely from https://github.com/JieZheng-ShanghaiTech/TMELand.

systems biology↗

bioRxiv2023

Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

Structural variations (SVs) are a major source of domestication and improvement traits, however SV profiles of duck and their phenotypic impacts largely hidden. We present the first duck pan-genome constructed using five genome assemblies capturing [~]40.98 Mb new sequences. This pan-genome together with high-depth sequencing data ([~]46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to ducks domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of IGF2BP1 and generate a novel transcript of MITF, shaping bodyweight and white plumage. In the IGF2BP1 locus, the TE-derived SV explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). Our findings highlight the importance of using a pan-genome as a reference in genomics studies and explore the roles of TE-derived SVs in trait formation and in livestock breeding.

genetics↗

bioRxiv2022

Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks

Diseases that have a complex genetic architecture tend to suffer from considerable amounts of genetic variants that, although playing a role in the disease, have not yet been revealed as such. Two major causes for this phenomenon are genetic variants that do not stack up effects, but interact in complex ways; in addition, as recently suggested, the omnigenic model postulates that variants interact in a holistic manner to establish disease phenotypes. We present DiseaseCapsule, as a capsule network based approach that explicitly addresses to capture the hierarchical structure of the underlying genome data, and has the potential to fully capture the non-linear relationships between variants and disease. DiseaseCapsule is the first such approach to operate in a whole-genome manner when predicting disease occurrence from individual genotype profiles. In experiments, we evaluated DiseaseCapsule on amyotrophic lateral sclerosis (ALS) and Parkinsons disease (PD), with a particular emphasis on ALS because known known to have a complex genetic architecture, so being affected by considerable missing heritability (40%). On ALS, Disease-Capsule achieves 86.9% accuracy on held out test data in predicting disease occurrence, thereby outperforming all other approaches by large margins. Also, DiseaseCapsule required sufficiently less training data for reaching optimal performance. Last but not leaset, the systematic exploitation of the network architecture yielded 922 genes of particular interest, and 644 "non-additive" genes that are crucial factors in DiseaseCapsule, but have no effect within linear schemes.

bioinformatics↗

bioRxiv2022

DHHC3 mediated Cadm4 palmitoylation regulates myelination in CNS

Cell adhesion molecule 4 (Cadm4) plays important roles on plasma membrane (PM) to regulate myelin formation and the downregulation of Cadm4 is a prominent feature in many demyelination diseases. However, how Cadm4 maintains its level on PM has been elusive. Here, we identify that Cadm4 is palmitoylated at cysteine-347 (C347) and palmitoylation regulates the stable localization of Cadm4 on PM, as blocking palmitoylation by mutating C347 into alanine (C347A) results in the dissociation of Cadm4 from PM and targeting for degradation. Intriguingly, blocking Cadm4 palmitoylation by introducing C347A (Cadm4-KI) causes myelin abnormalities in CNS, characterized by loss of myelination, myelin infoldings and hypermyelination. Moreover, it is uncovered that Cadm4 palmitoylation is catalyzed by DHHC3, reducing Cadm4 palmitoylation by the deletion of DHHC3 renders the redistribution of Cadm4 for degrading. Consistently, the genetic deletion of DHHC3 leads to downregulated Cadm4 palmitoylation and defects in CNS myelination, virtually phenocopies that of the Cadm4-KI mice. Our findings suggest a mechanism that the stable localization of Cadm4 on PM regulated by protein palmitoylation is vital for myelination in CNS.

neuroscience↗

bioRxiv2022

A Mechanistic Study on the Cellular Uptake, Intracellular Trafficking, and Antisense Gene Regulation of Bottlebrush Polymer-Conjugated Oligonucleotides

We have developed a non-cationic transfection vector in the form of a bottlebrush polymer-antisense oligonucleotide (ASO) conjugate. Termed pacDNA (polymer-assisted compaction of DNA), these agents show improved biopharmaceutical characteristics and antisense potency in vivo while suppressing non-antisense side effects. Nonetheless, there still lacks a mechanistic understanding regarding the cellular uptake, subcellular trafficking, and gene knockdown with pacDNA. Here, we show that the pacDNA enters human non-small cell lung cancer cells (NCI-H358) predominantly by scavenger receptor-mediated endocytosis and macropinocytosis, and trafficks via the endolysosomal pathway within the cell. The pacDNA significantly reduces a target gene expression (KRAS) in the protein level but not in the mRNA level, despite that the transfection of free ASOs causes ribonuclease H1 (RNase H)-dependent degradation of KRAS mRNA. In addition, the antisense activity of pacDNA is independent of ASO chemical modification, suggesting that the pacDNA functions as a steric blocker. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/496353v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@56e08eorg.highwire.dtl.DTLVardef@1b09510org.highwire.dtl.DTLVardef@a785corg.highwire.dtl.DTLVardef@1641874_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

VeChat: Correcting errors in long reads using variation graphs

Error correction is the canonical first step in long-read sequencing data analysis. The current standard is to make use of a consensus sequence as a template. However, in mixed samples, such as metagenomes or organisms of higher ploidy, consensus induced biases can mask true variants affecting haplotypes of lower frequencies, because they are mistaken as errors. The novelty presented here is to use graph based, instead of sequence based consensus as a template for identifying errors. The advantage is that graph based reference systems also capture variants of lower frequencies, so do not mistakenly mask them as errors. We present VeChat, as a novel approach to implement this idea: VeChat distinguishes errors from haplotype-specific true variants based on variation graphs, which reflect a popular type of data structure for pangenome reference systems. Upon initial construction of an ad-hoc variation graph from the raw input reads, nodes and edges that are due to errors are pruned from that graph by way of an iterative procedure that is based on principles from frequent itemset mining. Upon termination, the graph exclusively contains nodes and edges reflecting true sequential phenomena. Final re-alignments of the raw reads indicate where and how reads need to be corrected. Extensive benchmarking experiments demonstrate that PacBio and ONT reads corrected by VeChat contain 4 to 15, or, respectively, 2 to 10 times less errors than when corrected state of the art approaches. VeChat is implemented in an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat.

bioinformatics↗

bioRxiv2021

Reversible regulation of Cas12a activities by AcrVA5-mediated acetylation and CobB-mediated deacetylation

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated (Cas) system protects bacteria and archaea from the invasion of foreign genetic elements. To cope with the host CRISPR systems, phages have evolved many strategies, including the anti-CRISPR (Acr) proteins, to inactivate the Cas nucleases. Recently, it has been reported that the type V-A Cas12a effector can be acetylated and inactivated by AcrVA5, which is a GNAT-family acetyltransferase. However, it is unclear whether the host has any coping strategies to reactivate the defense system. Here we show that the AcrVA5-acetylated Cas12a can be deacetylated by bacterial deacetylase CobB, reactivating Cas12a for both in vitro cleavage of target DNA sequences and in vivo protection of the host from invasion of foreign nucleic acids. Therefore, this study not only shows the reversible regulation of Cas12a activities by post-translational modification but also reveals CobB as a secondary safeguard to bacterial CRISPR defense systems. In addition, we demonstrate that AcrVA5 is a wide-spectrum acetyltransferase, acetylating a large number of target proteins besides Cas12a, and the AcrVA5-acetylated targets can also be deacetylated by CobB.

molecular biology↗

bioRxiv2021

CCR5 closes the temporal window for memory linking

Real world memories are formed in a particular context and are not acquired or recalled in isolation 1-5. Time is a key variable in the organization of memories, since events experienced close in time are more likely to be meaningfully associated, while those experienced with a longer interval are not1-4. How does the brain segregate events that are temporally distinct? Here, we report that a delayed (12-24h) increase in the expression of the C-C chemokine receptor type 5 (CCR5), an immune receptor well known as a co-receptor for HIV infection6,7, following the formation of a contextual memory, determines the duration of the temporal window for associating or linking that memory with subsequent memories. This delayed CCR5 expression in mouse dorsal CA1 (dCA1) neurons results in a decrease in neuronal excitability, which in turn negatively regulates neuronal memory allocation, thus reducing the overlap between dCA1 memory ensembles. Lowering this overlap affects the ability of one memory to trigger the recall of the other, thus closing the temporal window for memory linking. Remarkably, our findings also show that an age-related increase in CCL5/CCR5 expression leads to impairments in memory linking in aged mice, which could be reversed with a CCR5 knockout and an FDA approved drug that inhibits this receptor, a result with significant clinical implications. All together the findings reported here provide the first insights into the molecular and cellular mechanisms that shape the temporal window for memory linking.

neuroscience↗

bioRxiv2021

Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore

Nanopore sensors could revolutionize single-molecule proteomics by providing a means for identification of known proteins through fingerprinting or by de novo sequencing. However, the complex chemical and physical properties of proteins present multiple challenges to the conventional nanopore sensing method, predominantly, the single-file threading of a protein chain into a nanopore and its transport through it. Herein we describe a general approach for realizing unidirectional transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore platform and a high concentration guanidinium chloride buffer enables protein unfolding and unidirectional transport through a pore, propelled by an electroosmotic effect that largely owes to the guanidinium chloride presence. The uniform and slow (~10 {micro}s/amino acid) single-file transport, when combined with supervised machine learning of the electrical current signatures obtained, allows us to use to discern the protein threading orientation and identity. In conjunction with a method for tail-modification of native proteins and higher-resolution nanopores, our approach could offer a path towards direct single-molecule protein fingerprinting without the requirement of a motor enzyme.

biophysics↗

bioRxiv2021

Specific phenotypic, genomic, and fitness evolutionary trajectories toward antibiotic resistance induced by pesticide co-stressors in Escherichia coli

To explore how co-occurring non-antibiotic environmental stressors affect evolutionary trajectories toward antibiotic resistance, we exposed susceptible Escherichia coli K-12 populations to environmentally relevant levels of pesticides and streptomycin for 500 generations. The coexposure substantially changed the phenotypic, genotypic, and fitness evolution trajectories, resulting in much stronger streptomycin resistance (>15-fold increase) of the populations. Antibiotic target modification mutations in rpsL and rsmG, which emerged and dominated at late stages of evolution, conferred the strong resistance even with less than 1% abundance, while the off-target mutations in nuoG, nuoL, glnE, and yaiW dominated at early stages only led to mild resistance (2.5 - 6-fold increase). Moreover, the strongly resistant mutants exhibited lower fitness costs even without the selective pressure and had lower minimal selection concentrations than the mildly resistant ones. Removal of the selective pressure did not reverse the strong resistance of coexposed populations at a later evolutionary stage. The findings suggest higher risks of the selection and propagation of strong antibiotic resistance in environments potentially impacted by antibiotics and pesticides.

microbiology↗