Biology subjects

Akbar, S.

Publications and source records attributed to Akbar, S..

9 recordsLinked to original sources

bioRxiv2026

Ribosome collisions trigger tmRNA-mediated rescue through mRNA disengagement

Ribosome rescue pathways maintain translation during normal growth and contribute to stress tolerance. In Escherichia coli, HrpA is a ribosome-collision recognition factor that mediates antibiotic tolerance by resolving stalled ribosomes, yet the fate of the resulting ribosomal intermediate, with a topologically trapped peptidyl-tRNA in the 50S nascent peptide exit tunnel, has remained unclear. Using in vivo single-molecule tracking, we show that under antibiotic treatment, HrpA-dependent collision processing promotes recruitment of tmRNA and Hsp15 as downstream rescue factors. Cryo-electron microscopy of affinity-purified native complexes from tmRNA-deficient cells reveals accumulation of aberrant 70S{middle dot}peptidyl-tRNA complexes and shows that Hsp15, previously thought to interact exclusively with 50S{middle dot}peptidyl-tRNA, binds to 70S complexes lacking mRNA in the E site. This intermediate can be resolved by the canonical tmRNA pathway, thereby connecting HrpA-dependent collision processing to canonical tmRNA-mediated rescue.

molecular biology↗

bioRxiv2026

Bioactive Natural Products Produced by Streptomyces from the Microbiome of Cadaveric Fly Larvae

Streptomyces are prolific producers of bioactive compounds and increasingly recognized as members of insect microbiomes, yet the microbiome of cadaveric fly larvae remain an overlooked system for discovering metabolically versatile Streptomyces species. Here, we conduct targeted bacterial isolations from the microbiome of fly larvae collected from pig cadavers, generating 42 Streptomyces isolates of interest, and systematically evaluated their metabolic potential through genomic analysis, antimicrobial screening, biosynthetic gene cluster assessment, untargeted LC-MS/MS metabolomics, and compound purification. The Streptomyces isolates spanned nine species, including underrepresented lineages for which we added genomic representatives. Streptomyces from carrion fly larvae exhibited broad-spectrum antimicrobial activity and substantial BGC diversity, supported by metabolomic detection of antimycins, surugamides, and macrotetrolides. From a deep phylogenetic lineage, we purified JBIR-68 and Simamycin and demonstrated their potent anthelmintic activity against Brugia malayi microfilariae. GNPS molecular networking revealed three additional JBIR-68 analogs, establishing the first taxonomically resolved Streptomyces lineage capable of producing these rare metabolites. Our findings position cadaveric fly larvae as a rich ecological reservoir for discovering Streptomyces with the potential to produce chemically diverse natural products with biomedical applications.

biochemistry↗

bioRxiv2025

Soil and water microbial communities: A source of novel antibiotics for sustainable plant disease control

Pathogenic microorganisms pose a significant threat to plant health and agricultural productivity worldwide. Herein, this study explores the potential of natural microbial communities as sources of biopesticides. We analyzed 20 soil and water samples from remote areas, isolating 121 colonies using nutrient agar. Antibacterial activity was assessed through agar diffusion, revealing that 12 colonies exhibited significant inhibitory effects against various pathogenic bacteria. Measurement of inhibition zones indicated that these colonies could produce antibiotics. Subsequently, molecular characterization with 16S rRNA and BLAST searches of 12 unidentified sequences highlighted substantial microbial diversity within the samples. This research underscores the promise of these natural microbial communities in developing biocontrol agents for managing plant diseases in greenhouse and field environments. Extraction and purification techniques could further refine these antibiotics, advancing sustainable agricultural practices.

microbiology↗

bioRxiv2024

Doublet decoding of tRNASer3 demonstrates plasticity of ribosomal decoding center

Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNASer3GCU was in the 1980s shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. It has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. We here performed single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNASer3 bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet-decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon.

molecular biology↗

bioRxiv2023

Indigenous probiotics Lactobacillus reuteri and Enterococcus faecium exhibit positive growth performance and disease prevention against extended-spectrum cephalosporin and fluoroquinolones resistant Salmonella enterica in broiler chicks.

ABSTRACTThe rapid increase in antibiotic resistance poses a global threat to public health, necessitating the development of effective antimicrobial alternatives. This study compared an indigenous probiotic mix containing Lactobacillus reuteri and two strains of Enterococcus faecium to a commercial probiotic blend ProtexinR on the growth performance, mortality rate, histomorphology, serum immunoglobulins, and intestinal microflora of broiler chickens challenged with two multi drug resistant Salmonella serovars, Typhimurium and Enteritidis. Two hundred and forty day-old broiler chicks were randomly assigned to six treatment groups for 4 weeks: the treatment groups were; birds continuously supplemented with only indigenous probiotic strains (108 CFU/mL) (IPRO-); birds challenged with Salmonella serovars 106 (CFU/mL) (PC+); birds continuously supplemented with indigenous probiotic strains and challenged with Salmonella serovars (IPRO+); birds supplemented with ProtexinR and challenged with Salmonella serovars (CM+); birds supplemented with only ProtexinR (CM-); and birds with no Salmonella challenge or probiotics (negative control; PC-). The results revealed that IPRO- diets significantly improved feed conversion ratio (FCR) and increased body weight (BW) (P [≤] 0.05). No effect of probiotic treatments was observed on IPRO- and CM- on relative organ weights as compared to the negative control (PC-). The Salmonella- challenged group PC+ had the highest (20%) mortality rate and lowest BW. The IPRO- had significantly lower FCR (1.55) compared to PC- (1.86) and PC+ (1.95). The broilers in the IPRO- group showed significantly increased serum concentrations of IgA and IgG relative to both control groups (P [≤] 0.05). Morphological analysis of the ileum revealed significant increases (P [≤] 0.05) in the villus height and villus height/crypt depth in birds fed IPRO- compared with the PC+. Cecal Lactobacillus and Enterococcus counts were the highest (P [≤] 0.05) and Salmonella counts were the lowest (P [≤] 0.05) in the IPRO- group compared to the Salmonella infected group PC+. These results indicated that indigenous probiotic strains Lactobacillus reuteri and Enterococcus faecium can be an effective and low-cost alternative compared to commercial probiotics in the Pakistan poultry industry.

microbiology↗

bioRxiv2021

Differential response to prey quorum signals indicates predatory range of myxobacteria

A potential keystone taxa, myxobacteria contribute to the microbial food web as generalist predators. However, the extent of myxobacterial impact on microbial community structure remains unknown. The chemical ecology of these predator-prey interactions provides insight into myxobacterial production of biologically active specialized metabolites used to benefit consumption of prey as well as the perception of quorum signals secreted by prey. Using comparative transcriptomics and metabolomics, we compared how the predatory myxobacteria Myxococcus xanthus and Cystobacter ferrugineus respond to structurally distinct exogenous quorum signaling molecules. Investigating acylhomoserine lactone (AHL) and quinolone type quorum signals used by the clinical pathogen Pseudomonas aeruginosa, we identified a general response to AHL signals from both myxobacteria as well as a unique response from C. ferrugineus when exposed to the quinolone signal 4-hydroxy-2-heptylquinolone (HHQ). Oxidative detoxification of HHQ in C. ferrugineus was not observed from M. xanthus. Subsequent predation assays indicated P. aeruginosa to be more susceptible to C. ferrugineus predation. These data indicate that as generalist predators myxobacteria demonstrate a common response to the ubiquitous AHL quorum signal class, and we suggest this response likely involves recognition of the homoserine lactone moiety of AHLs. We also suggest that oxidation of HHQ and superior predation of P. aeruginosa observed from C. ferrugineus provides an example of how prey signaling molecules impact predatory specialization of myxobacteria by influencing prey range. SummaryMultiomic analysis of transcriptional and metabolic responses from the predatory myxobacteria Myxococcus xanthus and Cystobacter ferrugineus exposed to prey signaling molecules of the acylhomoserine lactone and quinolone quorum signaling classes provided insight into myxobacterial specialization associated with predatory eavesdropping. We suggest that the general response observed from both myxobacteria exposed to acylhomoserine lactone quorum signals is likely due to the generalist predator lifestyles of myxobacteria and ubiquity of acylhomoserine lactone signals. We also provide data that indicates the core homoserine lactone moiety included in all acylhomoserine lactone scaffolds to be sufficient to induce this general response. Comparing both myxobacteria, unique transcriptional and metabolic responses were observed from Cystobacter ferrugineus exposed to the quinolone signal 4-hydroxy-2-heptylquinoline (HHQ) natively produced by Pseudomonas aeruginosa. We suggest that this unique response and ability to metabolize quinolone signals contribute to the superior predation of P. aeruginosa observed from C. ferrugineus. These results further demonstrate myxobacterial eavesdropping on prey signaling molecules and provide insight into how responses to exogenous signals might correlate with prey range of myxobacteria. Originality-Significance StatementThis manuscript provides the first multiomic analysis of how predatory myxobacteria respond to exogenous prey signaling molecules and details the differences observed by comparing responses from two myxobacteria.

microbiology↗

bioRxiv2020

Predatory selection of mucoid, antibiotic resistant Pseudomonas putida phenotype by myxobacterium Cystobacter ferrugineus

Predation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Predator-prey experiments utilizing myxobacteria have provided details into predatory mechanisms and features that facilitate consumption of prey. However, prey resistance to myxobacterial predation remains underexplored, and prey resistances have been observed exclusively from predator-prey experiments that included the model myxobacterium Myxococcus xanthus. Utilizing a predator-prey pairing that instead included the myxobacterium, Cystobacter ferrugineus, with Pseudomonas putida as prey, we infrequently observed surviving phenotypes capable of eluding predation. Comparative transcriptomics between P. putida unexposed to C. ferrugineus and the survivor phenotype suggested that increased expression of efflux pumps, genes associated with mucoid conversion, and various membrane features contribute to predator avoidance. The P. putida survivor phenotype was confirmed to be resistant to the antibiotics kanamycin, gentamicin, and tetracycline and to produce more alginate, pyoveridine, and phenazine-1-carboxylic acid than predator-unexposed P. putida. Unique features observed from the survivor phenotype including small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion overlap with traits associated with Pseudomonas aeruginosa predator avoidance and pathogenicity. The survivor phenotype also benefited from increased predator resistance during subsequent predation assays. These results demonstrate the utility of myxobacterial predator-prey models and provide insight into prey resistances in response to predatory stress might contribute to the phenotypic diversity and structure of bacterial communities.

microbiology↗

bioRxiv2019

Automated and Manual Quantification of Tumour Cellularity in Digital Slides for Tumour Burden Assessment

AimsThe residual cancer burden index is an important quantitative measure used for assessing treatment response following neoadjuvant therapy for breast cancer. It has shown to be predictive of overall survival and is composed of two key metrics: qualitative assessment of lymph nodes and the percentage of invasive or in-situ tumour cellularity (TC) in the tumour bed (TB). Currently, TC is assessed through eye-balling of routine histopathology slides estimating the proportion of tumour cells within the TB. With the advances in production of digitized slides and increasing availability of slide scanners in pathology laboratories, there is potential to measure TC using automated algorithms with greater precision and accuracy.\n\nMethodsWe describe two methods for automated TC scoring: 1) a traditional approach to image analysis development whereby we mimic the pathologists workflow, and 2) a recent development in artificial intelligence in which features are learned automatically in deep neural networks using image data alone.\n\nResultsWe show strong agreements between automated and manual analysis of digital slides. Agreements between our trained deep neural networks and experts in this study (0.82) approach the inter-rater agreements between pathologists (0.89). We also reveal properties that are captured when we apply deep neural network to whole slide images, and discuss the potential of using such visualisations to improve upon TC assessment in the future.\n\nConclusionsTC scoring can be successfully automated by leveraging recent advancements in artificial intelligence, thereby alleviating the burden of manual analysis.

pathology↗

bioRxiv2018

Cryo-EM structures reveal dynamic interplay of nascent chain-processing factors on the ribosome

During protein biosynthesis in bacteria, one of the earliest phenomena that a nascent polypeptide chain experiences is the co-translational enzymatic processing. The event includes two enzymatic pathways, deformylation of the N-terminal methionine followed by methionine excision catalyzed by peptide deformylase (PDF) and methionine aminopeptidase (MetAP). The ribosome tunnel exit serves as the podium for recruiting proteins involved in maturation processes of the nascent chain. During the process, the emerging nascent protein likely remains shielded by the chaperone trigger factor (TF).\n\nHere, we present the first cryo-EM structures of E. coli ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where proteins L22 and L32 are identified as primary anchoring sites for both proteins. Interestingly however, MetAP has a remarkable ability of repositioning itself to adjacent locations in the presence of PDF and TF at the tunnel exit. Thus, our results disclose an unexpected scanning mechanism that MetAP adopts for context-specific ribosome association.

biochemistry↗