Biology subjects

Yousuf, M.

Publications and source records attributed to Yousuf, M..

6 recordsLinked to original sources

bioRxiv2025

Chromatin stability safeguards mitochondrial homeostasis and prevents mTORC1 hyperactivation

Cells dynamically regulate chromatin in response to nutrient flux which promotes the transcriptional changes necessary for adaptation. The mechanistic target of rapamycin complex 1 (mTORC1) kinase integrates nutrient signaling with chromatin regulation, yet whether chromatin stability feeds back to mTORC1 activation and stress adaption remains unknown. We previously identified histone H3 at lysine 37 (H3K37) as essential for the response to mTORC1 stress such that mutation of H3K37 to alanine (H3K37A) causes cell death upon mTORC1 inhibition. Herein, we show that H3K37-dependent chromatin stability prevents proteasome-mediated histone degradation, restricts mTORC1 signaling, and safeguards mitochondrial homeostasis during mTORC1 stress. Genetic interaction analyses reveal that H3K37A combined with mutants that destabilize chromatin, including loss of the Set2 H3K36 methyltransferase, Rpd3S histone deacetylase, or multiple histone deposition pathways, causes synthetic lethality when mTORC1 is inhibited. Transcriptome analysis indicates that H3K37A misregulates the mitochondrial transcriptome during mTORC1 stress, which increases mitochondrial reactive oxygen species (ROS) and triggers lethal mitochondrial retrograde signaling. Inactivation of retrograde signaling, or ROS neutralization, rescues viability of H3K37A and chromatin stability mutants during mTORC1 stress. These findings establish chromatin stability as a key safeguard that restrains mTORC1 activity and prevents toxic mitochondrial stress during metabolic adaptation.

molecular biology↗

bioRxiv2024

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

Gene expression in bacterial cells is dependent on a genes position along the genome, mainly because of the effects of neighbouring genes expression, but also because of the local activity of nucleoid proteins, differing levels of DNA supercoiling and changes in gene copy number with growth rate and growth phase. This genome position dependence can be a source of specific regulation, however, in some cases it is necessary to have gene expression insulated from these local effects. Escherichia coli cells express ribosomal RNA from multiple operons found at different sites along the genome. The number of ribosomal operons varies in different strains and correlates with the maximal growth rate. rRNA promoters are under the regulation of Fis, H-NS, DNA supercoiling and ppGpp. These factors are known to result in growth phase and growth rate dependent regulation of gene expression. Here we show that the combined action of Fis and H-NS also provides insulation from the activity of both local and global regulatory factors. Furthermore, our results indicate that the presence of a divergently expressed gene can also act as an insulator revealing a DNA supercoiling gradient from the origin to the terminus. The organisation of ribosomal promoters therefore has been selected to allow for gene duplication independently of the influence of local genome organisation and neighbouring genes activity.

cell biology↗

bioRxiv2023

Basal forebrain activity predicts functional degeneration in the entorhinal cortex and decreases with Alzheimer's Disease progression

BACKGROUND AND OBJECTIVESRecent models of Alzheimers Disease (AD) suggest the nucleus basalis of Meynert (NbM) as the origin of structural degeneration followed by the entorhinal cortex (EC). However, the functional properties of NbM and EC regarding amyloid-{beta} and hyperphosphorylated tau remain unclear. METHODSWe analyzed resting-state (rs)fMRI data with CSF assays from the Alzheimers Disease Neuroimaging Initiative (ADNI, n=71) at baseline and two years later. RESULTSAt baseline, local activity, as quantified by fractional amplitude of low-frequency fluctuations (fALFF), differentiated between normal and abnormal CSF groups in the NbM but not EC. Further, NbM activity linearly decreased as a function of CSF ratio, resembling the disease status. Finally, NbM activity predicted the annual percentage signal change in EC, but not the reverse, independent from CSF ratio. DISCUSSIONOur findings give novel insights into the pathogenesis of AD by showing that local activity in NbM is affected by proteinopathology and predicts functional degeneration within the EC.

neuroscience↗

bioRxiv2020

Spontaneous emergence of azithromycin resistance in independent lineages of Salmonella Typhi in Northern India

BackgroundThe emergence and spread of antimicrobial resistance (AMR) pose a major threat to the effective treatment and control of typhoid fever. The ongoing outbreak of extensively drug resistant (XDR) Salmonella Typhi (S. Typhi) in Pakistan has left azithromycin as the only remaining broadly efficacious oral antimicrobial for typhoid in South Asia. Ominously, azithromycin resistant S. Typhi organisms have been subsequently reported in Bangladesh, Pakistan, and Nepal. MethodsHere, we aimed to understand the molecular basis of AMR in 66 S. Typhi isolated in a cross-sectional study performed in a suburb of Chandigarh in Northern India using whole genome sequencing (WGS) and phylogenetic analysis. ResultsWe identified seven S. Typhi organisms with the R717Q mutation in the acrB gene that was recently found to confer resistance to azithromycin in Bangladesh. Six out of the azithromycin-resistant S. Typhi isolates also exhibited triple mutations in gyrA (S83F and D87N) and parC (S80I) genes and were resistant to ciprofloxacin. These contemporary ciprofloxacin/azithromycin-resistant isolates were phylogenetically distinct from each other and from those reported from Bangladesh, Pakistan, and Nepal. ConclusionsThe independent emergence of azithromycin resistant typhoid in Northern India reflects an emerging broader problem across South Asia and illustrates the urgent need for the introduction of typhoid conjugate vaccines (TCVs) in the region. Key pointsWe identified ciprofloxacin/azithromycin-resistant Salmonella Typhi (S. Typhi) in Chandigarh in Northern India. The independent emergence of ciprofloxacin/azithromycin-resistant typhoid in Bangladesh, Pakistan, Nepal, and India and the continued spread of extensively-drug resistant (XDR) typhoid in Pakistan highlight the limitations of licensed oral treatments for typhoid fever in South Asia.

genomics↗

bioRxiv2019

Early fate of exogenous promoters in E. coli

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, and microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.

genomics↗

bioRxiv2018

Comparison of the structural organisation of reeler hippocampal CA1 region with wild type CA1.

The dendritic pattern defines the input capacity of a neuron. Existing methods such as Golgi impregnation or intracellular staining only label a small number of neurons. By using high-resolution imaging and 3D reconstruction of green fluorescent protein-expressing neurons, the present study provides an approach to investigate the anatomical organization of dendritic structures in defined brain regions. We characterized the structural organization of dendrites in the CA1 region of the mouse hippocampus by analyzing Sholl intersections, dendritic branches, branching and orientation angles of dendrites, and the different types of spine on the dendritic branches. Utilizing this quantitative imaging approach, we show that there are differences in the number of Sholl intersections and in the orientation of apical and basal dendrites of CA1 pyramidal neurons. Performing 3D reconstructions of the CA1 region of the reeler hippocampus, we show that neurons of this mutant display an arbitrary orientation of apical dendrites at angles ranging from -180 to +180 degrees in contrast to wild-type mice that show a preferred orientation angle. This methodology provides a way of analyzing network organization in wild type and mutant brains using quantitative imaging techniques. Here, we have provided evidence that in reeler a sparse, weakly connected network results from the altered lamination of CA1 pyramidal neurons and the variable orientation of their dendrites.\n\nHighlightsO_LIHigh-resolution imaging and 3D reconstruction of CA1 pyramidal neurons\nC_LIO_LIAnalysis of Sholl intersections\nC_LIO_LIAnalysis of the orientation of apical and basal dendrites of CA1 pyramidal neurons\nC_LIO_LIAltered dendrite orientation angle of apical dendrites in reeler mutant mice\nC_LIO_LIMore stubby spines compared to thin and mushroom spines in wild-type CA1\nC_LI

neuroscience↗