Biology subjects

Mohammed, S. A.

Publications and source records attributed to Mohammed, S. A..

7 recordsLinked to original sources

bioRxiv2026

Global Proteome Remodelling in Rhodococcus jialingiae RS1 to Decipher its Plant Growth-Promoting and Biofertilizer Properties: Gene Identification for Transgenics

1.Abiotic stresses like nitrogen deficiency and soil salinity are major factors contributing to low crop yields. The use of selective biofertilizers alleviates both types of stress. In this study, we investigated the biofertilizer activity and plant growth-promoting properties (PGP) of Rhodococcus jialingiae RS1 through cytosolic proteome remodelling. We cultured RS1 under two conditions, i) without and ii) with 6% NaCl, in nitrogen-deficient defined Burks medium. Under dual stress of nitrogen limitation and salt stress, Orbitrap LC-MS/MS proteomics revealed one-quarter of the proteome remodelling, particularly the upregulation of ribosomal synthesis and protein repair systems. As expected, we found high expression of EctC, an ectoine synthase, a key enzyme in osmolyte biosynthesis. Additionally, ribosomal and translational-associated factors, including RpsL, RpsS, RpsT, RpsR1, RplV, RplL, RplA, and elongation factor Tuf, were highly expressed, suggesting enhanced translational fidelity under dual stress. High levels of DNA protection protein, Dps suggest dual stress may lead to DNA damage. Upregulation of chaperones, environmental sensors (KinE), and redox transcriptional factors like WhiB3, Hsp18, AhpC, and MetE suggests protein misfolding and oxidative stress. Metabolic modulations were evident through high expression of IlvA, NAD-dependent glutamate dehydrogenase, lipid/envelope-remodelling enzymes, cutinase/esterases, lipases, endopeptidases like NlpC/P60 and transport systems. In contrast, proteins involved in urease structural components (urea-G), nitrogen regulators and ammonium transporters (GlnK and Amt) were downregulated. Dual stress may lead to an energy crisis, prompting strategic shifts away from high-ATP-dependent ureolytic nitrogen-scavenging pathways towards lower-energy nitrogen-assimilating routes, such as IlvA-mediated deamination and NAD-dependent glutamate dehydrogenation. Genetic manipulations of the above-mentioned genes or their homologues across the genera of microbes, plants, and crops may enhance resilience to abiotic stresses. Our studies reveal stress-responsive genes and biochemical pathways that could be used to improve transgenic efficacy in nitrogen-limited, saline soil and other (a)biotic stresses. Global Proteome Profiling of Rhodococcus jialingiae RS1 to Develop Transgenics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/724437v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1f29783org.highwire.dtl.DTLVardef@1b953e6org.highwire.dtl.DTLVardef@335951org.highwire.dtl.DTLVardef@12ce661_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

In Silico analysis of the structural and functional impact of deleterious nsSNPs in the human RETREG1 gene associated with congenital sensory neuropathy type II

BackgroundMutations in the RETREG1 gene are known to cause Hereditary Sensory and Autonomic Neuropathy type II (HSAN II), a severe congenital disorder affecting sensory neurons. However, the full spectrum of pathogenic single nucleotide polymorphisms (SNPs) and their specific structural consequences remain incompletely characterized. ObjectivesThis study aimed to elucidate pathogenic nsSNPs and their role in the Congenital Sensory Neuropathy (HSAN II) by employing in-silico analysis. MethodThe nsSNPs of RETREG1 were retrieved from the dbSNP in NCBI database. Different in silico tools, SIFT, PolyPhen-2, SNP&GO, PHD-SNP, SNAP2, I-mutant, Project Hope, MutPred, ConSurf, phyre2, Chimera, and GeneMANIA, were used for predicting the pathogenicity, protein stability, evolutionary conservation, structural alterations, and protein-protein interaction networks.for RETREG1 gene. ResultFive nsSNPs were identified as "damaging" or deleterious by using the above software (Y221C, G216R, G211R, L119V, W107C). Four SNPs (Y221C, G211R, L119V, and W107C) were predicted to decrease protein stability, while the fifth SNP (G216R) was expected to increase it. Structural modeling revealed that all five mutations are located within the critical Reticulon Homology Domain (RHD), where they are predicted to cause steric clashes, disrupt hydrophobic packing, and impair protein-membrane interactions. ConclusionThis integrated in silico analysis identifies four novel deleterious nsSNPs in RETREG1 (W107C, L119V, G211R, Y221C) and confirms the established G216R variant. These mutations are predicted to impair RETREG1 structure and function, providing mechanistic insight into HSAN II pathogenesis and prioritizing candidates for future experimental validation.

bioinformatics↗

bioRxiv2025

Non-invasive Free-breathing Gating-free Extracellular Cellular Volume Quantification for Repetitive Myocardial Fibrosis Evaluation in Rodents

BackgroundInterstitial myocardial fibrosis is a crucial pathological feature of many cardiovascular disorders. Myocardial fibrosis resulting in extracellular volume (ECV) expansion can be non-invasively quantified by cardiac MRI (CMR) with T1 mapping before and after gadolinium (Gd) contrast agent administration. However, longitudinal repetitive ECV measurements are challenging in rodents due to the prolonged scan time with cardiac and respiratory gating that is required for conventional T1 mapping and the invasive nature of the rodent intravenous lines. MethodsTo address these challenges, the objective of this study is to establish a fast, free- breathing, and gating-free ECV procedure with a non-invasive subcutaneous catheter for in- scanner Gd administration that can allow longitudinal repetitive ECV evaluations in rodent models. This is achieved by (1) IntraGate sequence for free-breathing gating-free cardiac imaging, (2) non-invasive subcutaneous in-scanner Gd administration, and (3) fast T1 mapping with varied flip angle (VFA) in conjunction with (4) triple jugular vein blood T1 normalization. Additionally, full cine CMR (multi-slice short-axis, long-axis 2-chamber, and long-axis 4- chamber) was acquired during the waiting period for comprehensive systolic cardiac functional and strain analysis. ResultsWe have successfully established a non-invasive fast ECV quantification protocol to enable longitudinal repetitive ECV quantifications in rodents. Non-invasive subcutaneous Gd bolus administration induced reasonable dynamic contrast enhancement (DCE) time course reaching a steady state in [~] 20 min for stable T1 quantification. The free-breathing gating-free VFA T1 quantification scheme allows for rapid cardiac ([~]2.5 min) and jugular vein (49 sec) T1 quantification with no motion artifacts. The triple jugular vein T1 acquisitions (1 pre-contrast and 2 post-contrast) immediately flanking the heart T1 acquisitions enable accurate myocardial ECV quantification. Our data demonstrated that left-ventricular myocardial ECV quantifications were highly reproducible with repeated scans, and the ECV values (0.25) are comparable to reported ranges among humans and rodents. This protocol was successfully applied to ischemic reperfusion injury model to detect myocardial fibrosis that was validated with histopathology. ConclusionWe have established a simple, fast, non-invasive, and robust CMR protocol in rodents that can enable longitudinal repetitive ECV quantifications for cardiovascular disease progression. It can be used to monitor disease regression with interventions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/664411v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14b44e5org.highwire.dtl.DTLVardef@985392org.highwire.dtl.DTLVardef@96cef7org.highwire.dtl.DTLVardef@ede47d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Improving MALDI Mass Spectrometry Imaging Performance: Low-Temperature Thermal Evaporation for Controlled Matrix Deposition and Improved Image Quality

The deposition of matrix compounds significantly influences the effectiveness of matrix-assisted laser desorption/ionization (MALDI) Mass Spectrometry Imaging (MSI) experiments, impacting sensitivity, spatial resolution, and reproducibility. Dry deposition methods offer advantages by producing homogeneous matrix layers and minimizing analyte delocalization without the use of solvents. However, refining these techniques to precisely control matrix thickness, minimize heating temperatures, and ensure high-purity matrix layers is crucial for optimizing MALDI-MSI performance. Here, we present a novel approach utilizing low-temperature thermal evaporation (LTE) for organic matrix deposition under reduced vacuum pressure. Our method allows for reproducible control of matrix layer thickness, as demonstrated by linear calibration for two organic matrices, 2,5-dihydroxybenzoic acid (DHB), and 1,5-Diaminonaphthalene (DAN). The environmental scanning electron microscopy images reveal a uniform distribution of small-sized matrix crystals, consistently on the submicrometer scale, across tissue slides following LTE deposition. Remarkably, LTE serves as an additional purification step for organic matrices, producing very pure layers irrespective of initial matrix purity. Furthermore, stability assessment of MALDI-MSI data from mouse brain sections coated with LTE-deposited DHB or DAN matrix indicates minimal impact on ionization efficiency, signal intensity, and image quality even after storage at - 80{degrees}C for two weeks, underscoring the robustness of LTE-deposited matrices for MSI applications. Comparative analysis with the spray-coating method highlights several advantages of LTE deposition, including enhanced ionization, reduced analyte diffusion, and improved MSI image quality.

bioengineering↗

bioRxiv2024

Chromatin Remodeling by the Histone Methyltransferase SETD2 Drives Lipotoxic Injury in Cardiometabolic Heart Failure with Preserved Ejection Fraction

BackgroundCardiometabolic heart failure with preserved ejection fraction (cHFpEF) is highly prevalent and associates with a poor outcome. Pathological gene expression in heart failure is accompanied by changes in active histone marks without major alterations in DNA methylation. Histone 3 trimethylation at lysine 36 (H3k36me3) - a chromatin signature induced by the histone methyltransferase SETD2 - strongly correlates with changes in gene expression in human failing hearts; however, its role is poorly understood. Here we investigate the role of SETD2 in cHFpEF. MethodsMice with cardiomyocyte-specific deletion of SETD2 (c-SETD2-/-) were generated and subjected to high fat diet feeding and L-NAME treatment for 15 weeks to induce cHFpEF. Cardiac function and exercise tolerance were assessed by echocardiography and Treadmill exhaustion test. Chromatin immunoprecipitation assays (ChIP) were performed to investigate SETD2/H3k36me3 enrichment on gene promoters. SETD2 gain- and loss-of-function experiments were performed in cultured cardiomyocytes (CMs) exposed to palmitic acid (PA). SETD2 expression was also investigated in left ventricular (LV) myocardial specimens from patients with cHFpEF and control donors. ResultsSETD2 was upregulated in cHFpEF mouse hearts and its chromatin mark H3k36me3 was enriched on the promoter of sterol regulatory element-binding transcription factor 1 (SREBP1) gene. SETD2 activation in cHFpEF led to SREBP1 upregulation, triglyceride accumulation and lipotoxic damage. Of note, cardiomyocyte-specific deletion of SETD2 in mice prevented HFpEF-related hypertrophy, diastolic dysfunction and lung congestion while improving exercise tolerance. SETD2 deletion blunted H3K36me3 enrichment on SREBP1 promoter thus leading to a marked rewiring of the cardiac lipidome and restoration of autophagic flux. SETD2 depletion in PA-treated CMs prevented SREBP1 upregulation, whereas SETD2 overexpression recapitulated lipotoxic damage. Finally, SETD2 was upregulated in LV specimens from cHFpEF patients and its pharmacological inhibition by EZM0414 attenuated CM stiffness. ConclusionsTherapeutic modulation of SETD2/H3k36me3 axis might prevent lipotoxic injury and cardiac dysfunction in cHFpEF.

physiology↗

bioRxiv2023

Tryptophan stress activates EGFR-RAS-signaling to MTORC1 and p38/MAPK to sustain translation and AHR-dependent autophagy

Tumours face tryptophan (Trp) depletion, but the mechanisms sustaining protein biosynthesis under Trp stress remain unclear. We report that Trp stress increases the levels of the translation repressor EIF4EBP1. Yet, at the same time, EIF4EBP1 is selectively phosphorylated by the metabolic master regulator MTORC1 kinase, preventing EIF4EBP1 from inhibiting translation. MTORC1 activity under Trp stress is unexpected because the absence of amino acids is typically linked with MTORC1 inhibition. EIF4EBP1-sensitive translation in Trp starved cells is sustained by EGFR and RAS signalling to MTORC1. Via this mechanism, Trp stress enhances the synthesis and activity of the aryl hydrocarbon receptor (AHR). This is noteworthy as Trp catabolites are known to activate AHR, and therefore Trp stress was previously considered to inhibit AHR. Trp stress-induced AHR enhances the expression of key regulators of autophagy, which sustains intracellular Trp levels and Trp-charged tRNAs for translation. Hence, Trp stress switches MTORC1 from its established inhibitory function into an enhancer of autophagy, acting through AHR. The clinical potential of this fundamental mechanism is highlighted by the activity of the mTORC1-AHR pathway and an autophagy signature in 20% of glioblastoma patients, opening up new avenues for cancer therapy.

biochemistry↗

bioRxiv2021

PPi plays a role in sugar starvation tolerance

H+-PPase acidifies the endo-membrane compartments utilizing the energy of PPi hydrolysis. This acidification creates an electrochemical proton gradient that powers the secondary active transport and allows for vacuolar accumulation of several materials against their concentration gradients. The hydrolysis of the cytosolic PPi is necessary for the forwardness of the PPi-generating reactions. However, information is lacking on the role of PPi in adaptation to sugar starvation and low energy status in plants. Here, several mutants lacking the functional H+-PPases were used to illuminate this role. Three alleles of fugu5 mutants defective in type I H+-PPase exhibited better tolerance to sugar starvation than wild-type plants, when grown on [1/2] and full-strength MS media under photosynthesis-constraining low light intensity. The PPi level in fugu5 mutants was significantly higher than its level in wild type and type II H+-PPase-defective mutants. SnRK1 (Sucrose-non-fermenting1-Related kinase-1) plays a central role in the coordination of the plant transcriptome to the energy signals. SnRK1 senses the energy depletion in plant cells, and controls the expression of genes and phosphorylation of proteins in a way that promotes catabolism, and inhibits anabolism. Sugar starvation significantly induced the SnRK1 phosphorylation activity in wild type and type II H+-PPase lacking mutants. Whereas the activity remained unchanged in sugar-starved fugu5 mutants. This is possibly achieved through activation of PPi-dependent enzymes. Results suggest that the high PPi level in fugu5 mutants might contribute to more efficiently use of low level of ATP under sugar starvation and low light conditions.

plant biology↗