Biology subjects

Iqbal, A.

Publications and source records attributed to Iqbal, A..

23 records · Page 2Linked to original sources

bioRxiv2019

Phytohormonal cross-talk modulate Bipolaris sorokiniana (Scc.)interaction with Zea mays

Besides acting as growth inducing molecule, Gibberellin (GA3) also confers the compatibility of microbial interactions with host. We inoculated 11 days old Z. mays seedlings grown under hydroponic conditions and high GA3 levels with Bipolaris sorokiniana (BIPOL) at the spore density (SD) of OD0.6. The high level of GA3 negatively affected the growth of the seedlings, accompanied by the high level of stress deducing secondary metabolites (proline, total flavanoids, phenylpropanoids, and glucosinolides). Moreover, high level of GA3 produced a hypersensitive response (HR) in the seedlings. The HR developed cross talks with IAA and trans-zeatins and triggered higher production of hypersensitive inducing biomolecules. The other HR co-related biological processes were demonstrated by high phytoalexins level and high protease activities. Such activities ultimately inhibited the colonization of BIPOL on the roots of maize seedlings. The products of the genes expressed at high GA3 also conferred the deterrence of BIPOL colonization at SD = OD0.6. Intriguingly, when we inhibited GA3 biosynthesis in the seedlings with aerially sprayed uniconizole, prior to BIPOL treatment, the BIPOL colonized and subsequently promoted the seedling growth. This low level of GA3 after BIPOL treatment checked the high level of secondary metabolites and hypersensitivity inducing molecules. The results, thus suggested that the aforementioned processes only happened in the BIPOL at SD (OD0.6), whereas the SD at lower levels (OD0.2 or OD0.4) neither promoted the growth of uniconizole pre-treated seedlings nor produced HR in control seedlings of maize plant.

physiology↗

bioRxiv2019

Identification of a small molecule antagonist for the Tudor domain of SMN

Survival of motor neuron (SMN), a Tudor-domain-containing protein, plays an important role in diverse biological pathways via recognition of symmetrically dimethylated arginine (Rme2s) on proteins by its Tudor domain, and deficiency of SMN leads to the motor neuron degenerative disease spinal muscular atrophy (SMA). Here we report a potent and selective antagonist with a 4-iminopyridine scaffold targeting the Tudor domain of SMN. Our structural and mutagenesis studies indicate that the sandwich stacking interactions of SMN and compound 1 play a critical role in selective binding to SMN. Various on-target engagement assays support that compound 1 recognizes SMN specifically in a cellular context. In cell studies display that the SMN antagonist prevent the interaction of SMN with R1810me2s of DNA-directed RNA polymerase II subunit POLR2A and results in transcription termination and R-loop accumulation, mimicking depletion of SMN. Thus, in addition to the antisense, RNAi and CRISPR/Cas9 techniques, the potent SMN antagonist could be used as an efficient tool in understanding the biological functions of SMN and molecular etiology in SMA.

biochemistry↗

bioRxiv2019

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Bartonella bacilliformis is the causative agent of Carrions disease, one of the truly neglected tropical diseases found in Peru, Colombia and Ecuador. Recent evidence predicts that Bartonella bacilliformis subsp. ver097 can emerge as an antibacterial resistant strain and hence identification of novel drug targets is a crying need. Subtractive genome analysis of B. bacilliformis subsp. ver097 was successfully done in order to address the challenges. Various computational tools and online based servers were used to screen out human homologous proteins of pathogen and proteins involved in common metabolic pathways of host and pathogen. Only 7 proteins involved in pathogen specific pathways were further analyzed to identify membrane proteins. Flagellar biosynthesis protein FlhA and ABC transporter permease were found to be novel as targets according to DrugBank database. To avoid side effects in human while administering drugs, human anti-targets analysis was performed to confirm non-homology of selected novel drug targets. Both predicted proteins also showed probability of antigenicity prediction through VaxiJen, however, Flagellar biosynthesis protein FlhA showed broad spectrum conservancy with Bartonella strains. Therefore, Flagellar biosynthesis protein FlhAcould facilitate the development of novel drugs and therapeutic compounds along with vaccines for efficient treatment of infections caused by Bartonella bacilliformis subsp. ver097.

bioinformatics↗

bioRxiv2019

Identification and Characterization of the First Fragment Hits for SETDB1 Tudor Domain

SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase, which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the TTD of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.

pharmacology and toxicology↗

bioRxiv2017

A genetic screen suggests an alternative mechanism for inhibition of SecA by azide

Sodium azide prevents bacterial growth by inhibiting the activity of SecA, which is required for translocation of proteins across the cytoplasmic membrane. Azide inhibits ATP turnover in vitro, but its mechanism of action in vivo is unclear. To investigate how azide inhibits SecA in cells, we used transposon directed insertion-site sequencing (TraDIS) to screen a library of transposon insertion mutants for mutations that affect the susceptibility of E. coli to azide. Insertions disrupting components of the Sec machinery generally increased susceptibility to azide, but insertions truncating the C-terminal tail (CTT) of SecA decreased susceptibility of E. coli to azide. Treatment of cells with azide caused increased aggregation of the CTT, suggesting that azide disrupts its structure. Analysis of the metal-ion content of the CTT indicated that SecA binds to iron and the azide disrupts the interaction of the CTT with iron. Azide also disrupted binding of SecA to membrane phospholipids, as did alanine substitutions in the metal-coordinating amino acids. Furthermore, treating purified phospholipid-bound SecA with azide in the absence of added nucleotide disrupted binding of SecA to phospholipids. Our results suggest that azide does not inhibit SecA by inhibiting the rate of ATP turnover in vivo. Rather, azide inhibits SecA by causing it to \"backtrack\" from the ADP-bound to the ATP-bound conformation, which disrupts the interaction of SecA with the cytoplasmic membrane.\n\nSignificance statementSecA is a bacterial ATPase that is required for the translocation of a subset of secreted proteins across the cytoplasmic membrane. Sodium azide is a well-known inhibitor of SecA, but its mechanism of action in vivo is poorly understood. To investigate this mechanism, we examined the effect of azide on the growth of a library of [~]1 million transposon insertion mutations. Our results suggest that azide causes SecA to backtrack in its ATPase cycle, which disrupts binding of SecA to the membrane and to its metal cofactor, which is iron. Our results provide insight into the molecular mechanism by which SecA drives protein translocation and how this essential biological process can be disrupted.

microbiology↗