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Patra, N.

Publications and source records attributed to Patra, N..

7 recordsLinked to original sources

Estimation of Absolute Protein-DNA Binding Free Energy using Streamlined Geometric Formalism

Protein-DNA complexes are involved in vital cellular functions like gene regulation, replication, transcription, packaging, rearrangement, and damage repair. In this work, streamlined geometric formalism for computing the absolute binding free energy was used to obtain chemical accurate in silico estimation of binding free energy of three Protein-DNA complexes. Additionally, molecular interactions between Protein and DNA involved hydrogen bonds, electrostatic, van der Waals, and hydrophobic interactions. Using this formalism, researcher can obtain the absolute binding free energy for a Protein-DNA complex with remarkable accuracy and modest computational cost.

biophysics↗

Structural insights into the mechanism of C3 side chain fragmentation in cephalosporins with SME-1 class A carbapenemase

Cephalosporins remain one of the largest classes of antibiotics used clinically, with a diverse group of dual substituents at C3 and C7 positions. The fragmentation of the C-3 side chain from the C3 position after hydrolysis by Serine or metallo-{beta} lactamase leaving an exo-methylene group has been introduced in the literature recently, but the exact mechnism by which it happens remains unclear until now. Our incrystallo findings suggest that the fragmentation of the C3 side chain will depend on the C3 atom and its hybridization state. A C3 carbon with sp2 hybridization will not allow fragmentation, but a sp3 hybridized carbon will facilitate the detachment of the side chain. Furthermore, heteroatoms like Sulfur, on C3 position, bearing vacant d-orbitals participate in {pi}-cloud delocalization, making the detachment of C3 side chain energetically unfeasible. For the sp3 hybridized carbon at C3, the fragmentation of the bond was independent of the C3 atom. We observed fragmentation of the C3-C3 bond for all three heteroatoms, Nitrogen, Oxygen, and sulfur, at the C3 position. We validated our crystallographic findings with mass spectrometry to confirm the fragmentation of the C3 side chain in sp3 carbon and the unfragmented side chain in sp2 carbon and sulfur at C3 position. QM/MM simulations on three types of enzyme-cephalosporin complexes with different C3 side chains confirm the mechanism of fragmentation. Beyond revealing C3 side chain fragmentation in cephalosporins, useful for inhibitor and diagnostic design, our QM/MM methods are useful on incrystallo complexes to show the enzyme catalysis.

biochemistry↗

Heterologous expression in Saccharomyces and Chlamydomonas reveals host-dependent activity of Brassica juncea fatty acid elongase1 isozymes

The fatty acid elongase1 (FAE1) genes of tetraploid Brassica juncea are the key determinant of high erucic acid (EA, C22:1) accumulation in its seed oil. While our previous work demonstrated near-zero EA content in mustard oil via CRISPR/Cas9 knockout of the two homeoalleles, BjFAE1.1 and BjFAE1.2; the contributory function of each isozymes towards EA biosynthesis remains elusive. This study investigated the heterologous expression of BjFAE1.1 and BjFAE1.2 from high EA B. juncea cultivar JD6 in two metabolically distinct eukaryotic microbial hosts: the green microalga Chlamydomonas reinhardtii and the budding yeast Saccharomyces cerevisiae. Despite confirmed protein expression, neither BjFAE1 isozyme produced detectable C20:1 or C22:1 very-long-chain fatty acids (VLCFAs) in transgenic lines of C. reinhardtii. In contrast, expression in S. cerevisiae resulted in significant de novo biosynthesis of VLCFAs, C20:1 ([~]9-11%) and C22:1 ([~]17-19%), confirming their enzymatic activity as functional {beta}-ketoacyl-CoA synthase. Substrate feeding experiments in yeast further validated their capability to elongate oleoyl-CoA (C18:1-CoA) to erucoyl-CoA (C22:1-CoA) via eicosenoyl-CoA (C20:1-CoA), with BjFAE1.1 showing slightly higher activity, as indicated by the enhanced VLCFAs accumulation. These findings highlight the critical influence of the heterologous hosts cellular environment on the enzyme functionality of plant genes involved in lipid metabolism, underscoring challenges for VLCFA production in microalgal platform.

plant biology↗

Phosphatidylinositol-3,5-bisphosphate mediated vacuolar morphology modulation is integral to ethanol stress response

Vacuoles enlarge in response to ethanol. We used quantitative imaging to show that even brief exposure to ethanol causes a rapid transition from multilobed vacuoles to a single compartment. Vacuole unlobing is essential as mutants restricted for vacuole fusion exhibit greater ethanol sensitivity. This response involves the inhibition of vacuole fission via downregulation of the activity of Fab1, a lipid kinase generating the signaling lipid phosphatidylinositol-3,5-bisphosphate. Ethanol exposure results in the redistribution of a phosphatidylinositol-3,5-bisphosphate sensor from the perivauolar dots to the cytoplasm and the dissociation of the effector of this lipid, Atg18, from the vacuolar membrane to the cytoplasm. Impaired Atg18 membrane recruitment also entails a loss of interaction between a scaffold of the Fab1 complex, Vac14, and Atg18. A hyperactive Fab1 mutant, with elevated pools of phosphatidylinositol-3,5-bisphosphate, shows delayed vacuole enlargement; the partial relocation of the phosphatidylinositol-3,5-bisphosphate probe to the perivacuolar dots and of Atg18 to the vacuole membrane. Since Atg18 is responsible for vacuole fragmentation, our results show that, under ethanol stress, cells actively regulate vacuole morphology by modulating phosphatidylinositol-3,5-bisphosphate levels.

cell biology↗

Divergent Functions of Late ESCRT Components in Giardia lamblia: Insights from Subcellular Distributions and Protein Interactions

Giardia lamblia, a human gut pathogen, possesses a minimal ESCRT (Endosomal Sorting Complex Required for Transport) machinery. Paradoxically, there are multiple paralogs of some late-ESCRT components. There are three paralogs for Vps4, GlVps4a, GlVps4b, and GlVps4c, and two for Vps46, GlVps46a, and GlVps46b. This study addressed whether these paralogs discharge overlapping and/or distinct cellular functions by determining the sub-cellular distribution of the paralogs in trophozoites and during encysting. Consistent with the distribution of orthologs in model organisms, most of these components were found to be associated with various cellular membranes, particularly in regions of acute membrane bending. Some of these paralogs are also associated with microtubule structures, such as cytoplasmic axonemes and the median body. Considering their diverse sub-cellular distributions, it is likely that they perform non-overlapping functions within the cell. Furthermore, their redistribution during encystation indicates that they may play a role in the morphological and functional changes accompanying this transition. The study also characterized GlIst1, an ESCRT-III accessory protein that undergoes unique post-translational myristoylation at lysine 43, potentially aiding its membrane recruitment. GlIst1 selectively interacts with GlVps4b through non-canonical MIT-MIM interactions. GlIst1 also exhibits selective interaction with GlVps46b. Such selective interaction of GlIst1 with only specific paralogs of GlVps4 and GlVps46 further underscores the distinct cellular roles of these paralogs. Author SummaryGiardia lamblia, a unicellular protozoan parasite, is the causative agent of giardiasis, a water-transmitted disease affecting millions globally. This disease poses a substantial threat to public health, especially in less developed countries, where clean water and proper sanitation are scarce. The parasite manifests in two morphologically distinct forms, trophozoites and cysts. Transformation between these forms is essential for the organisms survival, spread, and infection processes. Trophozoites, the active and motile form of Giardia, inhabit the small intestine of the host and trigger infections. These trophozoites can transform into cysts through encystation, enabling the parasite to endure harsh external environments and spread between hosts through contaminated water or food sources. The transition between these states necessitates extensive membrane restructuring. Such changes are likely to involve the Endosomal Sorting Complex Required for Transport (ESCRT) machinery, as it has been shown to participate in both prokaryotic and eukaryotic membrane remodeling events. Our research sheds light on the ESCRT machinery in G. lamblia, a crucial membrane-shaping system that may facilitate the transition between trophozoites and cysts. The ESCRT machinery in G. lamblia is distinct from that in yeast and humans, representing one of the most basic ESCRT systems. Our investigation provides valuable information about the intracellular distribution of various late-ESCRT components under different conditions, their potential functions, and their interactions with other late-ESCRT components. These findings may contribute significantly to our understanding of the basic operation of the ESCRT machinery in this parasite.

cell biology↗

Knockout of fatty acid elongase1 homeoalleles in amphidiploid Brassica juncea leads to undetectable erucic acid in seed oil

Indian mustard (Brassica juncea L.) is a major oilseed crop with significant economic and nutritional importance within the Indian subcontinent. While its seed oil offers valuable dietary benefits, including a balanced ratio of human essential fatty acids, the traditional high oil-yielding varieties contain an elevated level of erucic acid (EA, C22:1) that is associated with adverse health effects. Therefore, developing low erucic acid (LEA) mustard cultivars is crucial for broader utilization and consumer safety. In this study, we employed CRISPR/Cas9 genome editing tools to disrupt the fatty acid elongase1 (FAE1) gene that encodes a key enzyme in EA biosynthesis in two high erucic acid (HEA) B. juncea cultivars, PCR7 and JD6. Targeted knockout (KO) of BjFAE1 homeoalleles (BjFAE1.1 and BjFAE1.2) in this amphidiploid plant using CRISPR/Cas9 constructs, each carrying two guide RNAs led to monoallelic and biallelic mutations. Biallelic KO lines showed a near-complete elimination of EA (<0.5% in PCR7, undetectable in JD6) with a significant increase in nutritionally beneficial oleic acid ([~]30% in PCR7, [~]35% in JD6), while the content of essential fatty acids also increased significantly, suggesting rerouting of carbon flux from EA biosynthesis. Importantly, these LEA lines retained key agronomic traits like plant seed yield and oil content, matching the productivity of the control elite cultivars. Our findings underscore the effectiveness of CRISPR/Cas9 technology for editing B. juncea genome, producing LEA seed oil lines with improved nutritional quality and thus expanding the applications of this important oilseed crop.

plant biology↗

Two paralogues of N-ethylmaleimide sensitive factor: An exception to the minimal vesicular trafficking machinery of Giardia

Vesicular trafficking plays a critical role in the survival of the human gut pathogen Giardia lamblia as it drives nutrient uptake and morphological stage transition. Unlike most eukaryotes, Giardia has a minimal vesicular trafficking machinery. Herein, we report a rare exception to this minimalism wherein two paralogues of NSF, a crucial factor driving vesicular trafficking by uncoupling the cis-SNARE bundle, are present in this unicellular parasite. While GlNSF114776 and GlNSF112681 share very high sequence homology, they are likely to have distinct cellular roles as they exhibit differences in their affinities towards the Gl-SNAPs and display non-overlapping distribution in encysting trophozoites. Under multiple stress conditions (nutritional, oxidative and nitrosative), while GlNSF112681 remains at peripheral vesicles, GlNSF114776 relocalizes to the anterior flagella-associated striated fibres, indicating a possible role in regulating flagellar motility. At this location, GlNSF114776 is likely to perform a 20S complex independent function as neither Gl-SNAPs nor GlSNAREs are present there. The two paralogues are likely needed for stress adaptation as both copies have also been retained in Giardia genomes isolated from clinical samples. This non-canonical function of the GlNSF114776 may have evolved to support the unique architecture and motility of the anterior flagella.

cell biology↗