01851nas a2200169   4500008004100000245009800041210006900139260000800208300001000216490000800226520121500234100003201449700002501481700003101506700002101537856012301558       2018                        eng d00a Integrated constraints based analysis of an engineered violacein pathway in escherichia coli0 aIntegrated constraints based analysis of an engineered violacein  cSEP  a10-190 v1713 aStrategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Delta pgi & Delta pheA were validated using in silico gene deletion analysis. Phenotypic phase plane (PhPP) analysis highlighted sensitivity between tryptophan and NADPH for violacein synthesis at molar growth yields. A synthetic VioABCDE operon (SYNO) sequence was designed to maximize Codon Adaptive Index (CAI: 0.9) and tune translation initiation rates (TIR: 2-50 fold higher) in E. coli. All pSYN E. coli transformants produced higher violacein, with a maximum six-fold increase in yields. The rational design E. coli: Delta pheA SYN: gave the highest violacein titers (33.8 mg/I). Such integrated approaches targeting multiple molecular hierarchies in the cell can be extended further to increase violacein yields.1 aImmanuel, Selva, Rupa Chris1 aBanerjee, Deepanwita1 aRajankar, Mayooreshwar, P.1 aRaghunathan, Anu  uhttps://library.ncl.res.in/content/integrated-constraints-based-analysis-engineered-violacein-pathway-escherichia-coli01855nas a2200205   4500008004100000245011700041210006900158260000900227300000600236490000600242520110000248100003201348700002501380700003001405700001601435700001601451700003101467700002101498856013001519       2021                        eng d00aIntegrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells0 aIntegrated genetic and metabolic landscapes predict vulnerabilit  cJAN   a20 v73 a<p>Metabolic reprogramming and its molecular underpinnings are critical to unravel the duality of cancer cell function and chemo-resistance. Here, we use a constraints-based integrated approach to delineate the interplay between metabolism and epigenetics, hardwired in the genome, to shape temozolomide (TMZ) resistance. Differential metabolism was identified in response to TMZ at varying concentrations in both the resistant neurospheroidal (NSP) and the susceptible (U87MG) glioblastoma cell-lines. The genetic basis of this metabolic adaptation was characterized by whole exome sequencing that identified mutations in signaling pathway regulators of growth and energy metabolism. Remarkably, our integrated approach identified rewiring in glycolysis, TCA cycle, malate aspartate shunt, and oxidative phosphorylation pathways. The differential killing of TMZ resistant NSP by Rotenone at low concentrations with an IC50 value of 5 nM, three orders of magnitude lower than for U87MG that exhibited an IC50 value of 1.8 mM was thus identified using our integrated systems-based approach.</p>
1 aImmanuel, Selva, Rupa Chris1 aGhanate, Avinash, D.1 aParmar, Dharmeshkumar, S.1 aYadav, Ritu1 aUthup, Riya1 aPanchagnula, Venkateswarlu1 aRaghunathan, Anu  uhttps://library.ncl.res.in/content/integrated-genetic-and-metabolic-landscapes-predict-vulnerabilities-temozolomide-resistant