ATP alters protein folding and function of Escherichia coli uridine phosphorylase

Proteomic insight into growth and defense strategies under low ultraviolet-B acclimation in the cyanobacterium Nostoc sphaeroides

Prioritizing defense over growth often occurs under ultraviolet (UV)-B radiation while several studies showed its growth-promoting effects on photosynthetic organisms, how they overcome the growth-defense trade-off is unclear. This study deciphered the acclimation responses of the cyanobacterium Nostoc sphaeroides to low UV-B radiation (0.08 W m-2) using quantitative proteomic, physiological and biochemical analyses. We identified 628 significantly altered proteins, among which energy production and conversion related proteins dominated. The UV-B-acclimated cells exhibited a significant increase in the abundance of the phycoerythrin and chlorophyll synthesis related enzymes, along with enhanced linear and cyclic electron transport rates, which further led to a rise in light-induced NADPH generation (27 %) and ATP content (67 %). The enhanced photosynthetic energy supply could fuel both growth and defense in Nostoc sphaeroides. The UV-B-acclimated cells showed enhanced photosynthetic carbon fixation, as evidenced by an increase in extracellular carbonic anhydrase activity (142 %), ribulose-1,5-bisphosphate carboxylase/oxygenase activity (87 %) and the pH compensation point, compared to non-UV-B-acclimated cells. Low UV-B also induced ribosome heterogeneity, as indicated by significant changes in the abundance of core ribosomal proteins, RNA modification related enzymes, and ribosome biogenesis and translation related accessory factors. Additionally, low UV-B activated multiple defense strategies, such as significant upregulation of mycosporine-like amino acid synthesis, RecA-dependent DNA repair pathways and the glutathione redox system. Our findings suggested that growth and defense were balanced by enhancing the photosynthetic energy supply under low UV-B acclimation in the cyanobacterium Nostoc sphaeroides, which provides novel insight into mechanisms for overcoming growth-defense trade-offs.

Systems-level analysis of the global regulatory mechanism of CodY in Lactococcus lactis metabolism and nisin immunity modulation

Bacteria adapt to the constantly changing environment by regulating their metabolism. The global transcriptional regulator CodY is known to regulate metabolism in low G+C Gram-positive bacteria. Systems-level identification of its direct targets by proteome and ChIP-seq assays was rarely reported. Here, we identified CodY serves as an activator or a repressor of hundreds of genes involved in nitrogen metabolism, carbohydrate metabolism, and transcription through iTRAQ proteome and ChIP-seq. Combined with EMSA experiment, apart from the genes associated with amino acid biosynthesis (ilvD, leuA, optS, ybbD, dtpT, and pepN), genes involved in cell wall synthesis (murD and ftsW) and nisin immunity (nisI) were identified to be regulated by CodY. Moreover, it was demonstrated that CodY activated the transcription of nisI and contributed to the nisin immunity by nisin resistance assay. Intriguingly, CodY showed a self-regulation through binding to the motif 'AAAGGTGTGACAACT'in the CDS region of codY verified by DNase I footprinting assay and MEME analysis. In addition, a novel conserved AT-rich motif 'AATWTTCTGACAATT' was obtained in L. lactis F44. This study provides new insights into the comprehensive CodY regulation in L. lactis by controlling metabolism, nisin immunity and self-expression. Importance Lactococcus lactis, a widely used lactic acid bacteria (LAB) in the food fermentation, has been the model strain in genetic engineering, and its application has extended from food to microbial cell factory. CodY is a global regulator in low G+C Gram-positive bacteria. Its function and direct target genes in genome-level were rarely known in L. lactis. In this study, we described the comprehensive regulation mechanism of CodY. It widely modulated the metabolism of nitrogen and carbohydrate, cell wall synthesis and nisin immunity in L. lactis F44, and its expression level was regulated by feedback control.

Distinct functional properties of secretory l-asparaginase Rv1538c involved in phagosomal survival of Mycobacterium tuberculosis

The emergence of drug-resistant Mycobacterium tuberculosis (Mtb) stains has escalated the need for developing more efficient drugs and therapeutic strategies against tuberculosis. Here we functionally annotate a secretory mycobacterial asparaginase Rv1538c (MtA) and describe its biochemical properties. MtA primarily existed as dimer along with a minor population of multimers. Circular dichroism and fluorescence spectroscopy demonstrated a compact structure in Tris HCl buffer at pH 8.0. Under these conditions it also displayed optimum activity. It retained ∼40% activity at pH 5.5, supporting its physiological relevance in acidic phagosomal environment. MtA contravened classical Michaelis-Menten kinetics and exhibited product inhibition profile, yielding a K_cat of 869.4 s^-1 and an apparent K_m of 8.36 mM. We report the presence of several antigenic epitopes and a C-terminal YXXXD/E motif in MtA, hinting towards its potential to interact or influence host immune system. This was supported by our observation of morphological changes in MtA-treated human B lymphoblasts. We propose that MtA is a dual purpose enzyme used by Mtb to survive inside its host by; 1) ammonia-mediated neutralization of the phagosomal acidic pH and 2) inducing stress to primary immune cells and compromising the host immune response. Overall, this study contributes to our understanding of the biological role of mycobacterial asparaginase opening avenues for developing effective TB therapeutics.

Metabolites modulate the functional state of human uridine phosphorylase I

Metabolic pathways in cancer cells typically become reprogrammed to support unconstrained proliferation. These abnormal metabolic states are often accompanied by accumulation of high concentrations of ATP in the cytosol, a phenomenon known as the Warburg Effect. However, how high concentrations of ATP relate to the functional state of proteins is poorly understood. Here, we comprehensively studied the influence of ATP levels on the functional state of the human enzyme, uridine phosphorylase I (hUP1), which is responsible for activating the chemotherapeutic pro-drug, 5-fluorouracil. We found that elevated levels of ATP decrease the stability of hUP1, leading to the loss of its proper folding and function. We further showed that the concentration of hUP1 exerts a critical influence on this ATP-induced destabilizing effect. In addition, we found that ATP interacts with hUP1 through a partially unfolded state and accelerates the rate of hUP1 unfolding. Interestingly, some structurally similar metabolites showed similar destabilization effects on hUP1. Our findings suggest that metabolites can alter the folding and function of a human protein, hUP1, through protein destabilization. This phenomenon may be relevant in studying the functions of proteins that exist in the specific metabolic environment of a cancer cell.