Disruption of NAD+ binding site in glyceraldehyde 3-phosphate dehydrogenase affects its intranuclear interactions

Proteome and Metabolome Alterations in Radish (Raphanus sativus L.) Seedlings Induced by Inoculation with Agrobacterium tumefaciens

Infection of higher plants with agrobacteria (Agrobacterium tumefaciens) represents one of the most comprehensively characterized examples of plant-microbial interactions. Incorporation of the bacterial transfer DNA (T-DNA) in the plant genome results in highly efficient expression of the bacterial auxin, cytokinin and opine biosynthesis genes, as well as the host genes of hormone-mediated signaling. These transcriptional events trigger enhanced proliferation of plant cells and formation of crown gall tumors. Because of this, infection of plant tissues with A. tumefaciens provides a convenient model to address the dynamics of cell metabolism accompanying plant development. To date, both early and late plant responses to agrobacterial infection are well-characterized at the level of the transcriptome, whereas only little information on the accompanying changes in plant metabolism is available. Therefore, here we employ an integrated proteomics and metabolomics approach to address the metabolic shifts and molecular events accompanying plant responses to inoculation with the A. tumefaciens culture. Based on the acquired proteomics dataset complemented with the results of the metabolite profiling experiment, we succeeded in characterizing the metabolic shifts associated with agrobacterial infection. The observed dynamics of the seedling proteome and metabolome clearly indicated rearrangement of the energy metabolism on the 10th day after inoculation (d.a.i.). Specifically, redirection of the energy metabolism from the oxidative to the anaerobic pathway was observed. This might be a part of the plant's adaptation response to tumor-induced hypoxic stress, which most likely involved activation of sugar signaling.

Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus

Some metabolic enzymes normally occur in the nucleus and cytoplasm. These compartments differ in molecular composition. Since post-translational modification and interaction with allosteric effectors can tune enzyme activity, it follows that the behavior of an enzyme as a catalyst may differ between the cytoplasm and nucleus. We explored this possibility for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Homogenates of pristine nuclei and cytoplasms isolated from Xenopus laevis oocytes were used for whole compartment activity profiling in a near-physiological buffer. Titrations of NAD+ revealed similar whole compartment activity profiles for GAPDH in nuclear and cytoplasmic homogenates. Surprisingly however GAPDH in these compartments did not have the same behavior in assays of the dependence of initial velocity (v0) on G3P concentration. First, the peak v0 for nuclear GAPDH was up to 2.5-fold higher than the peak for cytoplasmic GAPDH. Second, while Michaelis Menten-like behavior was observed in all assays of cytoplasm, the v0 versus [G3P] plots for nuclear GAPDH typically exhibited a non-Michaelis Menten (sigmoidal) profile. Apparent Km and Vmax (G3P) values for nuclear GAPDH activity were highly variable, even between replicates of the same sample. Possible sources of this variability include in vitro processing of a metabolite that allosterically regulates GAPDH, turnover of a post-translational modification of the enzyme, and fluctuation of the state of interaction of GAPDH with other proteins. Collectively these findings are consistent with the hypothesis that the environment of the nucleus is distinct from the environment of the cytoplasm with regard to GAPDH activity and its modulation. This finding warrants further comparison of the regulation of nuclear and cytoplasmic GAPDH, as well as whole compartment activity profiling of other enzymes of metabolism with cytosolic and nuclear pools.

Age-related NAD+ decline

Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite that is reported to decline in concentration in tissues of aged animals. Strategies to increase NAD+ availability have shown promise in treating many conditions in rodents, including age-related degeneration, which has in turn driven intense interest in the effects of supplements on human health. However, many aspects of NAD+ metabolism remain poorly understood, and human data are limited. Here, we discuss the state of the evidence for an age-related decline in NAD+, along with potential mechanistic explanations, including increased consumption or decreased synthesis of NAD+ and changes in the composition of cells or tissues with age. Key challenges for the field involve the development of better tools to resolve information on the NAD+ content of specific cells and subcellular compartments as well as determining the threshold levels at which NAD+ depletion triggers physiological consequences in different tissues. Understanding how NAD+ metabolism changes with age in humans may ultimately allow the design of more targeted strategies to maintain its availability, such as inhibition of key consumers in specific tissues or direct delivery of precursors to sites of deficiency. In the meantime, human clinical trials with oral supplements are poised to provide some of the first direct evidence as to whether increasing NAD+ availability can impact human physiology. Thus, it is an exciting time for NAD+ research, with much remaining to be learned in terms of both basic biology and potential therapeutic applications.

Proteome-Wide Characterization of Phosphorylation-Induced Conformational Changes in Breast Cancer

Because of the close link between protein function and protein folding stability, knowledge about phosphorylation-induced protein folding stability changes can lead to a better understanding of the functional effects of protein phosphorylation. Here, the stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) techniques are used to compare the conformational properties of proteins in two MCF-7 cell lysates including one that was and one that was not dephosphorylated with alkaline phosphatase. A total of 168 and 251 protein hits were identified with dephosphorylation-induced stability changes using the SPROX and LiP techniques, respectively. Many protein hits are previously known to be differentially phosphorylated or differentially stabilized in different human breast cancer subtypes, suggesting that the phosphorylation-induced stability changes detected in this work are disease related. The SPROX hits were enriched in proteins with aminoacyl-tRNA ligase activity. These enriched protein hits included many aminoacyl-tRNA synthetases (aaRSs), which are known from previous studies to have their catalytic activity modulated by phosphorylation. The SPROX results revealed that the magnitudes of the destabilizing effects of dephoshporylation on the different aaRSs were directly correlated with their previously reported aminoacylation activity change upon dephosphorylation. This substantiates the close link between protein folding and function.