Biochemical and Structural Analysis of RraA Proteins To Decipher Their Relationships with 4‑Hydroxy-4-methyl-2-oxoglutarate/4-Carboxy-4-hydroxy-2-oxoadipate Aldolases

4-Hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolases are class II (divalent metal ion dependent) pyruvate aldolases from the <i>meta</i> cleavage pathways of protocatechuate and gallate. The enzyme from <i>Pseudomonas putida</i> F1 is structurally similar to a group of proteins termed regulators of RNase E activity A (RraA) that bind to the regulatory domain of RNase E and inhibit the ribonuclease activity in certain bacteria. Analysis of homologous RraA-like proteins from varying species revealed that they share sequence conservation within the active site of HMG/CHA aldolase. In particular, the <i>P. putida</i> F1 HMG/CHA aldolase has a D-X₂₀-R-D motif, whereas a G-X₂₀-R-D-X₂-E/D motif is observed in the structures of the RraA-like proteins from <i>Thermus thermophilus</i> HB8 (<i>Tt</i>RraA) and <i>Saccharomyces cerevisiae</i> S288C (Yer010Cp) that may support metal binding. <i>Tt</i>RraA and Yer010Cp were found to contain HMG aldolase and oxaloacetate decarboxylase activities. Similar to the <i>P. putida</i> F1 HMG/CHA aldolase, both <i>Tt</i>RraA and Yer010Cp enzymes required divalent metal ions for activity and were competitively inhibited by oxalate, a pyruvate enolate analogue, suggesting a common mechanism among the enzymes. The RraA from <i>Escherichia coli</i> (<i>Ec</i>RraA) lacked detectable C–C lyase activity. Upon restoration of the G-X₂₀-R-D-X₂-E/D motif, by site-specific mutagenesis, the <i>Ec</i>RraA variant was able to catalyze oxaloacetate decarboxylation. Sequence analysis of RraA-like gene products found across all the domains of life revealed conservation of the metal binding motifs that can likely support a divalent metal ion-dependent enzyme reaction either in addition to or in place of the putative RraA function

Fungal secondary metabolites rasfonin induces autophagy, apoptosis and necroptosis in renal cancer cell line

<p>Rasfonin (A304) is a fungal natural product isolated from the fermentation substrate of <i>Talaromyces</i> sp. 3656-A1, which was named according to its activity against the small G-protein Ras. In a former study, we demonstrated that it induced autophagy and apoptosis; however, whether rasfonin activated necroptosis remained unknown. Moreover, the interplay among different cell death processes induced by rasfonin was unexplored. In the present study, we revealed that, in addition of promoting autophagy and caspase-dependent apoptosis, rasfonin also activated necroptosis. Nectrostatin-1 (Nec-1), an inhibitor of necroptosis, affected rasfonin-induced autophagy in a time-dependent manner concurring with an increased caspase-dependent apoptosis. The aforementioned results were confirmed by knockdown of receptor-interacting protein 1 (RIP1), a crucial necrostatin-1-targeted adaptor kinase mediating cell death and survival. Taken together, the data presented indicate that rasfonin activates various cell death pathways, and RIP1 plays a critical role in rasfonin-induced autophagy and apoptosis.</p

Additional file 2 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 2: Supplementary table 1. Univariate and Multivariate analysis of prognostic factors affecting OS

Additional file 8 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 8

Additional file 3 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 3: Supplementary table 2. Univariate and Multivariate analysis of prognostic factors affecting CS

Additional file 1 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 1. Material and Methods

Additional file 7 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 7: Supplementary figure 3. Survival analysis of CSS and OS stratified by tumor size

Additional file 5 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 5: Supplementary table 3. Discriminatory ability of clinicopathological factors in predicting OS in gastric cancer

Additional file 1 of Rare and common coding variants in lipid metabolism-related genes and their association with coronary artery disease

Supplementary Material

Additional file 4 of Tumor size as a significant prognostic factor in T1 gastric cancer: a Surveillance, Epidemiology, and End Results (SEER) database analysis

Additional file 4: Supplementary figure 2. Heatmap of C-index of clinicopathological factors in predicting CSS and OS in gastric cancer