Deconjugation of Nedd8 from Cul1 Is Directly Regulated by Skp1-F-box and Substrate, and the COP9 Signalosome Inhibits Deneddylated SCF by a Noncatalytic Mechanism

COP9 signalosome (CSN) mediates deconjugation of the ubiquitin-like protein Nedd8 from the cullin subunits of SCF and other cullin-RING ubiquitin ligases (CRLs). This process is essential to maintain the proper activity of CRLs in cells. Here, we report a detailed kinetic characterization of CSN-mediated deconjugation of Nedd8 from SCF. CSN is an efficient enzyme, with a k(cat) of ～1 s(-1) and K(m)for neddylated Cul1-Rbx1 of ～200 nm, yielding a k(cat)/K(m) near the anticipated diffusion-controlled limit. Assembly with an F-box-Skp1 complex markedly inhibited deneddylation, although the magnitude varied considerably, with Fbw7-Skp1 inhibiting by ～5-fold but Skp2-Cks1-Skp1 by only ～15%. Deneddylation of both SCF(Fbw7) and SCF(Skp2-Cks1) was further inhibited ～2.5-fold by the addition of substrate. Combined, the inhibition by Fbw7-Skp1 plus its substrate cyclin E was greater than 10-fold. Unexpectedly, our results also uncover significant product inhibition by deconjugated Cul1, which results from the ability of Cul1 to bind tightly to CSN. Reciprocally, CSN inhibits the ubiquitin ligase activity of deneddylated Cul1. We propose a model in which assembled CRL complexes engaged with substrate are normally refractory to deneddylation. Upon consumption of substrate and subsequent deneddylation, CSN can remain stably bound to the CRL and hold it in low state of reduced activity.     

Natural Biased Coin Encoded in the Genome Determines Cell Strategy

Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.     

TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets

The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network.     

Functional activity of the mouse flavin-containing monooxygenase forms 1, 3, and 5

Three functional mouse flavin-containing monooxygenases (mFMOs) (i.e., mFMO1, mFMO3, and mFMO5) have been reported to be the major FMOs present in mouse liver. To examine the biochemical features of these enzymes, recombinant enzymes were expressed as maltose-binding protein fusion proteins (i.e., MBP-mFMO1, MBP-mFMO3, and MBP-mFMO5) in Escherichia coli and isolated and purified with affinity chromatography. The substrate specificity of these three mouse hepatic FMO enzymes were examined using a variety of substrates, including mercaptoimidazole, trimethylamine, S-methyl esonarimod, and an analog thereof, and a series of 10-(N,N-dimethylaminoalkyl)-2-(trifluoromethyl)phenothiazine analogs. The kinetic parameters of the three mouse FMOs for these substrates were compared in an attempt to explore substrate structure--function relationships specific for each mFMO. Utilizing a common phenothiazine substrate for all three enzymes, we compared the pH dependence for the recombinant enzymes under similar conditions. In addition, thermal stability for mFMO1, mFMO3, and mFMO5 enzymes was examined in the presence and absence of NADPH. The results revealed unique features for mFMO5, suggesting possible impact on the functional significance of this abundantly expressed FMO5 isoform in both human and mouse liver.     

Pre‐ and Postsurgery Behavioral Compliance,Patient Health,and Postbariatric Surgical Weight Loss

This study investigated the relationship between weight loss from gastric bypass surgery, patient characteristics, and compliance with physician instructions before and after surgery. A chart review of psychiatric and medical files was conducted for an initial cohort of 172 patients in a postsurgical management program. A total of 112 patients (primarily women (85%), white (79%), and well educated) from this cohort had presurgical data. Of these 112 subjects, 67 (60%) had postsurgical compliance information and BMI at 24 months postsurgery. The relationships between weight loss and a number of demographic, psychiatric, comorbid, and behavioral compliance factors were examined for these 67 patients. Missed appointments and noncompliance with exercise and weight loss plan instructions were high before and after surgery (65% vs. 72% for missed appointments, 39% vs. 51% for exercise, 42% vs. 57% for weight loss instructions). Although poor food choices were not frequently a problem before surgery (11%), they increased significantly after surgery: 37%, χ²(1) = 25.00, P < 0.001. Participants who lost the least weight at 2 years postsurgery were more likely to be nonwhite (r = 0.27, P = 0.039), have a lower socioeconomic status (SES) (r = 0.285, P = 0.02), and have a diagnosis of binge eating before surgery (r = 0.25, P = 0.039). Having more contact with patients and requiring adherence to behavioral changes, especially with respect to exercise and dietary restrictions, may improve the long‐term outcomes for bariatric procedures. In addition, those patients who are depressed and suffer from binge eating may need special attention from physicians during long‐term postoperative follow‐up.