Laser photolysis of carboxymethylated chitin derivatives in aqueous solution. Part 2. Reaction of OH* and SO4*- radicals with carboxymethylated chitin derivatives

The reactions of OH* or SO4*- radicals with carboxymethyl chitin (CM-chitin) and its deacetylated product, carboxymethyl chitosan (CM-chitosan), were investigated in aqueous solutions using a laser photolysis technique. The rate constants of the reactions of OH* and SO4*- radicals with CM-chitosan are always higher than those for CM-chitin, indicating that the amino-group could increase the reactivity of carboxymethylated chitin derivatives. The rate of the reactions of CM-chitin and CM-chitosan with OH* radical was found to decrease at lower pH when polymers chains tend to the coiled conformation. In comparison, the rate constant of the reaction of SO4*- radicals with CM-chitin or CM-chitosan decreased with pH, indicating that CM-chitin or CM-chitosan has a higher reactivity with the SO4*- radical at low pH due to the protonation of the amino group.     

MAGUK-Controlled Ubiquitination of CARMA1 Modulates Lymphocyte NF-κB Activity

The adaptor protein CARMA1 is required for antigen receptor-triggered activation of IKK and JNK in lymphocytes. Once activated, the events that subsequently turn off the CARMA1 signalosome are unknown. In this study, we found that antigen receptor-activated CARMA1 underwent lysine 48 (K48) polyubiquitination and proteasome-dependent degradation. The MAGUK region of CARMA1 was an essential player in this event; the SH3 and GUK domains contained the main ubiquitin acceptor sites, and deletion of a Hook domain (an important structure for maintaining inactive MAGUK proteins) between SH3 and GUK was sufficient to induce constitutive ubiquitination of CARMA1. A similar deletion promoted the ubiquitination of PSD-95 and Dlgh1, suggesting that a conserved mechanism may control the turnover of other MAGUK family protein complexes. Functionally, we demonstrated that elimination of MAGUK ubiquitination sites in CARMA1 resulted in elevated basal and inducible NF-κB and JNK activation as a result of defective K48 ubiquitination and increased persistence of this ubiquitination-deficient CARMA1 protein in activated lymphocytes. The coordination of degradation with the full activation of the CARMA1 molecule likely provides an intrinsic feedback control mechanism to balance lymphocyte activation upon antigenic stimulation.The CARD-containing MAGUK protein 1 (CARMA1, or CARD11) is regarded as an orchestrator of both T-cell-dependent and T-cell-independent immune responses due to its requirement in the activation of IKK and JNK signaling pathways downstream of antigen receptor (AR) ligation in B and T cells (3, 6, 8, 17). CARMA1 overexpression and/or mutations have also been associated with lymphomagenesis, as it promotes sustained activation of NF-κB-dependent cell survival (10, 16, 18). Structurally, CARMA1 is a multidomain adaptor protein containing a caspase recruitment (CARD) and a coiled-coil (CC) domain linked upstream of a region that is related to the MAGUK family of proteins. This MAGUK region contains a postsynaptic density 95/disc large/zona occludens 1 (PDZ), a SRC homology 3 (SH3), and a guanylate kinase-like (GUK) domain (2, 20). In addition, CARMA1 contains a flexible serine/threonine-rich linker that bridges the CC and MAGUK domains. Phosphorylation of this linker by protein kinase Cβ (PKCβ) or PKCθ controls the activation status of CARMA1 (13, 29, 30); thus, this region has been designated as the PKC-regulated domain (PRD) (22). It is likely that PRD phosphorylation destabilizes an inhibitory conformation in CARMA1 that exposes the various interaction domains required to assemble its downstream signaling components. Consistent with this model, deletion of the PRD results in a constitutively active CARMA1, resulting in high basal NF-κB activation (14, 30).Proximal downstream adaptors of CARMA1 include BCL10 and MALT1 (22). Genetic deletion of any of these proteins in cellular and animal models has revealed the importance of this pathway to immune cell function. While AR-induced activation of early signaling pathways, such as protein tyrosine phosphorylation, intracellular Ca²⁺ flux, and activation of extracellular signal-regulated kinase (ERK) and Akt are intact in CARMA1-, BCL10-, or MALT1-deficient lymphocytes, activation of NF-κB and JNK signaling pathways is markedly impaired (6, 24-26). This is manifested in defective lymphocyte proliferation and survival and in reduced immune responses.While the events leading to the activation of the IKK signaling complex downstream of CARMA1 have been well characterized, the signals that down-modulate this pathway are less well understood. Studies of BCL10 turnover have yielded some possible mechanisms (34). After cell activation, BCL10 is posttranslationally modified by both phosphorylation (possibly via IKKβ or CaMKII) and polyubiquitination (polyUb) and undergoes degradation that results in the down-modulation of NF-κB activity. Several ubiquitin protein ligases (E3s), including Itch, NEDD4, cIAP2, and βTrCP, have been reported to drive BCL10 ubiquitination in lymphocytes and to promote its degradation through either lysosomal or proteasomal pathways (7, 12, 27, 37). Overexpression of such E3s downregulates BCL10-dependent pathways, including NF-κB and the production of interleukin-2. Interestingly, antigen receptor-induced phosphorylation and degradation of BCL10 is not observed in the absence of CARMA1 (12), indicating a role for CARMA1 in BCL10 turnover.In this report, we demonstrate that endogenous CARMA1 is directly ubiquitinated and degraded by the proteasome in AR-activated lymphocytes. Structure-function analyses showed that the primary targets for ubiquitination within CARMA1 were localized within the MAGUK region. Mutation of all lysine residues (potential ubiquitin modification targets) to arginines within the MAGUK of CARMA1 produced a hyperactive molecule that promoted high NF-κB and JNK activation levels. Unlike the wild-type (WT) CARMA1 molecule, a lysine-to-arginine mutant CARMA1 was not modified by polyUb chains upon cell activation and had a resulting increase in protein stability. We identified a region between the SH3 and GUK domains that is highly similar to a region (termed the Hook region) that regulates the conformation of the MAGUK protein PSD-95. Notably, deletion of this Hook region was sufficient to trigger polyUb of CARMA1 as well as PSD-95 and Dlgh1, other MAGUK family proteins. These data suggest that activation of CARMA1 initiates a feedback mechanism controlled by the MAGUK domain that triggers ubiquitination and degradation of the CARMA1 signalosome, thereby limiting NF-κB and JNK signaling.     

Selenite reduction by the thioredoxin system: kinetics and identification of protein-bound selenide

Selenite (SeO(3)(2-)) assimilation into a bacterial selenoprotein depends on thioredoxin (trx) reductase in Esherichia coli, but the molecular mechanism has not been elucidated. The mineral-oil overlay method made it possible to carry out anaerobic enzyme assay, which demonstrated an initial lag-phase followed by time-dependent steady NADPH consumption with a positive cooperativity toward selenite and trx. SDS-PAGE/autoradiography using (75)Se-labeled selenite as substrate revealed the formation of trx-bound selenium in the reaction mixture. The protein-bound selenium has metabolic significance in being stabilized in the divalent state, and it also produced the selenopersulfide (-S-SeH) form by the catalysis of E. coli trx reductase (TrxB).     

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Background

Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.

Results

Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.

Conclusions

Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.     

Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil

The reductive pyrimidine catabolic pathway is absent in Escherichia coli. However, the bacterium contains an enzyme homologous to mammalian dihydropyrimidine dehydrogenase. Here, we show that E. coli dihydropyrimidine dehydrogenase is the first member of a novel NADH-dependent subclass of iron-sulfur flavoenzymes catalyzing the conversion of uracil to 5,6-dihydrouracil in vivo.     

Comparative survey of go/no-go results to identify the inhibitory control ability change of Japanese children

This research, conducted in 1998 and 2008, uses go/no-go data to investigate the fundamentals of cognitive functioning in the inhibitory control ability of Japanese children. 844 subjects from kindergarten to junior high school participated in go/no-go task experiments. Performance of go/no-go tasks, which are frequently used to investigate response inhibition, measures a variety of cognitive components besides response inhibition. With normal brain development, the ability to inhibit responses improves substantially in adolescence. An increase over time in the error rate during the go/no-go tasks of subjects of the same age indicates that these processes are not functioning properly. Comparisons between the 1998 and 2008 data revealed several differences in error rates. In 2008, there were increases in the number of errors in groups from each age range. The comparison also revealed that overall error rates peaked at later ages in the 2008 subjects. Taken together, these results show changing conditions in the inhibitory function of the prefrontal cortex. However, the reason for these changing conditions remains unclear. While a lifestyle questionnaire revealed several differences in factors such as bedtimes and hours spent watching TV, analysis did not reveal a significant correlation.     

High Salt Intake Damages the Heart through Activation of Cardiac (Pro) Renin Receptors Even at an Early Stage of Hypertension

Objective

It has not yet been fully elucidated whether cardiac tissue levels of prorenin, renin and (P)RR are activated in hypertension with a high salt intake. We hypothesized that a high salt intake activates the cardiac tissue renin angiotensin system and prorenin-(pro)renin receptor system, and damages the heart at an early stage of hypertension.

Methods

Wistar Kyoto rats (WKY) and spontaneously hypertensive rats (SHR) received regular (normal-salt diet, 0.9%) and high-salt (8.9%) chow for 6 weeks from 6 to 12 weeks of age. The systolic blood pressure, plasma renin activity (PRA) and plasma angiotensin II concentration were measured, and the protein expressions of prorenin, (pro)renin receptor, angiotensinogen, angiotensin II AT1 receptor, ERK1/2, TGF-β, p38MAPK and HSP27 in the myocardium were investigated. The cardiac function was assessed by echocardiography, and histological analysis of the myocardium was performed.

Results

The high-salt diet significantly increased the systolic blood pressure, and significantly reduced the PRA and plasma angiotensin II concentration both in the WKYs and SHRs. Cardiac expressions of prorenin, renin, (P)RR, angiotensinogen, angiotensin II AT1 receptor, phosphorylated (p)-ERK1/2, p-p38MAPK, TGF-β and p-HSP27 were significantly increased by the high salt diet both in the WKYs and SHRs. The high-salt diet significantly increased the interventricular septum thickness and cardiomyocyte size, and accelerated cardiac interstitial and perivascular fibrosis both in the WKYs and SHRs. On the other hand, dilatation of left ventricular end-diastolic dimension and impairment of left ventricular fractional shortening was shown only in salt loaded SHRs.

Conclusion

The high-salt diet markedly accelerated cardiac damage through the stimulation of cardiac (P)RR and angiotensin II AT1 receptor by increasing tissue prorenin, renin and angiotensinogen and the activation of ERK1/2, TGF-β, p38MAPK and HSP27 under higher blood pressure.