Disulfide formation and stability of a cysteine-rich repeat protein from Helicobacter pylori

Helicobacter pylori cysteine-rich proteins (Hcps) are disulfide-containing repeat proteins. The repeating unit is a 36-residue, disulfide-bridged, helix-loop-helix motif. We use the protein HcpB, which has four repeats and four disulfide bridges arrayed in tandem, as a model to determine the thermodynamic stability of a disulfide-rich repeat protein and to study the formation and the contribution to stability of the disulfide bonds. When the disulfide bonds are intact, the chemical unfolding of HcpB at pH 5 is cooperative and can be described by a two-state reaction. Thermal unfolding is reversible between pH 2 and 5 and irreversible at higher pH 5. Differential scanning calorimetry shows noncooperative structural changes preceding the main thermal unfolding transition. Unfolding of the oxidized protein is not an all-or-none two-state process, and the disulfide bonds prevent complete unfolding of the polypeptide chain. The reduced protein is significantly less stable and does not unfold in a cooperative way. During oxidative refolding of the fully reduced protein, all the possible disulfide intermediates with a correct disulfide bond are formed. Formation of "wrong" (non-native) disulfide bonds could not be demonstrated, indicating that the reduced protein already has some partial repeating structure. There is a major folding intermediate with disulfides in the second, third, and fourth repeat and reduced cysteines in the first repeat. Disulfide formation in the first repeat limits the overall rate of oxidative refolding and contributes about half of the thermodynamic stability to native HcpB, estimated as 27 kJ mol(-1) at 25 degrees C and pH 7. The high contribution to stability of the first repeat may be explained by the repeat acting as a cap to protect the hydrophobic interior of the molecule.     

Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics

A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L. johnsonii. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis cluster. On microarray hybridizations, Lactobacillus gasseri strains showed a shift to significantly lower fluorescence intensities than the L. johnsonii test strains, and only genes encoding very conserved cellular functions from L. acidophilus hybridized to the L. johnsonii array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of L. johnsonii with L. gasseri, L. acidophilus, and Lactobacillus delbrueckii; moderate synteny with Lactobacillus casei; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the L. acidophilus group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.     

Male reproductive toxicity of trichloroethylene: sperm protein oxidation and decreased fertilizing ability

The objective of the present study was to characterize and investigate potential mechanisms for the male reproductive toxicity of trichloroethylene (TCE). Male rats exposed to TCE in drinking water exhibited a dose-dependent decrease in the ability to fertilize oocytes from untreated females. This reduction in fertilizing ability occurred in the absence of treatment-related changes in combined testes/epididymides weight, sperm concentration, or sperm motility. In addition, flow cytometric analysis showed that there were no treatment-related differences in sperm mitochondrial membrane potential or acrosomal stability. TCE caused slight histological changes in efferent ductule epithelium, coinciding with the previously reported ductule localization of cytochrome P450 2E1. However, no alterations were noted in the testis or in any segment of the epididymis. Because there were no treatment-related changes to sperm indices and no clear pathological lesions to explain the reduced fertilization, the present study investigated TCE-mediated sperm oxidative damage. Oxidized proteins were detected by immunochemical techniques following the derivatization of sperm protein carbonyls with dinitrophenyl hydrazine. Immunochemical staining of whole, intact sperm showed the presence of halos of oxidized proteins around the head and midpiece of sperm from TCE-treated animals. The presence of oxidized sperm proteins was confirmed by Western blotting using in vitro-oxidized sperm as a positive control. Thiobarbituric acid reactive substances analyses showed a dose-dependent increase in the level of lipid peroxidation in sperm from treated animals, as well. Oxidative damage to sperm may explain the diminished fertilizing capacity of exposed animals and provide another mechanism by which TCE can adversely affect reproductive capabilities in the male.     

Pigment stratigraphy and trophic status: An evaluation of radionuclide‐dated lacustrine sediment

Sediment cores from the profundal region of relatively young (ca. 45 years), warm‐monomictic Lake Vechten were dated with Cs and ²¹⁰Pb and analyzed for major carotenoids, chlorophyll, and pheophytin. Vertical sediment accretion rates determined from a clay/sand horizon and from the radionuclide datings varied between 0.60 and 0.74 cm/year. Sedimentation rates based on paniculate matter collected in sediment traps agreed with results of the ¹³⁷Cs method with average values of respectively 2.9 and 2.3 kg dry weight m^‐2 year^‐1. It was concluded that the profundal sediment is fairly undisturbed. Pigments showed a severalfold increase from the deepest to the superficial sediment layers. Their profiles were compared with limnological data obtained during previous studies of Lake Vechten. Evidence was provided that the distribution of pigments reflected grossly the trophic history of the lake, which became more eutrophic during the last two decades. Pigment analyses of sediment cores may be a useful tool to rapidly obtain rough basic information on the recent trophic development of stratified lakes liable to eutrophication.     

Time course and extent of functional recovery during the first postoperative year after minimally invasive total hip arthroplasty with two different surgical approaches--a randomized controlled trial

While others have reported short-term comparisons between various minimally invasive surgical (MIS) approaches to total hip arthroplasty (THA) and their conventional analogues, longer-term data is lacking, as is information indicating whether MIS approaches to THA provide a biomechanically complete recovery. Furthermore, different MIS approaches have not been compared. Our approaches of interest were a one-incision modified Watson-Jones, and a two-incision approach. Hypotheses: (1) There are significant differences in gait recovery patterns between the two surgical groups and (2) THA subjects have significant differences in function one year after surgery compared to control subjects. To test these hypotheses, THA candidates (n=26) were randomized to receive one of these MIS approaches and evaluated preoperatively, and postoperatively at 3 weeks, and at 3, 6 and 12 months. Evaluations included three-dimensional gait analysis and 24-hour step-counts. The same data were obtained from 25 control subjects. Recovery time-course was assessed using repeated measures ANOVA. T-tests were used to compare controls with the pooled group of THA subjects. We found no differences between the two THA surgical groups regarding the time-course of recovery (p≥0.591). Although recovery was statistically complete by 3 months postoperatively for all variables, there were significant differences from controls at 12 months. Most notably, the external hip adduction moment, which reflects hip abductor function, was more than one standard deviation below normal (p<0.001). THA subject inactivity could not explain the gait differences, since one year after surgery daily step counts were not significantly different from controls (p=0.346). More work is necessary to determine ways to improve biomechanical outcomes for today's patients with high expectations for function and implant longevity.     

Targeting neddylation induces DNA damage and checkpoint activation and sensitizes chronic lymphocytic leukemia B cells to alkylating agents

Microenvironment-mediated upregulation of the B-cell receptor (BCR) and nuclear factor-κB (NF-κB) signaling in CLL cells resident in the lymph node and bone marrow promotes apoptosis evasion and clonal expansion. We recently reported that MLN4924 (pevonedistat), an investigational agent that inhibits the NEDD8-activating enzyme (NAE), abrogates stromal-mediated NF-κB pathway activity and CLL cell survival. However, the NAE pathway also assists degradation of multiple other substrates. MLN4924 has been shown to induce DNA damage and cell cycle arrest, but the importance of this mechanism in primary neoplastic B cells has not been studied. Here we mimicked the lymph node microenvironment using CD40 ligand (CD40L)-expressing stroma and interleukin-21 (IL-21) to find that inducing proliferation of the primary CLL cells conferred enhanced sensitivity to NAE inhibition. Treatment of the CD40-stimulated CLL cells with MLN4924 resulted in deregulation of Cdt1, a DNA replication licensing factor, and cell cycle inhibitors p21 and p27. This led to DNA damage, checkpoint activation and G2 arrest. Alkylating agents bendamustine and chlorambucil enhanced MLN4924-mediated DNA damage and apoptosis. These events were more prominent in cells stimulated with IL-21 compared with CD40L alone, indicating that, following NAE inhibition, the culture conditions were able to direct CLL cell fate from an NF-κB inhibition to a Cdt1 induction program. Our data provide insight into the biological consequences of targeting NAE in CLL and serves as further rationale for studying the clinical activity of MLN4924 in CLL, particularly in combination with alkylating agents.The ubiquitin–proteasome system ensures timely destruction of intracellular proteins. In the past decade, protein degradation has become a pharmacologic target: proteasome inhibitors (e.g., bortezomib) are currently being used in therapy of plasma and B-cell neoplasms. Inhibiting the ubiquitination process upstream of the proteasome represents a promising alternative approach. In this regard, ubiquitin-like modifiers (Ubl) such as NEDD8, ISG15 (interferon-stimulated gene 15), and SUMO (small ubiquitin-like modifier) regulate diverse cellular processes, depending on the exact Ubl and substrate involved. One such Ubl, NEDD8, modulates Cullin-RING E3 ubiquitin ligase (CRL) activity through covalent modification, neddylation.¹Chronic lymphocytic leukemia (CLL) B cells are highly dependent on cell–cell interactions in the lymph node and bone marrow microenvironment.² Stromal-mediated upregulation of B-cell receptor (BCR) and nuclear factor-κB (NF-κB) signaling in CLL cells resident in these niches ensures apoptosis evasion and promotes proliferation and clonal expansion.³ We recently reported that MLN4924 (pevonedistat), an investigational inhibitor of the NEDD8-activating enzyme (NAE), successfully abrogates NF-κB pathway activity, CLL cell survival and chemoresistance in an in vitro co-culture model that mimics the lymph node microenvironment.⁴ NAE adenylates NEDD8 at its C-terminus and allows its transfer to a specific cysteine within NAE, thus initiating a process of neddylation. Active NEDD8 is then transferred to the cysteine of the ubiquitin-conjugating enzyme (E2) specific for the pathway (Ubc12), and is finally conjugated to the CRLs.⁵ CRLs are responsible for ubiquitination and degradation of their substrate proteins. NAE–NEDD8 interaction is disrupted when a covalent adduct is formed between NEDD8 and MLN4924.⁶ Ultimately, this prevents ubiqitination of CRL target proteins, extending their half-life, thereby increasing levels of inhibitor of NF-κB (IκB), a negative pathway modulator.^{6, 7, 8} However, CRLs process a variety of proteins that, in addition to signal transduction (IκBα, DEPTOR, β-catenin, hypoxia-inducible factor-1α) and apoptosis (NOXA, Bim_EL), are important regulators of cell cycle and DNA replication (e.g., p21^Cip1, p27^Kip1, Wee1, Cyclin D1 and Cdt1).^{9, 10, 11, 12, 13, 14} Because of the diversity of CRL target substrates, the biological consequences of their inhibition are tissue dependent. In adherent solid tumor cell lines, inhibition of neddylation resulted in characteristic deregulation of cell cycle with DNA re-replication, checkpoint activation and cell cycle arrest, thought to be secondary to stabilization of the replication-licensing protein Cdt1 (chromatin licensing and DNA replication factor 1) and cyclin-dependent kinase (CDK) inhibitor p21^Cip1.^{11, 15, 16, 17} However, the importance of this mechanism in primary neoplastic B cells has not been studied. Here we determined that, under the conditions promoting cell replication and growth, MLN4924 induces checkpoint activation and cell cycle arrest in primary CLL B -cells. This mechanism complements abrogation of NF-κB pathway activity to induce apoptosis in CLL.     

Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I)

The proton-pumping NADH:ubiquinone oxidoreductase is the first of the respiratory chain complexes in many bacteria and the mitochondria of most eukaryotes. In general, the bacterial complex consists of 14 different subunits. In addition to the homologues of these subunits, the mitochondrial complex contains approximately 31 additional proteins. While it was shown that the mitochondrial complex is assembled from distinct intermediates, nothing is known about the assembly of the bacterial complex. We used Escherichia coli mutants, in which the nuo-genes coding the subunits of complex I were individually disrupted by an insertion of a resistance cartridge to determine whether they are required for the assembly of a functional complex I. No complex I-mediated enzyme activity was detectable in the mutant membranes and it was not possible to extract a structurally intact complex I from the mutant membranes. However, the subunits and the cofactors of the soluble NADH dehydrogenase fragment of the complex were detected in the cytoplasm of some of the nuo-mutants. It is discussed whether this fragment represents an assembly intermediate. In addition, a membrane-bound fragment exhibiting NADH/ferricyanide oxidoreductase activity and containing the iron-sulfur cluster N2 was detected in one mutant.     

Paternal chromosome incorporation into the zygote nucleus is controlled by maternal haploid in Drosophila

maternal haploid (mh) is a strict maternal effect mutation that causes the production of haploid gynogenetic embryos (eggs are fertilized but only maternal chromosomes participate in development). We conducted a cytological analysis of fertilization and early development in mh eggs to elucidate the mechanism of paternal chromosome elimination. In mh eggs, as in wild-type eggs, male and female pronuclei migrate and appose, the first mitotic spindle forms, and both parental sets of chromosomes congress on the metaphase plate. In contrast to control eggs, mh paternal sister chromatids fail to separate in anaphase of the first division. As a consequence the paternal chromatin stretches and forms a bridge in telophase. During the first three embryonic divisions, damaged paternal chromosomes are progressively eliminated from the spindles that organize around maternal chromosomes. A majority of mh embryos do not survive the deleterious presence of aneuploid nuclei and rapidly arrest their development. The rest of mh embryos develop as haploid gynogenetic embryos and die before hatching. The mh phenotype is highly reminiscent of the early developmental defects observed in eggs fertilized by ms(3)K81 mutant males and in eggs produced in incompatible crosses of Drosophila harboring the endosymbiont bacteria Wolbachia.