Dealing with DNA lesions: When one cell cycle is not enough

Subversion of genome integrity fuels cellular adaptation and is a prerequisite for organismal evolution, yet genomic lesions are also the harmful driving force of cancer and other age-related human diseases. Genome integrity maintenance is inherently linked to genome organization and nuclear architecture, which are substantially remodeled during the cell cycle. Here we discuss recent findings on how actively dividing cells cope with endogenous genomic lesions that occur frequently at repetitive, heterochromatic, and late replicating regions as byproducts of genome duplication. We discuss how such lesions, rather than being resolved immediately when they occur, are dealt with in subsequent cell cycle phases, and even after mitotic cell division, and how this in turn affects genome organization, stability, and function.     

When too much is not enough: obsessive-compulsive disorder as a pathology of stopping, rather than starting

Background

In obsessive-compulsive disorder (OCD), individuals feel compelled to repeatedly perform security-related behaviors, even though these behaviours seem excessive and unwarranted to them. The present research investigated two alternative ways of explaining such behavior: (1) a dysfunction of activation—a starting problem—in which the level of excitation in response to stimuli suggesting potential danger is abnormally strong; versus (2) a dysfunction of termination—a stopping problem—in which the satiety-like process for shutting down security-related thoughts and actions is abnormally weak.

Method

In two experiments, 70 patients with OCD (57 with washing compulsions, 13 with checking compulsions) and 72 controls were exposed to contamination cues—immersing a hand in wet diapers —and later allowed to wash their hands, first limited to 30 s and then for as long as desired. The intensity of activation of security motivation was measured objectively by change in respiratory sinus arrythmia. Subjective ratings (e.g., contamination) and behavioral measures (e.g., duration of hand washing) were also collected.

Results

Compared to controls, OCD patients with washing compulsions did not differ significantly in their levels of initial activation to the threat of contamination; however, they were significantly less able to reduce this activation by engaging in the corrective behavior of hand-washing. Further, the deactivating effect of hand-washing in OCD patients with checking compulsions was similar to that for controls, indicating that the dysfunction of termination in OCD is specific to the patient''s symptom profile.

Conclusions

These results are the first to show that OCD is characterized by a reduced ability of security-related behavior to terminate motivation evoked by potential danger, rather than a heightened initial sensitivity to potential threat. They lend support to the security-motivation theory of OCD (Szechtman & Woody, 2004) and have important implications both for research into the biological mechanisms underlying OCD and for the development of new treatment approaches.     

Thoughts of a Travelling Ecologist, 5. When the "worst case" is not bad enough

The condition of our Earth is changing,and it ischanging due to human dominance.We realised thatour influence on biota is overwhelming,building up toa mass extinction,the sixth in the history of life onEarth.The later this realisation is turned into action todecrease our fatal influence,the worse are the chancesof the survival of the human race.How can we fail?Oneplausible scenario is that this can happen via the loss ofecological services     

When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees.

The geranyl-modified tryptophan residue is crucial for ComXRO-E-2 pheromone biological activity

The ComX pheromone is an isoprenoidal oligopeptide containing a modified tryptophan residue, which stimulates natural genetic competence in gram-positive bacteria, Bacillus. We have reported the structure of the ComX_RO-E-2 pheromone, which is produced by the RO-E-2 strain of Bacillus subtilis. ComX_RO-E-2 analogs with substituted amino acids and isoprenoid modified tryptophan residues (e.g., prenyl, geranyl, and farnesyl), were synthesized and examined for biological activity. These results indicate that Phe-Trp^∗(Ger)-NH₂ is the minimum pharmacophore of the ComX_RO-E-2 pheromone. Furthermore, the length of the isoprenoid moiety (i.e., modification style), and the presence of double bonds, are crucial for biological activity. The modification style of the ComX pheromone is more important than the peptide sequence with respect to biological activity.     

When sex is not enough: ecological correlates of resprouting capacity in congeneric tropical forest shrubs

In moist tropical forests resprouting may be an important component of life history, contributing to asexual reproduction through the clonal spread of individuals derived from shoot fragments. However, in contrast to other ecosystems where resprouting is common, the ecological correlates of resprouting capacity in tropical forests remain largely unexplored. In this study we characterized shade tolerance, resprouting capacity and sexual reproductive success of eight co-occurring Piper species from lowland forests of Panama. In field experiments we found that shade-tolerant Piper species had a higher capacity to regenerate from excised or pinned stem fragments than light-demanding species in both gap and understory light conditions. In contrast, shade-tolerant species had lower recruitment probabilities from seeds, as a consequence of lower initial seed viability, and lower seedling emergence rates. All Piper species needed gap conditions for successful seedling establishment. Of 8,000 seeds sown in the understory only 0.2% emerged. In gaps, seed germination of light-demanding species was between 10 and 50%, whereas for shade-tolerant species it was 0.5–9.8%. We propose that the capacity to reproduce asexually from resprouts could be adaptive for shade-tolerant species that are constantly exposed to damage from falling litter in the understory. Resprouting may allow Piper populations to persist and spread despite the high rate of pre-dispersal seed predation and low seed emergence rates. Across Piper species, we detected a trade-off between resprouting capacity and the annual viable seed production per plant but not with annual seed mass produced per plant. This suggests that species differences in sexual reproductive success may not necessarily result from differential resource allocation. Instead we suggest that low sexual reproductive success in the understory may in part reflect reduced genetic diversity in populations undergoing clonal growth, resulting in self-fertilization and in-breeding depression.     

Protein array staining methods for undefined protein content, manufacturing quality control, and performance validation

Methods to assess the quality and performance of protein microarrays fabricated from undefined protein content are required to elucidate slide-to-slide variability and interpolate resulting signal intensity values after an interaction assay. We therefore developed several simple total- and posttranslational modification-specific, on-chip staining methods to quantitatively assess the quality of gel element protein arrays manufactured with whole-cell lysate in vitro protein fractions derived from two-dimensional liquid-phase fractionation (PF2D) technology. A linear dynamic range of at least 3 logs was observed for protein stains and immobilized protein content, with a lower limit of detection at 8 pg of protein per gel element with Deep Purple protein stain and a field-portable microarray imager. Data demonstrate the successful isolation, separation, transfer, and immobilization of putative transmembrane proteins from Yersinia pestis KIM D27 with the combined PF2D and gel element array method. Internal bovine serum albumin standard curves provided a method to assess on-chip PF2D transfer and quantify total protein immobilized per gel element. The basic PF2D array fabrication and quality assurance/quality control methods described here therefore provide a standard operating procedure and basis for developing whole-proteome arrays for interrogating host-pathogen interactions, independent of sequenced genomes, affinity tags, or a priori knowledge of target cell composition.     

ADP-ribosyltransferase from beef liver which ADP-ribosylates elongation factor-2

Fragment A of diphtheria toxin and Pseudomonas toxin A intoxicate cells by ADP-ribosylating the diphthamide residue of elongation factor-2 (EF-2) resulting in an inhibition of protein synthesis [1-3]. A cellular enzyme from polyoma virus transformed baby hamster kidney (pyBHK) cells ADP-ribosylates EF-2 in an identical manner [4]. Here we describe a similar cellular enzyme from beef liver which transfers [adenosine-14C]ADP-ribose from NAD to EF-2. The 14C-label can be removed from the EF-2 by snake venom phosphodiesterase as a soluble product which comigrates with AMP on TLC plates, indicating the 14C-label is present on EF-2 as monomeric units of ADP-ribose. Furthermore, the forward transferase reaction catalyzed by the beef liver ADP-ribosyltransferase is reversible by excess diphtheria toxin fragment A, with the formation of 14C-labeled NAD, indicating that both transferases ADP-ribosylate the same site on the diphthamide residue of EF-2. Thus, beef liver and pyBHK mono(ADP-ribosyl)transferases both modify the diphthamide residue of EF-2, in a manner identical to diphtheria toxin fragment A and Pseudomonas toxin A. These results suggest the cellular enzyme is probably ubiquitous among eukaryotic cells.     

UBE2D2 is not involved in MuRF1-dependent muscle wasting during hindlimb suspension

The Ubiquitin Proteasome System (UPS) is mainly responsible for the increased protein breakdown observed in muscle wasting. The E3 ligase MuRF1 is so far the only enzyme known to direct the main contractile proteins for degradation (i.e. troponin I, myosin heavy chains and actin). However, MuRF1 does not possess any catalytic activity and thus depends on the presence of a dedicated E2 for catalyzing the covalent binding of polyubiquitin (polyUb) chains on the substrates. The E2 enzymes belonging to the UBE2D family are commonly used for in vitro ubiquitination assays but no experimental data suggesting their physiological role as bona fide MuRF1-interacting E2 enzymes are available. In this work, we first found that the mRNA levels of critical E3 enzymes implicated in the atrophying program (MuRF1, MAFbx, Nedd4 and to a lesser extent Mdm2) are tightly and rapidly controlled during the atrophy (up regulation) and recovery (down regulation) phases in the soleus muscle from hindlimb suspended rats. By contrast, E3 ligases (Ozz, ASB2β and E4b) implicated in other processes (muscle development or regeneration) poorly responded to atrophy and recovery. UBE2B, an E2 enzyme systematically up regulated in various catabolic situations, was controlled at the mRNA levels like the E3s implicated in the atrophying process. By contrast, UBE2D2 was progressively repressed during atrophy and recovery, which makes it a poor candidate for a role during muscle atrophy. In addition, UBE2D2 did not exhibit any affinity with MuRF1 using either yeast two-hybrid or Surface Plasmon Resonance (SPR) approaches. Finally, UBE2D2 was unable to promote the degradation of the MuRF1 substrate α-actin in HEK293T cells, suggesting that no functional interaction exists between these enzymes within a cellular context. Altogether, our data strongly suggest that UBE2D2 is not the cognate ubiquitinating enzyme for MuRF1 and that peculiar properties of UBE2D enzymes may have biased in vitro ubiquitination assays.     

CCN2 is not required for skin development

Mice lacking the pro-adhesive matricellular protein connective tissue growth factor (CTGF/CCN2) display an embryonic lethal phenotype due to defects in bone and cartilage. However, the specific role of CCN2 in skin development is unknown. Here, we generated mice deleted for CCN2 in the entire body (using a cre/lox system in which CCN2 is deleted in the entire body due to the presence of a constitutively expressed cre recombinase). We found that CCN2 was not required for the development of skin as defined by skin thickness measurements, trichrome staining and immunostaining with anti-CD31 (to detect endothelial cells) and anti-α−SMA (to detect smooth muscle cells and pericytes) antibodies. Thus, although recently we have shown that CCN2 is required for fibrogenesis in postnatal mice, CCN2 is not required for skin development during embryogenesis.     

Ruthenium (II) tris-bathophenanthroline disulfonate is well suitable for Tris-Glycine PAGE but not for Bis-Tris gels

Pre-cast bis(2-hydroxyethyl)iminotris(hydroxymethyl)methane (Bis-Tris) gels have proven to be very suitable for pre-fractionation for LC-MS/MS analysis due to high reliability and long stability. To visualize proteins within gels fluorescence dyes proved to be a good tradeoff between sensitivity and MS-compatibility. The custom-made ruthenium dye represents a low-cost alternative regarding fluorescence-based protein visualization with high sensitivity. We demonstrate, that this dye is incompatible with Bis-Tris gels, while using Tris-Glycine gels a competitive sensitivity to commercially available stains can be achieved.     

Cytochrome b561 is not fatty acylated but acetylated at amino terminus in chromaffin vesicle membranes: an approach for the identification of posttranslational modification of transmembrane proteins

Summary.  We examined the nature of the posttranslational modification of bovine cytochrome b ₅₆₁, a membrane-spanning protein and an essential component of neuroendocrine secretory vesicles. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS) showed two populations in the partially digested fragments of cytochrome b ₅₆₁, which were obtained by controlled treatment of cytochrome b ₅₆₁-proteoliposomes with trypsin. One population, containing the posttranslationally modified amino-terminal region, showed molecular masses which were by about 40 Da larger than the theoretical molecular masses. The other population, without the modified amino-terminal region, showed a reasonable matching with the theoretical masses. This result suggested that the posttranslational modification occurred only in the amino-terminal region. The amino-terminal peptide was isolated by tryptic peptide mapping followed by treatment with acylamino-acid-releasing enzyme. Amino acid sequence and MALDI-TOF-MS analyses of the amino-terminal peptide showed that the initial Met residue was acetylated. There was no other posttranslational modification in the amino-terminal region, such as covalent fatty acylation through an ester linkage to Ser or Thr residues. Received May 9, 2002; accepted July 26, 2002; published online May 21, 2003 RID="*" ID="*" Correspondence and reprints: Department of Molecular Science, Graduate School of Science and Technology, Kobe University, Rokkodai-cho 1-1, Nada-ku, Hyogo 657-8501, Japan.     

Quantitative and qualitative 2D electrophoretic analysis of differentially expressed mitochondrial proteins from five mouse organs

Mitochondria fulfill many tissue‐specific functions in cell metabolism. We set out to identify differences in the protein composition of mitochondria from five tissues frequently affected by mitochondrial disorders. The proteome of highly purified mitochondria from five mouse organs was separated by high‐resolution 2DE. Tissue‐specific spots were identified through nano‐LC/ESI‐MS/MS and quantified by densitometry in ten biological replicates. We identified 87 consistently deviating spots representing 48 proteins. The percentage of variant spots ranged between 4.2% and 6.0%; 21 proteins having tissue‐specific isospots. Consistent tissue‐specific processing/regulation was seen for carbamoyl‐phosphate‐synthase, aldehyde‐dehydrogenase 2, ATP‐synthase α‐chain, and isocitrate‐dehydrogenase α‐subunit. Thirty tissue‐specific proteins were associated with mitochondrial disorders in humans. We further identified alcohol‐dehydrogenase, catalase, quinone‐oxidoreductase, cyclophilin‐A, and Upf0317, a potential biotin‐carboxyl‐carrier protein, which had not been annotated as “mitochondrial” in Gene Ontology or MitoCarta databases. Their targeting to the mitochondria was verified by transfection of full‐length GFP‐tagged plasmids. Given the high evolutionary conservation of mitochondrial metabolic pathways, these data further annotate the mitochondrial proteome and advance our understanding of the pathophysiology and tissue‐specificity of symptoms seen in patients with mitochondrial disorders. The generation of 2D electrophoretic maps of the mitochondrial proteome using tissue specimens in the milligram range facilitates this technique for clinical applications and biomarker research.     

A study in glycation of a therapeutic recombinant humanized monoclonal antibody: where it is, how it got there, and how it affects charge-based behavior

The glycated form of a basic recombinant humanized monoclonal antibody (rhuMAb) was separated and quantitated by boronate affinity chromatography using optimized shielding reagents. Characterization on the isolated glycated material by peptide mapping analysis, using liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS) sequencing techniques, identified eight reactive lysine primary amine sites. The glycation reaction extent was similar among the various reactive sites, ranging from approximately 1 to 12%, and a single histidine residue separated the most and least reactive sites. Boronate chromatography run in a linear gradient mode separated monoglycated rhuMAb from higher order glycated species and indicated that the majority ( approximately 90%) of glycated rhuMAb is monoglycated. Low-level glycation on a heavy chain lysine located within a complementarity-determining region (CDR) did not significantly affect binding activity in potency measurements. The glycated forms also behaved as slightly more acidic than the nonglycated antibody in charge-based separation techniques, observable by capillary isoelectric focusing (cIEF) and ion exchange chromatography (IEC). The boronate column has significantly increased retention of aggregated rhuMAb material under separation conditions optimized for the monomer form. Recombinant protein glycation initially occurred during production in mammalian cell culture, where feed sugar and protein concentrations contribute to the total overall glycation on this antibody product.     

An alpha-subunit loop structure is required for GM2 activator protein binding by beta-hexosaminidase A

The alpha- and/or beta-subunits of human beta-hexosaminidase A (alphabeta) and B (betabeta) are approximately 60% identical. In vivo only beta-hexosaminidase A can utilize GM2 ganglioside as a substrate, but requires the GM2 activator protein to bind GM2 ganglioside and then interact with the enzyme, placing the terminal GalNAc residue in the active site of the alpha-subunit. A model for this interaction suggests that two loop structures, present only in the alpha-subunit, may be critical to this binding. Three amino acids in one of these loops are not encoded in the HEXB gene, while four from the other are removed posttranslationally from the pro-beta-subunit. Natural substrate assays with forms of hexosaminidase A containing mutant alpha-subunits demonstrate that only the site that is removed from the beta-subunit during its maturation is critical for the interaction. Our data suggest an unexpected biological role for such proteolytic processing events.     

Rat CYP2D2, not 2D1, is functionally conserved with human CYP2D6 in endogenous morphine formation

The assumption that CYP2D1 is the corresponding rat cytochrome to human CYP2D6 has been revisited using recombinant proteins in direct enzyme assays. CYP2D1 and 2D2 were incubated with known CYP2D6 substrates, the three morphine precursors thebaine, codeine and (R)-reticuline. Mass spectrometric analysis showed that rat CYP2D2, not 2D1, catalyzed the 3-O-demethylation reaction of thebaine and codeine. In addition, CYP2D2 incubated with (R)-reticuline generated four products corytuberine, pallidine, salutaridine and isoboldine while rat CYP2D1 was completely inactive. This intramolecular phenol-coupling reaction follows the same mechanism as observed for CYP2D6. Michaelis-Menten kinetic parameters revealed high catalytic efficiencies for rat CYP2D2. These findings suggest a critical evaluation of other commonly accepted, however untested, CYP2D1 substrates.