Biochemical and structural consequences of a glycine deletion in the α-8 helix of protoporphyrinogen oxidase

A rare Gly210 deletion in protoporphyrinogen oxidase (PPO) was recently discovered in herbicide-resistant Amaranthus tuberculatus. According to the published X-ray structure of Nicotiana tabacum PPO, Gly210 is adjacent to, not in, the PPO active site, so it is a matter of interest to determine why its deletion imparts resistance to herbicides. In our kinetic experiments, this deletion did not affect the affinity of protoporphyrinogen IX nor the FAD content, but decreased the catalytic efficiency of the enzyme. The suboptimal K_cat was compensated by a significant increase in the K_is for inhibitors and a switch in their interactions from competitive to mixed-type inhibition. In our protein modeling studies on herbicide-susceptible PPO and resistant PPO, we show that Gly210 plays a key role in the αL helix-capping motif at the C-terminus of the α-8 helix which helps to stabilize the helix. In molecular dynamics simulations, the deletion had significant architecture consequences, destabilizing the α-8 helix-capping region and unraveling the last turn of the helix, leading to enlargement of the active site cavity by ∼ 50%. This seemingly innocuous deletion of Gly210 of the mitochondrial PPO imparts herbicide resistance to this dual-targeted protein without severely affecting its normal physiological function, which may explain why this unusual mutation was the favored evolutionary path for achieving resistance to PPO inhibitors.     

Integrating titania enrichment,iTRAQ labeling,and Orbitrap CID‐HCD for global identification and quantitative analysis of phosphopeptides

Recent advances in MS instrumentation and progresses in phosphopeptide enrichment, in conjunction with more powerful data analysis tools, have facilitated unbiased characterization of thousands of site‐specific phosphorylation events. Combined with stable isotope labeling by amino acids in cell culture metabolic labeling, these techniques have made it possible to quantitatively evaluate phosphorylation changes in various physiological states in stable cell lines. However, quantitative phosphoproteomics in primary cells and tissues remains a major technical challenge due to the lack of adequate techniques for accurate quantification. Here, we describe an integrated strategy allowing for large scale quantitative profiling of phosphopeptides in complex biological mixtures. In this technique, the mixture of proteolytic peptides was subjected to phosphopeptide enrichment using a titania affinity column, and the purified phosphopeptides were subsequently labeled with iTRAQ reagents. After further fractionation by strong‐cation exchange, the peptides were analyzed by LC‐MS/MS on an Orbitrap mass spectrometer, which collects CID and high‐energy collisional dissociation (HCD) spectra sequentially for peptide identification and quantitation. We demonstrate that direct phosphopeptide enrichment of protein digests by titania affinity chromatography substantially improves the efficiency and reproducibility of phosphopeptide proteomic analysis and is compatible with downstream iTRAQ labeling. Conditions were optimized for HCD normalized collision energy to balance the overall peptide identification and quantitation using the relative abundances of iTRAQ reporter ions. Using this approach, we were able to identify 3557 distinct phosphopeptides from HeLa cell lysates, of which 2709 were also quantified from HCD scans.     

Prevalence of allosuckling behaviour in Subantarctic fur seal pups

Non-offspring maternal care should be rare due to the high costs of raising offspring, particularly lactation, but nonetheless occurs in a variety of taxa. Misguided parental care, associated with recognition errors and/or inattentiveness by lactating females, has been hypothesized as an explanation for allolactation in mammals. In an extension of this hypothesis, we suggest that milk-stealing is parasitism instigated by non-filial offspring, and that maternal behaviour is of secondary interest in an evolutionary context if she is unaware of the interaction. We provide evidence for frequent milk-stealing attempts by Subantarctic fur seal (Arctocephalus tropicalis) pups, including an example of sustained non-maternal care (> three months) for one pup during the confirmed absence of his mother, leading to a weaning mass equal to the population mean. We also present only the second account of fostering/twins in the species at this locality. We suggest that rather than the hitherto suggested rare and anomalous behaviour, milk-stealing behaviour (while not always successful) is common.     

Modeling Rett syndrome with stem cells

The discovery that somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) raised the exciting possibility of modeling diseases with patient-specific cells. Marchetto et?al. (2010) now use iPSC technology to generate, characterize, and treat an in?vitro model for the autism spectrum disorder Rett syndrome.     

Broad-Host-Range Plasmids for Red Fluorescent Protein Labeling of Gram-Negative Bacteria for Use in the Zebrafish Model System

To observe real-time interactions between green fluorescent protein-labeled immune cells and invading bacteria in the zebrafish (Danio rerio), a series of plasmids was constructed for the red fluorescent protein (RFP) labeling of a variety of fish and human pathogens. The aim of this study was to create a collection of plasmids that would express RFP pigments both constitutively and under tac promoter regulation and that would be nontoxic and broadly transmissible to a variety of Gram-negative bacteria. DNA fragments encoding the RFP dimeric (d), monomeric (m), and tandem dimeric (td) derivatives d-Tomato, td-Tomato, m-Orange, and m-Cherry were cloned into the IncQ-based vector pMMB66EH in Escherichia coli. Plasmids were mobilized into recipient strains by conjugal mating. Pigment production was inducible in Escherichia coli, Pseudomonas aeruginosa, Edwardsiella tarda, and Vibrio (Listonella) anguillarum strains by isopropyl-β-d-thiogalactopyranoside (IPTG) treatment. A spontaneous mutant exconjugant of P. aeruginosa PA14 was isolated that expressed td-Tomato constitutively. Complementation analysis revealed that the constitutive phenotype likely was due to a mutation in lacI^q carried on pMMB66EH. DNA sequence analysis confirmed the presence of five transitions, four transversions, and a 2-bp addition within a 14-bp region of lacI. Vector DNA was purified from this constitutive mutant, and structural DNA sequences for RFP pigments were cloned into the constitutive vector. Exconjugants of P. aeruginosa, E. tarda, and V. anguillarum expressed all pigments in an IPTG-independent fashion. Results from zebrafish infectivity studies indicate that RFP-labeled pathogens will be useful for the study of real-time interactions between host cells of the innate immune system and the infecting pathogen.The use of fluorescent proteins as probes has proven to be a vital tool in elucidating spatial and temporal patterns of gene expression, protein localization, and protein-protein interactions in vivo. In addition to well-known contributions to cell biology and biochemistry, the use of fluorescent proteins to label bacteria has provided insight into complex host-pathogen interactions and routes of entry (14, 23, 29).The zebrafish has become an attractive model for in vivo infection studies. As an optically clear organism at the embryo and larval developmental stages, zebrafish are amenable to visualization during challenge with fluorescently labeled pathogens. In addition, fertilization in the zebrafish occurs ex utero, thereby simplifying infection by either static immersion or microinjection. The visualization of infection in situ can be conducted on the whole embryo using confocal or wide-field epifluorescence microscopy, an approach not possible in other model systems. To date, several zebrafish infection models have been established employing both fish and mammalian pathogens, including Edwardsiella tarda (21), E. ictaluri (14, 23), Staphylococcus aureus (16), Streptococcus pyogenes and S. iniae (18), and Pseudomonas aeruginosa (4). Illustrating the value of fluorescently labeled bacteria in studies of microbial pathogenesis, Van der Sar and colleagues established the zebrafish as a model for Salmonella enterica serovar Typhimurium infections using DsRed-labeled bacteria (30). Similarly, O''Toole and colleagues made use of a green fluorescent protein (GFP)-labeled strain of Vibrio (Listonella) anguillarum to elucidate the natural route of invasion of this fish pathogen (20). However, obstacles to the construction of fluorescently labeled microbes have prevented many from taking advantage of this technique to permit the real-time in situ analysis of infection. These obstacles include the nontransformable nature of many pathogens and the toxicity of RFP expression from high-copy-number plasmids.Recently, two transgenic lines of zebrafish that express GFP in cells of the myeloid lineage have been developed. Lawson et al. described a transgenic (Tg) zebrafish that utilizes the protooncogene fli1 promoter to drive the expression of enhanced GFP (EGFP) (15). The fli1 gene is preferentially expressed in endothelial and hematopoietic cells. Intended for the study of vascular development, Tg(fli1::EGFP) zebrafish not only have fluorescent endothelial cells but also macrophages (15), making this zebrafish line attractive to those who study innate immunity. It has been shown that zebrafish macrophages possess strong phagocytic properties and migrate to sites of bacterial infection (13). In 2006, Renshaw and his colleagues engineered a novel Tg(mpo::GFP) zebrafish that expresses GFP under the control of the neutrophil-specific myeloperoxidase promoter (22). In this study, they characterized the GFP-labeled neutrophils, noting their capability of chemotaxis at wound sites (22). Given the recent progress in zebrafish genetics with regard to these GFP-expressing transgenic lines, there was a clear need for a simple method for the RFP labeling of Gram-negative bacteria. Such a method would facilitate further studies of microbial pathogenesis in the zebrafish and could further elucidate phagocyte (GFP labeled)-pathogen (RFP labeled) interactions, kinetics of bacterial clearance, and mechanisms of phagocyte migration to sites of bacterial infection.For the purposes of this study, we employed dimeric (d) and monomeric (m) red fluorescent protein variants d-Tomato, td-Tomato, m-Orange, and m-Cherry, which were constructed by Shaner et al. (25). These variants were chosen based on combinations of their high relative brightness and decreased RFP maturation times compared to those of the original RFPs (25). We describe here a simple method for the RFP labeling of Gram-negative bacteria.     

Regulation of the promoter region of the human adiponutrin/PNPLA3 gene by glucose and insulin

Previous biochemical, cardiovascular and behavioral work has given evidence for the existence of antagonistic galanin receptor-5-HT1A receptor interactions in the brain. In this study we investigated the existence of GalR1-5-HT1A receptor heteromers and their functional characteristics. In mammalian cells transfected with GFP2-tagged 5-HT1A receptor and YFP-tagged GalR1 receptor, a proximity-based fluorescence resonance energy transfer technique was used and it has been demonstrated that GalR1-5-HT1A receptors heteromerize. Furthermore, signaling by either the mitogen-activated protein kinase (MAPK) or adenylyl cyclase (AC) pathways by these heteromers indicates a trans-inhibition phenomenon through their interacting interface via allosteric mechanisms that block the development of an excessive activation of G_i/o and an exaggerated inhibition of AC or stimulation of MAPK activity. The presence of these heteromers in the discrete brain regions is postulated based on the existence of GalR-5-HT1A receptor-receptor interactions previously described in the brain and gives rise to explore possible novel therapeutic strategies for treatment of depression by targeting the GalR1-5-HT1A heteromers.     

Detection of organometallic and radical intermediates in the catalytic mechanism of methyl-coenzyme M reductase using the natural substrate methyl-coenzyme M and a coenzyme B substrate analogue

Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the terminal step in methanogenesis using coenzyme B (CoBSH) as the two-electron donor to reduce methyl-coenzyme M (methyl-SCoM) to form methane and the heterodisulfide, CoBS-SCoM. The active site of MCR contains an essential redox-active nickel tetrapyrrole cofactor, coenzyme F(430), which is active in the Ni(I) state (MCR(red1)). Several catalytic mechanisms have been proposed for methane synthesis that mainly differ in whether an organometallic methyl-Ni(III) or a methyl radical is the first catalytic intermediate. A mechanism was recently proposed in which methyl-Ni(III) undergoes homolysis to generate a methyl radical (Li, X., Telser, J., Kunz, R. C., Hoffman, B. M., Gerfen, G., and Ragsdale, S. W. (2010) Biochemistry 49, 6866-6876). Discrimination among these mechanisms requires identification of the proposed intermediates, none of which have been observed with native substrates. Apparently, intermediates form and decay too rapidly to accumulate to detectible amounts during the reaction between methyl-SCoM and CoBSH. Here, we describe the reaction of methyl-SCoM with a substrate analogue (CoB(6)SH) in which the seven-carbon heptanoyl moiety of CoBSH has been replaced with a hexanoyl group. When MCR(red1) is reacted with methyl-SCoM and CoB(6)SH, methanogenesis occurs 1000-fold more slowly than with CoBSH. By transient kinetic methods, we observe decay of the active Ni(I) state coupled to formation and subsequent decay of alkyl-Ni(III) and organic radical intermediates at catalytically competent rates. The kinetic data also revealed substrate-triggered conformational changes in active Ni(I)-MCR(red1). Electron paramagnetic resonance (EPR) studies coupled with isotope labeling experiments demonstrate that the radical intermediate is not tyrosine-based. These observations provide support for a mechanism for MCR that involves methyl-Ni(III) and an organic radical as catalytic intermediates. Thus, the present study provides important mechanistic insights into the mechanism of this key enzyme that is central to biological methane formation.     

Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides

Understanding the rate at which various parts of a molecular chain come together to facilitate the folding of a biopolymer (e.g., a protein or RNA) into its functional form remains an elusive goal. Here we use experiments, simulations, and theory to study the kinetics of internal loop closure in disordered biopolymers such as single-stranded oligonucleotides and unfolded proteins. We present theoretical arguments and computer simulation data to show that the relationship between the timescale of internal loop formation and the positions of the monomers enclosing the loop can be recast in a form of a universal master dependence. We also perform experimental measurements of the loop closure times of single-stranded oligonucleotides and show that both these and previously reported internal loop closure kinetics of unfolded proteins are well described by this theoretically predicted dependence. Finally, we propose that experimental deviations from the master dependence can then be used as a sensitive probe of dynamical and structural order in unfolded proteins and other biopolymers.     

Senescent mouse cells fail to overtly regulate the HIRA histone chaperone and do not form robust Senescence Associated Heterochromatin Foci

Background

Cellular senescence is a permanent growth arrest that occurs in response to cellular stressors, such as telomere shortening or activation of oncogenes. Although the process of senescence growth arrest is somewhat conserved between mouse and human cells, there are some critical differences in the molecular pathways of senescence between these two species. Recent studies in human fibroblasts have defined a cell signaling pathway that is initiated by repression of a specific Wnt ligand, Wnt2. This, in turn, activates a histone chaperone HIRA, and culminates in formation of specialized punctate domains of facultative heterochromatin, called Senescence-Associated Heterochromatin Foci (SAHF), that are enriched in the histone variant, macroH2A. SAHF are thought to repress expression of proliferation-promoting genes, thereby contributing to senescence-associated proliferation arrest. We asked whether this Wnt2-HIRA-SAHF pathway is conserved in mouse fibroblasts.

Results

We show that mouse embryo fibroblasts (MEFs) and mouse skin fibroblasts, do not form robust punctate SAHF in response to an activated Ras oncogene or shortened telomeres. However, senescent MEFs do exhibit elevated levels of macroH2A staining throughout the nucleus as a whole. Consistent with their failure to fully activate the SAHF assembly pathway, the Wnt2-HIRA signaling axis is not overtly regulated between proliferating and senescent mouse cells.

Conclusions

In addition to the previously defined differences between mouse and human cells in the mechanisms and phenotypes associated with senescence, we conclude that senescent mouse and human fibroblasts also differ at the level of chromatin and the signaling pathways used to regulate chromatin. These differences between human and mouse senescence may contribute to the increased propensity of mouse fibroblasts (and perhaps other mouse cell types) to become immortalized and transformed, compared to human cells.