Genetic and Biochemical Characterization of Human AP Endonuclease 1 Mutants Deficient in Nucleotide Incision Repair Activity

Background

Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair enzyme involved in both base excision repair (BER) and nucleotide incision repair (NIR) pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 5′ to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells.

Methodology/Principal Finding

We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 3′→5′ exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites. Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase β and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells.

Conclusion/Significance

Taken together, these data further substantiate the role of NIR as a distinct and separable function of APE1 that is essential for processing of potentially lethal oxidative DNA lesions.     

Identifying Fishes through DNA Barcodes and Microarrays

Background

International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.

Methodology/Principal Findings

This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.

Conclusions/Significance

Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.     

Silencing of Ribosomal Protein S9 Elicits a Multitude of Cellular Responses Inhibiting the Growth of Cancer Cells Subsequent to p53 Activation

Background

Disruption of the nucleolus often leads to activation of the p53 tumor suppressor pathway through inhibition of MDM2 that is mediated by a limited set of ribosomal proteins including RPL11 and RPL5. The effects of ribosomal protein loss in cultured mammalian cells have not been thoroughly investigated. Here we characterize the cellular stress response caused by depletion of ribosomal protein S9 (RPS9).

Methodology/Principal Findings

Depletion of RPS9 impaired production of 18S ribosomal RNA and induced p53 activity. It promoted p53-dependent morphological differentiation of U343MGa Cl2:6 glioma cells as evidenced by intensified expression of glial fibrillary acidic protein and profound changes in cell shape. U2OS osteosarcoma cells displayed a limited senescence response with increased expression of DNA damage response markers, whereas HeLa cervical carcinoma cells underwent cell death by apoptosis. Knockdown of RPL11 impaired p53-dependent phenotypes in the different RPS9 depleted cell cultures. Importantly, knockdown of RPS9 or RPL11 also markedly inhibited cell proliferation through p53-independent mechanisms. RPL11 binding to MDM2 was retained despite decreased levels of RPL11 protein following nucleolar stress. In these settings, RPL11 was critical for maintaining p53 protein stability but was not strictly required for p53 protein synthesis.

Conclusions

p53 plays an important role in the initial restriction of cell proliferation that occurs in response to decreased level of RPS9. Our results do not exclude the possibility that other nucleolar stress sensing molecules act upstream or in parallel to RPL11 to activate p53. Inhibiting the expression of certain ribosomal proteins, such as RPS9, could be one efficient way to reinitiate differentiation processes or to induce senescence or apoptosis in rapidly proliferating tumor cells.     

Phospholipase C Gamma 2 Is Critical for Development of a Murine Model of Inflammatory Arthritis by Affecting Actin Dynamics in Dendritic Cells

Background

Dendritic cells (DCs) are highly specialized cells, which capture antigen in peripheral tissues and migrate to lymph nodes, where they dynamically interact with and activate T cells. Both migration and formation of DC-T cell contacts depend on cytoskeleton plasticity. However, the molecular bases governing these events have not been completely defined.

Methodology/Principal Findings

Utilizing a T cell-dependent model of arthritis, we find that PLCγ2−/− mice are protected from local inflammation and bone erosion. PLCγ2 controls actin remodeling in dendritic cells, thereby affecting their capacity to prime T cells. DCs from PLCγ2−/− mice mature normally, however they lack podosomes, typical actin structures of motile cells. Absence of PLCγ2 impacts both DC trafficking to the lymph nodes and migration towards CCL21. The interaction with T cells is also affected by PLCγ2 deficiency. Mechanistically, PLCγ2 is activated by CCL21 and modulates Rac activation. Rac1/2−/− DCs also lack podosomes and do not respond to CCL21. Finally, antigen pulsed PLCγ2−/− DCs fail to promote T cell activation and induce inflammation in vivo when injected into WT mice. Conversely, injection of WT DCs into PLCγ2−/− mice rescues the inflammatory response but not focal osteolysis, confirming the importance of PLCγ2 both in immune and bone systems.

Conclusions/Significance

This study demonstrates a critical role for PLCγ2 in eliciting inflammatory responses by regulating actin dynamics in DCs and positions the PLCγ2 pathway as a common orchestrator of bone and immune cell functions during arthritis.     

The induction of preterm labor in rhesus macaques is determined by the strength of immune response to intrauterine infection

Intrauterine infection/inflammation (IUI) is a major contributor to preterm labor (PTL). However, IUI does not invariably cause PTL. We hypothesized that quantitative and qualitative differences in immune response exist in subjects with or without PTL. To define the triggers for PTL, we developed rhesus macaque models of IUI driven by lipopolysaccharide (LPS) or live Escherichia coli. PTL did not occur in LPS challenged rhesus macaques, while E. coli–infected animals frequently delivered preterm. Although LPS and live E. coli both caused immune cell infiltration, E. coli–infected animals showed higher levels of inflammatory mediators, particularly interleukin 6 (IL-6) and prostaglandins, in the chorioamnion-decidua and amniotic fluid (AF). Neutrophil infiltration in the chorio-decidua was a common feature to both LPS and E. coli. However, neutrophilic infiltration and IL6 and PTGS2 expression in the amnion was specifically induced by live E. coli. RNA sequencing (RNA-seq) analysis of fetal membranes revealed that specific pathways involved in augmentation of inflammation including type I interferon (IFN) response, chemotaxis, sumoylation, and iron homeostasis were up-regulated in the E. coli group compared to the LPS group. Our data suggest that the intensity of the host immune response to IUI may determine susceptibility to PTL.     

Dealing with detection error in site occupancy surveys: what can we do with a single survey?

Aim Site occupancy probabilities of target species are commonly used in various ecological studies, e.g. to monitor current status and trends in biodiversity. Detection error introduces bias in the estimators of site occupancy. Existing methods for estimating occupancy probability in the presence of detection error use replicate surveys. These methods assume population closure, i.e. the site occupancy status remains constant across surveys, and independence between surveys. We present an approach for estimating site occupancy probability in the presence of detection error that requires only a single survey and does not require assumption of population closure or independence. In place of the closure assumption, this method requires covariates that affect detection and occupancy.Methods Penalized maximum-likelihood method was used to estimate the parameters. Estimability of the parameters was checked using data cloning. Parametric boostrapping method was used for computing confidence intervals.Important findings The single-survey approach facilitates analysis of historical datasets where replicate surveys are unavailable, situations where replicate surveys are expensive to conduct and when the assumptions of closure or independence are not met. This method saves significant amounts of time, energy and money in ecological surveys without sacrificing statistical validity. Further, we show that occupancy and habitat suitability are not synonymous and suggest a method to estimate habitat suitability using single-survey data.     

Global resource acquisition patterns of invasive and native plant species do not hold at the regional scale in Mediterranean type ecosystems

Invasive species may outperform native species by acquiring more resources or by efficiently using limited resources. Studies comparing leaf traits as a metric of carbon capture strategies in native and invasive species have come to different conclusions. Some studies suggest that invasive species are better at acquiring resources, but that native and invasive species use resources similarly. Other studies have found that native and invasive species differ in resource use efficiency, which implies different biochemical or physiological mechanisms of carbon capture. To resolve this debate, we examined relationships among four leaf traits (photosynthetic rate, specific leaf area, foliar nitrogen, foliar phosphorus) in co-occurring native and invasive species from eight plant communities across five Mediterranean-climate ecosystems. We performed standardized major axis regression for all trait combinations within and across sites, testing for slope homogeneity and shifts in elevation (y-intercept) or along a common slope between species groups. Across the global dataset, native and invasive species had similar carbon capture strategies (i.e., similar slopes), with invasive species occupying a position of greater resource acquisition. However, these patterns did not hold when regions were analyzed individually. Regional differences may be driven by differences in life form between native and invasive species, and variation in soil resource availability among regions. Our context-dependent results reveal not only that management of invasive species will differ across regions but also that global comparisons of invasive and native species can be misleading.     

Season of birth affects juvenile survival of giraffe

Variation in timing of reproduction and subsequent juvenile survival often plays an important role in population dynamics of temperate and boreal ungulates. Tropical ungulates often give birth year round, but survival effects of birth season for tropical ungulate species are unknown. We used a population of giraffe in the Tarangire Ecosystem of northern Tanzania, East Africa to determine whether calf survival varied by season of birth. Variation in juvenile survival according to season of birth was significant, with calves born during the dry season experiencing the highest survival probability. Phenological match may confer a juvenile survival advantage to offspring born during the dry season from greater accumulated maternal energy reserves in mothers who conceive in the long rainy season, high-protein browse in the late dry-early short rainy seasons supplementing maternal and calf resources, reduced predation due to decreased stalking cover, or some combination of these. Asynchrony is believed to be the ancestral state of all ungulates, and this investigation has illustrated how seasonal variation in vegetation can affect juvenile survival and may play a role in the evolution of synchronous births.