The E2 Ubiquitin-conjugating Enzymes Direct Polyubiquitination to Preferred Lysines

The ubiquitin-proteasome pathway plays a crucial role in many cellular processes by degrading substrates tagged by polyubiquitin chains, linked mostly through lysine 48 of ubiquitin. Although polymerization of ubiquitin via its six other lysine residues exists in vivo as part of various physiological pathways, the molecular mechanisms that determine the type of polyubiquitin chains remained largely unknown. We undertook a systematic, in vitro, approach to evaluate the role of E2 enzymes in determining the topology of polyubiquitin. Because this study was performed in the absence of an E3 enzyme, our data indicate that the E2 enzymes are capable of directing the ubiquitination process to distinct subsets of ubiquitin lysines, depending on the specific E2 utilized. Moreover, our findings are in complete agreement with prior analyses of lysine preference assigned to certain E2s in the context of E3 (in vitro and in vivo). Finally, our findings support the rising notion that the functional unit of E2 is a dimer. To our knowledge, this is the first systematic indication for the involvement of E2 enzymes in specifying polyubiquitin chain assembly.     

A one-enzyme strategy to release an antimicrobial peptide from the LFampin-domain of bovine lactoferrin

Antimicrobial peptides have been found throughout living nature, yet antimicrobial sequences may still lie hidden within a wide variety of proteins. A rational strategy was developed to select interesting domains, based on the presumed common features of antimicrobial peptides, and to release these from accessible and safe proteins. In silico proteolysis simulations of bovine lactoferrin (bLF) with selected endoproteinases predicted the liberation of peptides that encompasses a cationic amphipathic alpha-helix. Three predicted peptides were synthesized and tested for their biological activity, demonstrating that one single enzyme was sufficient to obtain an antimicrobial peptide. The proof of principle demonstrated that a 32-mer fragment isolated from the endoproteinase AspN digestion of bLF possessed strong antimicrobial activity. Moreover, desalted crude digest had improved activity over native bLF. Hence, selective digestion of bLF increases its antimicrobial activity by release of antimicrobial stretches.     

Interleukin 2 regulation following semi-allogeneic bone marrow transplantation in mice

Success of allogeneic and autologous bone marrow transplantation (BMT) is hampered by susceptibility to infection during the first two post-treatment years. Further, in treating malignant diseases, impaired anti-host reactivity for donor cells may contribute to a high rate of relapse. Both complications are a consequence of immune deficiency involving B and T lymphocytes. The present study evaluates several key parameters of the immunologic reconstitution mechanism in mice subjected to myeloablative total body irradiation following semi-allogeneic (parental) BMT. This resulted in a gradual reduction of splenic CD3, CD4 and CD8 cells until day 45 post-BMT. Concomitantly, there was an increase in monocytes and CD4⁺/CD8⁺ (double positive) cells, accompanied by a persistent elevation in the percentage of B lymphocytes. The total thymic and splenic T cell populations were reduced until day +30. The cellular reduction correlated with the poor proliferative response of the thymic and splenic cells. A decrease occurred in IL-2 mRNA expression in thymic cells during days 15–20 post-transplant, corresponding with the low level of IL-2 secretion in the spleen and thymus of the transplanted mice. In conclusion, following semi-allogeneic BMT, there was an overall immune down-regulation in the cells, gene and protein levels. Reduced immunological responsiveness following BMT reinforces the need for improving the immune dysfunction by immunotherapy post-BMT.     

A developmentally regulated lipocalin-like gene is overexpressed in Tomato yellow leaf curl virus-resistant tomato plants upon virus inoculation, and its silencing abolishes resistance

To discover genes involved in tomato resistance to Tomato yellow leaf curl virus (TYLCV), we previously compared cDNA libraries from susceptible (S) and resistant (R) tomato lines. Among the genes preferentially expressed in R plants and upregulated by TYLCV infection was a gene encoding a lipocalin-like protein. This gene was termed Solanum lycopersicum virus resistant/susceptible lipocalin (SlVRSLip). The SlVRSLip structural gene sequence of R and S plants was identical. SlVRSLip was expressed in leaves during a 15-day window starting about 40?days after sowing (20?days after planting). SlVRSLip was upregulated by Bemisia tabaci (the TYLCV vector) feeding on R plant leaves, and even more strongly upregulated following whitefly-mediated TYLCV inoculation. Silencing of SlVRSLip in R plants led to the collapse of resistance upon TYLCV inoculation and to a necrotic response along the stem and petioles accompanied by ROS production. Contrary to previously identified tomato lipocalin gene DQ222981, SlVRSLip was not regulated by cold, nor was it regulated by heat or salt. The expression of SlVRSLip was inhibited in R plants in which the hexose transporter gene LeHT1 was silenced. In contrast, the expression of LeHT1 was not inhibited in SlVRSLip-silenced R plants. Hence, in the hierarchy of the gene network conferring TYLCV resistance, SlVRSLip is downstream of LeHT1. Silencing of another gene involved in resistance, a Permease-I like protein, did not affect the expression of SlVRSLip and LeHT1; expression of the Permease was not affected by silencing SlVRSLip or LeHT1, suggesting that it does not belong to the same network. The triple co-silencing of SlVRSLip, LeHT1 and Permease provoked an immediate cessation of growth of R plants upon infection and the accumulation of large amounts of virus. SlVRSLip is the first lipocalin-like gene shown to be involved in resistance to a plant virus.     

Relationships between head morphology, bite performance and ecology in two species of Podarcis wall lizards

Understanding the relationship between form and function is central to our comprehension of how phenotypic diversity evolves. Traits involved in multiple activities, such as social interactions and ecological resource use, are under the influence of different evolutionary forces potentially acting in opposite directions. Such systems provide the opportunity of understanding how potential constraints on morphological variation may influence whole-organism performance. In this study we examined morphology and bite performance in two closely related species of Podarcis wall lizards with divergent microhabitat preferences, to investigate how natural and sexual selection interact to shape the evolution of head traits. Our results show that although head morphology is markedly different between species and sexes, only sexes differ in bite force, indicating that the ecological differentiation between species is reflected in their morphology but does not constrain performance. Rather, the modification of the relative size of head components between species and a shift in the form-function relationship provide a potential explanation of how equal performance is attained by different morphological configurations. Geometric morphometrics provide a clear, biomechanically meaningful image of how this is achieved and show a bisexual pattern of head shape-bite force association in both species. This, together with a strong allometry of head size on body size and head shape on head size, provides indirect morphological evidence for the importance of sexual selection in shaping morphological and functional patterns. Finally, our findings suggest that the differences observed between species and sexes in head traits and bite performance are not reflected in their dietary ecology, implying that if trophic niche segregation between groups occurs, the reasons behind it are not primarily related to head morphology and functional variation.     

Molecular diversity of nitrogen-fixing bacteria associated with Chrysopogon zizanioides (L.) Roberty (vetiver), an essential oil producer plant

The essential oil produced by vetiver can vary in amount and composition depending on the bacterial community associated with its roots. Some of these bacteria could also promote plant growth by fixing nitrogen. This study aimed to analyze the diversity of diazotrophic bacteria tightly associated with roots of different vetiver genotypes. nifH-based PCR-denaturing gradient gel electrophoresis (DGGE) and clone libraries were used. DGGE profiles obtained from bulk and rhizosphere soils and root DNA amplified with nifH primers showed that samples from rhizosphere soil and root were separated at 68% similarity. Twelve bands were excised from the DGGE and sequenced. High similarity with nifH sequences of Bradyrhizobium sp., Pseudacidovorax sp. and Xanthobacter sp. was observed. Moreover, three nifH clone libraries were generated using polF/polR-primers from root DNA samples obtained from vetiver genotypes UFS-VET001, UFS-VET003 and UFS-VET004. In UFS-VET001, 24.2% of 95 clones were affiliated with sequences of Mesorhizobium loti while in UFS-VET003 41.5% of 89 clones were affiliated with Sphingomonas azotifigens, and in UFS-VET004 36.4% of 85 clones were affiliated with Klebsiella pneumoniae. The data obtained can be used to guide the isolation of diazotrophic bacteria, which may contribute to plant growth promotion and improvement of the production of essential oil in vetiver.     

Periodontitis in established rheumatoid arthritis patients: a cross-sectional clinical,microbiological and serological study

Introduction

The association between rheumatoid arthritis (RA) and periodontitis is suggested to be linked to the periodontal pathogen Porphyromonas gingivalis. Colonization of P. gingivalis in the oral cavity of RA patients has been scarcely considered. To further explore whether the association between periodontitis and RA is dependent on P. gingivalis, we compared host immune responses in RA patients with and without periodontitis in relation to presence of cultivable P. gingivalis in subgingival plaque.

Methods

In 95 RA patients, the periodontal condition was examined using the Dutch Periodontal Screening Index for treatment needs. Subgingival plaque samples were tested for presence of P. gingivalis by anaerobic culture technique. IgA, IgG and IgM antibody titers to P. gingivalis were measured by ELISA. Serum and subgingival plaque measures were compared to a matched control group of non-RA subjects.

Results

A higher prevalence of severe periodontitis was observed in RA patients in comparison to matched non-RA controls (27% versus 12%, p < 0.001). RA patients with severe periodontitis had higher DAS28 scores than RA patients with no or moderate periodontitis (p < 0.001), while no differences were seen in IgM-RF or ACPA reactivity. Furthermore, RA patients with severe periodontitis had higher IgG- and IgM-anti P. gingivalis titers than non-RA controls with severe periodontitis (p < 0.01 resp. p < 0.05), although subgingival occurrence of P. gingivalis was not different.

Conclusions

Severity of periodontitis is related to severity of RA. RA patients with severe periodontitis have a more robust antibody response against P. gingivalis than non-RA controls, but not all RA patients have cultivable P. gingivalis.