Cryptic in vitro ubiquitin ligase activity of HDMX towards p53 is probably regulated by an induced fit mechanism

HDMX and its homologue HDM2 are two essential proteins for the cell; after genotoxic stress, both are phosphorylated near to their RING domain, specifically at serine 403 and 395, respectively. Once phosphorylated, both can bind the p53 mRNA and enhance its translation; however, both recognize p53 protein and provoke its degradation under normal conditions. HDM2 has been well-recognized as an E3 ubiquitin ligase, whereas it has been reported that even with the high similarity between the RING domains of the two homologs, HDMX does not have the E3 ligase activity. Despite this, HDMX is needed for the proper p53 poly-ubiquitination. Phosphorylation at serine 395 changes the conformation of HDM2, helping to explain the switch in its activity, but no information on HDMX has been published. Here, we study the conformation of HDMX and its phospho-mimetic mutant S403D, investigate its E3 ligase activity and dissect its binding with p53. We show that phospho-mutation does not change the conformation of the protein, but HDMX is indeed an E3 ubiquitin ligase in vitro; however, in vivo, no activity was found. We speculated that HDMX is regulated by induced fit, being able to switch activity accordingly to the specific partner as p53 protein, p53 mRNA or HDM2. Our results aim to contribute to the elucidation of the contribution of the HDMX to p53 regulation.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of <Emphasis Type="Italic">Pisum sativum in vitro</Emphasis> and <Emphasis Type="Italic">in vivo</Emphasis>

Six pea (Pisum sativum L.) cultivars (Adept, Komet, Lantra, Olivin, Oskar, Tyrkys) were transformed via Agrobacterium tumefaciens strain EHA105 with pBIN19 plasmid carrying reporter uidA (β-glucuronidase, GUS, containing potato ST-LS1 intron) gene under the CaMV 35S promoter, and selectable marker gene nptII (neomycin phosphotransferase II) under the nos promoter. Two regeneration systems were used: continual shoot proliferation from axillary buds of cotyledonary node in vitro, and in vivo plant regeneration from imbibed germinating seed with removed testa and one cotyledon. The penetration of Agrobacterium into explants during co-cultivation was supported by sonication or vacuum infiltration treatment. The selection of putative transformants in both regeneration systems carried out on media with 100 mg dm⁻³ kanamycin. The presence of introduced genes was verified histochemically (GUS assay) and by means of PCR and Southern blot analysis in T₀ putative transformants and their seed progenies (T₁ to T₃ generations). Both methods, but largely in vivo approach showed to be genotype independent, resulting in efficient and reliable transformation system for pea. The in vivo approach has in addition also benefit of time and money saving, since transgenic plants are obtained in much shorter time. All tested T₀ – T₃ plants were morphologically normal and fertile.This research was supported by the National Agency for Agricultural Research (grants No. QE 0046 and QF 3072) and Ministry of Education of the Czech Republic (grant No. ME 433).     

Both epiphytic and endophytic strains of <Emphasis Type="Italic">Rhodococcus fascians</Emphasis> influence transporter gene expression and cytokinins in infected <Emphasis Type="Italic">Pisum sativum</Emphasis> L. seedlings

Some strains of the soil bacterium Rhodococcus fascians maintain an epiphytic life style while others become endophytic. Virulent, endophytic strains cause multiple shoot growth and inhibit root growth of seed-inoculated Pisum sativum L. We were interested in assessing, at the molecular level, the impact of strains of contrasting niche on the emerging shoots and roots of inoculated seeds. The presence of R. fascians was monitored microscopically, endogenous cytokinin and chlorophyll levels were measured, and the expression of genes monitored by RT-qPCR. The expression of the pea sugar transporter genes (SWEET and SUT), amino acid (AAP) transporters and cell wall invertase gene family members, as well as expression of plant and bacterial cytokinin biosynthesis (IPT), activation (LOG) and degradation (CKX) genes were monitored. Both the virulent strain and the epiphytic strain affected the expression of the transporter genes, with less obvious differences between the strains on the shoot compared with the effect on the root. Strong expression of the R. fascians genes, RfIPT, RfLOG and RfCKX, in pea seedlings at 15 days post inoculation was mirrored by increased expression of transporter gene family members in the plant. However, the elevated levels of isopentenyl adenine-type and zeatin-type cytokinins were not consistently associated with the virulent strain. In conclusion, while both the virulent strain and the epiphytic strain impacted the expression of transporter genes in the shoots and roots, only the virulent strain affected morphology. The inhibited root growth, the greening of the roots, and the expression of the pea response regulators in the infected roots are indicative of a response to cytokinin, but a role for the ‘classical’ cytokinins as virulence determinants was not established.     

Effects of canonical Wnt signaling on dorso-ventral specification of the mouse telencephalon

Wnt signaling is involved in numerous processes during vertebrate CNS development. In this study, we used conditional Cre/loxP system in mouse to ablate or activate beta-catenin in the telencephalon in two time windows: before and after the onset of neurogenesis. We show that beta-catenin mediated Wnt signals are required to maintain the molecular identity of the pallium. Inactivation of beta-catenin in the telencephalon before neurogenesis results in downregulated expression of dorsal markers Emx1, Emx2 and Ngn2, and in ectopic up-regulation of ventral markers Gsh2, Mash1 and Dlx2 in the pallium. In contrast, ablation of ss-catenin after the onset of cortical neurogenesis (E11.5) does not result in a dorso-ventral fate shift. In addition, activation of canonical Wnt signaling in the subpallium leads to a repression of ventral telencephalic cell identities as shown by the down-regulation of subpallial markers Dlx2, Nkx2.1, Gsh2, Olig2 and Mash1. This was accompanied with an expansion of dorsal identities ventrally as shown by the expanded expression domains of pallial markers Pax6 and Ngn2. Thus, our data suggest that canonical Wnt signals are involved in maintaining the identity of the pallium by controlling expression of dorsal markers and by suppressing ventral programs from being activated in pallial progenitor cells.     

Endogenous cytokinin and auxin profiles during in vitro organogenesis from vegetative buds of Pinus radiata adult trees

In Pinus radiata D. Don, the transition from the juvenile to the mature phase is characterized by a reduction in the tree's organogenic potential, which is usually reverted in breeding programs by reinvigoration procedures to enable vegetative propagation. In this work, we have determined the best culture conditions for in vitro reinvigoration of radiata pine buds, tested different cytokinin (CK) types [N⁶‐benzyladenine (BA), meta‐topolin (mT) and trans‐zeatin] and concentrations (25 and 50 µM), and studied the effect of culture conditions on endogenous CK and indole‐3‐acetic acid (IAA) levels at different stages of the organogenic process. To this end, the levels of 43 CKs and IAA were determined in P. radiata buds before and during the reinvigoration process. When BA or mT was applied to the induction medium, we did not observe any significant increase or decrease in endogenous isoprenoid CK content. We also report for the first time the presence of O‐glucosides in non‐treated P. radiata explants from the field and remark the importance of O‐glucosides as storage forms.     

microRNA-342, microRNA-191 and microRNA-510 are differentially expressed in T regulatory cells of type 1 diabetic patients

Regulatory T cells (Tregs) are critical regulators of autoimmune diseases, including type 1 diabetes mellitus. It is hypothesised that Tregs’ function can be influenced by changes in the expression of specific microRNAs (miRNAs). Thus, we performed miRNAs profiling in a population of Tregs separated from peripheral blood of five type 1 diabetic patients and six healthy donors. For more detailed molecular characterisation of Tregs, we additionally compared miRNAs expression profiles of Tregs and conventional T cells. Tregs were isolated according to CD3+, CD4+, CD25^hi+ and CD127− by flow cytometry, and miRNA expression profiling was performed using TaqMan Array Human MicroRNA Panel-1 (384-well low density array). In Tregs of diabetic patients we found significantly increased expression of miRNA-510 (p = 0.05) and decreased expression of both miRNA-342 (p < 0.0001) and miRNA-191 (p = 0.0079). When comparing Tregs and T cells, we revealed that Tregs had significant higher expression of miRNA-146a and lower expression of eight specific miRNAs (20b, 31, 99a, 100, 125b, 151, 335, and 365). To our knowledge, this is the first study demonstrating changes in miRNA expression profiles occurring in Tregs of T1D patients and a miRNAs signature of adult Tregs.     

How too much care kills species: Grassland reserves,agri-environmental schemes and extinction of <Emphasis Type="Italic">Colias myrmidone</Emphasis> (Lepidoptera: Pieridae) from its former stronghold

We describe a rapid extirpation of a strong population of globally threatened butterfly, Colias myrmidone, from the White Carpathians, Czech Republic. The area is renowned for a high plant and insect diversity associated with savannah-like Carpathian meadows, traditionally managed by mowing once a year and subsequent autumn grazing. Although many meadows fell victim to land consolidation schemes in the 1970s and 1980s, over 2000 hectares have been preserved in a dense network of reserves. The reserve management practised since the mid-1990s has consisted of uniform machine mowing of entire areas and this was further accelerated after accession of the Czech Republic to the EU, when agri-environmental schemes (AES) required two cuts per year. This starkly conflicted with the life history of C. myrmidone, because both spring and autumn cuts interfere with larval development. Despite intensive surveys, only five and then two C. myrmidone individuals were seen in the area in 2005 and 2006, respectively, rendering the species effectively extinct. Conservation authorities failed by neglecting early warning signals issued by amateur entomologists, and by ignoring the basic tenets of conservation of insect diversity, such as the need to maintain heterogeneity of resources. Unless AES provide for this crucial aspect of habitat suitability for invertebrates, they may turn from a great hope into a massive failure.     

Determination of the absolute configurations of natural products via density functional theory calculations of vibrational circular dichroism, electronic circular dichroism, and optical rotation: the iso-schizozygane alkaloids isoschizogaline and isoschizogamine

The development of density functional theory (DFT) methods for the calculation of vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and transparent spectral region optical rotation (OR) has revolutionized the determination of the absolute configurations (ACs) of chiral molecules using these chiroptical properties. We report the concerted application of DFT calculations of VCD, ECD, and OR to the determination of the ACs of the isoschizozygane alkaloid natural products, isoschizogaline, and isochizogamine, whose ACs have not previously been determined. The ACs of naturally occurring (-)-isoschizogaline and (-)-isoschizogamine, are both determined definitively to be 2R, 7R, 20S, 21S.     

Nutrient use by tropical ant communities varies among three extensive elevational gradients: A cross-continental comparison

Aim

Many studies demonstrate that climate limits invertebrates along tropical elevational gradients, but we have only a rudimentary understanding of the role of nutrient limitation and climatic seasonality. Here we examined the relationships between ant community structure, nutrient use and season along three undisturbed elevational gradients, each from a different continent.

Location

Ecuador (South America), Papua New Guinea (PNG: Oceania), Tanzania (Africa).

Time period

2011–2014.

Major taxa studied

Ants.

Methods

Along each of the three gradients, we placed six distinct nutrient types (amino acid, sucrose, sucrose + amino acid, lipid, NaCl, H₂O). In total, we distributed 2370 baits at 38 sites from 203 m to 3972 m. We used generalized linear models to test for the effects of elevation and season on ant species richness and activity and relative nutrient use. We also tested if changes in ant trophic guilds corresponded to changes in the use of particular nutrients.

Results

Both species richness and activity decreased with elevation along each gradient. However, there were significant interaction effects among elevation, region and season, as ant activity in the dry season was higher in Ecuador and Tanzania but lower in PNG. Relative nutrient use varied among regions: ant preference for some nutrients changed with increasing elevation in Ecuador (decrease in lipid use) and Tanzania (decrease in amino acid and H₂O use), while season affected nutrient use in PNG. There were common trends in trophic guilds along the three elevational gradients (e.g. proportional increase of predators), but these did not explain most of the nutrient use patterns.

Main conclusion

While the structure of ant communities changed similarly with elevation, both the seasonal and elevational effects on nutrient use by ants differed between continents. We argue that regional differences in climate and nutrient availability rather than ant functional composition shape nutrient use by ants.     

A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues

Renal cell carcinoma (RCC) represents 2.2% of all cancer incidences; however, prognostic or predictive RCC biomarkers at protein level are largely missing. To support proteomics research of localized and metastatic RCC, we introduce a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of 86 initially localized RCC, 75 metastatic RCC and 17 adjacent non-cancerous fresh frozen tissue lysates were trypsin digested, pooled, and fractionated using hydrophilic chromatography. The fractions were analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition (DDA) mode. A resulting spectral library contains 77,817 peptides representing 7960 protein groups (FDR = 1%). Further, we confirm applicability of this library on four RCC datasets measured in data-independent acquisition (DIA) mode, demonstrating a specific quantification of a substantially increased part of RCC proteome, depending on LC-MS/MS instrumentation. Impact of sample specificity of the library on the results of targeted DIA data extraction was demonstrated by parallel analyses of two datasets by two pan human libraries. The new RCC specific library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets.