Genomic organization, expression analysis, and chromosomal localization of the mouse PEX3 gene encoding a peroxisomal assembly protein

The peroxin Pex3p has been identified as an integral peroxisomal membrane protein in yeast where pex3 mutants lack peroxisomal remnant structures. Although not proven in higher organisms, a role of this gene in the early peroxisome biogenesis is suggested, We report here the cDNA cloning and the genomic structure of the mouse PEX3 gene. The 2 kb cDNA encodes a polypeptide of 372 amino acids (42 kDa). The gene spans a region of 30 kb, contains 12 exons and 11 introns and is located on band A of chromosome 10, The putative promoter region exhibits characteristic housekeeping features. PEX3 expression was identified in all tissues analyzed, with the strongest signals in liver and in testis, and could not be induced by fenofibrate. The data presented may be useful for the generation of a mouse model defective in PEX3 in order to clarify the yet unknown functional impact of disturbances in early peroxisomal membrane assembly

Sustainable Phenylalanine-Derived SAILs for Solubilization of Polycyclic Aromatic Hydrocarbons

The solubilization capacity of a series of sustainable phenylalanine-derived surface-active ionic liquids (SAILs) was evaluated towards polycyclic aromatic hydrocarbons—naphthalene, anthracene and pyrene. The key physico-chemical parameters of the studied systems (critical micelle concentration, spectral properties, solubilization parameters) were determined, analyzed and compared with conventional cationic surfactant, CTABr. For all studied PAH solubilization capacity increases with extension of alkyl chain length of PyPheOCn SAILs reaching the values comparable to CTABr for SAILs with n = 10–12. A remarkable advantage of the phenylalanine-derived SAILs PyPheOCn and PyPheNHCn is a possibility to cleave enzymatically ester and/or amide bonds under mild conditions, to separate polycyclic aromatic hydrocarbons in situ. A series of immobilized enzymes was tested to determine the most suitable candidates for tunable decomposition of SAILs. The decomposition pathway could be adjusted depending on the choice of the enzyme system, reaction conditions, and selection of SAILs type. The evaluated systems can provide selective cleavage of the ester and amide bond and help to choose the optimal decomposition method of SAILs for enzymatic recycling of SAILs transformation products or as a pretreatment towards biological mineralization. The concept of a possible practical application of studied systems for PAHs solubilization/separation was also discussed focusing on sustainability and a green chemistry approach

Design of sustainable ionic liquids based on l-phenylalanine and l-alanine dipeptides: Synthesis, toxicity and biodegradation studies

A series of dipeptide ionic liquids (ILs) with l-phenylalanine and l-alanine fragments in structure were synthesized and their possible degradation pathways were analyzed. Based on this analysis, potential transformation products (PTPs) were proposed and synthesized. All of these compounds (25 in total) went through microbial toxicity screening and aerobic biodegradation testing. Obtained results demonstrated that by investigating ILs and PTPs with a dipeptide fragment (in tandem with single amino acid analogues), the design of ILs with high biodegradation values in closed bottle test can be accomplished. One finding was that within the scope of the compounds studied, l-phenylalanine containing compounds were more biodegradable than l-alanine derivatives. In addition to the choice of amino acid residue, its position in the dipeptide IL structure also had a significant effect on biodegradability. PyCH2CO-Phe-Ala-OEt IL, where l-phenylalanine was in close proximity to the positively charged pyridinium sub-unit, gave higher biodegradation percentages compared to PyCH2CO-Ala-Phe-OEt IL, where alanine was closer to pyridinium than the phenylalanine residue. Analysis of PTPs data showed that the presence of an alanine residue resulted in undesirable (less green) PTPs more often compared to PTPs containing phenylalanine, especially when alanine was in close proximity to the pyridinium headgroup. Based on both toxicity and biodegradation testing results preferable and less preferable subunits can be chosen for the design of new sustainable chemicals based on amino acids. Results from this study demonstrate a potential of designing new sustainable chemicals using amino acid moieties as part of their structure

An increased proportion of transgenic plants in the progeny of rapeseed (<i>Brassica napus</i> L.) transformants

Cotyledon and leaf explants of two spring rapeseed varieties were transformed with Agrobacterium tumefaciens harboring a genetic construct with the gfp marker gene. In order to reduce the proportion of hyperhydrated shoots, which appeared during regenerant formation, we optimized sucrose content in the regeneration media. Analysis of the progeny obtained from T0 regenerants showed that in a number of lines the distribution of the gfp marker did not follow Mendelian segregation of a monogenic trait in self-pollinated plants, while in the progeny of the other lines of transgenic plants, the gfp marker was completely absent, although its presence had been confirmed in all selected T0 plants. We also found that in individual transformants gfp is randomly inherited throughout the central peduncle; its presence in the genome of seedlings does not depend on the location of the pod. Thus, both transformed and non-transformed cells were involved in the formation of gametes in T0 plants. In addition, marker segregation was different in plants of the T1 line obtained by nodal cuttings of a primary transformant, depending on the location of the cuttings on the stem of the original plant, indicating that the nature of T1 generation plants was also chimeric. Furthermore, we showed that propagation of plants by cutting followed by propagation by seeds formed as a result of self-pollination led to an increase in the proportion of transgenic plants in subsequent generations. The results obtained during the course of this study show that the transformants were chimeric, i. e. their tissues contained both transgenic and non-transgenic cells, and this chimeric nature was passed on to subsequent generations. We found that, in addition to nutrient media composition, other factors such as plant genotype and explant type also contribute to the rising of chimeric plants during transformation. Based on these results, we developed a simplified method, which consists of several rounds of a combination of cutting, seed production by self-pollination, and subsequent culling of wild-type plants, which significantly enriched descendent populations of the original rapeseed transformants with plants transgenic for the gfp marker

Expression of rice OsMyb4 transcription factor improves tolerance to copper or zinc in canola plants.

The effects of copper and zinc salts on transgenic canola plants expressing rice transcription factor (TF) OsMYB4 were investigated. Transgenic plants (TPs), which showed a high OsMyb4 expression in response to either Cu or to Zn excess, were used for the current study. In leaves of TPs, the content of Cu was equal and the content of Zn was significantly higher than in non-transformed plants (NTPs). The TPs grown on an extremely high concentration of heavy metals (HMs; 150 mu De CuSO4 or 5 000 mu De ZnSO4) were able to survive for more than 15 d, while NTPs died after 7 - 9 d of incubation. This indicates that expression of OsMyb4 in canola plants improved their HM tolerance. The TPs tolerance to HMs was confirmed by a higher shoot biomass than that in NTPs. Excess of HMs caused oxidative stress (indicated by increase in malondialdehyde content) especially in leaves of NTPs. This data suggests a protective role of the OsMyb4 TF in oxidative stress. The HMs caused a lower decrease in activities of superoxide dismutase and guaiacol peroxidase in TPs than in NTPs. Higher tolerance of TPs to HMs was also suggested by a considerable increase in the content of low-molecular phenolic compounds, including flavonoids and anthocyanins, as well as proline (a potential antioxidant and chaperone). These data suggest that OsMYB4 may play a role as a positive regulator of phenylpropanoid pathway and proline synthesis. The created canola OsMyb4 TPs may be useful for future applications in phytoremediation of HM-polluted soils

Pex11p Plays a Primary Role in Medium-Chain Fatty Acid Oxidation, a Process That Affects Peroxisome Number and Size in Saccharomyces cerevisiae

The Saccharomyces cerevisiae peroxisomal membrane protein Pex11p has previously been implicated in peroxisome proliferation based on morphological observations of PEX11 mutant cells. Pex11p-deficient cells fail to increase peroxisome number in response to growth on fatty acids and instead accumulate a few giant peroxisomes. We report that mutants deficient in genes required for medium-chain fatty acid (MCFA) β-oxidation display the same phenotype as Pex11p-deficient cells. Upon closer inspection, we found that Pex11p is required for MCFA β-oxidation. Disruption of the PEX11 gene results in impaired formation of MCFA-CoA esters as measured in intact cells, whereas their formation is normal in cell lysates. The sole S. cerevisiae MCFA-CoA synthetase (Faa2p) remains properly localized to the inner leaflet of the peroxisomal membrane in PEX11 mutant cells. Therefore, the in vivo latency of MCFA activation observed in Pex11p-deficient cells suggests that Pex11p provides Faa2p with substrate. When PEX11 mutant cells are shifted from glucose to oleate-containing medium, we observed an immediate deficiency in β-oxidation of MCFAs whereas giant peroxisomes and a failure to increase peroxisome abundance only became apparent much later. Our observations suggest that the MCFA oxidation pathway regulates the level of a signaling molecule that modulates the number of peroxisomal structures in a cell

Multi-layered control of peroxisomal activity upon salt stress in Saccharomyces cerevisiae

[EN] Peroxisomes are dynamic organelles and the sole location for fatty acid ß-oxidation in yeast cells. Here, we report that peroxisomal function is crucial for the adaptation to salt stress, especially upon sugar limitation. Upon stress, multiple layers of control regulate the activity and the number of peroxisomes. Activated Hog1 MAP kinase triggers the induction of genes encoding enzymes for fatty acid activation, peroxisomal import and ß-oxidation through the Adr1 transcriptional activator, which transiently associates with genes encoding fatty acid metabolic enzymes in a stress- and Hog1-dependent manner. Moreover, Na+ and Li+ stress increases the number of peroxisomes per cell in a Hog1-independent manner, which depends instead of the retrograde pathway and the dynamin related GTPases Dnm1 and Vps1. The strong activation of the Faa1 fatty acyl-CoA synthetase, which specifically localizes to lipid particles and peroxisomes, indicates that adaptation to salt stress requires the enhanced mobilization of fatty acids from internal lipid stores. Furthermore, the activation of mitochondrial respiration during stress depends on peroxisomes, mitochondrial acetyl-carnitine uptake is essential for salt resistance and the number of peroxisomes attached to the mitochondrial network increases during salt adaptation, which altogether indicates that stress-induced peroxisomal ß-oxidation triggers enhanced respiration upon salt shock. peroxisomes, mitochondrial acetyl-carnitine uptake is essential for salt resistance, and the percentage of peroxisomes attached to the mitochondrial network increases during salt adaptation, which altogether indicates that stress-induced peroxisomal &#946;-oxidation triggers enhanced respiration upon salt shock.We thank E. Hettema for the kind gift of GFP-PTS1 expressing yeast strains and E. de Nadal and F. Posas for the kind gift of Hog1-GFP wt and kinase dead alleles. This work was supported only in the initial phase by a grant from Ministerio de Economia y Competitividad (BFU2011-23326). The authors declare no conflict of interest. MP and AP-A conceived and designed the study, SM-E, JE-B, BA, MP and AP-A acquired, analyzed and interpreted data, MP wrote the manuscript.Manzanares-Estreder, S.; Espí Bardisa, J.; Pascual-Ahuir Giner, MD.; Proft, MH. (2016). Multi-layered control of peroxisomal activity upon salt stress in Saccharomyces cerevisiae. Molecular Microbiology. 104(5):851-868. https://doi.org/10.1111/mmi.13669S851868104

On gene dosage balance in protein complexes: a comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression.

A comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol. 2008;2:

Adr1 and Cat8 Mediate Coactivator Recruitment and Chromatin Remodeling at Glucose-Regulated Genes

Adr1 and Cat8 co-regulate numerous glucose-repressed genes in S. cerevisiae, presenting a unique opportunity to explore their individual roles in coactivator recruitment, chromatin remodeling, and transcription.We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1. Through combined expression and recruitment data, along with analysis of chromatin remodeling at two of these genes, ADH2 and FBP1, we clarified how these activators achieve this wide range of co-regulation. We find that Adr1 and Cat8 are not intrinsically different in their abilities to recruit coactivators but rather, promoter context appears to dictate which activator is responsible for recruitment to specific genes. These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone. Although over-expression of Adr1 can compensate for loss of Cat8 at many genes in terms of both activation and chromatin remodeling, this over-expression cannot complement all of the cat8Delta phenotypes.Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators

Phylogenetic and Preliminary Phenotypic Analysis of Yeast PAQR Receptors: Potential Antifungal Targets

Proteins belonging to the Progestin and AdipoQ Receptor (PAQR) superfamily of membrane bound receptors are ubiquitously found in fungi. Nearly, all fungi possess two evolutionarily distinct paralogs of PAQR protein, which we have called the PQRA and PQRB subtypes. In the model fungus Saccharomyces cerevisiae, these subtypes are represented by the Izh2p and Izh3p proteins, respectively. S. cerevisiae also possesses two additional PQRA-type receptors called Izh1p and Izh4p that are restricted to other species within the “Saccharomyces complex”. Izh2p has been the subject of several recent investigations and is of particular interest because it regulates fungal growth in response to proteins produced by plants and, as such, represents a new paradigm for interspecies communication. We demonstrate that IZH2 and IZH3 gene dosage affects resistance to polyene antifungal drugs. Moreover, we provide additional evidence that Izh2p and Izh3p negatively regulate fungal filamentation. These data suggest that agonists of these receptors might make antifungal therapeutics, either by inhibiting fungal development or by sensitizing fungi to the toxic effects of current antifungal therapies. This is particularly relevant for pathogenic fungi such as Candida glabrata that are closely related to S. cerevisiae and contain the same complement of PAQR receptors