Engineering Pichia pastoris for the Production of Carotenoids.

Carotenoids are one of the most diverse and widely distributed classes of pigments in the biosphere and exhibit a variety of functions in the nature. Their importance and biotechnological applications are higher and higher, but their sources are not increasing in the same exponential way. Here we describe the process of bioengineering the yeast Pichia pastoris by sequential transformation to get an astaxanthin producer.

Combination of cGMP analogue and drug delivery system provides functional protection in hereditary retinal degeneration.

Inherited retinal degeneration (RD) is a devastating and currently untreatable neurodegenerative condition that leads to loss of photoreceptor cells and blindness. The vast genetic heterogeneity of RD, the lack of "druggable" targets, and the access-limiting blood-retinal barrier (BRB) present major hurdles toward effective therapy development. Here, we address these challenges (i) by targeting cGMP (cyclic guanosine- 3',5'-monophosphate) signaling, a disease driver common to different types of RD, and (ii) by combining inhibitory cGMP analogs with a nanosized liposomal drug delivery system designed to facilitate transport across the BRB. Based on a screen of several cGMP analogs we identified an inhibitory cGMP analog that interferes with activation of photoreceptor cell death pathways. Moreover, we found liposomal encapsulation of the analog to achieve efficient drug targeting to the neuroretina. This pharmacological treatment markedly preserved in vivo retinal function and counteracted photoreceptor degeneration in three different in vivo RD models. Taken together, we show that a defined class of compounds for RD treatment in combination with an innovative drug delivery method may enable a single type of treatment to address genetically divergent RD-type diseases.

Increased Plasma cGMP in a Family With Autosomal Recessive Retinitis Pigmentosa Due to Homozygous Mutations in the PDE6A Gene.

PURPOSE: To describe genotype and phenotype in a family with autosomal recessive retinitis pigmentosa (arRP) carrying homozygous mutations in the gene for the α-subunit of cyclic guanosine monophosphate (cGMP)-hydrolyzing phosphodiesterase 6 (PDE6A). Moreover, to compare their plasma cGMP levels to controls, exploring the possible role for cGMP in RP diagnostics. METHODS: Seven siblings and their parents were recruited. Microarray, verified by Sanger sequencing, was used for genotyping. Investigations included slit lamp and fundus examination, Goldmann perimetry, full-field and multifocal electroretinography (ERG), and optical coherence tomography (OCT). Cyclic GMP was measured with an immunoassay kit. RESULTS: All siblings and their father were homozygous, and the mother heterozygous, for IVS6+1G>A in PDE6A. Seven family members also carried c1532G>A in ABCA4. Visual fields were constricted with mere central remnants in older subjects and additional temporal crescents in younger subjects. Visual acuity ranged from 0.8 to amaurosis. Full-field ERGs showed extinguished rod responses and minimal cone responses. Multifocal ERGs were severely reduced. Optical coherence tomography revealed either general attenuation or central macular edema. Mean plasma cGMP in patients was approximately twice that in controls. CONCLUSIONS: To our knowledge, this is the first phenotypic description of arRP due to homozygous IVS6+1G>A mutations in PDE6A and these seem here to be associated with severe RP leading to early extinction of rod responses as well as reduced macular function. Additionally, patients showed increased plasma levels of cGMP, indicating a possible role for cGMP measurements as part of the clinical tests for this and, after further investigations, maybe other forms of RP.

Influence of extracellular matrix components on the expression of integrins and regeneration of adult retinal ganglion cells.

PURPOSE: Retinal ganglion cells (RGCs) are exposed to injury in a variety of optic nerve diseases including glaucoma. However, not all cells respond in the same way to damage and the capacity of individual RGCs to survive or regenerate is variable. In order to elucidate factors that may be important for RGC survival and regeneration we have focussed on the extracellular matrix (ECM) and RGC integrin expression. Our specific questions were: (1) Do adult RGCs express particular sets of integrins in vitro and in vivo? (2) Can the nature of the ECM influence the expression of different integrins? (3) Can the nature of the ECM affect the survival of the cells and the length or branching complexity of their neurites? METHODS: Primary RGC cultures from adult rat retina were placed on glass coverslips treated with different substrates: Poly-L-Lysine (PL), or PL plus laminin (L), collagen I (CI), collagen IV (CIV) or fibronectin (F). After 10 days in culture, we performed double immunostaining with an antibody against ßIII-Tubulin to identify the RGCs, and antibodies against the integrin subunits: αV, α1, α3, α5, ß1 or ß3. The number of adhering and surviving cells, the number and length of the neurites and the expression of the integrin subunits on the different substrates were analysed. RESULTS: PL and L were associated with the greatest survival of RGCs while CI provided the least favourable conditions. The type of substrate affected the number and length of neurites. L stimulated the longest growth. We found at least three different types of RGCs in terms of their capacity to regenerate and extend neurites. The different combinations of integrins expressed by the cells growing on different substrata suggest that RGCs expressed predominantly α1ß1 or α3ß1 on L, α1ß1 on CI and CIV, and α5ß3 on F. The activity of the integrins was demonstrated by the phosphorylation of focal adhesion kinase (FAK). CONCLUSIONS: Adult rat RGCs can survive and grow in the presence of different ECM tested. Further studies should be done to elucidate the different molecular characteristics of the RGCs subtypes in order to understand the possible different sensitivity of different RGCs to damage in diseases like glaucoma in which not all RGCs die at the same time.

Phenotypic map of porcine retinal ganglion cells.

PURPOSE: Porcine retina is an excellent model for studying diverse retinal processes and diseases. The morphologies of porcine retinal ganglion cells (RGCs) have, however, not yet been described comprehensively. The aim of the present study was to créate a classification of the RGCs using the 1, 1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) tracing method. METHODS: About 170 RGCs were retrogradely labeled by injecting DiI into the optic nerve of postmortem eyes and statistically analyzed by two different clustering methods: Ward's algorithm and the K-means clustering. Major axis length of the soma, soma area size, and dendritic field area size were selected as main parameters for cluster classification. RESULTS: RGC distribution in clusters was achieved according to their morphological parameters. It was feasible to combine both statistical methods, thereby obtaining a robust clustering distribution. Morphological analysis resulted in a classification of RGCs in three groups according to the soma size and dendritic field: A (large somas and large dendritic fields), B (medium to large somas and medium to large dendritic fields), C (medium to small somas and medium to small dendritic fields). Within groups, fine clustering defined several subgroups according to dendritic arborization and level of stratification. Additionally, cells stratifying in two different levels of the inner plexiform layer were observed within the clusters. CONCLUSIONS: This comprehensive study of RGC morphologies in the porcine retina provides fundamental knowledge about RGC cell types and provides a basis for functional studies toward selective RGC cell degeneration in retinal disorders.

Neuroprotective effects of topical CB1 agonist WIN 55212-2 on retinal ganglion cells after acute rise in intraocular pressure induced ischemia in rat.

Neuroprotection in retinal experimental work consists primarily of preventing retinal ganglion cell (RGC) loss after exposure to a hostile event. We have studied the neuroprotective effect on RGCs in an ischemia-reperfusion model by activation of the cannabinoid receptor CB1 using topical application of WIN 55212-2. Intraocular pressure (IOP) was increased by continuous infusion of phosphate buffer saline (PBS) into the anterior chamber of the eye. Mean intraocular pressure was increased up to 88.5 ± 0.29 mm Hg (control normal IOP 15.1 ± 0.25 mm Hg), for 35 min. Animals were distributed in 3 groups. Left eyes underwent acute rise in intraocular pressure. First group was treated with topical Tocrisolve™ 100 in both eyes. Second group was treated with 1% solution of CB1 agonist WIN 55212-2 in both eyes. Third group was treated with WIN 55212-2 1% and CB1 antagonist AM 251 1% solutions in both eyes. Subsequently, RGCs were immunolabeled with Brn3a and automated quantification of retinal mosaics of RGCs were performed. The ischemic damage led to a mean loss in RGC density of 12.33%. After topic administration of WIN 55212-2, mean loss of RGCs was of 2.45%. Co-treatment with CB1 antagonist AM 251 abolished almost completely the neuroprotective effect of WIN 55212-2. Topic 1% WIN 55212-2 showed a neuroprotective effect on RGC degeneration after ischemia-reperfusion without pre-activation of CB1 receptors.

Cloning and characterization of the beer foaming gene CFG1 from Saccharomyces pastorianus.

Foam production is an essential characteristic of beer, generated mainly from the proteins present in the malt and, to a minor extent, from the mannoproteins in brewer's yeast cell walls. Here, we describe the isolation and characterization of the novel fermentation gene CFG1 (Carlsbergensis foaming gene) from Saccharomyces pastorianus. CFG1 encodes the cell wall protein Cfg1p, a 105 kDa protein highly homologous to Saccharomyces cerevisiae cell wall mannoproteins, particularly those involved in foam formation, such as Awa1p and Fpg1p. Further characterization of Cfg1p revealed that this novel protein is responsible for beer foam stabilization. This report represents the first time that a brewing yeast foaming gene has been cloned and its action fully characterized.

Analysis of canthaxanthin production by Gordonia jacobaea.

Commercial interest in the use of natural pigments isolated from microorganisms has increased in recent years; hence, molecules belonging to the polyisoprenoid group (i.e., ß-carotene, astaxanthin, and canthaxanthin) have been the focus of much attention. The bacterium Gordonia jacobaea readily synthesizes and accumulates large amounts of canthaxanthin (ß-ß'-carotene-4,4'-dione), which is widely used in the food and cosmetics industries. In the present work, the integral process of canthaxanthin production by G. jacobaea is analyzed together with its application as natural sources for the industry. A great influence of culture media is observed on canthaxanthin levels. Also, the ability is found of extract the pigments with ethanol from bacteria. The concentration of the samples is a crucial point of the process, being mandatory to discard any process of heating the samples, because this provoked the pigment degradation. Despite this, the described method allows to consider G. jacobaea as a potential canthaxanthin producer for the industry.

Construction of a novel Pichia pastoris strain for production of xanthophylls.

In this study, we used the yeast carotenogenic producer Pichia pastoris Pp-EBIL strain, which has been metabolically engineered, by heterologously expressing ß-carotene-pathway enzymes to produce ß-carotene, as a vessel for recombinant astaxanthin expression. For this purpose, we designed new P. pastoris recombinant-strains harboring astaxanthin-encoding genes from carotenogenic microorganism, and thus capable of producing xanthophyllic compounds. We designed and constructed a plasmid (pGAPZA-WZ) containing both the ß-carotene ketolase (crtW) and ß-carotene hydroxylase (crtZ) genes from Agrobacterium aurantiacum, under the control of the GAP promoter and containing an AOX-1 terminator. The plasmid was then integrated into the P. pastoris Pp-EBIL strain genomic DNA, producing clone Pp-EBILWZ. The recombinant P. pastoris (Pp-EBILWZ) cells exhibited a strong reddish carotenoid coloration and were confirmed, by HPLC, to produce not only the previous described carotenoids lycopene and ß-carotene, but also de novo synthesized astaxanthin.

A new disruption vector (pDHO) to obtain heterothallic strains from both Saccharomy cescerevisiae and Saccharomyces pastorianus

Yeasts are responsible for several traits in fermented beverages, including wine and beer, and their genetic manipulation is often necessary to improve the quality of the fermentation product. Improvement of wild-type strains of Saccharomyces cerevisiae and Saccharomyces pastorianus is difficult due to their homothallic character and variable ploidy level. Homothallism is determined by the HO gene in S. cerevisiae and the Sc-HO gene in S. pastorianus. In this work, we describe the construction of an HO disruption vector (pDHO) containing an HO disruption cassette and discuss its use in generating heterothallic yeast strains from homothallic Saccharomyces species (AU)

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cDNA cloning of a novel gene codifying for the enzyme lycopene ß-cyclase from Ficus carica and its expression in Escherichia coli.

Lycopene beta-cyclase (ß-LCY) is the key enzyme that modifies the linear lycopene molecule into cyclic ß-carotene, an indispensable carotenoid of the photosynthetic apparatus and an important source of vitamin A in human and animal nutrition. Owing to its antioxidant activity, it is commercially used in the cosmetic and pharmaceutical industries, as well as an additive in foodstuffs. Therefore, ß-carotene has a large share of the carotenoidic market. In this study, we used reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE)-PCR to obtain and clone a cDNA copy of the gene Lyc-ß from Ficus carica (Lyc-ß Fc), which codes for the enzyme lycopene ß-cyclase (ß-LCY). Expression of this gene in Escherichia coli produced a single polypeptide of 56 kDa of weight, containing 496 amino acids, that was able to cycle both ends of the lycopene chain. Amino acid analysis revealed that the protein contained several conserved plant cyclase motifs. ß-LCY activity was revealed by heterologous complementation analysis, with lycopene being converted to ß-carotene as a result of the enzyme's action. The ß-LCY activity of the expressed protein was confirmed by high-performance liquid chromatography (HPLC) identification of the ß-carotene. The lycopene to ß-carotene conversion rate was 90%. The experiments carried out in this work showed that ß-LYC is the enzyme responsible for converting lycopene, an acyclic carotene, to ß-carotene, a bicyclic carotene in F. carica. Therefore, by cloning and expressing ß-LCY in E. coli, we have obtained a new gene for ß-carotene production or as part of the biosynthetic pathway of astaxanthin. So far, this is the first and only gene of the carotenoid pathway identified in F. carica.

Oily yeasts as oleaginous cell factories.

Oily yeasts have been described to be able to accumulate lipids up to 20% of their cellular dry weight. These yeasts represent a minor proportion of the total yeast population, and only 5% of them have been reported as able to accumulate more than 25% of lipids. The oily yeast genera include Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon, and Lipomyces. More specifically, examples of oleaginous yeasts include the species: Lipomyces starkeyi, Rhodosporidium toruloides, Rhodotorula glutinis, and Yarrowia lipolytica. Yeast do exhibit advantages for lipid production over other microbial sources, namely, their duplication times are usually lower than 1 h, are much less affected than plants by season or climate conditions, and their cultures are more easily scaled up than those of microalgae. Additionally, some oily yeasts have been reported to accumulate oil up to 80% of their dry weight and can indeed generate different lipids from different carbon sources or from lipids present in the culture media. Thus, they can vary their lipid composition by replacing the fatty acids present in their triglycerides. Due to the diversity of microorganisms and growth conditions, oily yeasts can be useful for the production of triglycerides, surfactants, or polyunsaturated fatty acids.

FPG1, a gene involved in foam formation in Saccharomyces cerevisiae.

Foam formation in fermentations conducted by Saccharomyces cerevisiae, either at the beginning of the fermentation process or at the end in the case of sparkling wines, is due, to a large extent, to cell wall mannoproteins, which provide hydrophobicity to the yeast cells and favour their floating index as well as stabilization of the foam. The foam may be an undesirable by-product if it accumulates on top of the fermentation tanks, but its formation is a good property in either beer or sparkling wines. It is therefore important to know the yeast genes involved in foam formation, in order to suppress or potentiate their expression according to the end product to be obtained. The present study identified and characterized, for the first time in an oenological S. cerevisiae strain, a gene involved in foam formation, named FPG1 (foam-promoting gene). The protein encoded by FPG1 is a mannoprotein precursor present in the cell wall and somewhat homologous to Awa1p, a foaming protein described in a sake S. cerevisiae strain. A foamless strain was prepared by FPG1 deletion, and a foam hyper-producing strain was also constructed, thus allowing the conclusion that Fpg1p is a mannoprotein involved in yeast frothing.

A new disruption vector (pDHO) to obtain heterothallic strains from both Saccharomyces cerevisiae and Saccharomyces pastorianus.

Yeasts are responsible for several traits in fermented beverages, including wine and beer, and their genetic manipulation is often necessary to improve the quality of the fermentation product. Improvement of wild-type strains of Saccharomyces cerevisiae and Saccharomyces pastorianus is difficult due to their homothallic character and variable ploidy level. Homothallism is determined by the HO gene in S. cerevisiae and the Sc-HO gene in S. pastorianus. In this work, we describe the construction of an HO disruption vector (pDHO) containing an HO disruption cassette and discuss its use in generating heterothallic yeast strains from homothallic Saccharomyces species.

Role of TolC in Klebsiella oxytoca resistance to antibiotics.

OBJECTIVES: The Gram-negative human pathogen Klebsiella oxytoca is often resistant to several antibiotics such as fluoroquinolones, erythromycin, tetracycline, chloramphenicol and others. The aim of this study was to look at the mechanisms leading to this resistance and particularly the role of TolC and efflux mechanisms in determining resistance. METHODS: Ciprofloxacin accumulation was measured spectrofluorometrically. Growth inhibition assays were performed in the presence or absence of carbonyl cyanide m-chlorophenylhydrazone (10 mg/L, final concentration). The genome of K. oxytoca was analysed for the existence of loci encoding tolC by PCR using primers for the Enterobacter aerogenes tolC gene and subsequently sequenced. A plasmid named pUC18TolC was constructed and inserted into Escherichia coli C600tolC,Tn5, and the function of TolC was analysed. The structure modelling was performed using the Modeller program. RESULTS: The existence of the AcrAB efflux mechanism was demonstrated in the species, and a TolC-like protein, a channel-forming protein at the external membrane that allows the extrusion of antibiotics by the AcrAB efflux pump, was cloned, sequenced and a model proposed. CONCLUSIONS: K. oxytoca express a functional TolC that lacks a fragment of six amino acids characteristic of the external loops of TolC in E. coli. This makes this species resistant to a few colicins.

Genetic stabilization of Saccharomyces cerevisiae oenological strains by using benomyl.

Wild-type oenological strains of Saccharomyces cerevisiae are usually aneuploid and heterozygotes; thus, when they are used as starters in must fermentation the resulting wine characteristics may vary from year to year. Treatment of a wild-type S. cerevisiae oenological strain with benomyl (methyl-l-butylcarbamoyl-2-benzimidazole carbamate), an antifungal agent shown to cause chromosome loss in yeasts, resulted in a stable starter strain in which the parental oenological traits were unchanged. The oenological S. cerevisiae strain was treated with benomyl in two different ways (A and B), and sporulation ability and spore viability were subsequently assayed. Treatment A resulted in both the highest numbers of tetrads and a reduction in DNA cell content, while treatment B increased spore viability. Fermentation assays were carried out with spore clones obtained from treatment A, and the concentrations of glycerol, lactic acid, acetic acid, and ethanol resulting from the treated strains were found to be similar to those of the parental strain. Benomyl treatment thus achieved stable, highly sporulating oenological S. cerevisiae strains of low ploidy, but preserved the desirable oenological properties of the parental strain.

Genetic stabilization of Saccharomyces cerevisiae oenological strains by using benomyl

Wild-type oenological strains of Saccharomyces cerevisiae are usually aneuploid and heterozygotes; thus, when they are used as starters in must fermentation the resulting wine characteristics may vary from year to year. Treatment of a wild-type S. cerevisiae oenological strain with benomyl (methyl-l-butylcarbamoyl-2-benzimidazole carbamate), an antifungal agent shown to cause chromosome loss in yeasts, resulted in a stable starter strain in which the parental oenological traits were unchanged. The oenological S. cerevisiae strain was treated with benomyl in two different ways (A and B), and sporulation ability and spore viability were subsequently assayed. Treatment A resulted in both the highest numbers of tetrads and a reduction in DNA cell content, while treatment B increased spore viability. Fermentation assays were carried out with spore clones obtained from treatment A, and the concentrations of glycerol, lactic acid, acetic acid, and ethanol resulting from the treated strains were found to be similar to those of the parental strain. Benomyl treatment thus achieved stable, highly sporulating oenological S. cerevisiae strains of low ploidy, but preserved the desirable oenological properties of the parental strain (AU)

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Putative ancient microorganisms from amber nuggets.

Evolutionary microbiology studies based on the isolation of ancient DNA and/or microbial samples are scarce due to the difficulty of finding well preserved biological specimens. However, amber is a fossil resin with natural preserving properties for microbial cells and DNA. The visualization by transmission electron microscopy of different microorganism-like specimens found in amber nuggets from both the Miocene and the Cretaceous periods was accompanied by studies of ancient DNA obtained from the nuggets. After the design of specific primers based on the present sequences of both genes in Saccharomyces cerevisiae, the ancestral AGP2 sequence from the Miocene, as well as the 18S rRNA from the Cretaceous, were amplified.

Putative ancient microorganisms from amber nuggets

Evolutionary microbiology studies based on the isolation of ancient DNA and/or microbial samples are scarce due to the difficulty of finding well preserved biological specimens. However, amber is a fossil resin with natural preserving properties for microbial cells and DNA. The visualization by transmission electron microscopy of different microorganism-like specimens found in amber nuggets from both the Miocene and the Cretaceous periods was accompanied by studies of ancient DNA obtained from the nuggets. After the design of specific primers based on the present sequences of both genes in Saccharomyces cerevisiae, the ancestral AGP2 sequence from the Miocene, as well as the 18S rRNA from the Cretaceous, were amplified (AU)

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Enzybiotics: a look to the future, recalling the past.

The discovery and development of antibiotics was one of the greatest successes of Medicine in the 20th century and allowed the control of many diseases caused by microorganisms. Nevertheless, it is necessary to search constantly for new therapeutic tools in the continuing fight against disease-causing microorganisms and this probably leads us to today's concept of enzybiotics. Although microorganism-degrading enzymes have been known since the beginning of the last century, their use was soon forgotten because of the widespread use of antibiotics. The term enzybiotic is a hybrid word from "enzyme" and "antibiotic" and refers to phages: that is, viruses that attack and lyse bacteria and that can potentially help us to fight bacterial diseases. If the concept of enzybiotic is extended to antifungal enzymes, an enormous potential in the struggle against microorganism-due diseases may become available in the foreseeable future.