The red yeast X. dendrorhous is one of the few natural sources of astaxanthin, a carotenoid used in aquaculture for salmonid fish pigmentation and in the cosmetic and pharmaceutical industries for its antioxidant properties. Genetic control of carotenogenesis is well characterized in this yeast; however, little is known about the regulation of the carotenogenesis process. Several lines of evidence have suggested that carotenogenesis is regulated by catabolic repression, and the aim of this work was to identify and functionally characterize the X. dendrorhous MIG1 gene encoding the catabolic repressor Mig1, which mediates transcriptional glucose-dependent repression in other yeasts and fungi. The identified gene encodes a protein of 863 amino acids that demonstrates the characteristic conserved features of Mig1 proteins, and binds in vitro to DNA fragments containing Mig1 boxes. Gene functionality was demonstrated by heterologous complementation in a S. cerevisiae mig1- strain; several aspects of catabolic repression were restored by the X. dendrorhous MIG1 gene. Additionally, a X. dendrorhous mig1- mutant was constructed and demonstrated a higher carotenoid content than the wild-type strain. Most important, the mig1- mutation alleviated the glucose-mediated repression of carotenogenesis in X. dendrorhous: the addition of glucose to mig1- and wild-type cultures promoted the growth of both strains, but carotenoid synthesis was observed only in the mutant strain. Transcriptomic and RT-qPCR analyses revealed that several genes were differentially expressed between X. dendrorhous mig1- and the wild-type strain when cultured with glucose as the sole carbon source. The results obtained in this study demonstrate that catabolic repression in X. dendrorhous is an active process in which the identified MIG1 gene product plays a central role in the regulation of several biological processes, including carotenogenesis.

BackgroundThe cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their activity, and the electrons are supplied by NAD(P)H through a P450 electron donor system, which is generally a cytochrome P450 reductase (CPR). The yeast Xanthophyllomyces dendrorhous has evolved an exclusive P450-CPR system that specializes in the synthesis of astaxanthin, a carotenoid with commercial potential. For this reason, the aim of this work was to identify and characterize other potential P450 genes in the genome of this yeast using a bioinformatic approach.ResultsThirteen potential P450-encoding genes were identified, and the analysis of their deduced proteins allowed them to be classified in ten different families: CYP51, CYP61, CYP5139 (with three members), CYP549A, CYP5491, CYP5492 (with two members), CYP5493, CYP53, CYP5494 and CYP5495. Structural analyses of the X. dendrorhous P450 proteins showed that all of them have a predicted transmembrane region at their N-terminus and have the conserved domains characteristic of the P450s, including the heme-binding region (FxxGxRxCxG); the PER domain, with the characteristic signature for fungi (PxRW); the ExxR motif in the K-helix region and the oxygen-binding domain (OBD) (AGxDTT); also, the characteristic secondary structure elements of all the P450 proteins were identified. The possible functions of these P450s include primary, secondary and xenobiotic metabolism reactions such as sterol biosynthesis, carotenoid synthesis and aromatic compound degradation.ConclusionsThe carotenogenic yeast X. dendrorhous has thirteen P450-encoding genes having potential functions in primary, secondary and xenobiotic metabolism reactions, including some genes of great interest for fatty acid hydroxylation and aromatic compound degradation. These findings established a basis for future studies about the role of P450s in the carotenogenic yeast X. dendrorhous and their potential biotechnological applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3942-9) contains supplementary material, which is available to authorized users.

BackgroundThe yeast Xanthophyllomyces dendrorhous produces carotenoids of commercial interest, including astaxanthin and β-carotene. Although carotenogenesis in this yeast and the expression profiles of the genes controlling this pathway are known, the mechanisms regulating this process remain poorly understood. Several studies have demonstrated that glucose represses carotenogenesis in X. dendrorhous, suggesting that this pathway could be regulated by catabolic repression. Catabolic repression is a highly conserved regulatory mechanism in eukaryotes and has been widely studied in Saccharomyces cerevisiae. Glucose-dependent repression is mainly observed at the transcriptional level and depends on the DNA-binding regulator Mig1, which recruits the co-repressor complex Cyc8–Tup1, which then represses the expression of target genes. In this work, we studied the regulation of carotenogenesis by catabolic repression in X. dendrorhous, focusing on the role of the co-repressor complex Cyc8–Tup1.ResultsThe X. dendrorhous CYC8 and TUP1 genes were identified, and their functions were demonstrated by heterologous complementation in S. cerevisiae. In addition, cyc8 − and tup1 − mutant strains of X. dendrorhous were obtained, and both mutations were shown to prevent the glucose-dependent repression of carotenogenesis in X. dendrorhous, increasing the carotenoid production in both mutant strains. Furthermore, the effects of glucose on the transcript levels of genes involved in carotenogenesis differed between the mutant strains and wild-type X. dendrorhous, particularly for genes involved in the synthesis of carotenoid precursors, such as HMGR, idi and FPS. Additionally, transcriptomic analyses showed that cyc8 − and tup1 − mutations affected the expression of over 250 genes in X. dendrorhous. ConclusionsThe CYC8 and TUP1 genes are functional in X. dendrorhous, and their gene products are involved in catabolic repression and carotenogenesis regulation. This study presents the first report involving the participation of Cyc8 and Tup1 in carotenogenesis regulation in yeast.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0597-1) contains supplementary material, which is available to authorized users.

Xanthophyllomyces dendrorhous is a carotenogenic yeast with a singular metabolic capacity to produce astaxanthin, a valuable antioxidant pigment. This yeast can assimilate several carbon sources and sustain fermentation even under aerobic conditions. Since astaxanthin biosynthesis is affected by the carbon source, the study of carotenogenesis regulatory mechanisms is key for improving astaxanthin yield in X. dendrorhous. This study aimed to elucidate the regulation of the metabolism of different carbon sources and the phenomenon of catabolic repression in this yeast. To this end, protein and transcript levels were quantified by iTRAQ (isobaric tags for relative and absolute quantification) and transcriptomic sequencing (RNA-seq) in the wild-type strain under conditions of glucose, maltose, or succinate treatment and in the mutant strains for genes MIG1, CYC8, and TUP1 under conditions of glucose treatment. Alternative carbon sources such as maltose and succinate affected the relative abundances of 14% of the wild-type proteins, which were mainly grouped into the carbohydrate metabolism category, with the glycolysis/gluconeogenesis and citrate cycle pathways being the most highly represented pathways. Each mutant strain showed significant proteomic profile changes, affecting approximately 2% of the total proteins identified, compared to the wild-type strain under glucose treatment conditions. Similarly to the results seen with the alternative carbon sources, the changes in the mutant strains mainly affected carbohydrate metabolism, with glycolysis/gluconeogenesis and the pentose phosphate and citrate cycle pathways being the most highly represented pathways. Our results showed convergence between carbon assimilation and catabolic repression in the strains studied. Interestingly, indications of cooperative, opposing, and overlapping processes during catabolic regulation were found. We also identified target proteins of the regulatory processes, reinforcing the likelihood of catabolic repression at the posttranscriptional level. IMPORTANCE The conditions affecting catabolic regulation in X. dendrorhous are complex and suggest the presence of an alternative mechanism of regulation. The repressors Mig1, Cyc8, and Tup1 are essential elements for the regulation of the use of glucose and other carbon sources. All play different roles but, depending on the growth conditions, can work in convergent, synergistic, and complementary ways to use carbon sources and to regulate other targets for yeast metabolism. Our results reinforced the belief that further studies in X. dendrorhous are needed to clarify a specific regulatory mechanism at the domain level of the repressors as well as its relationship with those of other metabolic repressors, i.e., the stress response, to elucidate carotenogenic regulation at the transcriptomic and proteomic levels in this yeast.

Carotenoids are naturally produced by plants, algae, and some bacteria and fungi, fulfilling functions as accessory photosynthetic pigments and antioxidants. Among carotenoids, the xanthophyll astaxanthin stands out for its antioxidant and nutraceutical properties, which are beneficial to human health, and also for its use in the aquaculture industry as nutritional supplement of salmonid fish. Many studies have focused on the search of natural sources of astaxanthin as an alternative production that guarantees the beneficial properties of this compound. In nature, few astaxanthin-producing organisms are known, being the microalgae Haematococcus pluvialis and the yeast Xanthophyllomyces dendrorhous the most promising microbiological systems for the biotechnological production of this carotenoid. In this chapter, we describe the carotenogenic pathways in these microorganisms and the proposed carotenogenesis regulation mechanisms. As an example, the influence of the carbon source, the regulation by catabolic repression and by sterols in the carotenogenesis in the yeast X. dendrorhous is described.

Pseudomonas syringae is a Gram-negative bacterium that infects a wide range of plants, causing significant economic losses in agricultural production. The pathogen exhibits a high degree of genetic and phenotypic diversity, which has led to the classification of P. syringae strains into different pathovars based on their host range and disease symptoms. Copper-based products have traditionally been used to manage infections in agriculture, but the emergence of copper-resistant strains has become a significant concern. Biological control is a promising strategy to manage P. syringae, as it offers an environmentally friendly and sustainable approach to disease management. The review includes an overview of the biology and epidemiology of P. syringae, and of the mechanisms of action of various biological control agents, mainly microorganisms (antagonistic bacteria, and fungi) and bacteriophages. Specifically, this review highlights the renewed interest in bacteriophages (bacteria-infecting viruses) due to their advantages over other eco-friendly management methods, thanks to their bactericidal properties and potential to target specific pathogenic bacteria. The potential benefits and limitations of biological control are also examined, along with research directions to optimize the use of this approach for the management of P. syringae.

Pistachio crops have a great economic potential, as their global production has increased dramatically over the past few decades. Therefore, it is important to maintain the healthy phytosanitary status of pistachio crops. In a Chilean pistachio orchard, a dieback of the trees was observed, with blighting of twigs and severe necrosis in the trunk and twigs. Bacterial isolation, pathogenicity tests and molecular characterization were conducted to determine the causal agent of the observed disease. The bacterial isolation and analysis of 16S rRNA gene led to the identification of Pantoea genus bacteria. Pathogenicity tests carried out on fruits inoculated with Pantoea isolates induced large necrosis seven days post-inoculation. Further inoculations were carried out on pruning cuttings and on the trunk of 18-month-old pistachio plants. Thirty-one weeks after inoculation, necrotic lesions were observed in the wood of pistachio plants. Sequence analysis of housekeeping genes enabled the isolated bacterium to be identified as Pantoa agglomerans, and to verify its role as the causal agent of the pistachio dieback with necrotic lesions. This is the first report of an occurrence of P. agglomerans inducing dieback in pistachio.

Tomatoes are susceptible to bacterial diseases, mainly related to some Pseudomonas syringae pathovars. Many Pseudomonas species are considered innocuous, but some have shown the ability to opportunistically infect tomato plants. Antimicrobial compounds have been used to control pathogenic organisms, and this can lead to environmental selection of phenotypically resistant bacteria. We assessed the diversity of Pseudomonas species associated with tomato plants from Chilean orchards and analyzed antimicrobial resistance among the isolated strains. A total of 64 Pseudomonas isolates (P. syringae, P. viridiflava, P. fluorescens, P. koreensis, P. gessardii, and P. azotoformans) were evaluated for their phenotypic resistance to seven antimicrobial compounds, including copper, streptomycin, and five other antibiotics typically not used in agriculture. The results showed that 95%, 86%, 70%, 53%, 45%, and 1.6% of the isolates were resistant to rifampin, ampicillin, copper, chloramphenicol, streptomycin, and tetracycline, respectively, with no isolates being resistant to gentamicin. A total of 96.9% of Pseudomonas isolates exhibited a multiresistant phenotype to at least two of the antimicrobials tested. The most frequent multiresistance phenotype was Cu-Str-Amp-Cm-Rif (23.4%). The presence of Pseudomonas strains tolerant to conventional bactericides, metals, and other antimicrobials makes these bacteria an emerging threat to the agriculture industry and to human health.