Draft Genome Sequence of Rhodotorula mucilaginosa, an Emergent Opportunistic Pathogen

Wine is a complex beverage, comprising thousands of metabolites that are produced through the action of a plethora of yeasts and bacteria during fermentation of grape must. These microbial communities originate in the vineyard and the winery and reflect the influence of several factors including grape variety, geographical location, climate, vineyard spraying, technological practices, processing stage and season (pre-harvest, harvest, post-harvest). Vineyard and winery microbial communities have the potential to participate during fermentation and influence wine flavour and aroma. Therefore, there is an enormous interest in isolating and characterising these communities, particularly non-Saccharomyces yeast species to increase wine flavour diversity, while also exploting regional signature microbial populations to enhance regionality. In this review we describe the role and relevance of the main non-Saccharomyces yeast species found in vineyards and wineries. This includes the latest reports covering the application of these species for winemaking; and the biotechnological characteristics and potential applications of non-Saccharomyces species in other areas. In particular, we focus attention on the species for which molecular and genomic tools and resources are available for study. Copyright © 2016 John Wiley & Sons, Ltd.

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“…graminis (Firrincieli et al ., ) and R . ‬ mucilaginosa ‬ (Deligios et al ., ). The genomes of the Rhodotorula spp.…”

Section: Rhodotorula Sppmentioning

confidence: 97%

“…Genome sequences are available for R. toruloides (synonym, R. gracilis) (Kumar et al, 2012a;Morin et al, 2014), R. glutinis (Paul et al, 2014), R. graminis (Firrincieli et al, 2015) and R. mucilaginosa (Deligios et al, 2015). The genomes of the Rhodotorula spp.…”

Section: Rhodotorula Sppmentioning

confidence: 99%

Yeasts found in vineyards and wineries

Varela

Borneman

2016

Yeast

116

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“…glutinis and recently ascribed to the species R . mucilaginosa (Deligios et al ., ), deposited at the Yeast Collection of Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Universita` Politecnica delle Marche (Ancona, Italy); and 400A15 and 200A6, primary mutants of C2.5 t1 deposited at the Culture Collection of the Dipartimento di Agraria, Università degli Studi di Sassari (Sassari, Italy). Mutants were obtained by UV mutagenesis, as described by Cutzu et al .…”

Section: Methodsmentioning

confidence: 99%

“…Three alternative sequence databases were used for peptide identification from gel spots: S‐DB, comprising all UniProtKB (v. 2015_02) sequences belonging to the order Sporidiobolales (13 005 sequences); C‐DB, comprising all UniProtKB (v. 2015_02) sequences related to the carotenoid biosynthesis pathway (starting from acetyl‐coenzyme A acetyltransferase to lycopene cyclase), irrespective of the organism of provenience, with clustering at 90% homology (243 146 sequences); and G‐DB, comprising all sequences generated upon genome sequencing of the C2.5t1 strain, as described in Deligios et al . () (6412 sequences, of which 4352 associated to a UniProt Accession No. upon blastp alignment).…”

Section: Methodsmentioning

confidence: 99%

“…Recently, the draft genome sequence of R . mucilaginosa has been released (Deligios et al ., ). However, although our knowledge on red yeasts is expected to increase in the near future, due to the renewed interest on their biotechnological potential and the recent development of molecular and ‐omic tools (Mannazzu et al ., ), this species is still poorly characterized at the genomic and proteomic level.…”

Section: Introductionmentioning

confidence: 97%

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Proteomic analysis of Rhodotorula mucilaginosa: dealing with the issues of a non‐conventional yeast

Addis

Tanca

Landolfo

et al. 2016

Yeast

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Red yeasts ascribed to the species Rhodotorula mucilaginosa are gaining increasing attention, due to their numerous biotechnological applications, spanning carotenoid production, liquid bioremediation, heavy metal biotransformation and antifungal and plant growth-promoting actions, but also for their role as opportunistic pathogens. Nevertheless, their characterization at the 'omic' level is still scarce. Here, we applied different proteomic workflows to R. mucilaginosa with the aim of assessing their potential in generating information on proteins and functions of biotechnological interest, with a particular focus on the carotenogenic pathway. After optimization of protein extraction, we tested several gel-based (including 2D-DIGE) and gel-free sample preparation techniques, followed by tandem mass spectrometry analysis. Contextually, we evaluated different bioinformatic strategies for protein identification and interpretation of the biological significance of the dataset. When 2D-DIGE analysis was applied, not all spots returned a unambiguous identification and no carotenogenic enzymes were identified, even upon the application of different database search strategies. Then, the application of shotgun proteomic workflows with varying levels of sensitivity provided a picture of the information depth that can be reached with different analytical resources, and resulted in a plethora of information on R. mucilaginosa metabolism. However, also in these cases no proteins related to the carotenogenic pathway were identified, thus indicating that further improvements in sequence databases and functional annotations are strictly needed for increasing the outcome of proteomic analysis of this and other non-conventional yeasts.

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Impairment of carotenoid biosynthesis through CAR1 gene mutation results in CoQ10, sterols, and phytoene accumulation in Rhodotorula mucilaginosa

Tkáčová

Zara

Ianiri

et al. 2021

Appl Microbiol Biotechnol

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Red yeasts, mainly included in the genera Rhodotorula, Rhodosporidiobolus, and Sporobolomyces, are renowned biocatalysts for the production of a wide range of secondary metabolites of commercial interest, among which lipids, carotenoids, and other isoprenoids. The production of all these compounds is tightly interrelated as they share acetyl-CoA and the mevalonate pathway as common intermediates. Here, T-DNA insertional mutagenesis was applied to the wild type strain C2.5t1 of Rhodotorula mucilaginosa for the isolation of albino mutants with impaired carotenoids biosynthesis. The rationale behind this approach was that a blockage in carotenoid biosynthetic pathway could divert carbon flux toward the production of lipids and/or other molecules deriving from terpenoid precursors. One characterized albino mutant, namely, strain W4, carries a T-DNA insertion in the CAR1 gene coding for phytoene desaturase. When cultured in glycerol-containing medium, W4 strain showed significant decreases in cell density and fatty acids content in respect to the wild type strain. Conversely, it reached significantly higher productions of phytoene, CoQ 10 , and sterols. These were supported by an increased expression of CAR 2 gene that codes for phytoene synthase/lycopene cyclase. Thus, in accordance with the starting hypothesis, the impairment of carotenoids biosynthesis can be explored to pursue the biotechnological exploitation of red yeasts for enhanced production of secondary metabolites with several commercial applications. Key points• The production of lipids, carotenoids, and other isoprenoids is tightly interrelated. • CAR1 gene mutation results in the overproduction of phytoene, CoQ 10 , and sterols. • Albino mutants are promising tools for the production of secondary metabolites.

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Draft Genome Sequence of Rhodotorula mucilaginosa, an Emergent Opportunistic Pathogen

Cited by 27 publications

References 20 publications

Yeasts found in vineyards and wineries

Yeasts found in vineyards and wineries

Proteomic analysis of Rhodotorula mucilaginosa: dealing with the issues of a non‐conventional yeast

Impairment of carotenoid biosynthesis through CAR1 gene mutation results in CoQ10, sterols, and phytoene accumulation in Rhodotorula mucilaginosa

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