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

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to validating the monophyly of the genus Rhodotorula. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

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Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

10.7287/peerj.preprints.3219v2 ◽

2017 ◽

Author(s):

Han Ming Gan ◽

Bolaji N Thomas ◽

Nicole T Cavanaugh ◽

Grace H Morales ◽

Ashley N Mayers ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Homing Endonuclease ◽

Antibacterial Properties ◽

Nuclear Genome ◽

Carotenoid Biosynthesis ◽

Open Reading Frames ◽

Whole Genome ◽

Rhodotorula Mucilaginosa ◽

Carotenoid Production ◽

Genome Phylogeny

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to validating the monophyly of the genus Rhodotorula. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

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Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

10.7287/peerj.preprints.3219v1 ◽

2017 ◽

Author(s):

Han Ming Gan ◽

Bolaji N Thomas ◽

Nicole T Cavanaguh ◽

Grace H Morales ◽

Ashley N Mayers ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Homing Endonuclease ◽

Antibacterial Properties ◽

Nuclear Genome ◽

Carotenoid Biosynthesis ◽

Open Reading Frames ◽

Whole Genome ◽

Rhodotorula Mucilaginosa ◽

Carotenoid Production ◽

Genome Phylogeny

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to validating the monophyly of the genus Rhodotorula. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

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Effects of some factors on carotenoid biosynthesis by Rhodotorula Muclaginosa

ENGINEERING AND TECHNOLOGY ◽

10.46223/hcmcoujs.tech.en.9.1.352.2019 ◽

2020 ◽

Vol 9 (1) ◽

pp. 62-69

Author(s):

Ly Thi Minh Hien ◽

Pham Thi Hang Nga

Keyword(s):

Yeast Extract ◽

Nutrient Concentration ◽

Aqueous Media ◽

Carotenoid Biosynthesis ◽

Natural Antioxidants ◽

Rhodotorula Mucilaginosa ◽

Fermentation Time ◽

Stress Environment ◽

H2o2 Solution ◽

Fermentation Media

Carotenoid compounds are the popular natural antioxidants which are often isolated from plants. There have been more and more researches on carotenoid biosynthesis towards lowering product prices. In this study, in order to produce carotenoid, Rhodotorula mucilaginosa was grown on aqueous media composed of carbon source (glucose, glycerol), nitrogen source (yeast extract, (NH4)2SO4). The optimum nutrient concentration was 10g/L glucose, 10g/L glycerol, the ratio of yeast extract and (NH4)2SO4 (3:7). The fermentation time for obtaining the highest carotenoid yield was 10 days in our research condition. Additionally, some oxidative stress environment for Rhodotorula mucilaginosa was be studied. The result has shown that the low level of Cu2+ (4.5mM) or 1% H2O2 solution (% v/v) in the fermentation media could increase the carotenoid biosynthesis.

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Peer Review #2 of "Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis (v0.1)"

10.7287/peerj.4030v0.1/reviews/2 ◽

2017 ◽

Keyword(s):

Whole Genome Sequencing ◽

Peer Review ◽

Genome Sequencing ◽

Carotenoid Biosynthesis ◽

Whole Genome ◽

Rhodotorula Mucilaginosa

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Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

PeerJ ◽

10.7717/peerj.4030 ◽

2017 ◽

Vol 5 ◽

pp. e4030 ◽

Cited By ~ 12

Author(s):

Han Ming Gan ◽

Bolaji N. Thomas ◽

Nicole T. Cavanaugh ◽

Grace H. Morales ◽

Ashley N. Mayers ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Homing Endonuclease ◽

Antibacterial Properties ◽

Nuclear Genome ◽

Carotenoid Biosynthesis ◽

Open Reading Frames ◽

Whole Genome ◽

Rhodotorula Mucilaginosa ◽

Carotenoid Production ◽

Genome Phylogeny

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced Rhodotorula species. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

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Effect of Selected Cations and B Vitamins on the Biosynthesis of Carotenoids by Rhodotorula mucilaginosa Yeast in the Media with Agro-Industrial Wastes

Applied Sciences ◽

10.3390/app112411886 ◽

2021 ◽

Vol 11 (24) ◽

pp. 11886

Author(s):

Anna Maria Kot ◽

Stanisław Błażejak ◽

Rita Brzezińska ◽

Wioletta Sęk ◽

Marek Kieliszek

Keyword(s):

Raw Materials ◽

Potato Starch ◽

Pantothenic Acid ◽

Carotenoid Biosynthesis ◽

Culture Conditions ◽

B Vitamins ◽

Industrial Wastes ◽

Biodiesel Production ◽

Rhodotorula Mucilaginosa ◽

Β Carotene

In recent years, there has been an increase in the search for novel raw materials for the production of natural carotenoids. Among yeasts, Rhodotorula species have the ability to synthesize carotenoids, mainly β-carotene, torulene, and torularhodin, depending on the culture conditions. This study aimed to determine the effect of selected cations (barium, zinc, aluminum, manganese) and B vitamins (biotin, riboflavin, niacin, pantothenic acid) on the biosynthesis of carotenoids by Rhodotorula mucilaginosa MK1 and estimate the percentages of β-carotene, torulene, and torularhodin synthesized by the yeast. The cultivation was carried out in a medium containing glycerol (waste resulting from biodiesel production) as a carbon source and potato wastewater (waste resulting from potato starch production) as a nitrogen source. Carotenoid biosynthesis was stimulated by the addition of aluminum (300 mg/L) or aluminum (300 mg/L) and niacin (100 µg/L) to the medium. The number of carotenoids produced by R. mucilaginosa MK1 in the medium containing only aluminum and in the medium with aluminum and niacin was 146.7 and 180.5 µg/gd.m., respectively. This content was 101% and 147% higher compared to the content of carotenoids produced by yeast grown in the control medium (73.0 µg/gd.m.). The addition of aluminum and barium seemed to have a positive effect on the biosynthesis of torulene, and the percentage of this compound increased from 31.86% to 75.20% and 68.24%, respectively. Niacin supplementation to the medium increased the percentage of torularhodin produced by the yeast from 23.31% to 31.59–33.79%. The conducted study showed that there is a possibility of intensifying carotenoid biosynthesis by red yeast and changing the percentages of individual carotenoids fractions by adding cations or B vitamins to the medium. Further research is needed to explain the mechanism of action of niacin on the stimulation of torularhodin biosynthesis.

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