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Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.

Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL - Front Microbiol (2015)

View Article: PubMed Central - PubMed

Affiliation: Department for Innovation Biological, Agro-Food and Forest System, University of Tuscia Tuscia, Italy.

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Here we present the genome sequence of Rhodotorula graminis WP1, a pink-pigmented, encapsulated yeast strain belonging to the Basidiomycota phylum that was isolated from within stems of Populus trichocarpa growing in its native riparian environment alongside the Snoqualmie River in Western Washington state(Xin et al., )... Although numerous bacterial endophytes, the microorganisms living fully within plants, have been characterized, relatively few endophytic yeast strains have been studied (Doty, )... The genome of strain WP1 was the first endophytic yeast to be sequenced, and has been included in several genomic analyses (Spatafora et al., ; Nagy et al., ; Pendleton et al., )... Rhodotorula graminis strain WP1 was isolated from surface-sterilized shoot cuttings of poplar (P. trichocarpa) collected at the Three Forks Natural Area in King County, WA in the riparian zone of the Snoqualmie River (+47° 31′ 14.30″, −121° 46′ 28.32″) in August 2002, and glycerol stocks were frozen at −70°C... Sequenced reads were QC filtered for vector sequence, mitochondria, unanchored rDNA, and assembled with the Arachne assembler (Jaffe et al., )... The 21,013,998 bp assembly resulted in 26 scaffolds comprising 323 contigs with average read depth coverage of 8.55x (Table 1)... A common feature of endophytic bacteria and fungi is the production of phytohormones (Hardoim et al., ; Bulgarelli et al., ; Sukumar et al., ; Duca et al., )... Many of the beneficial plant-associated microorganisms that produce auxin rely on plant-exuded tryptophan as the precursor for biosynthesis of the auxin, indole-3-acetic acid (IAA) (Hardoim et al., )... Under aerobic conditions, the synthesis of (R,R)-2,3-butandiol (KEGG Entry: R02946) from (R)-acetoin by two putative NADH-dependent dehydrogenase (Protein ID: 39181; 46342) occurs through the spontaneous decarboxylation of 2-acetolactate into (R)-acetoin (Atsumi et al., )... In order to offer a more in depth overview about the presence of putative SSPs (aminoacidic seq. < 300) encoding genes, as supposed effectors involved in plant-microbe interactions (Rafiqi et al., ), we data mined the annotation file “SignalP” as described in Pendleton et al. but with slight modification... Since a putative CAP59 (Protein ID: 4796) and CAP10 (Protein ID: 7100) were detected in WP1, the genome sequence of non-pathogenic encapsulated yeast would be interesting for a comparative analysis between the capsule synthesis in WP1 and C. neoformans... The well-studied symbiotic Basidiomycota, Laccaria bicolor, begins the colonization of poplar roots using an array of effector proteins known as mycorrhiza-induced-cysteine-rich SSPs (MiSSPs) (Martin et al., )... A domain of the WP1 mRNA splicing factor Prp8 (ProteinID 49541) is partially homologous to the L. bicolor LbMiSSP17 effector protein (Protein ID: 332226)... The Laccaria-Populus interaction is a well-studied mycorrhizal mutualism at the molecular level (Podila et al., ; Aminov, ; Larsen et al., ; Plett et al., )... With comparative genomics studies of the bacteria, mycorrhizae, and yeast associated with Populus, an understanding of common themes in plant-mutualist interactions may emerge.

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Electron microscopy analysis of Rhodotorula graminis strain WP1; M, mitochondria; ER, endoplasmic reticulum; N, nucleus; Nu, nucleulus; V, vacuole; black triangles, capsule. Photo credit: Prof. Jimmie Lara, Department of Microbiology, University of Washington.
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Figure 1: Electron microscopy analysis of Rhodotorula graminis strain WP1; M, mitochondria; ER, endoplasmic reticulum; N, nucleus; Nu, nucleulus; V, vacuole; black triangles, capsule. Photo credit: Prof. Jimmie Lara, Department of Microbiology, University of Washington.

Mentions: An interesting feature of WP1 is the presence of a polysaccharidic capsule that surrounds the cellular body (Figure 1). A well-studied encapsulated yeast is represented by Cryptococcus neoformans, an opportunistic pathogen that causes meningoencephalitis in immunocompromised patients (Mitchell and Perfect, 1995). C. neoformans is ubiquitous in nature and the survival under different environmental conditions can be due to his biofilmogenic property. Within biofilms, microbial cells not only have an increased resistance and tolerance against a wide range of biotic and abiotic stress but also, under specific physiological and environmental conditions, can disperse and colonize new ecological niches (Ramage et al., 2009). The capability of C. neoformans to form a biofilm is dependent on the presence of the capsule. Deletion mutants in cap59 and cap10, two genes involved in the capsule synthesis and virulence, are unable to form biofilms, implicating that this structure exerts an important role in the adhesion and subsequent formation of cells aggregates (Garcia-Rivera et al., 2004; Martinez and Casadevall, 2005). Since a putative CAP59 (Protein ID: 4796) and CAP10 (Protein ID: 7100) were detected in WP1, the genome sequence of non-pathogenic encapsulated yeast would be interesting for a comparative analysis between the capsule synthesis in WP1 and C. neoformans.


Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.

Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL - Front Microbiol (2015)

Electron microscopy analysis of Rhodotorula graminis strain WP1; M, mitochondria; ER, endoplasmic reticulum; N, nucleus; Nu, nucleulus; V, vacuole; black triangles, capsule. Photo credit: Prof. Jimmie Lara, Department of Microbiology, University of Washington.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4585186&req=5

Figure 1: Electron microscopy analysis of Rhodotorula graminis strain WP1; M, mitochondria; ER, endoplasmic reticulum; N, nucleus; Nu, nucleulus; V, vacuole; black triangles, capsule. Photo credit: Prof. Jimmie Lara, Department of Microbiology, University of Washington.
Mentions: An interesting feature of WP1 is the presence of a polysaccharidic capsule that surrounds the cellular body (Figure 1). A well-studied encapsulated yeast is represented by Cryptococcus neoformans, an opportunistic pathogen that causes meningoencephalitis in immunocompromised patients (Mitchell and Perfect, 1995). C. neoformans is ubiquitous in nature and the survival under different environmental conditions can be due to his biofilmogenic property. Within biofilms, microbial cells not only have an increased resistance and tolerance against a wide range of biotic and abiotic stress but also, under specific physiological and environmental conditions, can disperse and colonize new ecological niches (Ramage et al., 2009). The capability of C. neoformans to form a biofilm is dependent on the presence of the capsule. Deletion mutants in cap59 and cap10, two genes involved in the capsule synthesis and virulence, are unable to form biofilms, implicating that this structure exerts an important role in the adhesion and subsequent formation of cells aggregates (Garcia-Rivera et al., 2004; Martinez and Casadevall, 2005). Since a putative CAP59 (Protein ID: 4796) and CAP10 (Protein ID: 7100) were detected in WP1, the genome sequence of non-pathogenic encapsulated yeast would be interesting for a comparative analysis between the capsule synthesis in WP1 and C. neoformans.

View Article: PubMed Central - PubMed

Affiliation: Department for Innovation Biological, Agro-Food and Forest System, University of Tuscia Tuscia, Italy.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Here we present the genome sequence of Rhodotorula graminis WP1, a pink-pigmented, encapsulated yeast strain belonging to the Basidiomycota phylum that was isolated from within stems of Populus trichocarpa growing in its native riparian environment alongside the Snoqualmie River in Western Washington state(Xin et al., )... Although numerous bacterial endophytes, the microorganisms living fully within plants, have been characterized, relatively few endophytic yeast strains have been studied (Doty, )... The genome of strain WP1 was the first endophytic yeast to be sequenced, and has been included in several genomic analyses (Spatafora et al., ; Nagy et al., ; Pendleton et al., )... Rhodotorula graminis strain WP1 was isolated from surface-sterilized shoot cuttings of poplar (P. trichocarpa) collected at the Three Forks Natural Area in King County, WA in the riparian zone of the Snoqualmie River (+47° 31′ 14.30″, −121° 46′ 28.32″) in August 2002, and glycerol stocks were frozen at −70°C... Sequenced reads were QC filtered for vector sequence, mitochondria, unanchored rDNA, and assembled with the Arachne assembler (Jaffe et al., )... The 21,013,998 bp assembly resulted in 26 scaffolds comprising 323 contigs with average read depth coverage of 8.55x (Table 1)... A common feature of endophytic bacteria and fungi is the production of phytohormones (Hardoim et al., ; Bulgarelli et al., ; Sukumar et al., ; Duca et al., )... Many of the beneficial plant-associated microorganisms that produce auxin rely on plant-exuded tryptophan as the precursor for biosynthesis of the auxin, indole-3-acetic acid (IAA) (Hardoim et al., )... Under aerobic conditions, the synthesis of (R,R)-2,3-butandiol (KEGG Entry: R02946) from (R)-acetoin by two putative NADH-dependent dehydrogenase (Protein ID: 39181; 46342) occurs through the spontaneous decarboxylation of 2-acetolactate into (R)-acetoin (Atsumi et al., )... In order to offer a more in depth overview about the presence of putative SSPs (aminoacidic seq. < 300) encoding genes, as supposed effectors involved in plant-microbe interactions (Rafiqi et al., ), we data mined the annotation file “SignalP” as described in Pendleton et al. but with slight modification... Since a putative CAP59 (Protein ID: 4796) and CAP10 (Protein ID: 7100) were detected in WP1, the genome sequence of non-pathogenic encapsulated yeast would be interesting for a comparative analysis between the capsule synthesis in WP1 and C. neoformans... The well-studied symbiotic Basidiomycota, Laccaria bicolor, begins the colonization of poplar roots using an array of effector proteins known as mycorrhiza-induced-cysteine-rich SSPs (MiSSPs) (Martin et al., )... A domain of the WP1 mRNA splicing factor Prp8 (ProteinID 49541) is partially homologous to the L. bicolor LbMiSSP17 effector protein (Protein ID: 332226)... The Laccaria-Populus interaction is a well-studied mycorrhizal mutualism at the molecular level (Podila et al., ; Aminov, ; Larsen et al., ; Plett et al., )... With comparative genomics studies of the bacteria, mycorrhizae, and yeast associated with Populus, an understanding of common themes in plant-mutualist interactions may emerge.

No MeSH data available.


Related in: MedlinePlus