Genomics of alternative sulfur utilization in ascomycetous yeasts

Linder, Tomas

doi:10.1099/mic.0.060285-0

Cited by 19 publications

(29 citation statements)

References 47 publications

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“…Kluveromyces, Lodderomyces and Nakaseomyces are sexual stages of commonly occurring Candida spp. in the wastewater or the sewage sludge (Kutty and Philip 2008; Linder 2012). In addition to this, occurrence of these Candida spp.…”

Section: Discussionmentioning

confidence: 99%

Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

Samson

Rajput

Shah

et al. 2019

Preprint

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38River confluences are a hub of biodiversity with limited information with respect to the structure and the 39 functions of the microbial communities. The 'River Ganges' is the national river of India, having manifold 40 significance such as social, mythological, historic, geographic and agro-economic. It forms a sacred confluence 41 (known as Triveni Sangam) with River Yamuna at Prayagraj, India. Recent reports indicated the presence of fecal 42 coliform bacteria, an indicator recognized for water contamination in Ganges River leading to pollution. However, 43Fungi are also gaining attention as potential biological indicators of the trophic status of some rivers globally, but 44 remain under-explored in terms of diversity, ecology and functional aspects. We performed whole long read, 45 metagenome sequencing (MinION) of the sediment samples collected in December 2017 from confluence zone of 46 Ganges and Yamuna Rivers spanning the pre-confluence, confluence and post-confluence zones. Mycobiome reads 47 revealed a plethora of fungal communities, extending from saprophytes, endoparasites and edible fungi, to human 48 pathogens, plant pathogens and toxin producers. The fungal genera recognized as bio-indicators of river pollution 49 (Aspergillus, Penicillium) and eutrophication (Kluveromyces, Lodderomyces, and Nakaseomyces), were present in 50 all samples. Functional gene analyses of myco-communities uncovered hits for neurodegenerative diseases and 51 xenobiotic degradation potential, supporting bio-indicators of pollution. This study forms a foundational basis for 52 understanding the impact of various anthropogenic activities on the mycobiome, as a bio-indicator of pollution 53 across the confluence of Ganges and Yamuna Rivers and post-confluence of River Ganges, and could be useful in 54 mitigating strategies for cleaning strategies of the Ganges River.55

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Section: Discussionmentioning

confidence: 99%

Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

Samson

Rajput

Shah

et al. 2019

Preprint

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“…A sulfur-limited glucose medium (SLD) with only trace amounts of sulfate (≤6 μM) was used for assaying growth on individual sulfur-containing compounds [ 5 ]. SLD medium consisted of 1.2 g yeast nitrogen base without amino acids, ammonium sulfate, or magnesium l −1 (Formedium Ltd., Norfolk, UK), 4 g ammonium chloride l −1 , 0.84 g magnesium chloride hexahydrate l −1 , and 20 g glucose l −1 .…”

Section: Methodsmentioning

confidence: 99%

“…Many microorganisms can also assimilate non-amino acid organosulfur compounds such as sulfoxides, sulfones, sulfonates, and sulfate esters [ 5 , 14 ], which are abundant in nature [ 1 , 10 ]. These compounds are first desulfurized to release inorganic sulfur, usually in the form of either sulfate or sulfite [ 3 – 5 , 14 ], which can then be assimilated through the inorganic sulfur assimilation pathway. In the common Baker’s yeast Saccharomyces cerevisiae , the JLP1 gene, which encodes an α-ketoglutarate-dependent dioxygenase, is responsible for the desulfurization of sulfonates [ 3 ] and possibly sulfate esters as well (Fig.…”

Section: Introductionmentioning

confidence: 99%

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ATP Sulfurylase is Essential for the Utilization of Sulfamate as a Sulfur Source in the Yeast Komagataella pastoris (syn. Pichia pastoris)

Linder

2017

Curr Microbiol

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The methylotrophic yeast Komagataella pastoris (syn. Pichia pastoris) is one of the few known yeasts that can utilize sulfamate () as a sulfur source. The biochemical pathway responsible for the catabolism of sulfamate has yet to be identified. The present study sought to investigate whether sulfamate catabolism proceeds through either of the inorganic sulfur intermediates sulfate () or sulfite () before its assimilation and subsequent incorporation into sulfur-containing amino acids and their derivatives. Two key genes in the K. pastoris inorganic sulfur assimilation pathway were deleted separately and the ability of each deletion mutant to utilize sulfamate and other selected sulfur sources was studied. Deletion of the MET3 gene (which encodes the enzyme ATP sulfurylase) did not affect growth on l-methionine, sulfite, methanesulfonate, or taurine but completely abolished growth on sulfate, methyl sulfate and sulfamate. Deletion of the MET5 gene (which encodes the β subunit of the enzyme sulfite reductase) abolished growth on all tested sulfur sources except l-methionine. These results suggest that the catabolism of sulfamate proceeds through a sulfate intermediate before its assimilation.

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“…cerevisiae species of budding yeast are typically referred to as “nonconventional yeasts”. Nonconventional yeasts have been shown to possess a wider range of metabolic pathways for the assimilation of carbon (Riley et al, ), nitrogen (Large, ), and sulfur (Linder, ) compared with Sac. cerevisiae .…”

Section: Introductionmentioning

confidence: 99%

A genomic survey of nitrogen assimilation pathways in budding yeasts (sub‐phylum Saccharomycotina)

Linder

2018

Yeast

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Sequenced genomes of 149 species of budding yeast (including 62 species with draft genomes that currently lack gene annotations) were surveyed for the presence of 24 genes associated with the assimilation of amines, uracil, dihydropyrimidines, purines, uric acid, allantoin, and nitrate as nitrogen sources. Genes for the assimilation of primary amines were distributed broadly across the Saccharomycotina while choline assimilation appeared to be mostly restricted to the families Debaryomycetaceae, Metschnikowiaceae, and Pichiaceae. Conversely, the uracil catabolic pathway was completely absent in Debaryomycetaceae and Metschnikowiaceae but present in the majority of the remaining Saccharomycotina. The super-pathway for assimilation of purines, uric acid, and allantoin was present in the majority of surveyed species.Genes for the assimilation of nitrate were restricted to a minority of species in families Phaffomycetaceae, Pichiaceae, and Trichomonascaceae as well as some currently unassigned genera. This study also successfully identified yeast homologs of all six previously known eukaryotic genes involved in the biosynthesis of the molybdenum cofactor, which is required for the activity of the nitrogen assimilation-associated enzymes nitrate reductase and xanthine oxidoreductase. Analysis of 1,187 upstream intergenic regions identified three novel putative regulatory motifs for the assimilation of uracil, purines, and uric acid as well as a possible role for the MADS-box transcription factor Mcm1 in the regulation of amine assimilation genes.

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Genomics of alternative sulfur utilization in ascomycetous yeasts

Cited by 19 publications

References 47 publications

Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

ATP Sulfurylase is Essential for the Utilization of Sulfamate as a Sulfur Source in the Yeast Komagataella pastoris (syn. Pichia pastoris)

A genomic survey of nitrogen assimilation pathways in budding yeasts (sub‐phylum Saccharomycotina)

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