Molecular Characterization of the Relationships amongAmylomyces rouxii,Rhizopus oryzae, andRhizopus delemar

Kito, Hideki; Abe, Ayumi; Sujaya, I Nengah; Oda, Yuji; Asano, Kozo; Sone, Toshio

doi:10.1271/bbb.80773

Cited by 19 publications

(16 citation statements)

References 18 publications

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“…In addition, the domesticated form of R. microspores has been a widely used starter culture for the production of tempeh from fermented soybean (Hachmeister and Fung 1993). Its close relative, R. delemar , was also well known as efficient ethanol and fumaric acid producer by fermentation (Kito, et al 2009; Straathof and van Gulik 2012). P. blakesleeanus h was known for capable of fermenting sugar into β-carotene at an industrial scale, which is derived from the end product of glycolysis (Kaessmann, et al 2009).…”

Section: Resultsmentioning

confidence: 99%

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

Mullis¹,

Lü²,

Ye³

et al. 2019

Preprint

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9Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular 2 0 machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 2 1 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some 2 2 fungal species have maintained duplicate copies in most RP families. How the RP genes were 2 3 duplicated and maintained in these fungal species, and their functional significance remains 2 4 unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred 2 5 the timing and nature of gene duplication for all RP families. We found that massive duplications 2 6 of RP genes have independently occurred by different mechanisms in three distantly related 2 7 lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly 2 8 created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP 2 9 genes were likely generated by retroposition, which is unexpected considering their dosage 3 0 sensitivity. The sequences of most RP paralogs in each species have been homogenized by 3 1 repeated gene conversion, demonstrating parallel concerted evolution, which might have 3 2 facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and 3 3 retention of RP genes increased RP transcription abundance. Physiological data indicate that 3 4increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through 3 5 fermentation while maintaining high growth rates, providing selective advantages to these 3 6 species in sugar-rich environments.

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Section: Resultsmentioning

confidence: 99%

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

Mullis¹,

Lü²,

Ye³

et al. 2019

Preprint

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“…Of note, several possible identifications (up to four different species) were reported by two laboratories. In one case, corresponding to one R. oryzae-infected tissue sample, the reported identification based on sequence homology analysis with the GenBank entries was Rhizopus oryzae/Rhizopus japonicus/ Amylomyces rouxii (the last two names could be considered synonyms of R. oryzae [16,25]). In two other cases, both of which corresponded to R. microsporus-infected tissues, the identifications reported were Rhizopus microsporus/Rhizopus azygosporus/ Rhizopus sexualis/Rhizopus oryzae and Rhizopus microsporus var.…”

Section: Resultsmentioning

confidence: 99%

Molecular Detection and Identification of Zygomycetes Species from Paraffin-Embedded Tissues in a Murine Model of Disseminated Zygomycosis: a Collaborative European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Fungal Infection Study Group (EFISG) Evaluation

et al. 2010

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The present study was performed to assess the interlaboratory reproducibility of the molecular detection and identification of species of Zygomycetes from formalin-fixed paraffin-embedded kidney and brain tissues obtained from experimentally infected mice. Animals were infected with one of five species (Rhizopus oryzae, Rhizopus microsporus, Lichtheimia corymbifera, Rhizomucor pusillus, and Mucor circinelloides). Samples with 1, 10, or 30 slide cuts of the tissues were prepared from each paraffin block, the sample identities were blinded for analysis, and the samples were mailed to each of seven laboratories for the assessment of sensitivity. A protocol describing the extraction method and the PCR amplification procedure was provided. The internal transcribed spacer 1 (ITS1) region was amplified by PCR with the fungal universal primers ITS1 and ITS2 and sequenced. As negative results were obtained for 93% of the tissue specimens infected by M. circinelloides, the data for this species were excluded from the analysis. Positive PCR results were obtained for 93% (52/56), 89% (50/56), and 27% (15/56) of the samples with 30, 10, and 1 slide cuts, respectively. There were minor differences, depending on the organ tissue, fungal species, and laboratory. Correct species identification was possible for 100% (30 cuts), 98% (10 cuts), and 93% (1 cut) of the cases. With the protocol used in the present study, the interlaboratory reproducibility of ITS sequencing for the identification of major Zygomycetes species from formalin-fixed paraffin-embedded tissues can reach 100%, when enough material is available.

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“…The mucoromycotina fungus Rhizopus and Amylomyces are indispensable microorganisms for the production of fermented foods in Asia (Kito et al, 2009). A. rouxii belongs to the monotypic genus Amylomyces.…”

Section: Identification Of the Isolatesmentioning

confidence: 99%

“…R. oryzae is also considered as an alternative microorganism for lactic acid fermentation as it synthesizes L-lactic acid from starchy materials by the action of external amylases in the presence of ammonium salts as the sole nitrogen source (Watanabe and Oda, 2008). In their study related to phylogenetic analysis, Kito et al (2009) took twenty-one strains of A. rouxii isolated from starters of Asian fermented foods and concluded that the species A. rouxii is composed of two distinct types, derived from R. oryzae or R. delemar via domestication in the starters. A. rouxii shows by the formation of rhizoids, stolons, and black pigmented sporangia, and thereby suggesting its closeness to R. oryzae (Watanabe and Oda, 2008).…”

Section: Identification Of the Isolatesmentioning

confidence: 99%

Amylolytic fungi in starter cakes for rice beer production

Das

Miyaji

Deka

2017

J. Gen. Appl. Microbiol.

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Molecular Characterization of the Relationships amongAmylomyces rouxii,Rhizopus oryzae, andRhizopus delemar

Cited by 19 publications

References 18 publications

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

Molecular Detection and Identification of Zygomycetes Species from Paraffin-Embedded Tissues in a Murine Model of Disseminated Zygomycosis: a Collaborative European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Fungal Infection Study Group (EFISG) Evaluation

Amylolytic fungi in starter cakes for rice beer production

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