Identification and Diversity of Putative Aminoglycoside-Biosynthetic Aminotransferase Genes from Deep-Sea Environmental DNA

Aoki, Rie; Nagaya, Atsushi; Arakawa, Shizuka; Kato, Chiaki; Tamegai, Hideyuki

doi:10.1271/bbb.80033

Cited by 3 publications

(6 citation statements)

References 21 publications

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“…Three studies used PCR and cloning to detect the presence of the 2-deoxy-scyllo-inosose gene in TCDNA from Japanese soils (54 clones), and Pacific Ocean (34 clones). None of these sequences were closely related to the stsC gene from the streptomycin cluster, instead forming clades with genes from other biosynthetic clusters such as kanamycin or gentamycin [11], [46], [47].…”

Section: Discussionmentioning

confidence: 99%

Diversity Analysis of Streptomycetes and Associated Phosphotranspherase Genes in Soil

2012

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An attempt was made to verify the observation that Streptomyces griseus was prevalent in soil based on isolation work. A genus-specific PCR was developed for Streptomyces based on the housekeeping gene atpD and used to investigate species diversity within selected soils. The presence of S. griseus was investigated to determine coexistence of resistance-only streptomycin phosphotransferase (strA) in the same soil as streptomycin producers. Two additional PCR-based assays were developed; one specific for strA in association with production, the other for more diverse strA and other related phosphotranferases. Both the S. griseus atpD and strA genes were below the PCR detection limit in all soils examined. A number of more diverse phosphotransferase genes were amplified, a minority of which may be associated with streptomycin production. We conclude that neither streptomycin producers nor S. griseus are prevalent in the fresh or chitin and starch-amended soils examined (less than 0.1% of soil actinobacteria). One of the soil sites had received plantomycin (active ingredient: streptomycin) and diversity studies suggested that this altered the streptomycete populations present in the soil.

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Section: Discussionmentioning

confidence: 99%

Diversity Analysis of Streptomycetes and Associated Phosphotranspherase Genes in Soil

2012

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“…At least, this might be true for the K2 and MY1 samples, because genes encoding DOI synthase were not found in these samples, although we found putative aminotransferases in these same samples in a previous study. 15) The other possibility is that some of the btrS-homologous genes isolated from the same deep-sea environmental DNA were not from the aminoglycoside producers as discussed in our previous paper. 15) To investigate the diversity of aminoglycoside producers, additional exploration of both genes is required.…”

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confidence: 89%

“…13,14) Further, we have identified the genes encoding aminotransferase likely to be involved in the biosynthesis of aminoglycosides from deep-sea environmental DNA. 15) These genes were homologous to btrS of B. circulans, which encodes L-glutamine:DOI aminotransferase, which is required for the biosynthesis of DOS. 16) This suggests that aminoglycoside producers are widely distributed over Earth.…”

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confidence: 99%

“…Deep-sea environmental DNA was prepared in our previous study. 15 , and ML2 (10-17 cm from the bottom) were recovered from the same site with a single core mud sampler. K2 was recovered from almost the same location with a rake.…”

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confidence: 99%

“…Our previous results indicated that btrS-homologous genes from the same deep-sea environmental DNA showed as much diversity as similar genes from land-based environmental DNA. 15) Two possibilities might explain the difference in diversity of these genes. One is that producers of DOS-containing aminoglycoside are not dominant in these areas.…”

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confidence: 99%

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Genes Encoding Carbocycle-Forming Enzymes Involved in Aminoglycoside Biosynthesis in Deep-Sea Environmental DNA

Tamegai

Kanda

Kato

2010

Bioscience, Biotechnology, and Biochemistry

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We obtained 19 individual DNA fragments encoding 2-deoxy-scyllo-inosose synthase involved in the biosynthesis of aminoglycoside antibiotics from deep-sea sediments of the Pacific Ocean. Compared with genes from land-based environmental DNA, they showed low diversity. Combined with our previous study concerning the discovery of other aminoglycoside-biosynthetic genes from the same deep-sea samples, we suggest the importance of exploration of multiple biosynthetic genes to determine the diversity of aminoglycoside producers. We found that the deep sea is a useful source for screening of these genes.

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Using comparative genomics to uncover new kinds of protein‐based metabolic organelles in bacteria

Jorda¹,

López²,

Wheatley³

et al. 2013

Protein Science

101

174

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Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B 12 -independent, glycyl radical-based degradation of 1,2-propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical-based microcompartment binds an iron-sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical-based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.

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Identification and Diversity of Putative Aminoglycoside-Biosynthetic Aminotransferase Genes from Deep-Sea Environmental DNA

Cited by 3 publications

References 21 publications

Diversity Analysis of Streptomycetes and Associated Phosphotranspherase Genes in Soil

Diversity Analysis of Streptomycetes and Associated Phosphotranspherase Genes in Soil

Genes Encoding Carbocycle-Forming Enzymes Involved in Aminoglycoside Biosynthesis in Deep-Sea Environmental DNA

Using comparative genomics to uncover new kinds of protein‐based metabolic organelles in bacteria

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