Complete genome sequence of Actinosynnema mirum type strain (101T)

Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam; Chen, Feng; Copeland, Alex; Rio, Tijana Glavina del; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan‐Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Göker, Markus; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia C.; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Tindall, Brian J.; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter

doi:10.4056/sigs.21137

Cited by 37 publications

(33 citation statements)

References 16 publications

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“…Unsurprisingly, this analysis revealed a close relationship between S. espanaensis and A. mirum (Figure 2), currently the only other completely sequenced member [8] of the recently abolished family of the "Actinosynnemataceae" [23,24]. In the data some 38.4% of the best hits were against A. mirum .…”

Section: Resultsmentioning

confidence: 86%

Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

et al. 2012

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BackgroundThe genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast.ResultsTo better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified.ConclusionS. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis.

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Section: Resultsmentioning

confidence: 86%

Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

et al. 2012

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“…EDL82982.1). The homologues could also be detected in the genomes of other known NRdegrading bacteria, regardless of whether they grew adhesively (Nocardia farcinica IFM10152 [41,42]) or exhibited clear zoneforming abilities [Streptomyces coelicolor A3(2) (10, 43), Streptomyces flavogriseus ATCC 33331 (12), and Actinosynnema mirum DSM43827 (12,44)]. In the adjacent region of mcr, the genes encoding a putative ferredoxin reductase (orf1), a putative amidohydrolase (orf2), and a putative transcriptional regulator (orf3) were detected.…”

Section: Resultsmentioning

confidence: 95%

Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a

Luo

Hiessl

Steinbüchel

2013

Appl Environ Microbiol

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c Nocardia nova SH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 ؋ 10 7 CFU per g of plasmid DNA was achieved. By applying this optimized protocol to N. nova SH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an ␣-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, ␤-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP.

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“…Genome sequencing and automatic annotation have been described for Actinosynnema mirum [25], Catenulispora acidiphila [26], Cellulomonas flavigena [27], Jonesia denitrificans [28], Nocardiopsis dassonvillei [29], Stackebrandtia nassauensis [30], Streptosporangium roseum [31], Thermobispora bispora [32], Thermomonospora curvata [33], and Xylanimonas cellulosilytica [34]. Their genome sequences are available from GenBank.…”

Section: Methodsmentioning

confidence: 99%

Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria

et al. 2012

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Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms.

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Complete genome sequence of Actinosynnema mirum type strain (101T)

Cited by 37 publications

References 16 publications

Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a

Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria

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