Complete genome sequence of the glidobactin producing strain [Polyangium] brachysporum DSM 7029

Tang, Biao; Yu, Yucong; Zhang, Youming; Zhao, Guoping; Ding, Xiaoming

doi:10.1016/j.jbiotec.2015.06.417

Cited by 18 publications

(15 citation statements)

References 10 publications

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“…Based on the same reasoning, the other enzymes of type IIb are predicted to have PET-degrading activities similar to that of Is PETase. In addition to Is PETase, enzymes originating from bacteria, such as Acidovorax delafieldii 29 , [Polyangium] brachysporum DSM 7029 30 , and Burkholderiales bacterium RIFCSPLOWO2_02_FULL_57_36 31 , belong to type IIb. Interestingly, all four bacteria of type IIb enzymes belong to the order Burkholderiales , suggesting that these four bacteria seem to have similarly evolved.…”

Section: Resultsmentioning

confidence: 99%

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

et al. 2018

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Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified and suggested for possible use in degradation and/or recycling of PET. However, the molecular mechanism of PET degradation is not known. Here we report the crystal structure of I. sakaiensis PETase (IsPETase) at 1.5 Å resolution. IsPETase has a Ser–His-Asp catalytic triad at its active site and contains an optimal substrate binding site to accommodate four monohydroxyethyl terephthalate (MHET) moieties of PET. Based on structural and site-directed mutagenesis experiments, the detailed process of PET degradation into MHET, terephthalic acid, and ethylene glycol is suggested. Moreover, other PETase candidates potentially having high PET-degrading activities are suggested based on phylogenetic tree analysis of 69 PETase-like proteins.

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Section: Resultsmentioning

confidence: 99%

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

et al. 2018

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“…The gladiolus and human isolates occupied additional rhizomide BGCs and particularly, human isolates, including AU0032, AU29541, and AU30473, were rich in rhizomide BGCs more than any other strains. By spectroscopic characterization, production of rhizomide was identified from soil bacterium Burkholderiales DSM 7029, and Paraburkholderia rhizoxinica , intracellular symbionts of the phytopathogenic fungus [ 123 , 124 , 125 ]. Additionally, Burkholderia -originated rhizomide exhibited various actives such as antitumor activity, protective activity against cucumber downy mildew, antibacterial activity for gram-positive bacteria [ 123 ].…”

Section: Resultsmentioning

confidence: 99%

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli

et al. 2021

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Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.

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“…The primers for direct cloning were listed in Supplementary Data 1. Then, both plasmids were electroporated into the heterologous host Schlegelella brevitalea DSM 7029 (previous known as Burkholderiales strain DSM 7029 or Polyangium brachysporum K481-B101) 33,34,49 for functional expression according to the previous method 29,33 . The correct colonies were checked by colony PCR.…”

Section: Methodsmentioning

confidence: 99%

Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis

et al. 2021

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Nonribosomal peptide synthetases containing starter condensation domains direct the biosynthesis of nonribosomal lipopeptides, which generally exhibit wide bioactivities. The acyl chain has strong impacts on bioactivity and toxicity, but the lack of an in-depth understanding of starter condensation domain-mediated lipoinitiation limits the bioengineering of NRPSs to obtain novel derivatives with desired acyl chains. Here, we show that the acyl chains of the lipopeptides rhizomide, holrhizin, and glidobactin were modified by engineering the starter condensation domain, suggesting a workable approach to change the acyl chain. Based on the structure of the mutated starter condensation domain of rhizomide biosynthetic enzyme RzmA in complex with octanoyl-CoA and related point mutation experiments, we identify a set of residues responsible for the selectivity of substrate acyl chains and extend the acyl chains from acetyl to palmitoyl. Furthermore, we illustrate three possible conformational states of starter condensation domains during the reaction cycle of the lipoinitiation process. Our studies provide further insights into the mechanism of lipoinitiation and the engineering of nonribosomal peptide synthetases.

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Complete genome sequence of the glidobactin producing strain [Polyangium] brachysporum DSM 7029

Cited by 18 publications

References 10 publications

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli

Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis

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