Site-directed modification of the adenylation domain of the fusaricidin nonribosomal peptide synthetase for enhanced production of fusaricidin analogs

Han, Jae Woo; Kim, Eun Young; Lee, Jung Min; Kim, Yun Sung; Bang, Eunjung; Kim, Beom Seok

doi:10.1007/s10529-012-0913-8

Cited by 47 publications

(51 citation statements)

References 15 publications

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“…Of note is that none of the positions identified as critical to substrate preference in B . brevis gramicidin synthetase and Paenibacillus fusaricidin synthase were identified with high Group Entropy scores in NRPSs [77,78]. …”

Section: Resultsmentioning

confidence: 99%

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

et al. 2018

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Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.

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Section: Resultsmentioning

confidence: 99%

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

et al. 2018

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“…This observation implies that, whereas proper substrate positioning is important also for the nitration outcome, the requirement is not so stringent as to limit the scope of the reaction to a single substrate. Moreover, modification of adenylation modules for altered amino-acid specificity has been achieved 42,43 and could further expand the substrate scope. Finally, there is no a priori reason that the mechanistic strategy could not be extended to small-molecule substrates (in either natural or engineered enzymes), a possibility that we continue to explore.…”

Section: Discussionmentioning

confidence: 99%

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

et al. 2014

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Iron-dependent halogenases employ cis-halo-Fe(IV)-oxo (haloferryl) complexes to functionalize unactivated aliphatic carbon centers, a capability elusive to synthetic chemists. Halogenation requires (1) coordination of a halide anion (Cl− or Br−) to the enzyme's Fe(II) cofactor; (2) coupled activation of O2 and decarboxylation of α-ketoglutarate to generate the haloferryl intermediate; (3) abstraction of hydrogen (H•) from the substrate by the ferryl oxo group; and (4) transfer of the cis halogen as Cl• or Br• to the substrate radical. This enzymatic solution to an unsolved chemical challenge is potentially generalizable to installation of other functional groups, provided that the corresponding anions can support the four requisite steps. We show here that the wild-type halogenase SyrB2 can indeed direct aliphatic nitration and azidation reactions by the same chemical logic. The discovery and enhancement by mutagenesis of these previously unknown reaction types suggests unrecognized or untapped versatility in ferryl-mediated enzymatic C–H-bond activation.

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“…A single operon produces a variety of fusaricidins, differing in their incorporation of amino acids at three of the six positions in the peptide ring. The diversity here is due to relaxed substrate specificity of the NRPS [112], in contrast to the modular mixing of polymyxin synthases. Fusaricidins are active against fungi, including many important phytopathogens, and a variety of gram-positive bacteria.…”

Section: Antimicrobial Peptidesmentioning

confidence: 99%

Current knowledge and perspectives of Paenibacillus: a review

et al. 2016

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Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0603-7) contains supplementary material, which is available to authorized users.

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Site-directed modification of the adenylation domain of the fusaricidin nonribosomal peptide synthetase for enhanced production of fusaricidin analogs

Cited by 47 publications

References 15 publications

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

Current knowledge and perspectives of Paenibacillus: a review

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