المؤلفون: Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, P. Gomes, Paulo Wender, Caraballo-Rodriguez, Andres M, El Abiead, Yasin, Aron, Allegra T, Gentry, Emily C, Zemlin, Jasmine, Meehan, Michael J, Avalon, Nicole E, Cichewicz, Robert H, Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia-Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte CM, Jackrel, Sara L, Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A, Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C, Rimal, Bipin, Patterson, Andrew D, Traxler, Matthew F, Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis-Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S, Bandeira, Nuno, Gerwick, William H, Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C, Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M, Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J, Ding, Su, Sinninghe Damsté, Jaap S, Guan, Xue Li, Cui, Jerry J, Ju, Kou-San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector HF, Grundmann, Carlismari, Clement, Jason A

المصدر: Nature Microbiology. 9(2)

مصطلحات موضوعية: Microbiology, Biological Sciences, Good Health and Well Being, Humans, Tandem Mass Spectrometry, Metabolomics, Databases, Factual, Medical Microbiology

الوصف: microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4d47d56cTest

المؤلفون: Cui, Jerry J., Zhang, Yeying, Ju, Kou‐San

المساهمون: National Institute of General Medical Sciences

المصدر: Angewandte Chemie ; ISSN 0044-8249 1521-3757

الوصف: Phosphonate natural products, with their potent inhibitory activity, have found widespread use across multiple industries. Their success has inspired development of genome mining approaches that continue to reveal previously unknown bioactive scaffolds and biosynthetic insights. However, a greater understanding of phosphonate metabolism is required to enable prediction of compounds and their bioactivities from sequence information alone. Here, we expand our knowledge of this natural product class by reporting the complete biosynthesis of the phosphonoalamides, antimicrobial tripeptides with a conserved N ‐terminal l ‐phosphonoalanine (PnAla) residue produced by Streptomyces . The phosphonoalamides result from the convergence of PnAla biosynthesis and peptide ligation pathways. We elucidate the biochemistry underlying the transamination of phosphonopyruvate to PnAla, a new early branchpoint in phosphonate biosynthesis catalyzed by an aminotransferase with evolved specificity for phosphonate metabolism. Peptide formation is catalyzed by two ATP‐grasp ligases, the first of which produces dipeptides, and a second which ligates dipeptides to PnAla to produce phosphonoalamides. Substrate specificity profiling revealed a dramatic expansion of dipeptide and tripeptide products, while finding PnaC to be the most promiscuous dipeptide ligase reported thus far. Our findings highlight previously unknown transformations in natural product biosynthesis, promising enzyme biocatalysts, and unveil insights into the diversity of phosphonopeptide natural products.

الإتاحة: https://doi.org/10.1002/ange.202405052Test

المؤلفون: Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, Paulo, Paulo Wender, Caraballo-Rodriguez, Andres M., El Abiead, Yasin, Aron, Allegra T., Gentry, Emily C., Zemlin, Jasmine, Meehan, Michael J., Avalon, Nicole E., Cichewicz, Robert H., Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte C.M., Jackrel, Sara L., Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A., Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C., Rimal, Bipin, Patterson, Andrew D., Traxler, Matthew F., Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S., Bandeira, Nuno, Gerwick, William H., Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C., Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M., Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J., Ding, Su, Sinninghe Damsté, Jaap S., Guan, Xue Li, Cui, Jerry J., Ju, Kou San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector H.F., Grundmann, Carlismari, Clement, Jason A., Mohimani, Hosein, Broders, Kirk, McPhail, Kerry L., Ober-Singleton, Sidnee E., Rath, Christopher M., McDonald, Daniel, Knight, Rob, Wang, Mingxun, Dorrestein, Pieter C.

المصدر: Zuffa , S , Schmid , R , Bauermeister , A , Paulo , P W , Caraballo-Rodriguez , A M , El Abiead , Y , Aron , A T , Gentry , E C , Zemlin , J , Meehan , M J , Avalon , N E , Cichewicz , R H , Buzun , E , Terrazas , M C , Hsu , C Y , Oles , R , Ayala , A V , Zhao , J , Chu , H , Kuijpers , M C M , Jackrel , S L , Tugizimana ....

مصطلحات موضوعية: /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, name=SDG 3 - Good Health and Well-being

الوصف: microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health.

وصف الملف: application/pdf

العلاقة: https://orbit.dtu.dk/en/publications/71b90b22-dfc9-4882-940b-73337ef525aeTest

الإتاحة: https://doi.org/10.1038/s41564-023-01575-9Test
https://orbit.dtu.dk/en/publications/71b90b22-dfc9-4882-940b-73337ef525aeTest
https://backend.orbit.dtu.dk/ws/files/352044454/s41564-023-01575-9_1_.pdfTest

المؤلفون: Cuellar-Gaviria, Tatiana Z., García-Botero, Camilo, Ju, Kou-San, Villegas-Escobar, Valeska

المصدر: Frontiers in Microbiology ; volume 14 ; ISSN 1664-302X

مصطلحات موضوعية: Microbiology (medical), Microbiology

الوصف: Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, Bacillus tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms of adaptation that involve modifying the phyllosphere environment. Here, we report the complete genome of strain EA-CB0015, its precise taxonomic identity, and determined key genetic features that may contribute to its effective biocontrol of plant pathogens. We found that B. tequilensis EA-CB0015 harbors a singular 4 Mb circular chromosome, with 3,951 protein-coding sequences. Multi-locus sequence analysis (MLSA) and average nucleotide identity (ANI) analysis classified strain EA-CB0015 as B. tequilensis . Encoded within its genome are biosynthetic gene clusters (BGCs) for surfactin, iturin, plipastatin, bacillibactin, bacilysin, subtilosin A, sporulation killing factor, and other natural products that may facilitate inter-microbial warfare. Genes for indole-acetic acid (IAA) synthesis, the use of diverse carbon sources, and a multicellular lifestyle involving motility, biofilm formation, quorum sensing, competence, and sporulation suggest EA-CB0015 is adept at colonizing plant surfaces. Defensive mechanisms to survive invading viral infections and preserve genome integrity include putative type I and type II restriction modification (RM) and toxin/antitoxin (TA) systems. The presence of bacteriophage sequences, genomic islands, transposable elements, virulence factors, and antibiotic resistance genes indicate prior occurrences of genetic exchange. Altogether, the genome of EA-CB0015 supports its function as a biocontrol agent against phytopathogens and suggest it has adapted to thrive within phyllosphere environments.

الإتاحة: https://doi.org/10.3389/fmicb.2023.1135487Test

المؤلفون: Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, Gomes, Paulo Wender P., Caraballo-Rodriguez, Andres M., Abiead, Yasin El, Aron, Allegra T., Gentry, Emily C., Zemlin, Jasmine, Meehan, Michael J., Avalon, Nicole E., Cichewicz, Robert H., Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia-Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte C. M., Jackrel, Sara L., Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A., Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C., Rimal, Bipin, Patterson, Andrew D., Traxler, Matthew F., de Cassia Pessotti, Rita, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis-Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S, Bandeira, Nuno, Gerwick, William H., Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C., Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, dos Santos, Mariana Silva, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, de León, Arturo Vera Ponce, Pope, Phillip Byron, La Rosa, Sabina Leanti, Barbera, Giorgia La, Roager, Henrik M., Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J., Ding, Su, Sinninghe Damsté, Jaap S., Guan, Xueli Li, Cui, Jerry J., Ju, Kou-San, Silva, Denise Brentan, Ribeiro Silva, Fernanda Motta, da Silva, Gilvan Ferreira, Koolen, Hector H. F., Grundmann, Carlismari, Clement, Jason A., Mohimani, Hosein, Broders, Kirk, McPhail, Kerry L., Ober-Singleton, Sidnee E., Rath, Christopher M., McDonald, Daniel, Knight, Rob, Wang, Mingxun, Dorrestein, Pieter C.

الوصف: MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health.

العلاقة: https://nottingham-repository.worktribe.com/output/23475124Test; https://nottingham-repository.worktribe.com/file/23475124/1/2023.07.20.549584v1.fullTest

الإتاحة: https://nottingham-repository.worktribe.com/file/23475124/1/2023.07.20.549584v1.fullTest
https://nottingham-repository.worktribe.com/output/23475124Test

المؤلفون: Cui, Jerry, Ju, Kou-San

المساهمون: National Institute of General Medical Sciences

المصدر: ACS Chemical Biology ; ISSN 1554-8929 1554-8937

الإتاحة: https://doi.org/10.1021/acschembio.4c00190Test

المؤلفون: Ju, Kou-San, Nair, Satish K.

المساهمون: National Institutes of Health

المصدر: Current Opinion in Chemical Biology ; volume 71, page 102214 ; ISSN 1367-5931

مصطلحات موضوعية: Biochemistry, Analytical Chemistry

الإتاحة: https://doi.org/10.1016/j.cbpa.2022.102214Test
https://api.elsevier.com/content/article/PII:S1367593122000990?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S1367593122000990?httpAccept=text/plainTest

المؤلفون: Mahan, Kristina M, Penrod, Joseph T, Ju, Kou-San, Kass, Natascia Al, Tan, Watumesa A, Truong, Richard, Parales, Juanito V, Parales, Rebecca E

المصدر: Applied and Environmental Microbiology. 81(1)

مصطلحات موضوعية: Microbiology, Biological Sciences, Genetics, Comamonadaceae, Genetic Complementation Test, Mutation, Oxygenases, Selection, Genetic, Substrate Specificity, Toluene, Medical microbiology

الوصف: Acidovorax sp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/17738075Test

المؤلفون: Born, David A., Ulrich, Emily C., Ju, Kou-San, Peck, Spencer C., van der Donk, Wilfred A., Drennan, Catherine L.

المصدر: Science, 2017 Dec 01. 358(6368), 1336-1340.

الوصول الحر: https://www.jstor.org/stable/26401051Test

المؤلفون: Ju, Kou‐San, Parales, Rebecca E

المصدر: Microbial Biotechnology. 2(2)

مصطلحات موضوعية: Biological Sciences, Industrial Biotechnology, Bacterial Proteins, Biodegradation, Environmental, Comamonadaceae, Comamonas, Dioxygenases, Genetic Engineering, Nitrobenzenes, Ralstonia, Stereoisomerism, Substrate Specificity, Microbiology, Industrial biotechnology

الوصف: Widespread application of chloronitrobenzenes as feedstocks for the production of industrial chemicals and pharmaceuticals has resulted in extensive environmental contamination with these toxic compounds, where they pose significant risks to the health of humans and wildlife. While biotreatment in general is an attractive solution for remediation, its effectiveness is limited with chloronitrobenzenes due to the small number of strains that can effectively mineralize these compounds and their ability to degrade only select isomers. To address this need, we created engineered strains with a novel degradation pathway that reduces the total number of steps required to convert chloronitrobenzenes into compounds of central metabolism. We examined the ability of 2-nitrotoluene 2,3-dioxygenase from Acidovorax sp. strain JS42, nitrobenzene 1,2-dioxygenase (NBDO) from Comamonas sp. strain JS765, as well as active-site mutants of NBDO to generate chlorocatechols from chloronitrobenzenes, and identified the most efficient enzymes. Introduction of the wild-type NBDO and the F293Q variant into Ralstonia sp. strain JS705, a strain carrying the modified ortho pathway for chlorocatechol metabolism, resulted in bacterial strains that were able to sustainably grow on all three chloronitrobenzene isomers without addition of co-substrates or co-inducers. These first-generation engineered strains demonstrate the utility of nitroarene dioxygenases in expanding the metabolic capabilities of bacteria and provide new options for improved biotreatment of chloronitrobenzene-contaminated sites.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/3b92p3scTest