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Items: 32

1.

Applied evolution: phylogeny-based approaches in natural products research.

Adamek M, Alanjary M, Ziemert N.

Nat Prod Rep. 2019 Sep 1;36(9):1295-1312. doi: 10.1039/c9np00027e. Epub 2019 Sep 2.

PMID:
31475269
2.

The ADEP Biosynthetic Gene Cluster in Streptomyces hawaiiensis NRRL 15010 Reveals an Accessory clpP Gene as a Novel Antibiotic Resistance Factor.

Thomy D, Culp E, Adamek M, Cheng EY, Ziemert N, Wright GD, Sass P, Brötz-Oesterhelt H.

Appl Environ Microbiol. 2019 Oct 1;85(20). pii: e01292-19. doi: 10.1128/AEM.01292-19. Print 2019 Oct 15.

PMID:
31399403
3.

Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics.

Greule A, Izoré T, Iftime D, Tailhades J, Schoppet M, Zhao Y, Peschke M, Ahmed I, Kulik A, Adamek M, Goode RJA, Schittenhelm RB, Kaczmarski JA, Jackson CJ, Ziemert N, Krenske EH, De Voss JJ, Stegmann E, Cryle MJ.

Nat Commun. 2019 Jun 13;10(1):2613. doi: 10.1038/s41467-019-10384-w.

4.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T.

Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.

5.

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential.

Alanjary M, Steinke K, Ziemert N.

Nucleic Acids Res. 2019 Jul 2;47(W1):W276-W282. doi: 10.1093/nar/gkz282.

6.

Recovery of the Peptidoglycan Turnover Product Released by the Autolysin Atl in Staphylococcus aureus Involves the Phosphotransferase System Transporter MurP and the Novel 6-phospho-N-acetylmuramidase MupG.

Kluj RM, Ebner P, Adamek M, Ziemert N, Mayer C, Borisova M.

Front Microbiol. 2018 Nov 16;9:2725. doi: 10.3389/fmicb.2018.02725. eCollection 2018.

7.

Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites.

Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, Poehlein A, Ziemert N, König GM, Schäberle TF.

Sci Rep. 2018 Nov 9;8(1):16600. doi: 10.1038/s41598-018-34954-y.

8.

Assessing the Efficiency of Cultivation Techniques To Recover Natural Product Biosynthetic Gene Populations from Sediment.

Elfeki M, Alanjary M, Green SJ, Ziemert N, Murphy BT.

ACS Chem Biol. 2018 Aug 17;13(8):2074-2081. doi: 10.1021/acschembio.8b00254. Epub 2018 Jul 10.

PMID:
29932624
9.

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.

Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski J, Ziemert N.

BMC Genomics. 2018 Jun 1;19(1):426. doi: 10.1186/s12864-018-4809-4.

10.

Identification of a novel aminopolycarboxylic acid siderophore gene cluster encoding the biosynthesis of ethylenediaminesuccinic acid hydroxyarginine (EDHA).

Spohn M, Edenhart S, Alanjary M, Ziemert N, Wibberg D, Kalinowski J, Niedermeyer THJ, Stegmann E, Wohlleben W.

Metallomics. 2018 May 23;10(5):722-734. doi: 10.1039/c8mt00009c.

PMID:
29667664
11.

Function-related replacement of bacterial siderophore pathways.

Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N.

ISME J. 2018 Feb;12(2):320-329. doi: 10.1038/ismej.2017.137. Epub 2017 Aug 15.

12.

Genomic insights into specialized metabolism in the marine actinomycete Salinispora.

Letzel AC, Li J, Amos GCA, Millán-Aguiñaga N, Ginigini J, Abdelmohsen UR, Gaudêncio SP, Ziemert N, Moore BS, Jensen PR.

Environ Microbiol. 2017 Sep;19(9):3660-3673. doi: 10.1111/1462-2920.13867. Epub 2017 Aug 14.

13.

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery.

Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N.

Nucleic Acids Res. 2017 Jul 3;45(W1):W42-W48. doi: 10.1093/nar/gkx360.

14.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

Schorn MA, Alanjary MM, Aguinaldo K, Korobeynikov A, Podell S, Patin N, Lincecum T, Jensen PR, Ziemert N, Moore BS.

Microbiology. 2016 Dec;162(12):2075-2086. doi: 10.1099/mic.0.000386. Epub 2016 Oct 27.

15.

Mining Bacterial Genomes for Secondary Metabolite Gene Clusters.

Adamek M, Spohn M, Stegmann E, Ziemert N.

Methods Mol Biol. 2017;1520:23-47. doi: 10.1007/978-1-4939-6634-9_2.

PMID:
27873244
16.

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria.

Maansson M, Vynne NG, Klitgaard A, Nybo JL, Melchiorsen J, Nguyen DD, Sanchez LM, Ziemert N, Dorrestein PC, Andersen MR, Gram L.

mSystems. 2016 May 3;1(3). pii: e00028-15. eCollection 2016 May-Jun.

17.

Antibiotic drug discovery.

Wohlleben W, Mast Y, Stegmann E, Ziemert N.

Microb Biotechnol. 2016 Sep;9(5):541-8. doi: 10.1111/1751-7915.12388. Epub 2016 Jul 29. Review.

18.

The evolution of genome mining in microbes - a review.

Ziemert N, Alanjary M, Weber T.

Nat Prod Rep. 2016 Aug 27;33(8):988-1005. doi: 10.1039/c6np00025h. Epub 2016 Jun 8. Review.

PMID:
27272205
19.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

20.

Salinipyrone and Pacificanone Are Biosynthetic By-products of the Rosamicin Polyketide Synthase.

Awakawa T, Crüsemann M, Munguia J, Ziemert N, Nizet V, Fenical W, Moore BS.

Chembiochem. 2015 Jul 6;16(10):1443-7. doi: 10.1002/cbic.201500177. Epub 2015 May 15.

21.

Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species.

Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR.

Chem Biol. 2015 Apr 23;22(4):460-471. doi: 10.1016/j.chembiol.2015.03.010. Epub 2015 Apr 9.

22.

Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin.

Bonet B, Teufel R, Crüsemann M, Ziemert N, Moore BS.

J Nat Prod. 2015 Mar 27;78(3):539-42. doi: 10.1021/np500664q. Epub 2014 Nov 10.

23.

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora.

Ziemert N, Lechner A, Wietz M, Millán-Aguiñaga N, Chavarria KL, Jensen PR.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):E1130-9. doi: 10.1073/pnas.1324161111. Epub 2014 Mar 10.

24.

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules.

Kersten RD, Ziemert N, Gonzalez DJ, Duggan BM, Nizet V, Dorrestein PC, Moore BS.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):E4407-16. doi: 10.1073/pnas.1315492110. Epub 2013 Nov 4.

25.

Challenges and triumphs to genomics-based natural product discovery.

Jensen PR, Chavarria KL, Fenical W, Moore BS, Ziemert N.

J Ind Microbiol Biotechnol. 2014 Feb;41(2):203-9. doi: 10.1007/s10295-013-1353-8. Epub 2013 Oct 9.

26.

Phylogenetic approaches to natural product structure prediction.

Ziemert N, Jensen PR.

Methods Enzymol. 2012;517:161-82. doi: 10.1016/B978-0-12-404634-4.00008-5.

27.

The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity.

Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR.

PLoS One. 2012;7(3):e34064. doi: 10.1371/journal.pone.0034064. Epub 2012 Mar 29.

28.

Leader peptide and a membrane protein scaffold guide the biosynthesis of the tricyclic peptide microviridin.

Weiz AR, Ishida K, Makower K, Ziemert N, Hertweck C, Dittmann E.

Chem Biol. 2011 Nov 23;18(11):1413-21. doi: 10.1016/j.chembiol.2011.09.011.

29.

Exploiting the natural diversity of microviridin gene clusters for discovery of novel tricyclic depsipeptides.

Ziemert N, Ishida K, Weiz A, Hertweck C, Dittmann E.

Appl Environ Microbiol. 2010 Jun;76(11):3568-74. doi: 10.1128/AEM.02858-09. Epub 2010 Apr 2.

30.

Ribosomal synthesis of tricyclic depsipeptides in bloom-forming cyanobacteria.

Ziemert N, Ishida K, Liaimer A, Hertweck C, Dittmann E.

Angew Chem Int Ed Engl. 2008;47(40):7756-9. doi: 10.1002/anie.200802730. No abstract available.

PMID:
18683268
31.

Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium.

Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, de Marsac NT.

BMC Genomics. 2008 Jun 5;9:274. doi: 10.1186/1471-2164-9-274.

32.

Microcyclamide biosynthesis in two strains of Microcystis aeruginosa: from structure to genes and vice versa.

Ziemert N, Ishida K, Quillardet P, Bouchier C, Hertweck C, de Marsac NT, Dittmann E.

Appl Environ Microbiol. 2008 Mar;74(6):1791-7. doi: 10.1128/AEM.02392-07. Epub 2008 Feb 1.

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