antibiotics from microbial sources
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1 antibiotics from microbial sources 14-15/ 11/ 07 Margherita osio KtedoGen
2 outline 1. antibiotics producers: treptomyces and related actinomycetes 2. antibiotic biosynthesis 3. earch for novel antibiotics
3 ow are secondary metabolites made? application of genomic technologies requires knowledge of genes knowledge of genes requires understanding function 1 I 1 I n metabolite 1
4 gene clusters all genes required for biosynthesis, regulation and resistance size: kb
5 cluster genico (10- >120 k antibiotico
6 oligomerization reactions primary metabolites class I reactions class III reactions monomers amino acids carboxylic acids sugars isopentenyl diphosphate (IPP)
7 A β-alanina acido α-amino adipico ornitina 2 2 3,5-diidrossi-fenilglicina 4-idrossi-fenilglicina glicopeptidi, ramoplanina, CDA B DP ma mo pgt 2 prefenato 4-p-idrosssi-fenilglicina
8 C PEP + E4P - - P - P - 2 C 2 C 2 shikimic acid C 2 ABA amino acid aromatici ansamicin rifamicin
9 main classes of microbial secondary metabolites peptides polyketides terpenes oligosaccharides
10 ligopeptides ibosomal origin lantibiotics (e.g. nisin), microcins on ribosomal origin ß-lactams, glycopeptides, cyclosporin, bacitracin, etc. made by nonribosomal peptide synthetases (RP)
11 a lantibiotic: nisin
12 oligopeptides of ribosomal origin synthesis of a prepropeptide post-translational modifications + cleavage
13 Cl Cl 2 Cl (C 3 ) vancomicina, M r 1592 (Amycolatopsis orientalis) 2 ramoplanina, M r 2554 (Actinoplanes sp.) VGGGGGGGGGG C 2 GGQGG C 2 G C C GGG C G C GI Microcin B17, M r 1157 (E. coli )
14 2 2 2 Cl Cl 2
15 RP clusters gramicidin Phe-Pro-Val-rn-Leu cephalosporin Aaa-Cys-Val surfactin Glu-Leu-Leu-Val-Asn-Leu-Leu cyclosporin Ala-Leu-Leu-Val-Bmt-Abu-ar-Leu-Val-Leu-Ala
16 an RP module Minimal module Condensation Adenylation Thiolation
17 oligopeptide synthesis aa 1 -aa 2 -aa 3 M1 M2 M3 aa 3 aa 2 aa 1 3 AMP 3 ATP aa 1 aa 2 aa 3 aa 1 aa 2 aa 3 M1 M2 M3 M1 M2 M3 aa 1 aa 2 aa 3 M1 M2 M3
18 Modulo 1 Modulo 2 Modulo 3 Modulo n Iniziazione Elongazione Elongazione Terminazione A PCP C A PCP C A PCP C A PCP TE 2 R 1 R 2 R 3 n 2 R 1 R 2 R 3 2 R 1 R 2 2 R 1
19 additional domains Condensation Adenylation Thiolation Reductase Thioesterase eterocyclization -methylation Epimerization
20 dominio A 3 + ATP + 3 -AMP R R ominio PCP 3 R -AMP + PCP -ATP + 3 R PCP dominio C 3 R1 PCP1 2 R2 PCP2-2 3 R1 R2 PCP2
21 dominio E dominio Cy R PCP R PCP dominio Mt + 3 R PCP + AM 3 C R PCP dominio x
22
23 baca (15.8 kb) bacb (7.8 kb) bacc (19.1 kb) BacA BacB BacC modulo2 modulo 4 modulo 6 modulo 8 modulo 10 modulo 12 ulo 1 modulo 3 modulo 5 modulo 7 modulo 9 modulo 11 E E PCP C A PCP C A PCP C A PCP C A PCP C A PCP C A PCP C A PCP PCP C PCP C A E E A C A PCP C A PCP Te Bacitracina A 2 2 2
24 Examples le Cys Leu Glu Ile Lys rn Ile Phe is Asp Asn ca bacb bacc Ala Leu Leu Val Bmt Abu Gly Leu Val Leu Ala A Adenylation A domain Thiolation T domain Condensation C domain Epimerization E domain -methylation M domain eterocylization Cy domain Thioesterase Te domain Ile Leu Val Bmt Ile Cys Leu DGlu Ile Lys Drn 2 Asn 2 DPhe is DAsp Leu DAla Ala Leu Val Leu Abu Gly
25
26 main classes of microbial secondary metabolites peptides polyketides terpenes oligosaccharides
27 examples of polyketides C 3 3 C 2 3 C C 3 C 3 2
28 A 2 tetraciclina Me oleandomicina avermectina Me C 2 actinorodina
29 Polyketide synthases (PK) ype I PK multifunctional proteins iterative (e.g. in fungi) modular in bacteria ype II PK multienzyme complexes found in bacteria make mostly aromatic polyketides (e.g. tetracycline, daunomycin) ype III PK single enzyme, uses directly CoA derivatives typical of plants present also in bacteria (e.g. dihydroxyphenylglycine)
30 identifying the polyketide core C 3 C 3 Me erythromycin
31 polyketides and fatty acids
32 CoA R' ACP K R' AT R ACP R' R KR ACP ACP R' R D R R' new cycle ER K R' R transolaction ACP R' R
33 CoA R' ACP K R' AT R ACP R' R KR ACP ACP R' R D R R' new cycle ER K R' R ACP R' R
34 A CoA CoA CoA CoA acetyl CoA malonyl CoA propionyl CoA butyryl CoA CoA CoA CoA CoA methylmalonyl CoA isobutyryl CoA isovaleryl CoA benzoylcoa
35 A modulo minimo K AT ACP CoA R AT ACP AT ACP B R CoA K AT ACP K AT ACP K AT ACP K AT ACP R R R R C K AT ACP KR K AT ACP D KR K AT ACP ER D KR K AT ACP R R R R
36 modular PK AT K AT KR K AT KR K AT K AT D ER KR K AT KR K AT KR Te
37
38
39 manipulation of a modular PK AT K AT KR K AT KR K AT K AT D ER KR K AT KR K AT KR Te
40
41
42 P PK Unit Bond formation Activation Processing Prosthetic group amino acid C C AMP (-methylation) Pantetheine Carboxylic acid C C C -CoA none, KR, D, ER Pantetheine Racemization Modularity ize of module aa aa
43
44 2 Cl Cl CC 3 (C 3 ) Cl Cl
45
46 outline 1. antibiotics producers: treptomyces and related actinomycetes 2. antibiotic biosynthesis 3. earch for novel antibiotics
47 Combinatorial biosynthesis: the way Isolation of the biosynthesis gene cluster Characterization of genes and assignment of functions to the gene products Understanding natural product biosynthesis Engineering biosynthesis pathways Producer host onproducer host ovel compounds
48 Indolocarbazoles Rebeccamycin Cl Me Cl taurosporine Me C 3 Aureolic acids 3 C 3 C 3 C C 3 C 3 3 C 3 C C 3 3 C Mithramycin
49 Indolocarbazoles Lechevalieria aerocolonigenes treptomyces longisporoflavus Cl Cl Me Me Rebeccamycin DA topoisomerase I inhibitor C 3 taurosporine Protein kinase inhibitor
50 aglicone A B C D A C B D C 3 2 C 3 C 3 C 3 3 C 2 3 C 3 C 2 C 3 2 C 3 3 C 3 C 3 C C C 2 C 3
51 loading module DEB1 DEB2 DEB3 module 1 module 2 module 3 module 4 module 5 module 6 AT ACP KR K AT ACP KR K AT ACP K AT ACP ER D KR K AT ACP KR K AT ACP KR K AT ACP TE
52 Producer strains over 20,000 microbial metabolites have been described most of the metabolites are produced by either filamentous fungi or filamentous actinomycetes does this reflect superior biosynthetic ability by these strains? are there other microbes capable of producing secondary metabolites?
53 Increasing the odds in P research Increase the number of strains Employ novel assays Utilize novel approaches to strains novel strains metagenomic libraries genome mining
54 pportunities in P research nly a small fraction of the bacterial world has been cultivated Bacteria have had millions of years of evolution to experiment with chemistry to fight competing organisms biodiversity is a necessary requirement to access chemical diversity
55 novel strains from new habitats strains have been screened mostly from terrestrial sources, while marine habitats have been largely neglected marine strains have substantially diverged from terrestrial ones and are likely to produce different compounds
56 abyssomicin searched for compounds active against B. subtilis in MM whose activity could be reverted by paba addition screened a limited number of extracts from marine or rare strains isolated from a marine identified abyssomicin from the marine actinomycete Verrucosispora sp. Riedlinger et al. J Antibiotics 57: , 2004
57 novel strains from soil strains phylogenetically related to known antibiotic producers are likely to possess the same genetic potential for antibiotic production strains not represented in 16 rra databases are unlikely to have been intensively screened in the past search for previously uncultured actinomycetes
58 novel actinomycete taxa. thermoviolaceus treptomycetaceae T. alba Alpha Beta. dassonvillei ocardiopsaceae. albida A. herbida M. rosea. salmonea D. roseum A. auranticolor Delta A. erythreum Gamma treptosporangiaceae Thermomonosporaceae Micromonosporaceae Micrococcineae Catenulisporineae B. aggregatus Frankia sp. C10 A. alba eomycetes C. diphteriae Frankineae Pseudonocardineae Corynebacterineae
59 Ktedobacter racemifer A new division of filamentous, sporeforming, gram-positive bacteria
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