Genome mining indicates that the genus Xanthomonas is a promising reservoir for new bioactive non-ribosomally synthesized peptides

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Organizing Committee

CHAIR

Vasile 1. PARVUL ESCU (RO)

INTERNATIONAL ADVISORY BOARD

Martin E. MAIER (DE)

Ari KOSKINEN (F I)

Roderich SÜSSM UTH (DE)

Stephen CLARK (UK)

Antti POSO (IT)

Came lia BALA (RO)

SEC RETARIAT

Mihaela FLOREA (RO)

Bogdan COJOCARU (RO)

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ACTION CM0804. 22-24 May 20 \1, Bucharcst, Rem ani a

Genome mining indicates that the genus

Xanthomonas is a promising reservoir

for new bioactive non-ribosomally synthesized peptides

Monique Royer', Ralf Koebnik 2, Mélanie Marguerettaz', Valérie Barbe:', Guillaume P. Robin2,

Chrystelle Brin", Sébastien Carrere", Camila Gornez' , ManueJa Hügelland", Ginka Vôller", Julie Noëll', Isabelle Pieretti ' , Saskia Rausch", Valérie Verdie r', Stéphane Poussier ", Philippe Rott',

Roderich D. Süssmuth", Stéphane Cociancich 1

1CIRA D, UMR BGPI,F-34398Montpellier Cedex 5, France

21RD, UMR RPB, F-34394 Montpellier Cedex, France

3Genoscope , Centre National de Séquençage, F-91057 EVIY Cedex, France

4INRA , UM R IRHS, F-49071 Beaucouze, France

5

lNRA, UMR LlPM, F-31326 Castane t-Tolosan Cedex, France

"Ins ûnufûr Chemie, Technische Universit ât Berlin, D-l0623 Berlin, Germany

7Univers ité de la Réunion, UM R PVBMT, F-97715 Saint-Denis, La Réunion, France stephane. cocianc ich@ cirad. fr

In trod uction

Xanthomonas is a large genus of Gram-negati ve bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by non-ribosornal peptide synthesis (NRPS) in this genus is albicidin produced by Xanthomonas albilineans [1]. The DNA gyrase

inhibitor albicidin is not only an important virulence factor but also a possible lead structure for novel antibiotics [2]. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X albilineans and related species of Xanthomonas.

Experimental

ln silico analyses were performed on NRPS genes present in the pubJished finished genome

sequence of X albilineans strain GPE PC73 (accession n": NC_OI3722 .1), in the published draft genome sequence of Xanthomonas oryzae pv. oryzae strain X11-5A (accession n":

AFHKOOOOOOOO.I ), in the unpublished sequence of the 82-kb Jength region containing META-B in X oryza e pv. oryzae strain BAI-3 and in the unpublished draft genome sequence of strain

Xanthomonas spp. XaS3. Specificity of adenylation domains in NRPS and signatures were predicted using the web server NRPSpredictor2 [3].

Results and discussion

This study reveaJed four strains of the genus Xanthontonas possessing a novel homologous NRPS gene cluster, hereafter referred to as META-B. The sequence alignment of META-B gene clusters from Xanthomonas strains is indicative of the biosynthesis of lipopeptides or peptides linked to an other non-amino acid substrate, and involving the biosynthesi s and incorporation of the non proteinogenic amino acids Dpg (3,5-dihydroxyphenyJ-glycine), Dab (2,4-diamino butyric acid), ~

Hty (~-hydrox y-tyrosine) as weil as of amino acid(s) of unknown identity (Figure 1; [4]). This

study revealed that each sequence of the peptide is strain-specific. Ifthe biosynthetic pathways are functional, these peptides may exert different biological functions in plant-bacteria interactions.

Conclusions

This extensive in silico study shows that the genus Xanthomonas constitutes a promising reservoir for new non-ribosomall y synthesized peptides. Experimental elucidation ofthis

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COST ACTION CMOS04, 22-24 May 2012, Bucharest, Romania

promising biosynthetic potential should contribute ta the study of plant-bacteria interaction and also to the drug discovery.

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. .: genes Involved in l3-hydoxylation of tyrosine or other unknown amino-acids

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• : genes involved in the biosynthesis of an unknown amino acid

• : gene involved in the biosynthesis of Dab

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(number of genes, number of modules and amino acid specificity of modules are

different for each strain; exact number of genes and modules remains unknown for strains A and B because of draft sequences)

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strain Xll-SA;

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strain XaS3;

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strain GPE PC73;

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strain BAI3

Figure]. Schematic representation of the META-B gene clu ster in four strains of Xanthomonas

Acknowledgements

This project was supported by a joint research grant of the Deutsche Forschungsgemeinschaft to Roderich Süssmuth (DFG SU239/] ] -]) and the Agence Nationale pour la Recherche to Monique Royer (ANR-09-BLAN-0413-0 1).

References

[1] Royer, M., Coster. L., Vivien, E., Bes, M., Cousin, A., Damais, A., Picretti, 1., Savin. A., Megcssier, S., Viard, M., Frutos, R.. Gabriel, D.W" Rott, P.C., Molecular Plant-Microbe Interaction, 17 (2004), 414-427.

l2J Hushirni, S.M.. Wall, M.K., Smith, A.B.. Maxwell. A., Birch R.G., Antimicrobial Agents and Chcmothcrapy, 51 (2007). 181-187.

[3] Rëttig, M., Medema, M.H., Blin, K., Weber, T., Rausch, c., Kohlbacher, O., Nueleic Acids Research, 39 (2011),

362-367.

[4] Royer. M.. Koebnik, R.. Marguerettaz. M., Barbe, V.. Robin, G. P., Brin, C., Carrere, S., Gomez, c., Hügclland ,

M., Vëllcr. G.• Noëll. 1.. Piereui, 1.. Rausch. S.. Verdier. V.. Poussier. S.. Rott. P., Siissmuth. R.D.. Cociancich. S.,

Submitted to BMC Genomics.