1 Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber Lejla Pasic, Beltran Rodigruez-Mueller, Ana-Belen Martin-Cuadrado, Alex Mira, Forest Rohwer and Francisco Rodigruez-Valera BMC Genomics 2009, 10:570 I 690 Class Presentation – Week Presented By Neethu Shah March 23, 2010

2 Overview Introduction Background Methods Results Conclusion Additional references

3 Introduction Identify metagenomic islands of hyperhalophiles – S.ruber and H.walsbyi Understand the functions associated with these MGI How these MGI influence the living style of marine microbes

4 Genomic islands “Genomic islands are large chromosomal regions that are part of the flexible gene pool, previously transferred by other mobile genetic elements and are present in certain bacteria but are absent in most closely related variants” Dobrindt U, Hochhut B, Hentschel U, Hacker J. Genomic islands in pathogenic and environmental microorganisms. Nature Review Microbiology 2004, 2:

5 Common features of GIs Georgios S. Vernikos and Julian Parkhill, Resolving the structural features of genomic islands: A machine learning approach. Genome Research, 2008 February.

6 Islands and islands……….Mario Juhas1 et al, Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33 (2009) 376–393.

7 Identifying Genomic islands(A)The cumulative GC profile for the C. efficiens genome and (B) the distribution of the codon usage bias along the genome Zhang R et al, Genomic Islands in the Corynebacterium efficiens Genome. Applied and Environmental Microbiology, June 2005, p. 3126–3130

8 Identifying Genomic islands 2Zhang, R et al. Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis. Physiol. Genomics 16: The cumulative GC profiles of Bacillus cereus, Bacillus anthracis, and genomic islands. Identifying Genomic islands 2

9 Structural variation in GI.Georgios S. Vernikos and Julian Parkhill, Resolving the structural features of genomic islands: A machine learning approach. Genome Research, 2008 February.

10 Salinibacter ruber and metagenomic islandsMGI – The genomic islands identified when metagenomic reads were compared against a reference genome S.ruber grows in 20-25% salt concentration. Crystallizers are ideal for such studies Low diversity Dense population. 2.5 m Scanning electron micrograph of Salinibacter ruber strain M31 Josefa Anton, et al. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. International Journal of Systematic and Evolutionary Microbiology, 2002.

11 Data sets and methods Chula Vista Santa Pola454 sequencing Sanger sequencing reads sequences Phylogenetic analysis of the data sets Chula Vista BLASTX Reads assigned 10% H.walsbyi 23% Haloarcula marismortui N.pharanois 20% H.lacusprofundi 22% S.ruber 12%

12 Recruitment analysis MUMmer BLASTN Chula Vista Santa PolaNo bacterial recruitment H.walsbyi MUMmer Chula Vista S.ruber(14.6%) H.walsbyi(9.2%) Halobacterium salinarum H. marismortui…………. BLASTN Reference genome split into fragments of 50bp and compared against the reads.

13 Genome plasticity of Salinibater ruber.

14 Comparing MUMmer and BLAST

15 MGIs of H.walsbyi

16 Distribution of COGs in S.ruber

17 MGI 1 and Salinibacter ruber DSM 13855

18 MGI 1 109 kb Genes for exoplysaccharide biosynthesis Colanic acid Alginate Proteo-phosphoglycan MG1 2 70kp Genes for extracelluar polysaccharide assembly and synthesis, phage inhibition. Sialic acid Colanic acid Genes similar to pathogenic Gram negative bacteria. Lineage - specific set of genes MGI 3 42.8 kb Genes for recombination and repair Restriction modification enzymes Non-coding DNA Remnants of phage?

19 Convergence with MGIs of other microbesRecombination and DNA repair shared by islands of S.ruber, H.walsbyi, Prochlorococcus marinarus, Candidatus Accumulibacter phosphatis, Ferroplasma acidarmanus Biosynthesis of polysaccharide component of cell wall shared by S.ruber and Gram negative acquatic microbes.

20 Conclusion…….. MGIs have the classical features of genomic islandsMajority of the MGI genes are involved in biosynthesis of cell wall polysaccharides. Variation in these genes is a shared phenomenon in many other marine microbes Reflects defense mechanism of these microbes against phage predation

21 Additional referencesWilliam Hsiao et al. IslandPath: aiding detection of genomic islands in prokaryotes.Bioinformatics.19:3 2003,418–420 Langille MG etal. IslandViewer: An integrated interface for computational identification and visualization of genomic islands. Bioinformatics. 2009;25(5):664–665 Georgios S et al. Resolving the structural features of genomic islands: A machine learning approach. Genome Res February; 18(2): 331–342.

22 Thank you Red pigmentation by S.ruber in cyrstallizersSource :