a Whole Genome Array Approach - Jacobs University

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Background 1.2.1.2 Substrate spectrum Physiological studies on R. baltica showed optimal growth between 28 and 30°C. The bacterium is strictly aerobic, glucose will not be fermented and nitrate cannot serve as an electron acceptor. Growth experiments on liquid yielded that R. baltica can utilise a wide range of mono- and disaccharides (Tab 1) (Schlesner et al. 2004). Tab 1 Substrates tested on Rhodopirellula baltica modified after Schlesner et al. (Schlesner et al. 2004) Substrates used as carbon source Substrates not used as carbon source Monosaccharides C6: glucose, fructose, mannose, galactose, trehalose, C5: lyxose, ribose, xylose Monosaccharides C6: sorbose C5: - Modified monosaccarides methylated: rhamnose N-acetylated: N-acetylglucosamine Others: esculin, salicin Disaccharides cellobiose, lactose, maltose, sucrose, melibiose, amygdalin Trisaccharides melezitoase, raffinose Polysaccarides chondroitin sulphate, gelatine, starch, dextrin C1 - Others glycerol, gluconate, glucuronate Modified monosaccarides methylated: fucose N-acetylated: - Others: - Disaccharides - Trisaccharides - Polysaccarides cellulose, chitin, alginate C1 methylamine, methylsulfonate, methanol Others methanol, ethanol, erythritol, adonitol, arabitol, dulcitol, inositol, mannitol, sorbitol, acetate, adipate, benzoate, caproate, citrate, formiate, fumarate, glutarate, lactate, malate, 2- oxoglutarate, phthalate, propionate, pyruvate, succinate, tartrate, norleucine, ornithine, urea, indole, inulin, pectin, casein, tween 80, all 20 amino acids N-acetylglucosamine (NAG) can be used as the only energy and nitrogen source (Rabus et al. 2002). NAG is a main structural component in chitin and a substantial constituent of the 6
Background bacterial peptidoglycan cell wall. It is one of the main amino sugars in marine habitats (Riemann and Azam 2002). Additional growth studies show that R. baltica can grow on chondroitin sulphate (component of fish cartilage) (Schlesner et al. 2004) and iota-carrageenplates (algae) (Gurvan Michel pers. communication). The annotation process identified the standard pathways for heterotrophic bacteria including glycolysis, citrate cycle and oxidative phosphorylation. R. baltica SH1 T lacks the glyoxylate bypass and the Entner-Doudoroff pathway but exhibits the pentose phosphate cycle. Unexpected for an aerobic heterotrophic bacterium was the presence of all genes for heterolactic acid fermentation, though the organism has not yet been successfully cultured under anoxic conditions. Interestingly, key genes for the inter-conversion of C1-compounds were also found. Previously these were believed to occur only in methanogenic Archaea and methylotrophic Alphaproteobacteria (Glöckner et al. 2003; Bauer et al. 2004). 1.2.1.3 Sulphatases and their role The annotation results showed that the R. baltica genome harbours 110 genes encoding proteins with significant similarity to prokaryotic (82 genes; 75%) and eukaryotic (28 genes; 25%) sulphatases. For instance, similarities were found to alkylsulphatase of Pseudomonas aeruginosa, to arylsulphatases of Pseudomonas sp., to mucin-desulfating sulphatase of Prevotella sp., and to archaeal arylsulphatase, as well as to mammalian iduronate-2- sulphatase and arylsulphatases A and B. The annotation also revealed that in R. baltica the sulphatase genes are distributed across the genome in 22 clusters containing two to five genes. 59 sulphatases out of the set of 110 predicted sulphatases contain signal peptides prediction, indicating that most of these proteins are probably secreted. 11 predicted sulphatases have a high expression level prediction (PHX) (Lombardot 2004). In comparison, analysis of 70 published prokaryotic genomes with a specific Pfam profile revealed a maximum of only 6 sulphatases found in the Pseudomonas aeruginosa PAO1 genome and 30 in Bacteriodes thetaiotaomicron (Lombardot 2004). However, recent studies conclude that the number of genes and bacterial species encoding sulphatase enzymes is currently underestimated (Berteau et al. 2006). Until now, the 110 sulphatases found in R. baltica (15.3 per Mb) represents the highest number in any sequenced bacterial genome. In other planctomycetal genomes, genes encoding sulphatases were found in various numbers. Planctomyces maris DSM8797 T draft genome codes for 87 sulphatases (10.7/Mb), in Blastopirellula marina DSM3645 T 41 were found (6.16/Mb) and in the freshwater 7
Page 1: Ecological Aspects of the Marine Pl
Page 4 and 5: Background 3
Page 6 and 7: Background TABLE OF CONTENT 1 BACKG
Page 9 and 10: Background 1 BACKGROUND 1.1 Marine
Page 11 and 12: Background their nutritional specia
Page 13: Background rosettes. The latter are
Page 17 and 18: Background 1.3 Further outcome of t
Page 19 and 20: Background 1.5 Principle of DNA mic
Page 21 and 22: Background Fig 4 Flowchart of a typ
Page 23 and 24: Background Finally, cluster data ca
Page 25 and 26: Research Aims 2 RESEARCH AIMS 2.1 T
Page 27 and 28: Research Aims Zobellia galactanivor
Page 29 and 30: Results and Discussion 3 RESULTS AN
Page 31 and 32: Results and Discussion 3.1 Transcri
Page 33 and 34: Results and Discussion Abstract Bac
Page 35 and 36: Results and Discussion In summary,
Page 37 and 38: Results and Discussion Specific res
Page 39 and 40: Results and Discussion biosynthesis
Page 41 and 42: Results and Discussion fosmid 3FN [
Page 43 and 44: Results and Discussion conserved hy
Page 45 and 46: Results and Discussion exposed by R
Page 47 and 48: Results and Discussion Whole Genome
Page 49 and 50: Results and Discussion experiments,
Page 51 and 52: Results and Discussion References 1
Page 53 and 54: Results and Discussion 31. Aspedon
Page 55 and 56: Results and Discussion Figure legen
Page 57 and 58: Results and Discussion Each column
Page 59 and 60: Results and Discussion TABLE 2 Shar
Page 61 and 62: Results and Discussion TABLE 3 Shar
Page 63 and 64: Results and Discussion 3.2 The Rhod
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Results and Discussion Abstract Bac
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Results and Discussion and CzcR - b
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Results and Discussion of the expon
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Results and Discussion In the follo
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Results and Discussion successful c
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Results and Discussion RB3577, RB52
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Results and Discussion Conclusions
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Results and Discussion A detailed d
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Results and Discussion The setup of
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Results and Discussion 23. Kumar A:
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Results and Discussion R4 R4 R2 R3
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Results and Discussion FIG 7 A) Flu
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Results and Discussion FIG 7 C) Flu
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Results and Discussion TABLE 2 Numb
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Results and Discussion TABLE 4 Pres
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Results and Discussion Additional f
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Results and Discussion 3.3 Highly e
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Summary 4 SUMMARY In 2003, the comp
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Summary R. baltica. Results show th
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Summary 4.4 Fosmids of novel marine
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Establishing of the Microarray Pipe
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Contribution to the Research on Pla
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Outlook However, there will still b
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Reference Descamps, V., S. Colin, M
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Reference König, E., H. Schlesner
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Reference Rothberg, J. M. and J. H.
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Acknowledgement 9 ACKNOWLEDGEMENT
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Annex 10 ANNEX 111
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Heat Induced 10min ID Locus AA Nuc
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7098 RB12746 294 885 Formamidopyrim
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4326 RB7666 72 219 hypothetical pro
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4555 RB8076 173 522 Holliday juncti
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7197 RB12925 39 120 protein contain
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5700 RB10219 128 387 ATP synthase e
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5524 RB9907 433 1302 ISXo8 transpos
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Cold repressed 10min ID Locus AA Nu
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4428 RB7837 286 861 Ribosomal prote
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Salinity Induced 10min ID Locus STA
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1151 RB2186 1153993 1152692 433 130
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622 RB1179 603998 604384 128 387 hy
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Salinity repressed 10min ID Locus A
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2432 RB4386 349 1050 2259814 225876
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Cluster 1 Original row UID START ST
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1124 RB1190_integrase 607131 608009
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6247 RB8146_hypothetical protein 43
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Cluster 15 Original row UID START S
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Cluster 22 Original row UID START S
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The Rhodopirellula baltica life cyc
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62hvs44h_up ID Locus Ratio AA Nuc P
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82 h vs 62 h up ID Locus Ratio AA N
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92h vs 82h up ID Locus Ratio Parent
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240h vs 82h down ID Locus Ratio AA
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3871 RB6856 -1.574937983 62 189 hyp
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6606 RB11855 2.19926923 101 306 con
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2008 RB3662 2.034633667 43 132 hypo
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Cluster 3 Original row UID Start St
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1339 RB1225_dipeptidyl peptidase IV
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2860 RB2764_secreted protein contai
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Cluster 4 Original row UID Start St
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3513 RB378_periplasmic nitrate redu
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Cluster 13 Original row UID Start S
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