a Whole Genome Array Approach - Jacobs University

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Results and Discussion R. Rhodopirellula RB Rhodopirellula baltica ROS Reactive Oxygen Species ORF Open Reading Frame Competing interests The authors declare that they have no competing interests. Authors contribution PW conceived the study, initiated, conducted the experimental analysis, validated microarray and optimized experimental steps, wrote the manuscript, did the statistical analysis and analyzed the data. CK was involved in the chemostat cultivation of R. baltica and statistical analysis of the data AE wrote MADA the microarray analysis tool and designed the microarrays. CQ was responsible for the automatic reannotation of the genome and set up the web access PL and JH established the chemostat cultivation of R. baltica. JH supervised the chemostat cultivation. FOG contributed background information and was involved in writing and finishing the manuscript. All authors read and approved the final manuscript. Acknowledgements We thank Sylke Wohlrab for preliminary work and Matthias Gottschall for excellent technical assistance in the chemostat cultivation. The setup of the microarray and transcriptomic analysis of Rhodopirellula baltica was supported by European Commission contract GOCE-CT-2004-505403. 42
Results and Discussion References 1. Field D, Kyrpides N: The positive role of the ecological community in the genomic revolution. Microb Ecology 2007, 53(3):507-511. 2. Schlesner H, Rensmann C, Tindall BJ, Gade D, Rabus R, Pfeiffer S, Hirsch P: Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula. Int J Syst Evol Microbiol 2004, 54(Pt 5):1567-1580. 3. DeLong E, Franks D: Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 1993, 38:924-934. 4. Chatzinotas A, Sandaa R, W S, Amann R, FL D, Torsvik V, Zeyer J, Hahn D: Analysis of broad-scale differences in microbial community composition of two pristine forest soils. System Appl Microbiol 1998, 21(4):579-587. 5. Neef A, Amann R, Schlesner H, Schleifer K: Monitoring a widespread bacterial group: in situ detection of Planctomycetes with 16S rRNA-targeted probes. Microbiology 1998, 144(12):3257-3266. 6. Vergin KL, Urbach E, Stein JL, DeLong EF, Lanoil BD, Giovannoni SJ: Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol 1998, 64:3075-3078. 7. Crump BC, Armbrust EV, Baross JA: Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 1999, 65(7):3192-3204. 8. Giovannoni SJ, Scabtach E, Castenholz RW: Isosphaera pallida, gen. and comb. nov., a gliding, budding eubacterium from hot springs. Arch Microbiol 1987, 147:276-284. 9. Pimentel-Elardo S, Wehrl M, Friederich AB, Jensen PR, Henschel U: Isolation of Planctomycetes from aplysina sponges. Aqua Micro Ecol 2003, 33:239-245. 10. Fuerst JA, Gwilliam HG, Lindsay M, Lichanska A, Belcher C, Vickers JE, Hugenholtz P: Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Appl Environ Microbiol 1997, 63(1):254-262. 11. König E, Schlesner H, Hirsch P: Cell wall studies on budding bacteria of the Planctomyces/Pasteuria group and on a Prosthecomicrobium sp. Arch Microbiol 1984, 138:200-205. 12. Liesack W, König H, Schlesner H, Hirsch P: Chemical composition of the peptidoglycan-free cell envelopes of budding bacteria of the Pirella/Planctomyces group. Arch Microbiol 1986, 145:361-366. 13. Fuerst AJ: Intracellular compartmentation in Planctomycetes. Annu Rev Microbiol 2005, 59:299-328. 14. Tekniepe BL, Schmidt JM, Starr MP: Life cycle of a budding and appendaged bacterium belonging to morphotype IV of the Blastocaulis-Planctomyces group. Curr Microbiol 1981, 5:1-6. 15. Fuerst JA: The Planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 1995, 141 (Pt 7):1493-1506. 43
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 and 14: Background rosettes. The latter are
Page 15 and 16: Background bacterial peptidoglycan
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: Results and Discussion experiments,
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
Page 65 and 66: Results and Discussion Abstract Bac
Page 67 and 68: Results and Discussion and CzcR - b
Page 69 and 70: Results and Discussion of the expon
Page 71 and 72: Results and Discussion In the follo
Page 73 and 74: Results and Discussion successful c
Page 75 and 76: Results and Discussion RB3577, RB52
Page 77 and 78: Results and Discussion Conclusions
Page 79 and 80: Results and Discussion A detailed d
Page 81 and 82: Results and Discussion The setup of
Page 83 and 84: Results and Discussion 23. Kumar A:
Page 85 and 86: Results and Discussion R4 R4 R2 R3
Page 87 and 88: Results and Discussion FIG 7 A) Flu
Page 89 and 90: Results and Discussion FIG 7 C) Flu
Page 91 and 92: Results and Discussion TABLE 2 Numb
Page 93 and 94: Results and Discussion TABLE 4 Pres
Page 95 and 96: Results and Discussion Additional f
Page 98 and 99: 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
Page 112 and 113:
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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