a Whole Genome Array Approach - Jacobs University

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Results and Discussion Transcriptional response of the model planctomycete Rhodopirellula baltica SH1 T to changing environmental conditions Patricia Wecker 1,3 , Christine Klockow 1,3 , Andreas Ellrott 1 , Christian Quast 1 , Philipp Langhammer 2 , Jens Harder 2 , Frank Oliver Glöckner 1,3§ 1 Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany 2 Department of Microbiology, Max Planck Institute for Marine Microbiology, Microbiology, Celsiusstr. 1, 28359 Bremen, Germany 3 <strong>Jacobs</strong> <strong>University</strong> Bremen gGmbH, Campusring 1, 28759 Bremen, Germany § Corresponding author Keywords: Planctomycetes, Rhodopirellula baltica, marine, expression profiling, hypothetical genes, shift experiments, whole genome array, microarray, heat shock, cold shock, high salinity Email addresses: P. Wecker: pwecker@mpi-bremen.de C. Klockow: cklockow@mpi-bremen.de A. Ellrott: aellrott@mpi-bremen.de C. Quast: cquast@mpi-bremen.de P. Langhammer: phillanghammer83@yahoo.de J. Harder: jharder@mpi-bremen.de F.O. Glöckner: fog@mpi-bremen.de 24
Results and Discussion Abstract Background: The marine model organism Rhodopirellula baltica SH1 T was the first Planctomycete to be completely sequenced. The genome analysis predicted a complex life style and a variety of genetic opportunities to adapt to the marine environment. Its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray. Results: Stress responses to salinity and temperature shifts were monitored in time series experiments. Chemostat cultures grown on mineral medium at 28°C were compared to cultures that were shifted to either elevated (37°C) or reduced (6°C) temperatures as well as high salinity (59.5‰) and observed over 300 min. Heat shock showed the induction of several known chaperone genes. Cold shock altered the expression of genes in lipid metabolism and stress proteins. High salinity resulted in the modulation of genes coding for compatible solutes, ion transporter and morphology. In summary, over 3000 of the 7325 genes were affected by temperature and/or salinity changes. Conclusions: Transcriptional profiling confirmed that R. baltica is highly responsive to its environment. The distinct responses gave new insights into the complex adaptation machinery of an environmentally relevant marine bacterium. Our transcriptome study and previous proteome data suggest a set of genes of unknown functions that are most probably involved in the global stress response. This work lays the foundation for further bioinformatic and genetic studies which leads to a comprehensive understanding of the biology of a marine Planctomycete. 25
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
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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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