title: Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.
abstract: BACKGROUND
  Sphingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. Thus far, however, little is known about the adaptive strategies used by Sphingomonas bacteria to respond to changes in water potential. To improve our understanding, strain RW1 was perturbed with either the cell-permeating solute sodium chloride or the non-permeating solute polyethylene glycol with a molecular weight of 8000 (PEG8000). These solutes are assumed to simulate the solute and matric components of the total water potential, respectively. The responses to these perturbations were then assessed and compared using a combination of growth assays, transcriptome profiling, and membrane fatty acid analyses.
  
  
  RESULTS
  Under conditions producing a similar decrease in water potential but without effect on growth rate, there was only a limited shared response to perturbation with sodium chloride or PEG8000. This shared response included the increased expression of genes involved with trehalose and exopolysaccharide biosynthesis and the reduced expression of genes involved with flagella biosynthesis. Mostly, the responses to perturbation with sodium chloride or PEG8000 were very different. Only sodium chloride triggered the increased expression of two ECF-type RNA polymerase sigma factors and the differential expression of many genes involved with outer membrane and amino acid metabolism. In contrast, only PEG8000 triggered the increased expression of a heat shock-type RNA polymerase sigma factor along with many genes involved with protein turnover and repair. Membrane fatty acid analyses further corroborated these differences. The degree of saturation of membrane fatty acids increased after perturbation with sodium chloride but had the opposite effect and decreased after perturbation with PEG8000.
  
  
  CONCLUSIONS
  A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.
authors.affiliation: Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland. david.johnson@env.ethz.ch
authors.forename: David R
authors.initials: DR
authors.lastname: Johnson
authors.forename: Edith
authors.initials: E
authors.lastname: Coronado
authors.forename: Silvia K
authors.initials: SK
authors.lastname: Moreno-Forero
authors.forename: Hermann J
authors.initials: HJ
authors.lastname: Heipieper
authors.forename: Jan Roelof
authors.initials: JR
authors.lastname: van der Meer
mesh_terms: D002463:Cell Membrane Permeability; D005227:Fatty Acids / Q000032:analysis*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D011092:Polyethylene Glycols / Q000378:metabolism; D012965:Sodium Chloride / Q000378:metabolism; D020578:Sphingomonas / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D059467:Transcriptome; D014867:Water / Q000378:metabolism
chemical_list: D005227:Fatty Acids; D014867:Water; D011092:Polyethylene Glycols; D012965:Sodium Chloride
references.citation: Genes Dev. 1999 Mar 15;13(6):655-65
references.pmid: 10090722
references.citation: Annu Rev Microbiol. 2002;56:187-209
references.pmid: 12142477
references.citation: J Bacteriol. 2006 Nov;188(21):7617-25
references.pmid: 16916894
references.citation: Nature. 1987 Sep 24-30;329(6137):348-51
references.pmid: 3306410
references.citation: Microbiol Rev. 1994 Dec;58(4):755-805
references.pmid: 7854254
references.citation: Curr Microbiol. 2005 Mar;50(3):151-4
references.pmid: 15717227
references.citation: J Bacteriol. 2006 Jun;188(11):4068-78
references.pmid: 16707698
references.citation: Microbiol Rev. 1989 Mar;53(1):121-47
references.pmid: 2651863
references.citation: J Bacteriol. 2005 Apr;187(7):2501-7
references.pmid: 15774893
references.citation: Appl Environ Microbiol. 2004 Apr;70(4):1907-12
references.pmid: 15066779
references.citation: FEMS Microbiol Rev. 2000 Jul;24(3):263-90
references.pmid: 10841973
references.citation: J Lipid Res. 1964 Oct;5:600-8
references.pmid: 14221106
references.citation: Can J Biochem Physiol. 1959 Aug;37(8):911-7
references.pmid: 13671378
references.citation: Appl Environ Microbiol. 2008 May;74(9):2627-36
references.pmid: 18326668
references.citation: Appl Microbiol Biotechnol. 1998 May;49(5):489-99
references.pmid: 9650248
references.citation: Adv Microb Physiol. 2002;46:47-110
references.pmid: 12073657
references.citation: Plant Physiol. 1981 Jan;67(1):64-7
references.pmid: 16661635
references.citation: Mol Microbiol. 2004 May;52(3):735-50
references.pmid: 15101980
references.citation: Biodegradation. 1997;8(3):143-51
references.pmid: 9396169
references.citation: J Bacteriol. 1998 Aug;180(15):3954-66
references.pmid: 9683494
references.citation: J Bacteriol. 2007 Oct;189(19):6751-62
references.pmid: 17660288
references.citation: Appl Environ Microbiol. 2008 May;74(9):2864-72
references.pmid: 18310438
references.citation: Appl Environ Microbiol. 2005 Jul;71(7):3866-71
references.pmid: 16000799
references.citation: Appl Environ Microbiol. 1996 Aug;62(8):2773-7
references.pmid: 16535373
references.citation: FEMS Microbiol Rev. 2002 Mar;26(1):49-71
references.pmid: 12007642
references.citation: J Bacteriol. 1998 Aug;180(16):4171-6
references.pmid: 9696766
references.citation: Bioinformatics. 2005 Apr 15;21(8):1365-70
references.pmid: 15572465
references.citation: Annu Rev Microbiol. 2000;54:49-79
references.pmid: 11018124
references.citation: Appl Environ Microbiol. 1992 Apr;58(4):1284-91
references.pmid: 16348695
references.citation: FEMS Microbiol Lett. 2008 Apr;281(2):155-9
references.pmid: 18312578
references.citation: Annu Rev Microbiol. 2001;55:591-624
references.pmid: 11544368
references.citation: Nat Genet. 2001 Dec;29(4):365-71
references.pmid: 11726920
references.citation: Appl Environ Microbiol. 1996 Feb;62(2):367-71
references.pmid: 16535225
references.citation: Appl Environ Microbiol. 1992 Mar;58(3):1005-10
references.pmid: 1575472
references.citation: Appl Environ Microbiol. 1995 Oct;61(10):3701-4
references.pmid: 16535151
references.citation: Appl Environ Microbiol. 2000 Jun;66(6):2414-21
references.pmid: 10831419
references.citation: Plant Physiol. 1983 May;72(1):66-70
references.pmid: 16662983
references.citation: BMC Microbiol. 2010 May 26;10:153
references.pmid: 20504315
references.citation: Mol Microbiol. 2004 Mar;51(5):1321-32
references.pmid: 14982627
references.citation: J Bacteriol. 2003 Nov;185(21):6358-70
references.pmid: 14563871
references.citation: Appl Environ Microbiol. 1994 Feb;60(2):740-5
references.pmid: 16349202
references.citation: Annu Rev Genet. 1992;26:131-58
references.pmid: 1482109
references.citation: Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):281-292
references.pmid: 11321072
references.citation: Appl Environ Microbiol. 1999 May;65(5):2246-9
references.pmid: 10224029