title: Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism.
abstract: 'Candidatus Phytoplasma mali' is a phytopathogenic bacterium of the family Acholeplasmataceae assigned to the class Mollicutes. This causative agent of the apple proliferation colonizes in Malus domestica the sieve tubes of the plant phloem resulting in a range of symptoms such as witches'--broom formation, reduced vigor and affecting size and quality of the crop. The disease is responsible for strong economical losses in Europe. Although the genome sequence of the pathogen is available, there is only limited information on expression of selected genes and metabolic key features that have not been examined on the transcriptomic or proteomic level so far. This situation is similar to many other phytoplasmas. In the work presented here, RNA-Seq and mass spectrometry shotgun techniques were applied on tissue samples from Nicotiana occidentalis infected by 'Ca. P. mali' strain AT providing insights into transcriptome and proteome of the pathogen. Data analysis highlights expression of 208 genes including 14 proteins located in the terminal inverted repeats of the linear chromosome. Beside a high portion of house keeping genes, the recently discussed chaperone GroES/GroEL is expressed. Furthermore, gene expression involved in formation of a type IVB and of the Sec-dependent secretion system was identified as well as the highly expressed putative pathogenicity-related SAP11-like effector protein. Metabolism of phytoplasmas depends on the uptake of spermidine/putescine, amino acids, co-factors, carbohydrates and in particular malate/citrate. The expression of these transporters was confirmed and the analysis of the carbohydrate cycle supports the suggested alternative energy-providing pathway for phytoplasmas releasing acetate and providing ATP. The phylogenetic analyses of malate dehydrogenase and acetate kinase in phytoplasmas show a closer relatedness to the Firmicutes in comparison to Mycoplasma species indicating an early divergence of the Acholeplasmataceae from the Mollicutes.
authors.affiliation: Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Christin
authors.initials: C
authors.lastname: Siewert
authors.affiliation: Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Toni
authors.initials: T
authors.lastname: Luge
authors.affiliation: Institute of Pesticides and Environmental Protection, Belgrade, Serbia.
authors.forename: Bojan
authors.initials: B
authors.lastname: Duduk
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany.
authors.forename: Erich
authors.initials: E
authors.lastname: Seemüller
authors.affiliation: Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Carmen
authors.initials: C
authors.lastname: Büttner
authors.affiliation: Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Sascha
authors.initials: S
authors.lastname: Sauer
authors.affiliation: Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D054884:Host-Pathogen Interactions / Q000235:genetics; D010802:Phylogeny; D045582:Phytoplasma / Q000201:enzymology / Q000235:genetics / Q000378:metabolism* / Q000472:pathogenicity*; D021382:Protein Sorting Signals; D017433:Protein Structure, Secondary; D040901:Proteomics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome / Q000235:genetics; D014774:Virulence / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D021382:Protein Sorting Signals
references.citation: BMC Genomics. 2008 Jun 26;9:306
references.pmid: 18582369
references.citation: Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1217-1226
references.pmid: 15280295
references.citation: Nat Biotechnol. 2008 Dec;26(12):1367-72
references.pmid: 19029910
references.citation: Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1243-1255
references.pmid: 15280299
references.citation: Microbiology (Reading). 2012 Nov;158(Pt 11):2805-2814
references.pmid: 22936033
references.citation: Mol Cell Proteomics. 2013 Jul;12(7):1965-79
references.pmid: 23579186
references.citation: Curr Opin Microbiol. 2010 Oct;13(5):619-24
references.pmid: 20888288
references.citation: Microbiology (Reading). 2004 Jan;150(Pt 1):135-142
references.pmid: 14702406
references.citation: Int J Syst Bacteriol. 1995 Jul;45(3):449-53
references.pmid: 8590671
references.citation: Anal Biochem. 1987 Apr;162(1):156-9
references.pmid: 2440339
references.citation: Proteomics. 2013 Dec;13(23-24):3424-8
references.pmid: 24174276
references.citation: J Mol Microbiol Biotechnol. 2014;24(1):1-11
references.pmid: 24158016
references.citation: BMC Genomics. 2013 Aug 02;14:529
references.pmid: 23915186
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6416-21
references.pmid: 19329488
references.citation: Science. 2009 Jul 24;325(5939):388-90
references.pmid: 19628836
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: J Mol Microbiol Biotechnol. 2014;24(1):19-36
references.pmid: 24158107
references.citation: Phytopathology. 2009 Sep;99(9):1053-61
references.pmid: 19671007
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Bioinformatics. 2012 Feb 15;28(4):464-9
references.pmid: 22199388
references.citation: DNA Cell Biol. 2005 Dec;24(12):832-40
references.pmid: 16332180
references.citation: Int J Syst Evol Microbiol. 2005 Nov;55(Pt 6):2451-2463
references.pmid: 16280510
references.citation: PLoS One. 2011;6(8):e23242
references.pmid: 21858041
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W116-20
references.pmid: 15980438
references.citation: Comput Appl Biosci. 1994 Jun;10(3):301-7
references.pmid: 7922687
references.citation: Mol Biol Evol. 2008 Jul;25(7):1307-20
references.pmid: 18367465
references.citation: Proteins. 2003 Mar 1;50(4):526-30
references.pmid: 12577257
references.citation: J Proteome Res. 2011 Apr 1;10(4):1794-805
references.pmid: 21254760
references.citation: Nat Genet. 2004 Jan;36(1):27-9
references.pmid: 14661021
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D584-9
references.pmid: 23193261
references.citation: Front Microbiol. 2011 Jun 27;2:136
references.pmid: 21743810
references.citation: ScientificWorldJournal. 2012;2012:185942
references.pmid: 22550465
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Mol Plant Microbe Interact. 2012 Jul;25(7):889-95
references.pmid: 22432876
references.citation: Mol Plant Microbe Interact. 2009 Jan;22(1):18-30
references.pmid: 19061399
references.citation: J Bacteriol. 2006 May;188(10):3682-96
references.pmid: 16672622
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Int J Syst Evol Microbiol. 2013 Aug;63(Pt 8):2879-2894
references.pmid: 23334879
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: PLoS One. 2013 Apr 23;8(4):e62770
references.pmid: 23626855
references.citation: Genome Res. 2011 Sep;21(9):1552-60
references.pmid: 21690186
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W429-32
references.pmid: 17483518
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references.pmid: 22127870
references.citation: PLoS One. 2012;7(4):e36009
references.pmid: 22558305
references.citation: Nat Protoc. 2006;1(6):2856-60
references.pmid: 17406544
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):33-6
references.pmid: 10592175
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):E1254-63
references.pmid: 22065743
references.citation: Mol Microbiol. 2010 Sep;77(6):1406-15
references.pmid: 20662777
references.citation: Mol Plant Microbe Interact. 2013 Mar;26(3):367-76
references.pmid: 23387471
references.citation: DNA Cell Biol. 2007 Aug;26(8):557-64
references.pmid: 17688407
references.citation: Int J Syst Evol Microbiol. 2003 Nov;53(Pt 6):1925-9
references.pmid: 14657124
references.citation: J Bacteriol. 1969 May;98(2):547-51
references.pmid: 5784211
references.citation: Annu Rev Microbiol. 2000;54:221-55
references.pmid: 11018129
references.citation: Proteome Sci. 2010 Apr 08;8:20
references.pmid: 20377883
references.citation: Int J Syst Bacteriol. 1997 Apr;47(2):262-9
references.pmid: 9103609
references.citation: J Bacteriol. 2008 Jun;190(11):3979-91
references.pmid: 18359806
references.citation: Plant Dis. 2006 Oct;90(10):1313-1319
references.pmid: 30780938