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Series GSE6619 Query DataSets for GSE6619
Status Public on Dec 30, 2006
Title Transcriptome analysis of the phytobacterium Xylella fastidiosa growing under xylem-based chemical conditions
Platform organism Xylella fastidiosa
Sample organism Xylella fastidiosa 9a5c
Experiment type Expression profiling by array
Summary Xyllela fastidiosa (Xf) is a xylem-limited bacterium responsible for important plant diseases, such as citrus variegated chlorosis (CVC) in Brazil and grapevines Pierce´s disease in the USA. One intriguing aspect of this microorganism is its capacity to grow in an extremely harsh environment such as the xylem, mainly composed of water, minerals and few organic salts. In vitro growth of Xf cells in chemically-defined media that mimic xylem fluid has been recently achieved, allowing more detailed studies of metabolic processes used by xylem-dwelling bacteria to thrive in such a nutrient-poor environment. We employed microarray hybridization experiments to compare the transcriptomes of Xf cells grown in 3G10-R, a medium that resembles grape sap and in Periwinkle Wilt (PW), the complex medium traditionally used to cultivate Xf. We identified 317 transcripts modulated in response to growth in either of the two media. Some of these genes seem to be involved in plant colonization, virulence and competition with other microorganisms, and have also been shown, in independent studies, to be up-regulated in cells directly isolated from the xylem of infected plants. Xf cells also show an increase in aerobic respiration when cultivated in PW, which can be associated with enhanced bacterial growth rates. This finding raises the question of weather such a metabolic switch might be related to the onset of CVC in infected plants, when Xf population seems to increase dramatically.
Keywords: Diefential growth conditions
 
Overall design To evaluate and compare the bacterial transcriptome profiles from bacteria cultured in PW and 3G10R media, bacterial cultures were harvested for total RNA extraction at day 3 (PW) and day 13 (3G10R), which allowed us to compare bacterial cultures grown into similar cellular densities. Samples from the resulting RNAs were then used in competitive hybridizations against Xf microarrays. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium and since each microarray carried two replicas of each spotted gene, we ended up with a series of 8 independent readings for each gene present in the microarrays. Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with median values lower than the median local background plus two Standard Deviations have been flagged and excluded from further analyses. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium. For each pair of RNA preparations, two independent hybridizations were performed, with dye swaps within each pair. The results from each hybridization were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array. Finally, the results from each individual experiment were loaded into the software TIGR Multi-Experiment Viewer (TMEV), v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified with the aid of the one-class option of the Significance Analysis of Microarrays (SAM) test, described by Tusher et al. (2001). The δ factor of the SAM test was adjusted to guarantee a False Discovery Rate (FDR) < 1.
 
Contributor(s) Nunes LR, Oliveira RC
Citation(s) 20625415
Submission date Dec 28, 2006
Last update date Sep 25, 2012
Contact name Luiz R. Nunes
E-mail(s) luiz.nunes@ufabc.edu.br
Phone (55) (11) 4798-7104
Organization name UFABC - Universidade Federal do ABC
Department Centro de Ciências Naturais e Humanas
Lab Laboratório de Genômica Funcional e Estrutural
Street address Rua Santa Adélia 166
City Santo André
State/province SP
ZIP/Postal code 09210-170
Country Brazil
 
Platforms (1)
GPL4683 Xylella fastidiosa 9a5c Biochip v.2.0
Samples (8)
GSM153587 X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp1_Repl_1
GSM153589 X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp1_Repl_2
GSM153591 X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp2_Repl_1
Relations
BioProject PRJNA98843

Genes that displayed statistically significant modulation in expression header descriptions
ID
ORF
GENOME_ACC
GENOME_RANGE
PROBE_ID
PRIMARY_FUNCTIONAL_CATEGORY
Score (d)
Numerator (r)
Denominator (s+s0)
Average Expression Ratio [log2(3G10R/PW)]

Data table
ID ORF GENOME_ACC GENOME_RANGE PROBE_ID PRIMARY_FUNCTIONAL_CATEGORY Score (d) Numerator (r) Denominator (s+s0) Average Expression Ratio [log2(3G10R/PW)]
11 Xf1287 NC_002488 Xf1287 HYPOTHETICAL PROTEIN 15.2 KDA (ORF 1287) VIII.B - Hypothetical Proteins -1.6188726 -1.4038229 0.8671608 -1.403822896
21 Xf1250 NC_002488 Xf1250 ROCF - ARGININE DEAMINASE 33.6 KDA (ORF 1250) I.A.2 - Intermediary Metabolism - Degradation - Degradation of Small Molecules -3.2789433 -1.9981312 0.6093826 -1.998131125
32 Xf1164 NC_002488 Xf1164 RPLE OR RPL5 OR HI0790 - 50S RIBOSOMAL PROTEIN L5 20.0 KDA (ORF 1164) III.B.2 - Macromolecule Metabolism - RNA Metabolism - Ribosomal Proteins -1.4931098 -0.9124048 0.61107683 -0.9124048
42 Xf0493 NC_002488 Xf0493 HYPOTHETICAL PROTEIN 14.5 KDA (ORF 0493) VIII.B - Hypothetical Proteins 1.4022555 0.94926196 0.6769536 0.949261951
66 Xf0488 NC_002488 Xf0488; Xf0489 HYPOTHETICAL PROTEIN 10.1 KDA (ORF 0488); HYPOTHETICAL PROTEIN 18.0 KDA (ORF 0489) VIII.B - Hypothetical Proteins 1.8791466 1.2425488 0.6612304 1.502640035
73 Xf0037 NC_002488 Xf0037 HYPOTHETICAL PROTEIN 7.1 KDA (ORF 0037) VIII.B - Hypothetical Proteins -1.3802029 -1.16347 0.8429703 -1.116242818
78 Xf0264 NC_002488 Xf0264; Xf0265 HYPOTHETICAL PROTEIN 10.2 KDA (ORF 0264); HYPOTHETICAL PROTEIN 8.3 KDA (ORF 0265) VIII.B - Hypothetical Proteins 4.5025473 3.8706195 0.8596511 4.105172043
84 Xf1655 NC_002488 Xf1655 HYPOTHETICAL PROTEIN 22.5 KDA (ORF 1655) VIII.B - Hypothetical Proteins 1.4727284 0.81967807 0.5565711 0.81967804
91 Xf2450 NC_002488 Xf2450 CONSERVED HYPOTHETICAL PROTEIN 10.5 KDA (ORF 2450) VIII.A - Conserved Hypothetical Proteins -2.080298 -1.221592 0.5872197 -1.221591896
97 Xf0276 NC_002488 Xf0276 MPL - UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE 50.8 KDA (ORF 0276) "IV.B - Cell Structure - Murein Sacculus, Peptidoglycan" -1.4305509 -0.8794181 0.61474085 -0.879418066
98 Xf1108 NC_002488 Xf1108 GREA - TRANSCRIPTIONAL ELONGATION FACTOR 17.0 KDA (ORF 1108) "III.B.5 - Macromolecule Metabolism - RNA Metabolism - RNA Synthesis, Modification, DNA Transcription" -2.6430337 -1.73683 0.657135 -1.736830031
105 Xf0726 NC_002488 Xf0726 HYPOTHETICAL PROTEIN 40.9 KDA (ORF 0726) VIII.B - Hypothetical Proteins -1.4080606 -0.9311379 0.6612911 -1.171981
114 Xf2272 NC_002488 Xf2272 METE - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE HOMOCYSTEINE METHYLTRANSFERASE 85.6 KDA (ORF 2272) "II.A.2 - Biosynthesis of Small Molecules - Amino Acids Biosynthesis - Aspartate Family, Pyruvate Family" 1.9335023 1.4929034 0.7721239 1.43833289
118 Xf1554 NC_002488 Xf1554 FUMC - FUMARATE HYDRATASE 50.5 KDA (ORF 1554) "I.C.7 - Intermediary Metabolism - Energy Metabolism, Carbon - TCA Cycle" -2.0500622 -1.3635359 0.6651193 -1.3635359
136 Xf1011 NC_002488 Xf1011 FRPC - HEMOLYSIN-TYPE CALCIUM BINDING PROTEIN 173.0 KDA (ORF 1011) "VII.C - Pathogenicity, Virulence and Adaptation - Toxin Production and Detoxification" -2.1968863 -1.4472378 0.65876776 -1.447237853
140 Xf0428 NC_002488 Xf0428 TM0492 - TRYPTOPHANYL-TRNA SYNTHETASE 47.9 KDA (ORF 0428) "III.B.4 - Macromolecule Metabolism - RNA Metabolism - Aminoacyl tRNA Synthetases, tRNA Modification" -2.6367188 -1.8909166 0.71714765 -1.890916583
141 Xf0445 NC_002488 Xf0445 PROS OR DRPA - PROLYL-TRNA SYNTHETASE 64.7 KDA (ORF 0445) "III.B.4 - Macromolecule Metabolism - RNA Metabolism - Aminoacyl tRNA Synthetases, tRNA Modification" -1.6744448 -1.0837446 0.6472263 -1.083744578
158 Xf0088 NC_002488 Xf0088 HFLX - GTP-BINDING PROTEIN 50.3 KDA (ORF 0088) IX - ORFs with Undefined Category 1.5394286 1.3624072 0.8850084 1.362407174
204 Xf2701 NC_002488 Xf2701; Xf2702 HYPOTHETICAL PROTEIN 11.8 KDA (ORF 2701); HYPOTHETICAL PROTEIN 6.4 KDA (ORF 2702) VIII.B - Hypothetical Proteins -2.8379982 -1.6817478 0.5925824 -1.681747838
209 Xf1354 NC_002488 Xf1354 YYBA - TRANSCRIPTIONAL REGULATOR (MARR FAMILY) 16.4 KDA (ORF 1354) I.D - Intermediary Metabolism - Regulatory Functions 2.655148 1.5552752 0.5857584 1.555275225

Total number of rows: 299

Table truncated, full table size 54 Kbytes.




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