BioMed Research International

Research Article

Transcriptome Analysis of the Phytobacterium Xylella fastidiosa Growing under Xylem-Based Chemical Conditions

Table 1

List of genes that displayed statistically significant variation in gene expression. Genes with positive Log2 ratio are overexpressed in 3G10R, while genes with negative Log2 ratio are overexpressed in PW.
Functional GroupORFGeneGene ProductLog2
NumberName(3G10R/PW)
Intermediary Metabolism
Energy metabolism, carbon—Aerobic respirationXf0308nuoDNADH-ubiquinone oxidoreductase, NQO4 subunit − 0 . 9 3
Xf0310nuoFNADH-ubiquinone oxidoreductase, NQO1 subunit − 1 . 0 8
Xf0311nuoGNADH-ubiquinone oxidoreductase, NQO3 subunit − 1 . 1 4
Xf0317nuoMNADH-ubiquinone oxidoreductase, NQO13 subunit − 1 . 0 3
Xf0347dld1D-Lactate dehydrogenase 1 . 1 8
Energy metabolism, carbon—GlycolysisXf0303tpiA OR tpi Triosephosphate isomerase − 0 . 8 9
Energy metabolism, carbon—TCA cycleXf2548sucDSuccinyl-CoA synthetase, alpha subunit − 1 . 6 7
Xf1554fumCFumarate hydratase − 1 . 4 7
Xf1554fumCFumarate hydratase − 1 . 3 6
Energy metabolism, carbon—Electron TransportXf1990yneNThioredoxin − 1 . 1 4
Xf0620dsbDc-Type cytochrome biogenesis protein (Copper Tolerance) − 0 . 8 3
Degradation—Degradation of Small MoleculesXf1250rocFArginine deaminase − 2 . 0 0
Xf1740yliIGlucose dehydrogenase B 1 . 4 5
Xf2395axeAAcetylxylan esterase 1 . 7 5
Xf2432gtaBUTP-glucose-1-phosphate uridylyl transferase − 1 . 1 4
Xf0610galEUDP-glucose 4-epimerase − 1 . 4 4
Xf2210Dioxygenase 1 . 0 0
Regulatory FunctionsXf1354yybATranscriptional regulator (MARR Family) 1 . 2 7
Xf1354yybATranscriptional regulator (MARR Family) 1 . 5 5
Xf1254araLTranscriptional regulator (ARAC Family) − 1 . 1 0
Xf2344furTranscriptional regulator (FUR Family) 1 . 1 9
Xf2336colRTwo-component system regulatory protein 1 . 3 2
Xf2534colRTwo-component system regulatory protein − 0 . 9 5
Xf1752Transcriptional regulator (LYSR Family) 1 . 6 4
Xf1733AF0343Tryptophan repressor binding protein 1 . 1 3
Xf1749opdETranscriptional regulator 1 . 6 5
Xf1730yafCTranscriptional regulator (LYSR Family) 1 . 9 7
Sugar-Nucleotide Biosynthesis, ConversionsXf0260xanAPhosphoglucomutase/ Phosphomannomutase 0 . 9 2
Central Intermediary Metabolism—Pool, Multipourpose ConversionsXf0880yadFCarbonic anhydrase − 1 . 3 0
Xf2255acsAcetyl coenzyme A synthetase − 1 . 3 7
Central Intermediary Metabolism—Amino SugarsXf2355Exo II n-acetyl-beta-glucosaminidase 1 . 4 4
Biosynthesis of Small Molecules
Amino Acids Biosynthesis—Aspartate family, pyruvate familyXf2272metE5-methyltetrahydro pteroyltriglutamate–homocysteine methyltransferase 1 . 4 4
Xf1121metF OR AQ_14295,10-methylene tetrahydrofolate reductase 0 . 9 2
Xf2223thrCThreonine synthase 1 . 0 0
Xf0863met2Homoserine O-acetyltransferase 1 . 2 5
Amino Acids Biosynthesis—Aromatic Amino Acid FamilyXf0624aroEShikimate 5-dehydrogenase 1 . 6 4
Nucleotides Biosynthesis—Salvage of Nucleosides and NucleotidesXf2150apaHDiadenosine tetraphosphatase 1 . 1 4
Xf2354hptHypoxanthine-guanine phosphoribosyl transferase 1 . 0 8
Nucleotides Biosynthesis – 2 DeoxyribonucleotidesXf0580PH1695Thymidylate kinase − 0 . 9 3
Xf1196nrdA OR TP1008Ribonucleoside-diphosphate reductase alpha chain 1 . 1 0
Nucleotides Biosynthesis—Purine RibonucleotidesXf1503gmk OR spoRGuanylate kinase 0 . 8 6
Nucleotides Biosynthesis—Pyrimidine RibonucleotidesXf1107carB OR pyrACarbamoyl-phosphate synthase large chain − 0 . 9 9
Xf1106carACarbamoyl-phosphate synthase small chain − 0 . 9 6
Cofactors, Prosthetic Groups, Carriers Biosynthesis—Menaquinone, UbiquinoneXf1487ubiEUbiquinone menaquinone transferase − 1 . 6 4
Cofactors, Prosthetic Groups, Carriers Biosynthesis—PantothenateXf0229panB3-Methyl-2-oxobutanoate hydroxy methyltransferase − 1 . 5 0
Cofactors, Prosthetic Groups, Carriers Biosynthesis—ThiaminXf0783thiGThiamine biosynthesis protein − 0 . 8 7
Cofactors, Prosthetic Groups, Carriers Biosynthesis—RiboflavinXf1748MJ06715-amino-6-(5-phospho ribosylamino) uracil reductase 1 . 0 5
Cofactors, Prosthetic Groups, Carriers Biosynthesis—BiotinXf2477bioDDethiobiotin synthetase 1 . 0 8
Cofactors, Prosthetic Groups, Carriers Biosynthesis—OthersXf1916AF1671Coenzime F390 synthetase 1 . 2 1
Fatty Acid and Phosphatidic Acid BiosynthesisXf2269DRB00803-alpha-hydroxysteroid dehydrogenase − 0 . 9 3
Xf0572fabABeta-hydroxydecanoyl-ACP dehydratase 1 . 1 8
Macromolecule Metabolism
DNA metabolism—ReplicationXf0001dnaAChromosomal replication initiator − 1 . 0 2
Xf0002dnaNDNA polymerase III, beta chain − 1 . 3 9
Xf0002dnaNDNA polymerase III, beta chain − 1 . 1 5
Xfa0003topA OR supXTopoisomerase I − 1 . 6 0
Xf1353parCTopoisomerase subunit 0 . 9 8
DNA metabolism—RecombinationXf0425recDExodeoxyribonuclease V alpha chain − 0 . 9 6
Xf0425recDExodeoxyribonuclease V alpha chain − 1 . 0 2
Xf0423ecb OR rorAExodeoxyribonuclease V beta chain 1 . 3 0
DNA metabolism—RepairXf1902ruvB OR HL0312Holliday junction binding protein, DNA helicase − 1 . 2 0
Xf2692ungUracil-DNA glycosylase − 1 . 1 8
DNA Metabolism—Restriction, ModificationXf0935LLAIIAMethyltransferase − 0 . 8 3
Xf1804SPHIMSite-specific DNA-methyltransferase 1 . 1 2
Xf1774hpaIIMDNA methyltransferase − 0 . 8 1
DNA Metabolism—Structural DNA Binding ProteinsXf0446bbh3DNA-binding protein − 1 . 1 9
Xf1644ssbSingle-stranded DNA binding protein 1 . 0 5
RNA Metabolism—Ribosomes—Maturation and ModificationXf0441rimIRibosomal-protein-alanine acetyl transferase 1 . 8 7
Xf0939rluD OR sfhBRidosomal large subunit pseudoeridine synthase D − 1 . 0 2
RNA Metabolism—Ribosomal ProteinsXf1164rplE OR rpl5 OR HI079050S ribosomal protein L5 − 0 . 9 1
Xf0238rpsO OR secC30S ribosomal protein S15 − 1 . 2 3
Xf1166rpsH OR rps8 OR HI079230S ribosomal protein S8 − 1 . 4
Xf1169rpsE OR spc 30S ribosomal protein S5 − 1 . 1 4
RNA Metabolism—RNA Synthesis, Modification, DNA TranscriptionXf1108greATranscriptional elongation factor − 1 . 7 3
Xf0227pcnBPolynucleotide adenyltransferase − 1 . 3 1
Xf2632rpoC OR tabBRNA polymerase beta subunit 1 . 0 9
Xf2606rluCPseudourylate synthase − 1 . 0 8
RNA Metabolism—Aminoacyl tRNA Synthetases, tRNA ModificationXf0428TM0492Tryptophanyl-tRNA synthetase − 1 . 8 9
Xf0445proS OR drpAProlyl-tRNA synthetase − 1 . 0 8
Xf0134valS OR HI1391Valyl-tRNA synthetase − 0 . 9 6
Xf0169tyrS OR HI1610Tyrosyl-tRNA synthetase 1 . 9 3
Xf1314queAS-Adenosylmethionine tRNA ribosyltransferase-isomerase − 1 . 0 0
Xf0736thrSThreonyl-tRNA synthetase − 1 . 0 8
RNA Metabolism—RNA DegradationXf1505rphRibonuclease PH − 0 . 7 4
Xf1041rnhBRibonuclease HII − 1 . 0 0
Xf2615rnaSA3Ribonuclease 1 . 0 0
Protein Metabolism—Translation and ModificationXf0644mipPeptidyl-propyl cis-trans isomerase − 1 . 1 1
Xf2629fusAElongation factor G − 0 . 9 0
Protein Metabolism—Protein DegradationXf0220pepQProline dipeptidase − 1 . 1 3
Xf0453hflC OR HI0150Integral membrane proteinase 1 . 6 5
Xf2241mucDPeriplasmic protease − 0 . 8 7
Xf1479ptrB OR tlp Peptidase − 0 . 8 2
Xf2330slpDProteinase − 0 . 8 5
Cell Structure
Murein Sacculus, PeptidoglycanXf0416vacJLipoprotein precursor − 0 . 7 8
Xf0799ddlB OR ddl D-Alanine-D-alanine ligase B − 1 . 6 9
Xf0276mplUDP-N-acetylmuramate- L-alanine ligase − 0 . 8 8
Surface StructuresXf0487Fimbrillin 1 . 0 7
Xf2539Fimbrial protein − 1 . 0 2
Xf2544pilBPilus biogenesis protein − 0 . 7 9
Chemotaxis and Mobility—Surface Polysaccharides, Lipopolysaccharides and AntigensXf1289kdsA2-dehydro-3-deoxy phosphooctonate aldolase − 0 . 9 0
Xf1419lpxD OR firA OR omsAAcetyltransferase 1 . 0 5
Xf1646lpxD OR firAUDP-3-O-(R-3-hydroxy myristoyl)-glucosamine N-acyltransferase − 0 . 7 5
Xf1638Dolichyl-phosphate mannose synthase related protein − 1 . 0 2
Xf0879rfbULipopolysaccharide biosynthesis protein − 0 . 7 4
Xf2154opsXSaccharide biosynthesis regulatory protein − 1 . 0 0
Xf0105kdtA OR waaA3-deoxy-D-manno-octulosonic acid trasnferase 1 . 5 0
Membrane Components—Outer Membrane ConstituentsXf1024Outer membrane protein H.8 precursor − 1 . 1 9
Cellular Processes
Transport—CationsXf1903kup OR trkDPotassium uptake protein 1 . 0 1
Xf1903kup OR trkDPotassium uptake protein 1 . 4 0
Xf0599ybiLTONB-dependent receptor for iron transport 1 . 4 6
Xf0395bfrBacterioferritin − 1 . 2 2
Transport—Amino Acids, AminesXf1937gltPProton glutamate symport protein − 1 . 0 0
Transport—Protein, Peptide SecretionXf2685sppAProtease IV − 0 . 8 8
Xf2261HI0561 560Oligopeptide transporter − 1 . 1 2
Transport—Carbohydrates, Organic Acids, AlchoholsXf0976dctAC4-dicarboxylate transport protein − 1 . 1 0
Cell DivisionXf2281DR0012Chromosomepartitioning protein − 1 . 0 8
OtherXf2251ppaSolute Na+ symporter − 1 . 6 4
Xf1728F451Transport protein 1 . 1 1
Xf1604btuEABC transporter vitamin B12 uptake permease − 1 . 4 8
Xf1409HI1148ABC transporter ATP-binding protein 0 . 8 4
Mobile Genetic Elements
Transposon- and Intron-Related FunctionsXf1775IS629Reverse transcriptase 1 . 0 6
Xf0535Transposase ORFA − 0 . 8 0
Phage-Related Functions and ProphagesXf2522Phage-related protein 1 . 5 2
Xf2522Phage-related protein 1 . 0 2
Xfa0040trbIConjugal transfer protein − 0 . 9 8
Xf2291Phage-related protein 0 . 9 5
Xf0513lycVPhage-related endolysin − 1 . 5 2
Xf1786Phage-related protein 1 . 3 2
Xf1706GP37 Phage-related tail fiber protein 1 . 3 1
Xf0685Phage-related protein 0 . 8 6
Xf0704Phage-related protein 1 . 1 8
Xf1875Phage-related protein 1 . 4 4
Plasmid-Related FunctionsXfa0006traA OR virB3Conjugal transfer protein − 1 . 1 3
Xfa0013traAO OR virB9Conjugal transfer protein − 1 . 3 7
Xfa0008traAC OR virB5Conjugal transfer protein − 1 . 5 4
Pathogenicity,Virulence, and Adaptation
Toxin production and detoxificationXf0262cvaCColicin V precursor 7 . 2 9
Xf0263cvaCColicin V precursor 1 . 7 0
Xf1011frpCHemolysin-type calcium binding protein − 1 . 4 5
Xf1827ohr Organic hydroperoxide resistance protein − 1 . 4 3
Xf2614sodA OR sodSuperoxide dismutase (MN) − 1 . 4 7
Xf1210gst OR HI0111Glutathione S-transferase − 1 . 0 0
Xf1890gpoGlutathione peroxidase-like protein 0 . 8 6
Xf2135frnEPolyketide synthase (PKS) 1 . 8 0
Xf1897tolBTOLB protein precursor − 1 . 3 0
Xf1729DR1890Phenylacetaldehyde dehydrogenase 0 . 9 1
Host Cell Wall DegradationXf0818engXCAEndo-1,4-beta-glucanase − 0 . 8 9
Adaptation Atypical ConditionXf2682mdoGPeriplasmic glucan biosynthesis protein − 0 . 8 0
Xf2622tapBTemperature acclimation protein B − 1 . 3 0
Surface ProteinsXf1516uspA1Surface-exposed outer membrane protein − 1 . 2 8
ExopolysaccharydesXf2360gumMGumm protein − 1 . 0 8
OtherXf1529hsfSurface protein 1 . 9 6
Xf1532oxyROxidative stress transcriptional regulator 0 . 9 6
Xf2121vapEVirulence-associated protein E 1 . 2 4
Xf1987vacBVACB protein − 1 . 3 5
Xf1114rpfCRegulator of pathogenicity factors − 0 . 8 7
ORFs with Undefined Category
Xf1723yrpGSugar-phosphate dehydrogenase 1 . 3 0
Xf0088hflXGTP-binding protein 1 . 3 6
Hypothetical Proteins
Xf1287Hypothetical protein 1 . 4 0
Xf0493Hypothetical protein 0 . 9 4
Xf0037Hypothetical protein − 1 . 1 1
Xf1655Hypothetical protein 0 . 8 2
Xf0726Hypothetical protein − 1 . 1 7
Xf1835Hypothetical protein − 0 . 8 5
Xfa0031Hypothetical protein − 1 . 6 0
Xf2413Hypothetical protein 0 . 9 6
Xf0871Hypothetical protein 1 . 6 9
Xf2454Hypothetical protein − 0 . 9 7
Xf1769Hypothetical protein − 0 . 8 0
Xf1803Hypothetical protein − 2 . 0 0
Xf0512Hypothetical protein − 0 . 9 3
Xf0531Hypothetical protein − 1 . 7 2
Xf1868Hypothetical protein 1 . 1 1
Xf1881Hypothetical protein 1 . 1 8
Xf0917Hypothetical protein 1 . 2 5
Xf1738Hypothetical protein 1 . 3 7
Xf0242Hypothetical protein 1 . 2 7
Xf1228Hypothetical protein 1 . 0 1
Xf1279Hypothetical protein 1 . 1 1
Xf1575Hypothetical protein 1 . 1 4
Xf2597Hypothetical protein − 0 . 9 4
Xf0516Hypothetical protein 1 . 1 6
Xf2017Hypothetical protein − 1 . 5 1
Xf1989Hypothetical protein − 0 . 9 4
Xf2410Hypothetical protein − 1 . 6 0
Xf2304Hypothetical protein − 1 . 2 6
Xf0959Hypothetical protein 1 . 2 4
Xf2115Hypothetical protein 1 . 2 3
Xf1100Hypothetical protein 1 . 0 4
Xf1704Hypothetical protein 0 . 9 5
Xf0974Hypothetical protein − 1 . 2 6
Xf0491Hypothetical protein 1 . 3 1
Xf1060Hypothetical protein 1 . 7 7
Xf2151Hypothetical protein 1 . 7 3
Xf2449Hypothetical protein − 1 . 0 1
Xf2305Hypothetical protein − 0 . 7 7
Xf1721Hypothetical protein 1 . 1 4
Xf0626Hypothetical protein − 1 . 3 9
Xf2411Hypothetical protein 1 . 0 1
Xf1770Hypothetical protein − 0 . 8 7
Xf1364Hypothetical protein − 0 . 8 5
Xf1710Hypothetical protein 0 . 9 0
Xf1761Hypothetical protein 1 . 4 4
Xf1787Hypothetical protein 1 . 3 8
Xf0540Hypothetical protein − 1 . 3 0
Xf1788Hypothetical protein 1 . 0 6
Xf0646Hypothetical protein 1 . 0 3
Xf2543Hypothetical protein − 0 . 9 8
Xf0914Hypothetical protein − 1 . 3 3
Xf2702Hypothetical protein − 1 . 5 2
Xf0492Hypothetical protein 1 . 5 5
Xf1239Hypothetical protein 1 . 0 1
Xf0074Hypothetical protein − 1 . 0 7
Xfa0004Hypothetical protein − 1 . 7 8
Xf1687Hypothetical protein 1 . 3 2
Xf0388Hypothetical protein − 0 . 8 6
Xf0025Hypothetical protein − 1 . 2 3
Xf1434Hypothetical protein − 1 . 2 4
Xf2125Hypothetical protein 0 . 8 9
Xf1513Hypothetical protein 1 . 1 8
Xf2711Hypothetical protein 1 . 2 3
Xf0035Hypothetical protein 1 . 3 1
Xf1441Hypothetical protein − 1 . 4 1
Xf2514Hypothetical protein 1 . 7 1
Xf2626Hypothetical protein 1 . 4 4
Xf0687Hypothetical protein 1 . 0 7
Xf1917Hypothetical protein 1 . 9 0
Xf2271Hypothetical protein 1 . 5 0
Xf1036Hypothetical protein − 0 . 9 9
Xfa0017Hypothetical protein − 1 . 9 8
Xf0529Hypothetical protein 1 . 0 9
Xf2103Hypothetical protein − 1 . 0 5
Xf1986Hypothetical protein − 1 . 0 5
Xf1700Hypothetical protein 1 . 1 2
Xf1719Hypothetical protein 1 . 0 8
Xf1753Hypothetical protein 1 . 4 4
Xf0019Hypothetical protein 0 . 8 5
Xf0293Hypothetical protein − 1 . 1 5
Xf0300Hypothetical protein 1 . 6 7
Xf0279Hypothetical protein 1 . 7 9
Xf0735Hypothetical protein − 0 . 9 4
Xf1010Hypothetical protein − 0 . 9 7
Xf1580Hypothetical protein 0 . 8 0
Xf2021Hypothetical protein 1 . 2 1
Xf2738Hypothetical protein 1 . 4 9
Xf0877Hypothetical protein 1 . 2 8
Xf2270Hypothetical protein 1 . 1 3
Xf0488Hypothetical protein 1 . 5 0
Xf0264Hypothetical protein 4 . 1 0
Xf2701Hypothetical protein − 1 . 6 8
Xf2768Hypothetical protein 1 . 3 5
Xf0688Hypothetical protein 0 . 9 6
Xf0898Hypothetical protein 1 . 1 5
Xf0426Hypothetical protein − 1 . 2 3
Xf0443Hypothetical protein − 1 . 0 6
Xf1421Hypothetical protein − 1 . 4 0
Xf2193Hypothetical protein − 2 . 1 7
Xf2390Hypothetical protein 1 . 2 4
Xf1128Hypothetical protein − 1 . 1 6
Xf2116Hypothetical protein 1 . 5 2
Xf0467Hypothetical protein − 1 . 1 8
Xf1193Hypothetical protein − 0 . 8 0
Xf1032Hypothetical protein − 1 . 3 3
Xf2262Hypothetical protein − 1 . 6 0
Conserved Hypothetical Proteins
Xfa0045Conserved hypothetical protein − 2 . 2 2
Xf2450Conserved hypothetical protein − 1 . 2 2
Xf2609Conserved hypothetical protein − 0 . 8 7
Xf1754Conserved hypothetical protein 1 . 8 3
Xf0805Conserved hypothetical protein − 0 . 8 1
Xf2493Conserved hypothetical protein 1 . 1 3
Xf2088Conserved hypothetical protein 1 . 2 6
Xf0196Conserved hypothetical protein − 1 . 9 5
Xf1750Conserved hypothetical protein 1 . 3 6
Xf1745Conserved hypothetical protein 1 . 2 4
Xf2647Conserved hypothetical protein 1 . 1 3
Xf2252Conserved hypothetical protein − 2 . 8 1
Xf2010Conserved hypothetical protein − 1 . 0 6
Xf2237Conserved hypothetical protein − 0 . 8 5
Xfa0032SCJ21.16Conserved hypothetical protein − 1 . 0 6
Xf0758yjeEConserved hypothetical protein − 1 . 4 0
Xf0407yccWConserved hypothetical protein 0 . 9 8
Xf0552yraLConserved hypothetical protein − 0 . 9 2
Xf2651ycbYConserved hypothetical protein − 1 . 1 9
Xf2575DR0386Conserved hypothetical protein − 0 . 8 6
Xf0363yiaDConserved hypothetical protein − 1 . 7 8
Xf0066ylbKConserved hypothetical protein 1 . 1 0
Xf2179ybeNConserved hypothetical protein 1 . 2 9
Xf2153HI0260.1Conserved hypothetical protein − 1 . 1 4
Xf0553HI1655Conserved hypothetical protein − 1 . 2 9
Xf2014DR0566Conserved hypothetical protein 1 . 1 4
Xf0139yjgPConserved hypothetical protein 1 . 1 5
Xf2474yjeKConserved hypothetical protein − 0 . 7 9
Xf2096MTH1196Conserved hypothetical protein − 1 . 9 3
Xf1054TM1087Conserved hypothetical protein − 0 . 9 1
Xf0554yraNConserved hypothetical protein − 0 . 8 5
Xf0339btuB OR bfe OR cer Conserved hypothetical protein − 0 . 9 1
Xf1272RV1827 OR MTCY1A11.16CConserved hypothetical protein − 1 . 0 2
Xf1405yhbJConserved hypothetical protein − 0 . 8 8
Xf1808ybaBConserved hypothetical protein − 1 . 1 9
Xf1829RP471Conserved hypothetical protein − 1 . 0 5
Xf0941yuxKConserved hypothetical protein − 0 . 8 0