TABLE 4.

Genes differentially expressed in X. fastidiosa DAC1984 in vitro, organized by functional groups

Functional group and gened	ORF	Description	M/W ratioa,b	Expression level in mutantc
Cell structure
Membrane components/outer membrane; oprO	PD0264	Porin O precursor	0.24	Lower
Surface structures	PD1926	Fimbrial protein-pilus assembly protein	0.12	Lower
Cellular processes; transport/other; actP	PD1294	Acetate permease	0.337	Lower
Intermediary metabolism; energy metabolism and carbon/electron support	PD2039	Oxidoreductase	2.75	Higher
Biosynthesis of small molecules;	PD1688	Cytochrome P450-like enzyme	2.45	Higher
cofactors, prosthetic groups, and carrier biosynthesis/biotin; bioI	PD1703	Hypothetical protein-conserved domains: lysophospholipase	6.31	Higher
	PD1702	Hypothetical protein-conserved domains: secretory lipase	5.29	Higher
Pathogenicity, virulence, and adaptation
Toxin production and detoxification
cvaC	PD0215	Colicin V precursor: antibacterial polypeptide toxin	3.63	Higher
cvaCe	PD0216	Colicin V precursor: antibacterial polypeptide toxin	0.51	Lower
Outer membrane protein
xadA	PD0731	Outer membrane protein: autotransporter adhesion	0.11	Lower
hsf	PD0744	Surface protein: autotransporter adhesion	0.31	Lower
Exopolysaccharides; gumC	PD1395	Exopolysaccharide biosynthesis	3.17	Higher
Hypothetical conserved/hypothetical proteins	PD0243	Conserved domains: membrane fusion protein	3.01	Higher
	PD0244	Conserved domains: acriflavin resistance protein	2.7	Higher
	PD0956	V8-like Glu-specific endopeptidase	4.77	Higher
	PD1299	Conserved domains: polyvinyl alcohol dehydrogenase	6.18	Higher
	PD1295	Putative membrane protein: unknown function	0.20	Lower
	PD0521	Unknown	3.24	Higher
	PD0657	Unknown	3.28	Higher
	PD0743	Unknown	6.62	Higher
	PD0955	Unknown	2.67	Higher
Mobile genetic elements/phage-related	PD0911	Phage-related proteins: unknown function	6.04	Higher
functions and prophages	PD0912	Phage-related proteins: unknown function	8.41	Higher
	PD0917	Phage-related proteins: unknown function	3.94	Higher
	PD0924	Phage-related proteins: unknown function	6.39	Higher
	PD0925	Phage-related proteins: unknown function	9.12	Higher
	PD0930	Phage-related proteins: unknown function	3.96	Higher

^aThe hybridization signal intensity (mean for three technical replicates) obtained with the mutant was divided by that obtained with the wild type to obtain the M/W ratio.

^bThe normalized hybridization signals for those genes between the wild type and the mutant are all statistically significantly different, as analyzed by Student's t test (P < 0.001).

^cGenes having final M/W ratios of >1.5 or <0.66 were designated as having higher or lower expression levels in the mutant, respectively.

^dGenes were detected on the basis of X. fastidiosa Temecula1 genomic sequences at the NCBI website.

^eCurrently annotated as a colicin V precursor.