TABLE 4.

Genes differentially expressed in the X. fastidiosa algU::nptII mutant in vitro, organized by functional groups

Functional group and gened	ORF	Description	M/W ratioa,b	Expression in mutantc
Macromolecule metabolism
Protein metabolism/degradation
clpS	PD0664	ATP-dependent Clp protease adaptor; posttranslational modification	0.448	Lower
clpA	PD0665	ATP-dependent Clp protease subunit; posttranslational modification	0.485	Lower
clpB	PD1685	ATP-dependent Clp protease subunit; posttranslational modification	0.421	Lower
mucD	PD1286	Periplasmic protease	0.616	Lower
Protein metabolism/chaperones
grpE	PD1371	Heat shock protein GrpE	0.40	Lower
dnaK	PD1370	Heat shock protein Hsp70; cochaperones are DnaJ and GrpE	0.378	Lower
RNA metabolism/ribosomal proteins
rpmH	PD2123	50S ribosomal protein L34; unknown function	0.449	Lower
rplW	PD0439	50S ribosomal protein L23; unknown function	0.499	Lower
rplP	PD0444	50S ribosomal protein L16; unknown function	0.426	Lower
rpmC	PD0445	50S ribosomal protein L29; unknown function	0.479	Lower
rplN	PD0447	50S ribosomal protein L14; unknown function	0.477	Lower
rpsN	PD0450	30S ribosomal protein S14; unknown function	0.244	Lower
rpsH	PD0451	30S ribosomal protein S8; unknown function	0.256	Lower
rplF	PD0452	50S ribosomal protein L6; unknown function	0.323	Lower
rpsE	PD0454	30S ribosomal protein S5; unknown function	0.437	Lower
rpmD	PD0455	50S ribosomal protein L30; unknown function	0.348	Lower
rpsM	PD0458	30S ribosomal protein S13; unknown function	0.394	Lower
rpmB	PD0488	50S ribosomal protein L28; unknown function	0.436	Lower
rpmG	PD0489	50S ribosomal protein L33; unknown function	0.353	Lower
rpmE	PD0749	50S ribosomal protein L31; unknown function	0.350	Lower
Intermediary metabolism
Energy metabolism, carbon/tricarboxylic acid cycle
gltA	PD0750	Citrate synthase; energy production and conversion	0.496	Lower
Regulatory functions/sigma factors and other regulatory components
csrA	PD0095	RsmA homologue; regulates the production of virulence determinants	0.403	Lower
Regulatory functions/two-component systems
algR	PD1153	Two-component system; regulatory protein	0.617	Lower
Regulatory functions/activators/repressors
algH	PD1276	Transcriptional regulator	0.652	Lower
Cell structures
Surface structures
	PD1926	Fimbrial protein, pilus assembly protein	2.478	Higher
Membrane components/inner membrane
algC	PD0120	Phosphomannomutase	0.3	Lower
Membrane components/outer membrane
mopB	PD1709	Outer membrane protein	0.479	Lower
ompW	PD1807	Outer membrane protein	0.391	Lower
Cellular processes
Transport/protein, peptide secretion
secB	PD1065	Type II secretion system, preprotein translocase	0.409	Lower
Transport/carbohydrates, organic acids, alcohols
algS	PD0347	Sugar ABC transporter ATP-binding protein	0.41	Lower
Transport/cations
bfr	PD1672	Bacterioferritin; ferritin-like proteins	0.178	Lower
Mobile genetic elements
Phage-related functions and prophages
hfq	PD0066	Host factor-I protein; ubiquitous RNA-binding protein Hfq	0.32	Lower
Pathogenicity, virulence, and adaptation
Toxin production and detoxification
cvaCe	PD0216	Colicin V precursor; antibacterial polypeptide toxin	0.40	Lower
hspA	PD1280	Heat shock protein (Hsp)	0.469	Lower
Hypothetical/conserved hypothetical proteins
NDf	PD0159	Unknown	0.479	Lower
ND	PD0521	Unknown	0.439	Lower
ND	PD1354	Unknown	0.392	Lower
ND	PD0968	Unknown	0.495	Lower
ND	PD1028	Unknown	0.425	Lower
ND	PD1058	Putative transcriptional regulatory protein	0.484	Lower
ND	PD1295	Putative integral membrane protein; involved in cell shape determination	0.469	Lower
ND	PD1668	Putative integral membrane protein; involved in cell shape determination	0.413	Lower
ORFs with undefined category
ND	PD1667	HesB-like protein; unknown function	0.462	Lower

^aThe hybridization signal intensity (mean of 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 mutant are all statistically significantly different as analyzed by Student's t test (P < 0.001).

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

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

^eCurrently annotated as colicin V precursor.

^fND, no designation.