Infectious Diseases in Obstetrics and Gynecology

Research Article

Probiotic Interference of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 with the Opportunistic Fungal Pathogen Candida albicans

Table 2

Differentially expressed C. albicans genes in cocultures with L. rhamnosus GR-1 or L. reuteri RC-14. values for genes with at least three observed incidences of significant differential regulation in the tested conditions are shown. -values ≥3 and ≤−3 were considered significant (see Section 2). Values followed by the symbol ^† indicate gene induction when compared to C. albicans cultures without addition of lactobacilli. Downregulation values are followed by symbol ^#. Differential gene expression data from coculture experiments with L. rhamnosus GR-1 (GR1_a, b, c, d, e) and L. reuteri RC-14 (RC14_a, b) are grouped according to the C. albicans growth phase (log phase and late log to early stationary phase). Genes are ordered in functional groupings adapted from gene ontology (GO) annotations shown in the Candida Genome Database (http://www.candidagenome.org/). Differentially expressed genes are also divided into upregulated genes (a), genes with mixed regulation (b), and downregulated genes (c). Genes followed by the symbol * are further discussed in the text.

(a) Upregulated C. albicans genes


ORF^a	Gene	Molecular function^b	Log phase cocultures			Late log to early stationary phase cocultures
ORF^a	Gene	Molecular function^b	GR1_a	RC14_a	GR1_b	GR1_c	GR1_d	RC14_b	GR1_e

Amino acid metabolism^c
orf19.5610	ARG3	Ornithine carbamoyltransferase	0.49	2.43	−0.53	1.69	3.54^†	4.36^†	3.20^†

Carbohydrate metabolism
orf19.3675	GAL7	Putative galactose-1-phosphate uridyl transferase	0.69	2.12	1.55	6.12^†	3.40^†	4.11^†	0.47
orf19.1788	XKS1	Putative xylulokinase	0.39	2.26	0.37	3.24^†	2.91	4.33^†	3.06^†

Cell wall biosynthesis
orf19.3688		Putative chromatin DNA binding protein	7.69^†	1.66	0.35	0.19	10.34^†	4.25^†	−0.09
orf19.3674	GAL102	UDP-glucose 4,6-dehydratase with role in mannosylation of cell wall proteins	0.11	1.70	−0.06	3.63^†	4.48^†	4.75^†	0.21

Fatty acid metabolism
orf19.5640	PEX5	Putative peroxisomal targeting receptor	0.14	−2.14	3.31^†	5.21^†	3.34^†	4.03^†	1.03
orf19.5215	TES15	Putative acyl-CoA thioesterase	−0.91	−0.76	1.91	3.58^†	5.17^†	5.66^†	−2.00

Glycogen metabolism
orf19.3302		Putative type-1 protein phosphatase targeting subunit	−0.61	−0.98	0.58	3.03^†	6.26^†	3.28^†	1.32

Glycolysis
orf19.6116	GLK4	Glucokinase	−0.85	0.48	1.25	0.82	4.13^†	3.05^†	6.62^†

Intracellular transport
orf19.3233	HSE1	Putative SH3-domain-containing protein	−1.94	−0.81	2.30	3.34^†	5.24^†	3.66^†	−0.24
orf19.7086		Putative protein transporter	0.54	−1.18	−1.10	1.35	4.74^†	4.15^†	3.27^†
orf19.3841		Putative protein serine/threonine kinase	−2.91	−0.82	−0.68	4.07^†	4.94^†	4.92^†	−1.58

Oxidation/Reduction
orf19.5805*	DLD1 *	D-lactate dehydrogenase*	1.34	0.72	4.57^†	3.63^†	6.23^†	5.90^†	8.57^†
orf19.1048	IFD6	Aldo-keto reductase	−0.09	2.07	1.36	−0.92	5.16^†	3.41^†	6.71^†
orf19.742	ALD6	Putative aldehyde dehydrogenase	−1.27	0.96	−0.19	4.46^†	4.77^†	5.36^†	3.16^†
orf19.5288	IFE2	Alcohol dehydrogenase	1.03	−0.07	−0.66	5.77^†	6.75^†	6.04^†	0.33

Protein catabolism
orf19.1191		Possible ubiquitin-protein ligase	1.12	−0.91	3.14^†	2.25	3.64^†	4.31^†	−0.45
orf19.5752		Possible ubiquitin-protein ligase	−1.59	−0.66	0.17	4.35^†	3.16^†	3.29^†	2.38

Repair
orf19.1331	HSM3	Protein may be involved in DNA mismatch repair	−0.74	−2.27	−0.14	4.18^†	8.78^†	6.68^†	5.39^†

Respiration
orf19.4551	CTN1	Predicted carnitine acetyl transferase	1.21	1.97	0.08	11.85^†	3.64^†	7.52^†	2.61

RNA catabolism
orf19.5614	RNH1	Putative ribonuclease H1	−1.33	0.38	−0.07	3.06^†	4.11^†	2.96	3.22^†

Signaling
orf19.399		Putative serine/threonine protein kinase	−2.21	−2.59	−0.10	4.08^†	4.88^†	4.44^†	−0.22
orf19.5531	CDC37	Chaperone for Crk1 protein kinase	−0.45	0.95	0.80	2.13	5.46^†	3.19^†	6.05^†

Stress response
orf19.882*	HSP78 *	Heat-shock protein*	0.00	−1.35	0.06	4.21^†	4.52^†	5.81^†	4.66^†
orf19.3861*	SIS1 *	Putative Type II HSP40 co-chaperone*	−0.91	−0.40	0.79	1.65	3.92^†	4.78^†	3.10^†
orf19.5348*	TPS3 *	Trehalose-phosphate synthase subunit*	0.59	−0.26	−0.99	4.23^†	8.95^†	7.42^†	5.40^†

Transcriptional regulation
orf19.3047	SIP3	Protein kinase-related protein	1.23	0.77	0.66	3.62^†	3.69^†	4.84^†	4.52^†
orf19.909	STP4	Putative transcription factor	−0.52	−1.28	1.29	6.75^†	5.15^†	7.01^†	2.41
orf19.3190	HAL9	Putative transcription factor involved in salt tolerance	0.98	1.83	2.82	3.87^†	4.99^†	5.03^†	−0.59

Translation
orf19.154		Possible 90S pre-ribosome complex protein	9.04^†	1.52	−0.03	4.19^†	3.22^†	2.77	0.90

Transport
orf19.5079*	CDR4 *	ABC transporter*	2.77	3.79^†	−0.06	3.22^†	2.89	3.51^†	1.78
orf19.4802	FTH1	Putative high affinity iron transporter (vacuolar)	−0.45	0.76	1.10	4.54^†	5.95^†	7.85^†	−0.38
orf19.3668	HGT2	Putative glucose transporter	1.17	1.35	1.73	9.56^†	4.30^†	3.16^†	−2.49
orf19.5447	HGT19	Putative glucose/myo-inositol transporter	2.51	3.11^†	2.55	4.67^†	2.95	5.05^†	5.41^†
orf19.3526	ITR1	Inositol transporter	1.82	−0.20	1.69	3.52^†	5.21^†	5.25^†	2.91
orf19.1979	GIT1	Putative glycerophosphoinositol permease	0.97	6.75^†	−1.94	3.73^†	5.82^†	8.01^†	1.64
orf19.1027	PDR16	Phosphatidylinositol transfer protein	−0.47	−1.63	0.61	2.19	3.61^†	4.23^†	3.05^†
orf19.4737*	TPO3 *	Possible polyamine transporter*	0.08	−0.02	3.65^†	4.30^†	4.59^†	7.16^†	3.48^†
orf19.700*	SEO1 *	Similar to permeases (↑weak acid stress)*	−0.79	−1.34	4.50^†	4.90^†	2.88	5.02^†	−0.14

Unknown
orf19.2498		Unknown	−2.12	−1.08	0.29	3.03^†	3.05^†	3.99^†	−0.55
orf19.5245		Unknown	−0.36	−1.74	1.59	0.84	5.03^†	5.24^†	4.78^†
orf19.6321	PGA48	Putative GPI-anchored protein of unknown function	−1.55	−0.79	0.71	−1.46	5.14^†	3.50^†	3.62^†
orf19.5295		Unknown	−0.76	1.02	−2.03	5.83^†	3.06^†	3.51^†	−1.02
orf19.3448		Unknown	1.02	0.86	−0.59	5.89^†	2.51	3.32^†	3.52^†

(b) C. albicans genes with mixed regulation


ORF^a	Gene	Molecular function^b	Log phase cocultures			Late log to early stationary phase cocultures
ORF^a	Gene	Molecular function^b	GR1_a	RC14_a	GR1_b	GR1_c	GR1_d	RC14_b	GR1_e

Amino acid metabolism^c
orf19.3974	PUT2	1-Pyrroline-5-carboxylate dehydrogenase	−4.32^#	−0.86	−0.39	3.07^†	−3.25^#	−6.02^#	−1.68
orf19.105	HAL22	Put. phosphoadenosine-5′-phosphate phosphatase	−2.16	−4.51^#	3.44^†	3.62^†	−0.79	3.67^†	−3.38^#
orf19.5811	MET1	Putative uroporphyrin-3 C-methyltransferase	0.37	0.59	0.67	4.93^†	−1.93	3.53^†	−4.15^#

Carbohydrate metabolism
orf19.7481	MDH1	Malate dehydrogenase	−1.68	−2.14	1.19	3.97^†	−3.66^#	−3.34^#	−1.21

Cell morphogenesis
orf19.4892	TPK1	Subunit of cAMP-dependent protein kinase (PKA)	0.19	1.68	−3.02^#	−1.85	2.69	3.01^†	−3.77^#

Cell wall assembly
orf19.377	PHR3	Putative beta-1,3-glucanosyltransferase	−1.11	0.74	3.09^†	3.46^†	1.67	1.60	−3.52^#

Cytoskeleton maintenance
orf19.3505		Similar to S. cerevisiae phosphoinositide binding protein Slm2	−0.04	−4.18^#	−1.26	0.59	5.35^†	3.91^†	0.07

Filamentous growth
orf19.4246		Similar to S. cerevisiae Ykr070w protein	−1.10	−4.36^#	0.89	4.67^†	3.16^†	2.66	3.93^†
orf19.860	BMT8	Putative beta-mannosyltransferase	−4.31^#	1.93	3.88^†	1.90	−3.35^#	−2.13	−0.42

Oxidation/reduction
orf19.7323	CBP1	Corticosteroid binding protein	−1.74	3.42^†	0.83	0.26	−3.66^#	−3.27^#	−1.81
orf19.6139	FRE7	Putative ferric reductase	−1.25	0.17	4.56^†	−2.56	−3.14^#	−4.12^#	−0.42
orf19.6531	NUC2	NADH-ubiquinone oxidoreductase	−2.95	0.14	3.33^†	−2.10	−3.89^#	−4.12^#	−1.28

pH response
orf19.101	RIM9	Unknown, involved in cellular response to pH	−0.73	−0.50	−0.84	2.43	3.69^†	3.75^†	−3.08^#

Stress response
orf19.3707*	YHB1 *	Nitric oxide dioxygenase*	−0.61	−1.54	1.07	4.53^†	2.61	5.15^†	−3.06^#
orf19.6232*	NPR1 *	Predicted serine/threonine protein kinase*	−3.75^#	−1.63	4.49^†	3.98^†	−0.21	1.51	−0.30

Transcription
orf19.2831	RPC31	Putative RNA polymerase III subunit C31	−0.70	3.18^†	2.42	−3.33^#	−3.63^#	−2.32	−1.66
orf19.5908	TEC1	TEA/ATTS transcription factor	2.31	2.20	1.74	6.57^†	1.81	4.84^†	−4.97^#
orf19.5992	WOR2	Transcriptional regulator of white-opaque switching	−1.25	−3.19^#	−0.42	6.58^†	6.05^†	8.17^†	−3.00^#

Transport
orf19.6578		Predicted membrane transporter	0.28	−3.37^#	−0.56	4.20^†	6.39^†	3.27^†	0.01

tRNA aminoacylation
orf19.5239		similarity to alanyl-tRNA synthases	0.30	−4.73^#	−3.55^#	0.74	0.58	3.76^†	0.69

Unknown
orf19.925			−1.03	−1.59	3.42^†	−0.81	−4.07^#	−3.38^#	0.11
orf19.599			2.89	4.04^†	4.02^†	−3.40^#	0.51	0.33	2.02
orf19.4765	PGA6	Putative GPI-anchored cell wall adhesin-like protein	−0.67	5.78^†	−3.74^#	−0.92	−0.13	−4.12^#	2.61
orf19.6342			2.06	4.26^†	−3.63^#	−3.94^#	1.70	2.11	1.27

(c) Downregulated C. albicans genes


ORF^a	Gene	Molecular function^b	Log phase cocultures			Late log to early stationary phase cocultures
ORF^a	Gene	Molecular function^b	GR1_a	RC14_a	GR1_b	GR1_c	GR1_d	RC14_b	GR1_e

Adhesion^c
orf19.2122*	ALS12 *	ALS family protein; role in adhesion, biofilm formation, germ tube induction*	−1.84	−3.38^#	0.64	1.51	−3.68^#	−0.73	−3.71^#

Amino acid metabolism
orf19.646	GLN1	Putative glutamate synthase	−3.16^#	−0.50	0.45	1.56	−1.62	−3.20^#	−3.08^#
orf19.3846	LYS4	Homoaconitase	−2.68	−1.54	0.63	−4.04^#	−5.51^#	−4.80^#	−0.52
orf19.2360	URA2	Putative bifunctional carbamoylphosphate synthetase-aspartate transcarbamylase	−0.58	−5.46^#	−0.75	−1.48	−3.62^#	−4.30^#	−0.13
orf19.6257	GLT1	Putative glutamate synthase	−0.80	−3.46^#	0.19	−3.07^#	−5.30^#	−3.61^#	0.29

Cell wall organization
orf19.386	SAM4	Putative S-adenosylmethionine-homocysteine methyltransferase	−1.87	−1.60	0.64	−3.11^#	−3.40^#	−4.50^#	−2.44
orf19.3829*	PHR1 *	Glycosidase of cell surface*	−4.84^#	−4.20^#	−3.95^#	−7.74^#	−3.17^#	−6.66^#	−5.39^#
orf19.5171	PMT1	Protein mannosyltransferase,	−0.75	−0.20	0.42	−4.18^#	−3.67^#	−4.02^#	−0.86

Cytoskeleton organization
orf19.2286		Putative deoxyhypusine hydroxylase	−2.97	0.36	−1.06	−1.51	−3.07^#	−3.08^#	−3.49^#

DNA replication
orf19.5183*	POL3 *	Large subunit of DNA polymerase III*	−2.60	−4.03^#	0.98	−0.12	−4.07^#	−3.39^#	−2.58
orf19.6078	POL93	Putative gypsy-like reverse transcriptase	−3.48^#	−0.48	−0.43	−6.24^#	−1.66	−4.44^#	0.28
orf19.2885*	PRI2 *	Putative DNA primase*	0.27	−3.17^#	−3.27^#	−3.20^#	0.35	−2.05	0.31
orf19.3322	DUT1	dUTP pyrophosphatase	−3.24^#	−4.14^#	−0.28	−2.23	−3.38^#	−4.36^#	−0.44

Ergosterol biosynthesis
orf19.1631*	ERG6 *	Delta(24)-sterol C-methyltransferase*	−0.67	0.20	−3.61^#	−2.84	−6.05^#	−4.09^#	−1.34
orf19.2016*		Possible role in ergosterol biosynthesis*	−2.26	0.16	2.13	−3.22^#	−3.69^#	−3.14^#	1.05
orf19.922*	ERG11 *	Lanosterol 14-alpha-demethylase*	−1.29	−0.44	−0.73	−5.19^#	−4.14^#	−5.50^#	−2.26

Filamentous growth
orf19.815	DCK1	Putative guanine nucleotide exchange factor required for embedded filamentous growth	−1.76	−4.90^#	−0.07	0.47	−4.22^#	−1.11	−4.89^#
orf19.3669	SHA3	Putative serine/threonine kinase	−1.04	−2.35	−0.77	−3.24^#	−3.27^#	−1.55	−3.89^#
orf19.3575*	CDC19 *	Putative pyruvate kinase; mutation affects filamentation*	−2.04	−0.07	0.20	−3.09^#	−3.12^#	−3.97^#	0.49

Gluconeogenesis
orf19.7514*	PCK1*	Phosphoenolpyruvate carboxykinase*	−0.22	−3.90^#	2.82	1.21	−3.89^#	−3.66^#	−2.91

Glutathione biosynthetic process
orf19.5059	GCS1	Gamma-glutamylcysteine synthetase	−2.60	−3.06^#	−3.10^#	1.00	−2.27	−0.52	−3.85^#

Intracellular transport
orf19.4805		Putative membrane protein	−1.19	1.35	−0.56	−3.69^#	−3.87^#	−3.64^#	−2.47

Lipoate biosynthetic process
orf19.819		Possible role in lipoate biosynthesis	−1.06	−3.54^#	1.91	0.27	−4.15^#	−3.69^#	−0.94

NAD biosynthetic process
orf19.1460		Putative glutamine-dependent NAD synthetase	−2.41	−2.49	0.05	−0.79	−3.60^#	−3.23^#	−3.51^#

Oxidation/Reduction
orf19.5517		Similar to alcohol dehydrogenases	−2.94	−0.19	−0.85	−4.83^#	−6.56^#	−8.21^#	−0.07
orf19.2525	LYS12	Mitochondrial homoisocitrate dehydrogenase	−2.17	1.04	−1.19	−5.01^#	−5.72^#	−7.22^#	0.65

RNA processing
orf19.7215		Ortholog(s) have snoRNA binding activity	−2.83	−0.06	−0.38	−0.16	−5.20^#	−4.12^#	−3.23^#
orf19.3159	UTP20	Similar to S. cerevisiae nucleolar protein Utp10p	−1.27	−0.48	−0.20	−2.29	−5.60^#	−3.26^#	−3.15^#

Signaling
orf19.3453		Possible role in signal transduction	−1.58	−0.21	0.89	−4.27^#	−3.25^#	−4.07^#	0.09
orf19.6906*	ASC1 *	Protein described as part of 40S ribosomal subunit*	−3.30^#	−2.92	−1.91	0.37	−3.74^#	−4.70^#	−2.62

TCA cycle
orf19.6632	ACO2	Aconitate hydratase 2	−1.14	−0.25	0.55	−3.34^#	−6.53^#	−4.39^#	0.05

Translation
orf19.6253*	RPS23A *	Putative ribosomal protein*	−1.19	−3.68^#	−0.63	−3.51^#	−2.82	−2.86	−3.17^#
orf19.4152*	CEF3 *	Translation elongation factor 3*	−2.13	−3.35^#	0.54	0.12	−3.18^#	−1.03	−3.86^#

Transport
orf19.4599	PHO89	Putative phosphate permease	0.73	−0.06	−2.63	−11.05^#	−6.49^#	−5.80^#	−6.50^#
orf19.5170	ENA21	Possible sodium transporter sodium transporters	−0.77	−2.46	−1.35	−3.59^#	−4.30^#	−5.16^#	−1.38
orf19.6000*	CDR1 *	ABC transporter involved in multidrug resistance*	−0.09	−0.21	−2.97	−1.76	−5.00^#	−5.04^#	−3.82^#

Unknown
orf19.7413		MMS21-SMC5-SMC6 complex component	−3.01^#	−3.22^#	1.62	−3.10^#	−1.53	−1.75	0.55
orf19.1549		Unknown	−0.42	−1.89	−3.17^#	−3.96^#	−3.83^#	−2.95	−1.10
orf19.4651	PGA53	Putative GPI-anchored protein	−0.84	−1.33	−1.16	−3.73^#	−3.33^#	−3.75^#	0.35
orf19.5799		Unknown	0.24	−0.13	−1.23	−3.54^#	−4.95^#	−5.27^#	−1.11
orf19.915		Unknown	−0.56	1.05	−0.59	0.19	−3.60^#	−3.15^#	−3.21^#
orf19.5760	IHD1	Putative GPI-anchored protein	−2.64	−5.84^#	−0.54	−5.21^#	−3.27^#	−5.36^#	−5.36^#
orf19.3548		Unknown	−3.48^#	−1.88	−0.44	1.89	−3.13^#	−3.08^#	−0.96

^aFor further information on the open reading frames (ORFs) see the Candida Genome Database (CGD: [20]) (http://www.candidagenome.org/).
^bInformation on the molecular function is abridged. More information is available at the CGD website.
^cFunctional groupings derived from Biological Process GO annotations. Due to space restrictions, the groupings are simplified. Individual genes can be involved in multiple biological processes.