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Table 2 Selected Class 1 genes ordered into different biological processes

From: Genomic and functional analyses unveil the response to hyphal wall stress in Candida albicans cells lacking β(1,3)-glucan remodeling

Functional category

Locus name (ORF n)

Sc best hit

1 h

3 h

5 h

Description

RF

colour ratio

RF

colour ratio

RF

colour ratio

Cell wall

PGA23

   

22.2

R/G

65.6

R/G

GPI protein

 

orf19.750

   

11.1

R/G

36.0

R/G

In vitro substrate of Kex2p

 

RBR1

     

6.7

R/G

GPI protein

 

RBT4

PRY3

2.2

R/R

10

R/G

8.9

R/W

PRY family protein

 

ECM331

PST1

2.3

R/R

5.2

R/W

5.3

R/W

GPI protein

 

PGA6

CCW12

2.8

R/R

6.8

R/W

3.4

R/W

GPI protein

 

CHS8

CHS1

2.2

R/R

2.0

R/R

4.3

R/R

Chitin synthase

 

PGA13

   

4.1

R/W

3.7

R/R

GPI protein

 

CRH11

CRH1

4.7

R/R

4.2

R/W

3.3

R/R

GPI transglycosylase

 

PGA54

 

2.0

R/R

3.5

R/R

  

GPI protein

 

TOS1

TOS1

  

2.5

R/W

  

Putative β(1,3)-glucanase

 

PLB3

PLB1

  

2.3

R/W

  

GPI anchored phospholipase B

 

CHS2

CHS1

2.4

R/R

2.0

R/W

  

Chitin synthase

 

EXG2

EXG2

2.2

R/R

    

GPI-anchored exo-β-1,3-glucosidase

Protein folding/ modification

CHS7

CHS7

    

2.4

R/W

Export Chs3p from ER

 

CWH8

CWH8 a

    

2.0

R/R

Dolychyl-P-P phosphatase of the ER

 

MNT1

KTR1

2.4

R/W

    

Golgi α(1,2)-mannosyltransferase

 

orf19.6864

 

2.5

R/W

    

Ubiquitin ligase complex

Filamentous growth

orf19.1208

 

2.6

R/W

  

3.1

R/W

FGR6-related gene

 

orf19.6896

 

3.4

R/W

  

2.9

R/W

FGR6-related gene

 

FGR6-1

 

3.9

R/W

4.3

R/W

2.9

R/W

Member of FGR family

 

FGR6

 

2.9

R/W

4.6

R/W

2.5

R/W

Member of FGR family

 

FGR6-3

 

2.5

R/W

2.7

R/W

2.2

R/W

Member of FGR family

 

FGR6-10

 

3.3

R/W

  

2.1

R/W

Member of FGR family

 

FGR6-4

 

2.6

R/W

  

2.0

R/W

Member of FGR family

 

orf19.5775

 

6.7

R/W

    

FGR6-related gene

 

orf19.4246

YKR070W

2.7

R/W

    

Tn mutation affects filamentation

Stress response

DDR48

DDR48

  

4.5

R/G

3.4

R/W

Immunogenic stress-associated protein

 

orf19.2125

 

2.1

R/R

3.1

R/R

2.4

R/R

CipC-like antibiotic response protein

Signal transduction

CPP1

MSG5

    

5.2

R/W

MAPK phosphatase

 

SSK2

SSK2

  

2.1

R/W

4.7

R/W

MAPKKK regulates Hog1p

 

ARF3

ARF3

      

Small GTPase

Cell cycle

PCL1

PCL1

    

11.7

R/G

Cyclin homolog

 

PCL2

PCL2

    

6.7

R/G

Cyclin homolog

 

CCN1

CLB3

3.5

R/W

6.0

R/G

7.9

R/W

G1 cyclin

 

GIN4

GIN4

2.0

R/R

4.0

R/W

3.2

R/W

Phosphorylates Cdc11p

 

DUN1

DUN1

    

2.1

R/W

Cell-cycle checkpoint protein kinase

 

CDC28

CDC28

  

2.0

R/W

2.4

R/R

Cyclin-dependent kinase

 

HSL1

HSL1

2.9

R/W

2.2

R/W

  

Morphogenesis regulation

 

INT1

BUD4

  

2.1

R/W

  

Morphogenesis regulation

Cell polarity/ cytoskeleton

MLC1

MLC1

2.0

R/R

    

Cytokinetic ring in hyphae

 

orf19.3501

PXL1

  

2.1

R/W

  

Polarized growth

 

orf19.6610

STU2

    

2.9

R/W

Microtubule-associated protein

DNA replication/repair

POL30

POL30

2.6

R/W

  

2.6

R/W

PCNA

 

POL3

POL3

    

2.2

R/W

Catalytic subunit of DNA pol delta

 

RAD51

RAD51

  

3.3

R/W

  

Homologous recombination and repair

 

DUT1

DUT1

2.3

R/R

3.2

R/W

  

dTTP de novo biosynthesis

 

orf19.7425

UNG1

2.0

R/R

    

Uracil-N-glycosylase

 

MSH6

MSH6

  

3.1

R/W

  

Mismatch repair

 

RFA2

RFA2

  

2.4

R/W

  

Putative DNA replication factor A

 

RFA1

RFA1

2.2

R/W

2.1

R/W

  

Putative DNA replication factor A

 

RNR1

RNR1

2.0

R/R

    

Subunit of ribonucleotide reductase

 

orf19.2796

POL12

3.5

R/W

    

DNA Pol α/primase complex

 

POL1

POL1

3.2

R/W

    

DNA Pol α

 

CDC54

MCM4

2.4

R/W

    

Pre-replication helicase complex

 

CDC46

MCM5

2.6

R/W

    

MCM complex subunit

 

MCM6

MCM6

2.0

R/W

    

MCM complex component

Metabolism

GFA1

GFA1

2.8

R/R

2.1

R/R

2.3

R/R

Glucosamine-6P synthase

 

FAS1

FAS1

2.9

R/W

2.0

R/R

  

β-subunit of fatty acid synthase

 

ACC1

ACC1

2.6

R/W

2.0

R/R

  

Acetyl-coenzyme-A carboxylase

 

FAS2

FAS2

2.5

R/W

2.0

R/R

  

α-subunit of fatty acid synthase

 

DPP3

DPP1

3.1

R/R

    

DGPP phosphatase; farnesol synthesis

 

GNA1

GNA1

2.1

R/R

    

Glucosamine-6P acetyltransferase

 

RTA2

RSB1

4.8

R/G

    

Flippase for sphingolipid release

 

orf19.2761

GPI11

2.3

R/R

    

Putative GPI anchor assembly protein

Oxido-reduction processes

PUT1

PUT1

2.3

R/W

    

Proline oxidase

 

orf19.1340

YDL124W

  

3.1

R/R

  

Member of aldo-keto reductase family

 

GDH3

GDH3

  

2.5

R/R

  

NADP-glutamate dehydrogenase

 

orf19.2244

YJR096W

    

3.6

R/W

Member of aldo-keto reductase family

 

orf19.7306

YPR127W

    

2.0

R/R

Aldo-keto reductase

Chromatin/chromosome

HHF22

HHF2

2.2

R/R

2.6

R/W

  

Putative histone H4

 

orf19.1052

HTB1

  

3.2

R/W

  

Putative histone H2B

 

HHF1

HHF1

  

3.2

R/W

  

Putative histone H4

 

HTA1

HTA1

2.1

R/R

2.9

R/W

  

Histone H2A

 

HTA2

HTA1

  

2.4

R/W

  

Putative histone H2A

 

HTB1

HTB1

  

2.2

R/W

  

Histone H2B

 

IRR1

IRR1

2.3

R/W

    

Putative cohesin subunit

 

ASF1

ASF1

2.2

R/W

    

Nucleosome assembly factor

Pathogenesis

SAP6

BAR1

    

2.7

R/R

Secreted aspartyl protease

Transcription

SWI6

SWI6

2.4

R/W

    

Regulator of G1/S transition

 

YOX1

YOX1

2.2

R/W

2.3

R/R

3.8

R/R

Homeobox transcriptional repressor

 

WOR2

UME6

  

2.3

R/W

5.1

R/W

Zn2Cys6 regulator of W-O switching

Transport

CCC2

CCC2

    

4.2

R/W

Golgi Copper transporter

 

FRP3

ATO2

2.5

R/W

    

Ammonium transporter

 

FLC2

FLC2

2.5

R/W

2.5

R/W

2.2

R/W

FAD (or putative calcium) transporter

 

YVC1

YVC1

2.0

R/R

2.8

R/W

2.4

R/W

Calcium activated cation channel

 

orf19.5022

SMF2

2.0

R/W

    

Divalent metal transporter

  1. The data refer to Class 1 genes showing statistically significant RF (see Additional file 2 and criteria used as described in Methods). Only genes that were upregulated respect to time zero by two-fold in the mutant (expression ratio ≥ 2) are shown. The genes were further colour-labelled according to their expression pattern: R/G (Red/Green, induced in the mutant and repressed in the wild type), R/W (Red/White, induced in the mutant and unchanged in the wild type), R/R (Red/Red, induced in both strains but more in the mutant). Only genes with known function or participation to a biological process are listed. aThis gene has two names: CWH8 and CAX4