Expression of Saccharomyces’ ORF HO

 

The ORF HO is an endonuclease that mediates the switch of genes at the MAT locus with those at the HMR locus during Saccharomyces’ mating type switch (Kuplun 2000).  A search for the ORF HO on the Saccharomyces Genome Database's Expression Connection outlines the expression data for HO in microarray experiments involving HO's expression depending on alpha-factor concentration, in response to alpha-factor, during the diauxic shift, during sporulation, in response to histone depletion, and during the cell cycle. Data gathered in microarray experiments should reflect the hypothesis that the ORF is involved in mating type switching and thus repressed when exposed to pheromones and during sporulation.

 

Each experiment uses this scale to represent induction or repression:

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HO’s response to increased concentration of alpha-factor (Roberts et.al 2000)

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL227C

 

HO

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YLR314C

 

CDC3

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

structural protein of cytoskeleton

 

septin ring (sensu Saccharomyces)*

YFL068W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML034W

 

SRC1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR189W

 

SLY1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKR068C

 

BET3

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YMR002W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR289W

 

SNF5

 

 

chromatin modeling

 

non-specific RNA polymerase II transcription factor

 

nucleosome remodeling complex

YDL058W

 

USO1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR352W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCL034W

 

LSB5

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR083C

 

GCD2

 

 

protein synthesis initiation

 

translation initiation factor

 

ribosome

YOR326W

 

MYO2

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

microfilament motor

 

actin cap (sensu Saccharomyces)*

YDR545W

 

YRF1-1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YLL067C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL015W

 

BAR1

 

 

pheromone degradation

 

aspartic-type endopeptidase

 

periplasmic space (sensu Fungi)

YBL097W

 

BRN1

 

 

mitotic chromosome segregation*

 

molecular_function unknown

 

nucleus*

YJL013C

 

MAD3

 

 

mitotic spindle checkpoint

 

molecular_function unknown

 

nucleus

YDR013W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL214W

 

PEX17

 

 

peroxisome organization and biogenesis

 

protein binding

 

peroxisomal membrane

YOR082C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

          This image was taken from the SGD webpage's Expression Connection database.

 

• This experiment uses varying concentrations alpha- factor, which is a Saccharomyces' pheromone, to reveal resulting expression among genes.  HO is repressed when exposed to alpha factor. It is repressed most at the 5 nM concentration of aF.  HO expression pattern is similar to other genes involved in the cell cycle (SNF5, BRN1, MAD3), mating (BAR1) , and structural proteins(PEX17, MYO2, CDC3).

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HO’s expression in response to duration of exposure to alpha-factor (Roberts et.al 2000)

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL227C

 

HO

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YOR047C

 

STD1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YNL225C

 

CNM67

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YNL039W

 

TFC5

 

 

transcription initiation, from Pol III promoter

 

RNA polymerase III transcription factor

 

transcription factor TFIIIB

YEL065W

 

SIT1

 

 

transport

 

not yet annotated

 

not yet annotated

YBR104W

 

YMC2

 

 

transport

 

not yet annotated

 

not yet annotated

YDR176W

 

NGG1

 

 

not yet annotated

 

not yet annotated

 

SAGA complex

YPL105C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR018W

 

RLF2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKR095W

 

MLP1

 

 

protein-nucleus import

 

molecular_function unknown

 

nuclear membrane*

YOR368W

 

RAD17

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YNL231C

 

PDR16

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YDL003W

 

MCD1

 

 

mitotic chromosome condensation*

 

molecular_function unknown

 

cohesin

YPR104C

 

FHL1

 

 

rRNA processing*

 

transcription factor

 

nucleus

YER174C

 

GRX4

 

 

oxidative stress response

 

glutaredoxin

 

cellular_component unknown

YDL048C

 

STP4

 

 

tRNA splicing

 

molecular_function unknown

 

not yet annotated

YAR008W

 

SEN34

 

 

tRNA splicing

 

tRNA-intron endonuclease

 

nuclear inner membrane*

YGR109C

 

CLB6

 

 

G1/S transition of mitotic cell cycle*

 

cyclin

 

cellular_component unknown

YIR010W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCL013W

 

 

 

 

 

 

 

 

 

YKL089W

 

MIF2

 

 

mitosis

 

not yet annotated

 

not yet annotated

This image was taken from the SGD webpage’s Expression Connection database.

• This experiment uses duration of exposure to alpha-factor to reveal resulting expression among genes. HO is repressed for the entire duration of alpha-factor exposure. HO’s expression is similar to genes involved in protein synthesis(FHL1, STP4, SEN34, TFC5) , cell cycle (MIF2, CLB6, MCD1), metabolism(GRX4), transport (SIT1, YMC2), and structure (CNM67).

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HO’s expression during diauxic shift (DiRisi et.al 1997)

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL227C

 

HO

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YCL029C

 

BIK1

 

 

mitotic anaphase B*

 

microtubule binding

 

spindle pole body*

YCR060W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAR014C

 

BUD14

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL098C

 

SNU23

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDL077C

 

VAM6

 

 

not yet annotated

 

vacuolar carboxypeptidase Y

 

not yet annotated

YDR020C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL101C

 

DUN1

 

 

DNA repair

 

not yet annotated

 

not yet annotated

YCR085W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAR020C

 

PAU7

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCR064C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL102W

 

CDC2

 

 

nucleotide-excision repair*

 

delta DNA polymerase

 

delta DNA polymerase

YIL092W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR126C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR144C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL203C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCR089W

 

FIG2

 

 

mating (sensu Saccharomyces)

 

not yet annotated

 

not yet annotated

YCR041W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL221W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL090W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL065W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

This image was taken from the SGD webpage’s Expression Connection database.

 

· HO is initially induced and then repressed during the cells transition from anaerobic to aerobic metabolism. HO’s expression is similar to genes involved in mating (FIG2), DNA repair (CDC2, DUN1), and the cell cycle (BIK1). Many of the genes with this expression pattern have an unknown function.

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HO’s expression during sporulation (Chu et.al 1998)        

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL227C

 

HO

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKR104W

 

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YMR091C

 

NPL6

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YHL006C

 

SHU1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL064W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR192W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

This image was taken from the SGD webpage’s Expression Connection database.

 

· HO is slightly repressed during sporulation. Only five genes were reported as having similar expression patterns all of which are not yet annotated.

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H0’s expression as histone is depleted (Wyrick et.al 1999)

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL227C

 

HO

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YGR041W

 

BUD9

 

 

polar budding

 

molecular_function unknown

 

cell

YIL154C

 

IMP2'

 

 

DNA repair*

 

transcription factor

 

cellular_component unknown

YAL023C

 

PMT2

 

 

O-linked glycosylation

 

dolichyl-phosphate-mannose--protein mannosyltransferase

 

endoplasmic reticulum

YLR198C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL036C

 

FUN11

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YOR196C

 

LIP5

 

 

fatty acid metabolism

 

not yet annotated

 

not yet annotated

YAL041W

 

CDC24

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

signal transducer*

 

not yet annotated

YMR236W

 

TAF17

 

 

transcription initiation, from Pol II promoter*

 

general RNA polymerase II transcription factor

 

TFIID complex*

YPL057C

 

SUR1

 

 

mannose-inositol-P-ceramide (MIPC) metabolism

 

not yet annotated

 

not yet annotated

YOR107W

 

RGS2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YLR025W

 

SNF7

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YAL056W

 

GPE2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL121C

 

TOM70

 

 

mitochondrial translocation

 

protein transporter

 

mitochondrial outer membrane translocase complex

YAL022C

 

FUN26

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL042W

 

ERV46

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL178W

 

CBC2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YGR200C

 

ELP2

 

 

transcription

 

not yet annotated

 

not yet annotated

YML093W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL059W

 

ECM1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YAL011W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

This image was taken from the SGD webpage’s Expression Connection database.

 

· HO is repressed when histone is depleted. HO expression pattern under this condition is similar to the expression pattern of genes involved in asexual reproduction (BUD9), DNA repair (IMP2’), metabolism (LIP5, SUR1),  signal transduction (CDC24, TAF17), and cell cycle (ELP2).

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HO’s Expression during Cell Cycle (Spellman et.al 1999)

Name

Score

Peak

HO

2.861

G1

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

 

 

 

Plot of HO (YDL227C)

 

· This experiment analyzes the expression of genes during the cell cycle. HO is repressed and induced during different stages of the cell but with a little deviance from 1:1 fold expression.

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HO’s expression pattern in the experiments supports the assumption that it is involved in mating type switch. It is repressed in conditions in which the cell is committed to a mating type such as sporulation and when exposed to pheromones. The fact that its expression patterns are similar to DNA repair genes and structural genes is interesting and surprising in my opinion. Perhaps these genes function in the processes that HO is involved in when it is induced.

 

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