Expression of Saccharomyces' ORF YEL068C

 

YEL068C is an ORF with no known function (SGD 2001). The analysis YEL068C expression and its comparison to other genes' expression under certain conditions can provide clues as to the function of the YEL068C in the Saccharomyces' cell cycle. A search for ORF YEL068C on the Saccharomyces Genome Database's Expression Connection outlines the expression data for YEL068C in microarray experiments involving YEL068C's expression depending on alpha-factor concentration, in response to alpha-factor, during the diauxic shift, during sporulation, in response to histone depletion, during the cell cycle, and in response to glucose limitation in evolved strains.

 

Each experiment uses this scale to represent induction or repression:


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YEL068C’s response to increased concentration of alpha-factor

(Roberts et.al 2000)

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YEL068C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL218C

 

 

SRY1

 

 

serine metabolism

 

not yet annotated

 

not yet annotated

YEL012W

 

 

UBC8

 

 

polyubiquitylation*

 

ubiquitin conjugating enzyme

 

cellular_component unknown

YDR531W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR022W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL043W

 

 

ECM13

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YPL159C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL065C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL035C

 

 

 

 

 

 

 

 

 

 

YJL017W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL139W

 

 

CTK1

 

 

protein amino acid phosphorylation*

 

protein kinase

 

not yet annotated

YOR256C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR479C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL078C

 

 

AUT7

 

 

autophagy*

 

microtubule binding

 

microtubule associated protein

YJL103C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL058W

 

 

THI5

 

 

vitamin B1 biosynthesis

 

molecular_function unknown

 

cellular_component unknown

YCL005W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR005W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL093W

 

 

MBR1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YJL015C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL045C

 

 

FAD1

 

 

not yet annotated

 

FMN adenylyltransferase

 

not yet annotated

 

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

 

• This experiment uses varying concentrations alpha- factor, which is a Saccharomyces' pheromone, to reveal resulting expression among genes. YEL068C expression increases slightly with increased concentration of alpha -factor. YEL068C maximum induction occurred at 158 nM aF with 0.25 fold induction but decreased again at 500 nM aF to approximately 0.1 fold induction (AC Rosetta, 2001). Genes with similar induction patterns are located on different chromosomes (GO report, 2001). Many of the genes also have unknown biological processes, but SRY1, UBC8, CTK1, AUT7, and THI5 are all involved in metabolism.

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YEL068C’s expression in response to duration of exposure to alpha-factor (Roberts et.al 2000)

 

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YEL068C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR265W

 

 

PEX10

 

 

peroxisome organization and biogenesis

 

molecular_function unknown

 

cellular_component unknown

YCL048W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL005C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL269W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR201C

 

 

PET56

 

 

ribosomal large subunit assembly and maintenance

 

rRNA (guanine-N1-)-methyltransferase

 

mitochondrion

YFR057W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL214C

 

 

PRR2

 

 

MAPKKK cascade

 

receptor signaling protein serine/threonine kinase

 

cellular_component unknown

YKL099C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR040W

 

 

GLO4

 

 

carbohydrate metabolism

 

hydroxyacylglutathione hydrolase

 

mitochondrion*

YDL164C

 

 

CDC9

 

 

nucleotide-excision repair*

 

DNA ligase (ATP)

 

replication fork

YDL209C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR005W

 

 

MPT1

 

 

transcription, from Pol II promoter

 

RNA polymerase II transcription factor

 

TFIID complex

YLR366W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR204W

 

 

QRI5

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL170C

 

 

SPO74

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL079W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR381W

 

 

YRA1

 

 

mRNA processing

 

not yet annotated

 

not yet annotated

YDR150W

 

 

NUM1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YMR244W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR247W

 

 

 

 

 

biological_process unknown

 

molecular_function

 

 

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

 

• This experiment uses duration of exposure to alpha-factor to reveal resulting expression among genes. YEL068C expression was repressed slightly after 90 minutes of exposure to alpha-factor. The genes with a similar expression pattern to YEL068C include those involved in DNA repair and replication, mRNA processing, carbohydrate metabolism, MAP signal transduction pathway, and ribosome assembly and maintenance (GO report, 2001).

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YEL068C’s expression during diauxic shift (DiRisi et.al 1997)

Orf

 

Gene

 

 

Process

 

Function

 

Component

YEL068C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR016W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL035C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL029C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL007C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR101W

 

SNT309

 

 

mRNA splicing

 

not yet annotated

 

not yet annotated

YMR072W

 

ABF2

 

 

mitochondrial genome maintenance

 

not yet annotated

 

not yet annotated

YIL041W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR245C

 

CDD1

 

 

cytidine catabolism*

 

cytidine deaminase

 

cellular_component unknown

YJL175W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR183C

 

SSO2

 

 

non-selective vesicle fusion*

 

t-SNARE

 

integral plasma membrane protein

YPL228W

 

CET1

 

 

not yet annotated

 

polynucleotide 5'-phosphatase

 

not yet annotated

YJL181W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNR010W

 

CSE2

 

 

transcription, from Pol II promoter*

 

RNA polymerase II transcription mediator

 

mediator complex

YMR294W

 

JNM1

 

 

mitotic anaphase B

 

structural protein of cytoskeleton

 

dynactin complex

YOL027C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL176C

 

SWI3

 

 

chromatin modeling

 

non-specific RNA polymerase II transcription factor

 

nucleosome remodeling complex

YBR100W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR036C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL188W

 

POS5

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR039C

 

SUB1

 

 

transcription

 

not yet annotated

 

not yet annotated

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

· YEL068C is repressed at intervals during the time the cell under went the shift from anaerobic to respiratory metabolism. Many of the cells with similar expression patterns are not annotated; but SUB1, SWI3, SCSE2, JNM1, and SNT309 are involved in the cell cycle.

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YEL068C’s expression during sporulation (Chu et.al 1998)

Orf

 

Gene

 

 

Process

 

Function

 

Component

YEL068C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR087W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL041W

 

KRE26

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIR030C

 

DCG1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YGL259W

 

YPS5

 

 

not yet annotated

 

aspartic-type endopeptidase

 

not yet annotated

YPR139C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL237W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YEL066W

 

HPA3

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YEL067C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER030W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL218W

 

SAR1

 

 

ER to Golgi transport

 

SAR small monomeric GTPase

 

COPII vesicle coat

YJR012C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL005C

 

COD5

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER031C

 

YPT31

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YIL088C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR080C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL101W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR125W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL072W

 

RNH35

 

 

DNA replication

 

ribonuclease H

 

cell

YMR090W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR105C

 

SEN2

 

 

tRNA splicing

 

tRNA-intron endonuclease

 

nuclear inner membrane*

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

 

· YEL068C is repressed before two hours of exposure; then it is induced at two hours; and then it is repressed again for the entire of the duration. Genes with similar expression patterns to YEL068C during sporulation function in the cell cycle or in protein synthesis or are unknown.

 

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YEL068C’s expression as histone is depleted (Wyrick et.al 1999)

Orf

 

Gene

 

 

Process

 

Function

 

Component

YEL068C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL136W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR351W

 

SBE2

 

 

bud growth

 

molecular_function unknown

 

cell

YDR505C

 

PSP1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL033W

 

HCA4

 

 

35S primary transcript processing

 

ATP dependent RNA helicase

 

nucleolus

YKR068C

 

BET3

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKL076C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL051W

 

OAF1

 

 

transcription regulation, from Pol I promoter

 

specific RNA polymerase II transcription factor

 

nucleus

YLL020C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR089C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL185W

 

ASH1

 

 

pseudohyphal growth*

 

specific transcriptional repressor

 

nucleus

YKL205W

 

LOS1

 

 

tRNA splicing

 

not yet annotated

 

not yet annotated

YDL001W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR058C

 

APS2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YLR089C

 

 

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDL161W

 

ENT1

 

 

actin filament organization*

 

cytoskeletal adaptor

 

actin cortical patch (sensu Saccharomyces)

YNL068C

 

FKH2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR072C

 

SIS2

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YLL019C

 

KNS1

 

 

protein amino acid phosphorylation

 

protein serine/threonine kinase*

 

not yet annotated

YAL029C

 

MYO4

 

 

mRNA localization, intracellular

 

microfilament motor

 

actin cap (sensu Saccharomyces)

YAL056W

 

GPE2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

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

YEL068C is repressed for the entire duration of histone depletion. It has a similar expression pattern to genes involved in protein synthesis (MYO4, KNS1, LOS1, OAF1, HCA4) and structural genes (ENT1, ASH1, SBE2).

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YEL068C’s Expression during Cell Cycle (Spellman et.al 1999)

Name

Score

Peak

YEL068C

5.047

S

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 YEL068C

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

· This experiment analyzes the expression of genes during the cell cycle. YEL068C is repressed and induced during different stages of the cell but with a little deviance from 1:1 fold expression.

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YEL068C’s expression evolution through generations with limitations on glucose supply (Ferea et.al 1999)

 

 

Name

 

Process

 

Function

YEL068C

 

biological_process unknown

 

molecular_function unknown

SET5

 

biological_process unknown

 

molecular_function unknown

YDR491C

 

biological_process unknown

 

molecular_function unknown

ESP1

 

not yet annotated

 

not yet annotated

YLL064C

 

biological_process unknown

 

molecular_function unknown

YAL014C

 

biological_process unknown

 

molecular_function unknown

YCR041W

 

biological_process unknown

 

molecular_function unknown

YDR542W

 

biological_process unknown

 

molecular_function unknown

MSB3

 

actin filament organization*

 

RAB GTPase activator

TBS1

 

not yet annotated

 

molecular_function unknown

YAF9

 

biological_process unknown

 

molecular_function unknown

NUP82

 

mRNA-nucleus export*

 

structural protein

YOR072W

 

biological_process unknown

 

molecular_function unknown

YGL261C

 

biological_process unknown

 

molecular_function unknown

MFT1

 

protein-mitochondrial targeting

 

molecular_function unknown

HFI1

 

transcription

 

not yet annotated

CDH1

 

ubiquitin-dependent protein degradation*

 

enzyme activator

YNR077C

 

biological_process unknown

 

molecular_function unknown

PEX14

 

protein-peroxisome targeting

 

protein binding

SAP185

 

G1/S transition of mitotic cell cycle

 

protein serine/threonine phosphatase

BIK1

 

mitotic anaphase B*

 

microtubule binding

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

·This experiment regulates the glucose supply for yeast over several generations and then test the evolved colonies on a glucose limited medium to determine evolution of expression of genes. YEL068C is repressed in the evolved second generation in comparison to the parent generation. Genes with similar expression patterns are involved in the cell cyle and structure.

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Although nothing concrete can be assumed from the data generated in these microarrays about the function of YEL068C, the fact that it generally clustered with genes involved in cell cycle regulation, protein synthesis, and structure is very compelling.

 

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