1

PDD1

The PDD1 gene encodes Pdd1p, an abundant protein whose
expression is limited to the sexual phase of the
Tetrahymena life cycle. Somatic knockout cells lacking
Pdd1p during the early stages of conjugation and
macronuclear development exhibit defects in a variety
of developmental processes, including programmed DNA
elimination, macronuclear genome endoduplication, and
nuclear resorption. While Pdd1p is not required for
vegetative growth, exconjugants derived from matings of
somatic knockout cells are inviable. Originally
identified during a screen for proteins upregulated
during macronuclear development (which also led to the
cloning of PDD2 and PDD3), the gene encoding p65
(Pdd1p) was cloned and shown to encode a novel protein
composed of three chromodomains. Methylated histone
binding activity has been demonstrated in vitro for one
chromodomain of Pdd1p, specifically to methylated
lysine-9 residues of histone H3. This histone
modification is required for programmed DNA
elimination, and like Pdd1p, these modified histones
colocalize with chromatin containing the DNA sequences
destined for elimination. Distribution of Pdd1p in the
cell over time follows a remarkable pattern that is
suggestive of its major role in programmed DNA
elimination: Pdd1p is initially restricted to the old
macronucleus, then relocalizes to the developing
macronucleus when it is formed. Studies have long
suggested an epigenetic contribution from the parental
macronucleus that specifies the elimination of specific
DNA sequences. The timing of its localization and its
ability to bind chromatin suggests Pdd1p is directly
involved in communicating this information to the new
macronucleus.

2

TWI1,
HHT2,
PDD1,
PDD3,
DCL1

A proposed model for the mechanism of programmed DNA
elimination in Tetrahymena is based on the timing of
expression, cellular distribution, mutant phenotypes,
and predicted functions of the protein and RNA
components involved. In this model, both strands of the
micronuclear genome (or perhaps only the portions
containing internal eliminated sequences) are
transcribed early in conjugation to produce large
non-genic, double-stranded RNAs. This transcription is
likely performed by RNA Polymerase II, based on the
localization of its subunit Rpb3p to the micronucleus
during this time. These transcripts pass to the
cytoplasm where they are processed into short (~28
nucleotide) scan RNAs (scnRNA) by the dicer-like
protein Dcl1p, similar to the production of the small
inhibitory RNAs (siRNA) central to the RNA interference
(RNAi) pathway of other eukaryotes. The scnRNAs complex
with Twi1p, a member of the PPD (PAZ and Piwi Domain)
protein family, whose members are commonly involved in
RNAi and related processes. The scnRNA/Twi1p complexes
enter the old macronucleus, where scnRNAs homologous to
DNA sequences found there are degraded. The remaining
scnRNAs, comprised of micronuclear-restricted
sequences, are transferred to the developing
macronucleus. There, histone H3 proteins (Hht1p, Hht2p)
that are bound to sections of the genome sharing
identity to the scnRNAs are methylated on lysine-9.
This modification, which is often associated with the
formation of heterochromatin, is recognized by one or
more of the chromodomains belonging to Pdd1p and Pdd3p.
Regions of DNA associated with these modified histones
are eliminated from the developing macronuclear genome.

3

CDK1

Cyclin-dependent kinases (cdks) are a family of
serine-threonine kinases that are involved in cell
cycle control and cell division in eukaryotes. Cdks are
catalytic subunits that are activated by association
with proteins called cyclins, forming cyclin-cdk
complexes. Cdk kinase activity is regulated by cyclin
binding, phosphorylation and dephosphorylation, protein
degradation, protein-protein interactions with cdk
inhibitors, and subcellular localization.

4

CDK1

Tetrahymena thermophila Cdk1p shares homology with cdk
homologs from other eukaryotes. It contains 11
catalytic domains characteristic of protein kinases,
conserves all of the regulatory phosphorylation sites
found in cdks, and has a slightly modified
cyclin-binding PSTAIRE motif that is a hallmark of
cdks. The Tetrahymena thermophila Cdk1p was also found
to bind Saccharomyces cerevisiae p13suc1, a yeast
cyclin.

5

CDK1

The level of Cdk1p fluctuates over the vegetative cell
cycle, correlating with its histone H1 kinase activity.
Cdk1p is associated with the basal bodies of the
ciliary rows of the cell cortex and the oral apparatus.
This localization, along with the phenotype of a
partial CDK1 knockout phenotype of bent and buckled
ciliary rows, suggests that Cdk1p is involved in
cortical morphogenesis.

6

HEH2

HEH2 is expressed during vegetative growth of T.
thermophila and its protein product has been localized
to basal bodies. Interestingly, its protein product was
found to have high sequence similarity to the human
disease gene KIAA1279. Human KIAA1279 was also found to
have homologs in fruit fly, frog, rat, mouse, bee,
chicken, and Japanese puffer fish, but none in
Saccharomyces cerevisiae. Although the function of
KIAA1279 is not yet known, evidence suggests that
KIAA1279 is important in the development of the enteric
and central nervous system (CNS). KIAA1279 was
expressed in different parts of the adult CNS, and
mutations in KIAA1279 were associated with
Goldberg-Shprintzen syndrome (OMIM).

7

HEH2

HEH2 appears to be located on the right arm of
micronuclear chromosome 2 based on mapping REP6, a
locus upstream of HEH2.

8

HHO1,
MLH1

The HHO1 gene encodes the macronuclear linker histone
H1 protein; the MLH1 gene encodes a polyprotein
comprising a set of four micronuclear linker histone
proteins (alpha, beta, gamma, and delta) unrelated to
Hho1p. Histone H1 and the MLH proteins are chromatin
proteins that associate with the inter-nucleosomal
(linker) DNA. T. thermophila has two nuclei, one of
which is transcriptionally active (the macronucleus)
and one that is silent during most of the life cycle
(the micronucleus). Furthermore, the macronucleus
undergoes amitosis, whereas the micronucleus undergoes
typical mitosis. The fact that Hho1p and MLH proteins
are found exclusively in the macronucleus and
micronucleus, respectively, has led to studies of their
function, or lack of function, in transcription
regulation, mitosis, and amitosis. Surprisingly, an
HHO1 knockout showed this gene to be non-essential; its
main observable phenotype was an overall decondensation
of macronuclear chromatin. MLH1 knockouts, which are
also viable, showed a similar phenotype in the
micronucleus.

9

HHO1,
CDC2,
NgoA,
CYP1

HHO1 knockouts show no global increase or decrease in
the amount of transcription in the cell; however, these
same knockouts also show that Hho1p is important for
the transcriptional regulation of individual genes in
response to stimuli, such as starvation. The
differential regulation of Hho1p by phosphorylation
under vegetative growth and starvation conditions has
been well studied. During vegetative growth, Hho1p is
phosphorylated on five closely spaced residues,
preventing it from interacting with chromatin, likely
by interfering with its ability to bind DNA. Under
these conditions, expression is increased for CDC2, a
homolog of the cyclin dependent kinases responsible for
histone H1 phosphorylation, possibly creating a
positive feedback loop that promotes the cell cycle.
During starvation conditions, Hho1p is
dephosphorylated, allowing it to bind to chromatin.
This stimulates the expression of some genes, including
ngoA, and protease genes such as CYP1, while inhibiting
expression of other genes, such as CDC2. This decrease
in CDC2 expression may be responsible for cell cycle
arrest during starvation.

10

MYO1,
MYO2,
MYO3,
MYO4,
MYO5,
MYO4 ,
MYO9,
MYO10,
MYO11,
MYO12,
MYO13

Proteins of the myosin superfamily are ATP-dependent
molecular motors that travel unidirectionally along
actin filaments. The myosin heavy chain proteins are
comprised of three domains: a head (motor) domain
responsible for ATP hydrolysis at the N-terminus, a
neck (lever arm) region, and a C-terminal tail region.
Thirteen predicted myosin heavy chain genes have been
identified in the Tetrahymena genome and named
MYO1-MYO13. A phylogenetic analysis comparing these
predicted proteins with the 19 previously identified
myosin classes suggests that Myo1p-Myo12p belong to a
previously undescribed class of myosins. This new
family, designated Class XX, does not include Myo13p,
which did not branch with this class or any of the
other classes in the analysis. The neck and tail
regions of the Tetrahymena myosins include a variety of
domains characterized in other myosin classes, with
each protein containing one or more of the following
domains: coiled-coil (which may support dimerization);
IQ motif (binding sites for calmodulin or
calmodulin-like proteins); FERM domain (Four-point-one
protein, Ezrin, Radixin, Moesin homology); and MyTH4
domain (Myosin Tail Homology 4).

11

CMB1

A recessive gene determining temperature-sensitive
fission arrest was described in 1976 under the name
"mo1". Around 1979, following the (then) new
nomenclatural rules, it was re-named cdaA1 (CDA="cell
division arrest"). In the early 1980's, Y. Watanabe and
his associates made some remarkable findings reported
in 1986. Using 2D-gel electrophoresis, they found a
protein, which they called p85 (later renamed Cmb1p),
which was localized to the oral apparatus and also to
an apical filament ring and to structures (which turned
out to be basal-body couplets) located just posterior
to the division furrow. The equatorial localization was
observed in cdaA1 homozygotes at the permissive
temperature (when division took place), but not after a
shift to the restrictive temperature (when the division
furrow failed to develop). Based on these studies it
was naturally assumed that p85 was the protein product
of the cdaA gene, especially as p85 differed slightly
in mobility in 2D-gels made from wild-type and cdaA1
cell extracts. However, in 1999 the gene encoding p85
was cloned. This yielded a big surprise: "The cdaA1 p85
cDNA contained one open reading frame and its deduced
amino acid sequence, cdaA1 p85, was completely
identical to that of wild-type p85" (p. 116). There
were some differences in the 3'UTR and 5' UTRs, but
they "do not affect the transcription and translation
of the p85 gene, because the amounts of transcribed
mRNA and translated protein of cdaA1 p85 were
equivalent to those of wild type p85" (p. 118). The
authors conclude the Results section as follows: "Thus,
we suppose that the difference in molecular weight
between cdaA1 and wild-type p85 was caused by a
disorder of post-translational modification mechanisms
of p85 in cdaA1 cells." (p. 116). These results
demonstrate that p85 is likely not the product of the
cdaA1 gene, and that the gene mutated in the cdaA1
strain is more likely to be a protein responsible for
the post-translational modification of p85, which is
altered in the cdaA1 mutant. (Contributed by J.
Frankel, University of Iowa, 2005)

12

THD1

THD1, a homolog of the Saccharomyces cerevisiae Rpd3p,
a class I histone deacetylase (HDAC), is localized to
the macronucleus during vegetative growth, and
distributed to developing new macronuclei early in
their differentiation. Thd1p deacetylates all four core
histones in vitro. Thd1p is a 52kDa polypeptide in an
HDAC complex of approximately 160 kDa.

13

THD1

Tetrahymena cells with reduced Thd1p expression
exhibited phenotypes indicative of loss of chromatin
integrity, such as DNA fragmentation and extrusion of
chromatin from the macronucleus, variable macronuclear
size and shape, enlarged nucleoli, and reduced
phosphorylation of histone H1 from bulk chromatin.
Macronuclei in THD1 knockdown cells also contained more
DNA, suggesting Thd1p may play a role in regulating
macronuclear DNA content. The THD1 gene could not be
completely replaced by a disruption construct,
suggesting that THD1 is an essential gene.

14

FSF1

A macronuclear chromosome containing a fusion gene was
cloned from the spirotrichous ciliate Oxytricha
trifallax. The gene encodes a single polypeptide
containing homologs of two proteins that catalyze
sequential steps in the formaldehyde detoxification
pathway in Saccharomyces cerevisiae. These two proteins
are formaldehyde dehydrogenase (FALDH) and
S-formylglutathione hydrolase (SFGH); the fusion gene
is called FSF1 (FALDH/SFGH Fusion 1). A similar gene
was identified in the Tetrahymena thermophila genome
sequence, and a T. thermophila EST sequenced from both
ends showed that the fusion gene is expressed in this
species in vivo. FSF1 has not yet been identified in
other ciliates, but a fusion of these two genes has
been identified in another group of protists, the
diatoms. An EST from Phaeodactylum tricornutum and a
gene from the genome sequence of Thalassiosira
pseudonana both encode a fusion of these two genes, but
in the opposite orientation of the ciliate genes. In
diatoms, the SFGH domain is found N-terminal to the
FALDH domain, suggesting that these two fusion genes
evolved independently in ciliates and diatoms. The
diatom genes were named SFF1 to highlight these
differences.

15

SPO11

Spo11p induces DSBs and at the same time triggers the
elongation of meiotic nuclei (crescents) via an
ATR-dependent response in Tetrahymena. The crescent
resembles the conserved bouquet arrangement and the
fission yeast horsetail nucleus. It promotes meiotic
chromosome pairing. Thus, by nuclear elongation and the
ensuing close juxtapositioning of homologous chromosome
regions within the tubular nucleus, Spo11p ensures that
DSBs formed by its activity can be repaired by
homologous recombination.

16

HOPP2

HOP2B is a homolog of budding yeast HOmologous Pairing
2. It is essential for vegetative growth. HOP2B has a
meiosis-specific paralog in Tetrahymena (HOP2, HOP2A,
TTHERM_00794620) which is the yeast HOP2 ortholog.

17

ATR1

Knockout prevents SPO11-dependent elongation of meiotic
nuclei. Involved in the signaling of meiotic DSBs and
other DNA damage.

18

MBD1

MBD1 is a gene fusion of two genes involved in the
methionine salvage pathway:
methylthioribulose-1-phosphate dehydratase -mtnB; and
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase -
mtnD. These enzymes catalyze non-consecutive steps in
the pathway. Interestingly the gene that codes for the
intervening enzyme in the pathway, mtnC, is missing
from the genome of Tetrahymena. Complementation tests
in yeast were used to show that MBD1 from Tetrahymena
is able to do in one step what yeast does in three,
since it can rescue yeast knockouts of mtnB, mtnC, or
mtnD (Salim, Negritto and Cavalcanti 2009).

19

FLP11,
FLP5,
FLP7,
FLP4,
FLP12,
FLP9,
DNF1 ,
FLP1,
FLP2,
FLP10,
FLP13,
FLP6,
FLP14,
FLP15,
FLP16,
FLP8,
FLP17,
FLP18,
FLP19

The phospholipid flippase family of genes in
Tetrahymena contains 20 members, FLP1-FLP20.
Preliminary studies show that many of these genes are
differentially regulated in response to temperature
and/or the presence of a polycyclic aromatic
hydrocarbon (pyrene).

20

19

21

2

22

LIA4

LIA4 is expressed exclusively during conjugation and
Lia4p localizes to developing macronuclei. It is
required for completion of conjugation, DNA
rearrangement, chromosome breakage, and Pdd1 foci
(dumposome) formation (Horrell SA and Chalker DL,
unpublished data).

23

ABC3

ABC3 shares homology with ABC transporter proteins from
other eukaryotes. It contains an ATP-binding domain
that hydrolyzes ATP in to provide energy for the
protein to translocate various molecules across a
biological membrane. Paragraph by undergraduates at
the Keck Science Department, Pitzer College

24

STF1

Solute Transport Facilitator 1 (STF1) is a protein from
the major facilitator superfamily (MFS), one of the
largest families of membrane transports known, found in
archaea, bacteria, and eukaryotes. This protein is
predicted to have a MFS1 domain (E-value 1e-08), and is
likely to transport small solutes through the membrane
through either uniport, symport, or antiport. Paragraph
by: Lisette Espinosa and Charles McGregor
(undergraduates), Keck Science Department, Claremont
McKenna College

25

NHX1

NHX1 is an integral membrane protein that shares
homology with other proteins containing a sodium
hydrogen exchanger domain involved in transporting
sodium and hydrogen ions across the concentration
gradient between a cell and its surroundings.
Functioning as an antiporter for sodium and hydrogen
ions, the exchange function characteristic of this
domain is highly dependent on pH. Although the exact
molecular mechanisms responsible for this behavior are
not well understood, a prominent current inference is
that these exchanger proteins use ATP to transport ions
across membranes. Paragraph by: Samuel Rubin and Owen
Foster (undergraduates) Keck Science Deparment,
Claremont Colleges

26

NHX2

NHX2 belongs in the family of sodium-hydrogen
exchangers that act as antiporrters that maintain the
pH of actively metabolizing cells by controlling the
balance of sodium. THe antiporters have 10-12 regions
on the N-terminus and a large cytoplasmic region on the
C-terminus. The 10-12 transmembrane regions contain 2
highly conserved regions and most of the regions share
identities within the family , while the large
cytoplasmic region is noted to have little similarity
with other members in the family. Paragraph by: Chris
Fang and Deanna Liou (undergraduates) Keck Science
Department, The Claremont Colleges

27

GTP4

GTP4 has only one known functional domain and is a
member of the sugar transporter family, a subset of the
major facilitator superfamily (E-value: 5.4e-36). This
protein appears to be responsible for transporting
sugar across the plasma membrane in response to changes
in the electrochemical gradient, specifically in sugar
uptake. Paragraph by: Kathleen Beardsworth and Kristen
Keller (undergraduates), Keck Science Department,
Claremont Colleges.

28

ABC2

ABC2 shares homology with members of the ABC family
transporter proteins. This protein appears to have two
types of domains. It is thought that the two domains
function together to bind ATP to transport substances
such as glutathione, glucuronate, and sulfate across
the membrane. Using energy from ATP hydrolysis, both
domains of ABC transporters facilitate the transport of
a wide variety of materials out of the cell. Paragraph
by undergraduates from the Keck Science Department at
Claremont McKenna and Scripps Colleges

29

MAF4

Tetrahymena thermophila MAF4 is homologous with
proteins from the WD40 superfamily, mostly membrane and
flagellar associated proteins. It contains two
domains; the first domain (E-value=1.95E-5), in the
clathrin family, indicates that the protein could have
a membrane spanning domain due to repeated
alpha-helices. The second domain (E-value=7.46E-3) is
a kinase complex, which indicates possible movement
function, and correlates with the homologs being
flagellar associated proteins. It is possible that
this protein is an integral membrane protein that has a
function in flagellar movement. Paragraph by: Lauren
Mitten and Rebecca Dutta (undergraduates), Keck Science
Department, Scripps College

30

PKC2

PKC2 shares homology with a number of Protein Kinase C
related proteins in other ciliated prokaryotes. PKC2
contains only one single domain across its entire 517
amino acids. It conserves most of the protein kinase
domain, and contains a 241 amino acid region with
unknown function. PKC2 appears to play a role in
amplifying the message of signal transduction pathways
by phosphorylating serine and threonine. This induces
a conformational change in a targeted protein and
subsequently leads to a cellular response. Paragraph
by: Jacqueline Kroll and Rachel Brunetti
(undergraduates), Keck Science Department, The
Claremont Colleges.

31

PMR1

Tetrahymena thermophilia PMR1 (potential mRNA
regulator) is homologous to proteins from the LRR_RI
domain. The domain suggests that the protein is similar
to Leucine rich repeat, ribonucleus inhibiter (Evalue =
7.51 × 〖10〗^(-6)). The leucine rich protein may
form tight complexes with a certain ribonuclease, or
may be involved in other protein-protein interactions.
It is possible that the PMR plays a role in regulating
the lifetime of RNA like the ribonuclease inhibitor.
Paragraph provided by undergraduates at the Keck
Science Department of Claremont McKenna, Pitzer, and
Scripps Colleges.

32

Tetrahymena thermophile TIT1 is homologous with
proteins from a cation channel family. It contains one
domain: the ion transport protein (Evalue: 1x10⁻⁸)
whose function is to selectively transport ions through
the membrane. It is possible that this protein is an
integral membrane protein that has a critical function
in facilitating ion transport. Transmembrane Ion
Channel Family proteins that are found in eukaryotes
tend to have up to four additional transmembrane
helices. These additional helices help explain the
physical properties of the protein. We have determined
that TIT1 has a sequence that consists of 604 amino
acids, a relatively lengthy sequence. Paragraph by:
Kristiana Kim and Will Su(undergraduates), Keck Science
Department, Scripps College, Claremont McKenna College

33

TIC1

Tetrahymena thermophile TIT1 is homologous with
proteins from a cation channel family. It contains one
domain: the ion transport protein (Evalue: 1x10⁻⁸)
whose function is to selectively transport ions through
the membrane. It is possible that this protein is an
integral membrane protein that has a critical function
in facilitating ion transport. Transmembrane Ion
Channel Family proteins that are found in eukaryotes
tend to have up to four additional transmembrane
helices. These additional helices help explain the
physical properties of the protein. We have determined
that TIT1 has a sequence that consists of 604 amino
acids, a relatively lengthy sequence. Paragraph by:
Kristiana Kim and Will Su(undergraduates), Keck Science
Department, Scripps College, Claremont McKenna
College

34

Tetrahymena thermophila gene CUT1 (Common Unknown
Trans-membrane) protein is a trans-membrane protein
with unknown function. This gene is closely related to
a similar gene in Ichthyophthirius multifiliis. It
contains two CLPTM1 functional domains, one of which is
more strongly conserved than the other. When expressed
in the human genome, this domain is known to be linked
to cleft lip and palate. This family (CLPTM 1) is one
of many eukaryotic, trans membrane protein sequences
that are linked to cleft lip and palate; however,
specific function is unknown. Paragraph provided by
Kristina Millar and Caroline Hays, undergraduates at
the Keck Science Department of Claremont McKenna,
Pitzer, and Scripps Colleges.

35

PKD1

Tetrahymena thermophila PKD1 (protein kinase domain) is
homologous with other protein kinase-like proteins that
are involved in catalytic functions and phosphorylation
in cellular processes. PKD1 is located near the
C-terminus of the protein appears to contain only one
known domain (E-value= 1.2x10-42) in the protein kinase
family although the substrate specificity of the PKD1
is unknown. Paragraph by: Victoria Nguyen and Joseph
Grotts (undergraduates), Keck Science Department of
Claremont McKenna, Pitzer, and Scripps Colleges.

36

STP1

This protein is the in domain of sugar transporter with
an E-value of 1.5X10-66, indicating that the sequence
contains strongly conserved amino acids typical of the
domain. . These types of transporters come from the
Major Facilitator Superfamily (MFS) that are
responsible for binding and then transporting several
different molecules such as sugars, carbohydrates, and
small, biological acids. While much is unknown about
this specific transporter, it most likely is involved
in the binding and transport of sugars across the cell
membrane. Written by Jessica Thomas and Paul Gonzalez,
undergraduates at the Keck Science Department of
Claremont McKenna, Pitzer, and Scripps Colleges.

37

ATA2 from the eukaryote Tetrahymena thermophila is
similar to ATA homologs from other eukaryotes. It
contains two of each of the two types of domains, an
ATP binding cassette (ABC) and a less conserved
transmembrane domain (TMD), totaling four domains. The
3D structure of an ABC is a stubby L-shape with two
distinct arms. These transporters function as dimers.
The purpose of the binding cassettes (approximately 200
amino acid residues) is to bind and hydrolysis ATP,
which releases energy that enables the transporters to
transfer macromolecules and ions across cellular
membranes. This most commonly occurs in the transport
of essential nutrients to bacteria, but also is related
to diseases such as cystic fibrosis in humans. It is
clear that ATA2 is important as we can see that it is
strongly conserved across many organisms from Homo
sapiens to Drosophila. Paragraph provided by Aish
Subramanian and Travis Tu, undergraduates at the Keck
Science Department of Claremont McKenna, Pitzer, and
Scripps Colleges.

38

MSC1

Tetrahymena thermophilia MSC1 has similarities with
different protein solute carriers from bacterial
organisms. It contains only one domain characteristic
to UAA transporters, which has a specificity for
UDP-N-acetylglucosamine. The protein is largely located
on the membrane of the eukaryote. Investigation into
the family of UAA transporter proteins still remains
largely untouched. Paragraph provided by undergraduates
at the Keck Science Department of Claremont McKenna,
Pitzer, and Scripps Colleges.

39

CCT3

Tetrahymena thermophile ASH3 (Assistant for the
prevention of Shock due to Heat) is homologous with
TCP-1/cpn60 chaperonin family of heat shock proteins.
This family plays a major role in cell growth by
assisting with the folding of denatured or partially
denatured polypeptides when heat shock occurs in the
cell. Because they do not denature in a wide range of
temperatures, they are an important domain of heat
shock proteins, which are mainly found in prokaryotes,
chloroplasts, and mitochondria. Kate Jesse and Ashley
Gould, undergraduates at the Keck Science Department of
Claremont McKenna, Pitzer, and Scripps Colleges.

40

CUT1

Tetrahymena thermophila gene CUT1 (Common Unknown
Trans-membrane) protein is a trans-membrane protein
with unknown function. This gene is closely related to
a similar gene in Ichthyophthirius multifiliis. It
contains two CLPTM1 functional domains, one of which is
more strongly conserved than the other. When expressed
in the human genome, this domain is known to be linked
to cleft lip and palate. This family (CLPTM 1) is one
of many eukaryotic, trans membrane protein sequences
that are linked to cleft lip and palate; however,
specific function is unknown. Kristina Millar and
Caroline Hays, undergraduates at the Keck Science
Department of Claremont McKenna, Pitzer, and Scripps
Colleges.

41

MTP1

Two domains on Tetrahymena thermophila MTP1 suggest
that it belongs to the BT1 family. The proteins of this
family are transport proteins, suggesting that MTP1 is
also a transporter. Many proteins of this family are
thought to be pteridine transporters, so it is possible
that MTP1 also transports pteridine. By Nicole
Hohnstein and Emilie Fisher, undergraduates at the Keck
Science Department of Claremont McKenna, Pitzer, and
Scripps Colleges.

42

CCT2

APF1 (Assistant Protein Folder) is homologous with
members of the TCP-1/cpn60 chaperonin family and is
found in abundance in prokaryotes, chloroplasts and
mitochondria. It contains one domain (E-value=
7.8x10-136) that is possibly used to stabilize and
protect disassembled polypeptides under heat shock
conditions. In addition to its role as a heat shock
protein, they may also function to assist in amino acid
chain folding into their three-dimensional protein
structures. This paragraph was provided by Hannah Chia
and Jesse Honig, undergraduates at the Keck Science
Department of Claremont McKenna, Pitzer, and Scripps
Colleges.

43

ICT1

Tetrahymena thermophila ICT1 is homologous to the
natural resistance-associated macrophage protein
(NRAMP) family, composed of membrane proteins that are
divalent cation transporters. It contains one domain
(E-value=3.7x10-108), which is located in the middle of
the protein. Given the function of the homologous
proteins, it is likely that ICT1 is an integral
membrane protein and functions as a cation transporter.
Paragraph by: Alec Koh and Katherine Tully
(undergraduates), Keck Science Department, Claremont
McKenna College and Scripps College.

44

STD1

Tetrahymena thermophila STD1 (Sugar Transport and
Distribution) is homologous to proteins from the major
facilitator/general substrate transporter superfamily
of proteins. It contains a single domain (E-value = 9.6
* 10-42) categorized as “sugar_tr,” which is
responsible for sugar and other solute transportation
across a membrane. This implies that STD1 integral
membrane protein may be involved in the transport of
sugars across the T. thermophila membrane. Paragraph by
Daivik Vyas and Katie Liu, Keck Science Department,
Claremont McKenna College and Scripps College.

45

ATA2

ATA2 from the eukaryote Tetrahymena thermophila is
similar to ATA homologs from other eukaryotes. It
contains two of each of the two types of domains, an
ATP binding cassette (ABC) and a less conserved
transmembrane domain (TMD), totaling four domains. The
3D structure of an ABC is a stubby L-shape with two
distinct arms. These transporters function as dimers.
The purpose of the binding cassettes (approximately 200
amino acid residues) is to bind and hydrolyze ATP,
which releases energy that enables the transporters to
transfer macromolecules and ions across cellular
membranes. This most commonly occurs in the transport
of essential nutrients to bacteria, but also is related
to diseases such as cystic fibrosis in humans. It is
clear that ATA2 is important as we can see that it is
strongly conserved across many organisms from Homo
sapiens to Drosophila. Paragraph provided by Aish
Subramanian and Travis Tu at the Keck Science
Department of Claremont McKenna, Pitzer, and Scripps
Colleges.

46

AKM1

Tetrahymena thermophilia AKM1 (Advancer of K+ through
the cell Membrane) contains one identified functional
domain: the ion channel family (E-value 1.8 X 10
〖10〗^(-12)). It is most closely related to
Ichthyophthirius multifilis EGR28840.1, a
small-conductance, calcium-activated potassium channel
protein. It is likely that AKM1 has a similar
conformation as this protein. AKM1 is expected to be a
tetrameric potassium channel, located in the
phospholipid bilayer and contains a “loop” which is
involved in the selectivity of ions that may pass
through the channel. Paragraph by: Makari Krause and
Amanda McQuade (undergraduates), Keck Science
Department, Claremont McKenna, Pitzer, and Scripps
Colleges.

47

SFR1

The gene model is incorrect. The cDNA sequence, as
determined by RT-PCR,
is: ATGAGTTTAGTTTAGAGAACAATATAGGCTTATGAGAAGGATGAAAACAA
AAACTTCGAAGAGTTCATTGAAAAAAGTTTAAAAGCATTTAGAGAAGAAGGTATG
AAATTCGAGTAGTAAAAGGAGTGCAATTCGTAATAAATGTCTGATAACTAAAGAA
ACGAATGGGAAGAAAAAATAGCTAGTTTGGAAAGTCTTTTTAAAATGTTTTGTGT
GCTTAAAGGTTAAAAGAGAAAGAAATCAAGAGTCATGTATAACATTTGTGAGCAT
ATTTATGGAAAGAATTTACTAAAAAGAACATTTTGGTGCTGGAAAAGCCACCAGA
AGAATGAAGAATATCTGCGTTAGATGGAAGAGTAAGCAGATGTATTTTATAACAG
AAGGACACTAACAAAAATAATGAGAAGTTGGTAAGATGTTGTAATTGATGAGAAT
AAAACAATAGTTAAAAACACTGCCTTAAAGAAAACTGAGTTAGAATTGCAAAAAA
ATCAAAAGGAGTTTGAAAACCAAATTAAGAGTTTGGAAATTTTGCTATAATAAAA
AATATTAACACTGAGACATGAAGAATAACAATACAACATTTTATTCTAAAAATAA
TAGCTCCTTTCATAAAATTAAAAAATTGAATTTGATTGA The
corresponding protein sequence
is: MSLVQRTIQAYEKDENKNFEEFIEKSLKAFREEGMKFEQQKECNSQQMSD
NQRNEWEEKIASLESLFKMFCVLKGQKRKKSRVMYNICEHIYGKNLLKRTFWCWK
SHQKNEEYLRQMEEQADVFYNRRTLTKIMRSWQDVVIDENKTIVKNTALKKTELE
LQKNQKEFENQIKSLEILLQQKILTLRHEEQQYNILFQKQQLLSQNQKIEFD

48

SFR13

The gene prediction is incorrect. The cDNA sequence,
as determined by RT-PCR,
is: ATGGCATCCTTATTTAGGAGCGAGGAGCAAGCAATTTAAGAAATTATAAA
GCTTATCCCTAACAATAGCGAAGACATATCAATTTTCGATATTTTGAAAGCTTAC
GATACATATATAGAGGAAAGTGGAATTAGCTTTGAAGATCCTTTTGCATATGATG
TTTATGAAATTATCATTCATGCATCTAGAAGAGCACAAGACAATCAACTTAGGAG
TTTGTTGACAAATTACAAAGAAATATAAAAATTAAAAATGAAATAAAACAGAAAA
AATTCTGGGTATTCTGACAATAGTGATAACTCAGAGAAACCATATTCAAAGCAAA
AGTTAGCCAAGTAAAAAATATCAAGCAAGTTCAGCAGTAAAAATTAGTCACTTTC
ACCAACCAACTTTGGTGTGAATAATTAAAAAAATGATAGAAAAGAATACAACATA
TAGTTTAAAAATTTTGATACCAGCTCAGGTGAAGAAAACGATAATAATTTTGTAA
ATAAAGAAATAAATGAAATATAAGATATTGAGCATACTCCTAGCTCTCAATATGA
ATAATAATAAGTGAGAGGAAGACTTGGATAATACCAACAATTTGCATCTAAAATT
ATTAATTCAGGTTTGAAAATGTCTAATCCTTTTAATGATAATTTATATAGATATG
CAACAGAATAAGCAGATTAGCCTAATCGTTATAGCATTAGAAAGTATAGCTACTC
TCCAAACAATAAAATGGATAGTAATAATAATCTAAAAAGGTCAGCATCTCCTATT
TGTCATCCTAATAATAGAAGCCTTTCACCTCACTTAAACAATTCAAAACTCTCTA
ACTACCAAGCAAGATTAAACACTAGTAATTCTCACAATAATTCATTTAATAGTAG
TGTTAATTAGCAATAGTCTTAAAGAGTAAGATTTAATACACAGAATGCTGATGAA
TATGTCAATATTTAAAGCCCTTTAAATTCAATTAACAACTTTTAGGCCAACAGAT
AGATGAAAGGTAATTTGGAGCAAATATAATAAAGAAGATTTATCTAAGAAAATTA
GCACTAAACTCTCAATAGATCCATTGATAATTCAGATTTAAATTCAAAGGTAAAT
GGCATAGATAATAAAAAATATTTATCATTAGAACCTAAAGATTATCAATAATATT
AATTTATGCCAGCTAATCATAAAAAATATTTATCTCTTGATTCAAGCACTAAACA
AATGCTTAAGTATGAAAATTAAGATAACGAAAAATAAAACTAAGAAAATGTGTAG
TACAATTTTGAAAATAGACACAGAAGTATTGAGGAAATAGAGGAAGATATTGATT
TAGTTAGAAATGAAATGGCTCAAGGATTAAGAAGAAAATGGGTACTACATTACCA
TTTTGCAAACTGGAAAGATTATATTTAAAGATGGAAAGGAGCAACTGAATACATA
AATAAGGAGGAATAAGTAGAAAATTTTATTAAAATCAAGATTTAAAGGAAATTTT
TCGAAAAATGGGAATAATATGTATAAGAAGAAAATACTTGGAAAGAAGCAAAATT
AAATTTTGTTATGAAAAAAAGATAGAATATTTTAAGAAAATGCTTCAATGAATTA
AGAGATAGATTAAATGATGGAAAAATTGATAAATATACTTATTATGCAGCAAAAT
ACAAAAAAGAATAAGTTTTAAAGGAAAAGTACTTTTAAAAATTTTTATAGTTCTC
CAGAAATCATAGATCAAATAGGTTAAAATTGGAAAGGACACAATAAACTGCCTAA
AATAACTTAAAAAAACTAGCTTTTAATCATTTAAAATAGTTAAAATCTGAAAAAA
AAGAACGCCAGATAATAAAAGATGATATTAAAATGAAATAAAGTCTGCTTGAAAA
GAAAATATCATTTGACAGATTTATTAATAATATAAGATCCATTCTTTGTTTTAAG
AAGAAAAAAGAAATACTCAATAAAGCTATAGAAATATAGTTAAAATAGCATTCTC
TTTTATCTATGATAGATAACTTTAGAATCATTAAGTATTTCAAAATTTAAGATCA
AAGAGCAAGTGAATTTTATAATAAAAATTTATCATCTAAGTTTTTCTATCACTTG
AAGTTATTTTTATTTAATAACAGAGAAAGAGTTGAAAATACAGAGAGCTATAATT
AACTTAGAATTATAAATAAGCATCATAAATAATGGCAAAAATTTGTTTAACTGAA
TAAAAGTAAAGAATAAAAATACAAAGATGCGAGAATTCTTTACTTTTTGTATAGA
ATGATGATTATGATATTAAATGATAACGATTACTAAATTAGTCAGTAAAGAAATA
TTCAATTTGAGGCTTTTAAAGAATAAGTTTTATACTTATAAAAAATGAATTAAAT
ACTTAATAATTAGCAATAAAAAGAAAATTATTAGTCTTTTGGTAAAGGAGAGAGC
GAAGATGAATAAATTGATCCCACTCACTAATCTATGATGCAAAACTCAAGTAGCA
ATAATAATTTAATGTCAAATCATAAAAAATTACTGCCTAACTAAAAGAGTAAAAA
TTATTTATTCTCTAGAAGCACTCAAGCAACAGCTATGGGGAATAATGTTAATCCA
AATCAAGTTTTTGATACTGTTAGATCCTTCTCTCCTGCCCCTGCAAGATAACATG
ATAATAAAACTTCTAGAAATGAAAACCATAATCAAGATTAATAATTCTTATCAGA
AAATGACTAAAGCGATAATCAGCGTATGCAAAGAAATCTATCTGAATAAAATTTT
GTTTATTAAACTCAAAGATAGTCTTAGAGCAATATACTAAAAGTATATGAAAATT
AAGAGATGATGAATGAGTAATAAATAAATGAAGAAATTGCAATTTAAATAATAGG
ACATGGAATATTTTTTACTTATCCTAGTATACTATCTATAAATTATTATAACAAA
ACTCAAACAGAAAAATTATTTTAATCTCATAGAAATTTAAATCAATTCATTTTAA
GTAAGTCTTTTAAGAATTGGGTGACTTTCTTAAGATCAAGAAATGACTTTAGAAA
GAAGATGTTAAATAAAATTTATTAAAAACATTTTGATGCCATGAAAATTTATTCT
ACAAAATCTTAATGTTTAAGATTTTGTGTTGAAAAAATGCAGAAAAAGCTAAATA
AAAAGACTGTCGAAAATGTTTTTAGAGAAATGAGTTTAAGAGCTTAAGAGAGAAA
AAATTCAAGAAATGGTTTTAAAATAATAAGAGAAAAGATAGAGAAAAAATTACTT
TAAAAATACTTTAAGATTTATAGAAGAGAATTTTCTTCATCACGTGGATATTCTG
AAAACTATGAATAAGCTGGCATTTATTATAAAAAATGGCTTATTGTTTAATCTTT
CCAAGCTATCTAAAATTATGCAAATAGATAAAAAATGGTAAGAGATGTCATTTCA
ACAAAATTCTAAACTAAAAGCTAAAACTAAATGAGTAGAATATTCTTTGCCTGGA
GAATTTATTCTGATAAAAGAAGATAAAGAAACTTTATATATTAACAAATTAGATA
GATATATGAAAAAAAGGTTTATAAAGAATGTTTATTTGCATTAGCAAATTATAGA
GATAAACACTCAAAGTCAACAAAGAATAAAAATATTGTGAAATCTTATTTGTTTA
ACAAATATATTGTGAACACTTTCTAAAAAATACTAAATTATTCTAAAAGTCATAA
AATAAAAAGTATTTTGACTGATAAAATTAGAATTGCATATAAGCAAAAGCTTATG
TAGAATTATCTCCATAAACTTAAAGATTATAAAAATTATAGACAAAAGAAAGTAA
CTCTCCAAGCAAAAAATACTGAGAAAGTAGAAAAAGTATTTCAAAAAAAGCATTT
TAGGGCTTGGTACAAGCTAGGATGTAGAAATTAAAGCTTCCGTTACTTAGTTGAT
TTAGTAAAAAGACTATAATTAAGTAGATTTTTTGTTATCATGAAATATTTACGTT
AAAGGGATTTCTAAAAGCAAAAAATTATTAAAAGTGATCATCTAATCTTCTTAAA
ATTAACTATTTTTAATGCTTTTGTTAAGTATTACAGAAAAAGAAAATATGAAAGA
AAGAGTCTTGAATATATAAAATGTAGATAACAAATTAATTATGCCAAGTAATCTA
TGAAGTAATGGAAGAAATTGCATTCATACAATAAAAATGTAACATATTTATGTGC
AAAGTCAATCATAGCTATCAAAAACGAAATACTTTTAAAGTACTTTAATAAACTT
AAATAAAAATGGTTCTTAAAATCATAAGAAAACAAGTTTATAAAGGAAAATCAAA
TTAAGATGAAGAGAAAAATCTTACTTGGATTAAGAAAATATACAACTTATAAAAT
AAATAACTATGAAAACATGATAGCTATCAATGAAAAAAGAAAGAAATAGATTAAA
TAAAACATTCTATATATTTGGCTCAGAAAGTTATTTAATAAATAGCGTCAAGAAG
ACGTCTCTAGGGCTATTATTAAATACAGAAA

49

SFR13

The continuation of the cDNA sequence
is: GCATAAAGTACTTCAAACTTGGGCTGATTTGTTTAACATCAAAAATAACC
TACATAATCCAGTTAAAGTTTCTGATTTTCAAGGATTTAAGAGATTAGAAGAAAC
ATAAGAAATACATATCATCACAACAAATAGAGGCAAAAAAAGAAACTTAAGATAG
TTTTTCTTTAATATGTTGAAATTAAATTAAAAAATTTTACAACAAAAAGTCTTTT
CATGTTTAAAAAACTTAATTAATGAAAGAAAAATTGAGAATAAAAAATCAGATTA
AATTTAATTTAAATGTGAAACTGATTTATTAACAAAGTACCTTCTGCAATGGTAA
AAATCTAGTCAAAAGAAAATAAATAAGTATAATATGATAGTAAAATTACGAAGTG
TATTTTAAAAGTATTAAAAGAGGATTGGGTTTGAAGCTATTTAAGGATAAGAATA
AATTTATTTGGAATTAATACAAAAATCCAAAAAGGCTGTAACTTAAAGACAAAAA
TCCATTAAAATGAAAAGTTTTAACAAGCTTAAAGCATACTATCTTAAGAAAAGAA
AAATAGCTAAGAGAAAGCTGGAACTTGATGAACTTGTATAGAGAAATAACACTCT
AAATTTCTTTAAAAAGCTAAAGTTTTATGCATATAAAAAGTAGGAAAATAAATAA
AAGAATGTATATATCTAAGATTATTTATACTTAAATTTGCTTAAAAAGGTGTTTA
ATAAGATAAGAACATACTAAATAATTAAGTAGACTTTAGCTTAAAAATCTCTTAA
ACTTTAATCTTACTTAAATAAAAAGAAGCTTAGAAGAGGATTTAAATAAATTTAA
TAAAACTTTTCTGAAAGTAAAAGTGATATGTAAAATACCATTTAATCATTAAAGG
CTTACAGAATGAATCTTCAGCTTAAATCATTCGCTGTTCTAAGAAAATACATGAA
TATTTAAAAATTGAAAAGCTAAAAATATAATAGTGCTTTTAATAAATATTATTTT
AGTTTAGCTACAAGAATATTTGGAGCATTAAAGACATATATACTCAATAAAAATA
TTGAAAAAGATAATCATTTGTATATCCTTGATTAATATCGTTAAAGAAAATAAGT
CGAAATAAAGAAGGGAATTTTGATGGTTTGGAAATACTACACTAATTAAAGTATA
AATCAAGTCTAGCAATTTAGGTCTTGCATTGAAGCTTCAGTTCTAAAATCTAAGT
TTGTTGAATGGAAGATTAAGACTCATCTTCTCAAAGATAAGAGAATGAAATATAA
CATTATTAAAAATTCTAATAATTATAAGCTAAGAGCTAAGCTATTCAAATTATGG
TAGTAAAGGGCAAAGCTGAATTTAGTCCTTACAAATATTTTTGTCTATCATGCAA
AAATAGAAATTAAAAAAAGACTTTTAAAGTGGAATCAATCTAAAAACTTGTTGAA
AAAAATAGTGAACAAATCTTAATAACAAGTTATTTCTAAACCTAGATCAGCAGAT
GATATTTAAAAAATGAGATAAGTATTTTGCATGATCAAAGAAATGGCTTAAAATA
CACATTCAATTAAGAAGGATTAAAATTTAAGATAAAAGTAAATTAATGACCAAAA
TGTCTTTAAGTAGTTTACTTTGCAATTTAAAGCTTCATAATTAGCAGAAAAATTA
AATCAGCTAAGATACTTCTCTTCTGCTCAATAATTTATTTTTAATCTAAAGCAAA
TGTACATTTAAAAAAAGTAGGACAAAGCTCTTGCTAAGAAATCTGAAAGACTAAA
TTCTCCTAAATTCTAAAAAAACTAAATCAAGAATTCCATGATTTAGCAAACTCTT
AAAGAACAAAAGTTAAAGGATGAATTTTAAAAGTTAAGTAAATTAATAAGCAGAA
AGCAAAAAGAGTTACTCAGTGGTAGCTTGCTAAACTTAAAAGATTTTGTTAACTA
CTAAAATAATATTTAAATTCAAGCTAATTTACATCATGATAGGTAGCTACAGTAA
AAAACTTTCAAACTTTGGAAAAAGTTTGTTGAAAGTTCCAAGCAATTTTCAAGTG
TGCTAGGATAGGTGTTAACTAAGGCTTTAAAAAGATGCTAATAATAGAAATTGAG
AGATGCTTTTAGATAAATATAAATCAGATATATAAAAATTAAAGCTGCTAATATA
GTTTCTAGCTGTATTGATAGATCAGTAAAGCGCTAATACGCTTAAAAATTATTTG
AACTTTACGAGTAATTTAAATCAAAAACACAAGTACTAAGATATTTAATTGAAAA
CCATTAAATAAAAATGAACACATAAAGAGCAATTTAGTTCTTTAACATTCTAAAA
AATCTAAAAATTCAAGCTGAACGCTCAAAGATGAAGTGTAAAGAATATCTATTCA
TTAGAAGAATAAAATAAATGAAATCAGTCTTGACAATATTATAAATCTATACTCA
GTATAGAAGAAACAAAAATGACAGATACTAAAAAGCTCATTTATTTTGGGAAAAC
AAATCCAAATAAAAATACCTTTATTTCTGGGCCAGAGCTTATTAAAACGCCTAAC
AATATGAGGAATACTAATAAGATCAATTCGATTAGTAAGAATTTTATGAGTAACA
ATAAAAATTAGTTGAGAATGAACTTATGTAATAATTGGCTTTACACCATCAGCAA
TAAGTAAACTAATAAGGAAACATTTAGTAACTAACAAAATAAGAGCAAGAAGAGT
AGTTGCGTTATCTTTAGCAATAATATGAAATTTTGAAGTAGCAGTAGCAGTAAAT
GTTGTAAAAATAATAATAAACTTATCACCAATAAAACTAACAACAAAATTAAAGA
TATCTAAGTAATTAATCAGAATAATTTTAATCTGATGAGAACGAATATTATAATG
AAGAACCAGTAACTTACAGTGATGCAAATTACATAAATATACCTATTAACTATAA
TCCTAATTCCAATTATGATTAAAATATTGGTATTTAGTAAAAAATAAATTAAATT
TAGCAAGAGAATAAATATGATTATCAAGACTAAGACATGGCAGATTTACTTTTTG
ACAAACCAAGATAATATATTCCCTAATAGCAAAGACAGCAAATTTAGAGTTATGA
AAACATTTAAAAGCAATCAAACATAATTCAATAAGAACATCTCATTATCAAAGAG
CAAAGTGAGGAACATGAGTCAGGTAATGATTCTTAATTGTAAAAGTATTTGAGAG
AGTCCTAATCTTATAATTAAGAGAATTAAAATGACTCTTATTAAAATGATCAAGA
AAATAAATCTTAAGAAAGAGAAAGTAAAATAGAATCATATTAAATTTAAAGTTAA
AATGAGTCATATGAATAAATTCATTCCTACTAACAGTAAGATAAAGATATTCATT
AGCATGATCATGAATTAGTTTAATAAAATTAAAACTAAAGTTAAGGATAAGATTA
ACATGAAGAATAATAATACACATTTAGCTAAGACGAATAAAAAAGTTCATCTAAT
ACATCTAAAAATATTTTAAATAATAATTATGAACAATAACAATAAAATTTAAGTA
ATTAGTAATAAAATATGATATAATAATAGTAATTAATTCAATAACAGTAGTAGCA
ACTGTTATAATAGCTCTAGTAGGCTTAACAATAAAAACAAATAAACATGAGCTTT
GAGAATATTGATTAAAATTAAGCAGATAAATCTTAAGTAGAGGATTATAAGGAAG
ATGATTTTTATAATTAAGGCGAATTTTTGGAATAATCTGAAGAAGATTCTTAAGA
ATAAACAAATTTTATGCTTTAACAATATTTATTATAGAAGCAAGAGTCATTTGTT
CAAATGGTCTTCAATGTTTGGCGCAAATTTACTATAGACAAAAAAATTAAAAGAA
ATTAAGAAGAAGAAGCTATCGAAACAGCTTATTAAGTTTATGAAAATAATTTGAG
CAGGAGAGTATTTTTAGAGTGGAAAGAAGTATGCTAAGAAAGAATTAATATGAGC
AAGTAACAAATGAGATCCTACTTATATGCTTGCTTTTCAAGCTGGAAAATGTTTT
CTAAGGAAAAAAAATTACTAAAAAAATATTTATCTGAAGCTGAGTTGGATGAACA
ATTAGCCTACACTCCTTAAACAACCGACAGGCTAAATCTTCTTTTTAATAATAAC
GATCCTAGATCTTCTTAATAAAAATTTTAGAGATCTGGGTCTTATAATAATTTAG
AAGGATCTAACAAAACTTCCTCTGATTCATAAAAGAGTGTATCGTTAGCAAGCGC
ACTCTTTACTGGAAAGCTCAAAATTTAAGATACTTCTAATTTGGATAAAAATGCT
CCTCATTGA

50

SFR13

The predicted protein sequence based on the cDNA
sequence determined by RT-PCR
is: MASLFRSEEQAIQEIIKLIPNNSEDISIFDILKAYDTYIEESGISFEDPF
AYDVYEIIIHASRRAQDNQLRSLLTNYKEIQKLKMKQNRKNSGYSDNSDNSEKPY
SKQKLAKQKISSKFSSKNQSLSPTNFGVNNQKNDRKEYNIQFKNFDTSSGEENDN
NFVNKEINEIQDIEHTPSSQYEQQQVRGRLGQYQQFASKIINSGLKMSNPFNDNL
YRYATEQADQPNRYSIRKYSYSPNNKMDSNNNLKRSASPICHPNNRSLSPHLNNS
KLSNYQARLNTSNSHNNSFNSSVNQQQSQRVRFNTQNADEYVNIQSPLNSINNFQ
ANRQMKGNLEQIQQRRFIQENQHQTLNRSIDNSDLNSKVNGIDNKKYLSLEPKDY
QQYQFMPANHKKYLSLDSSTKQMLKYENQDNEKQNQENVQYNFENRHRSIEEIEE
DIDLVRNEMAQGLRRKWVLHYHFANWKDYIQRWKGATEYINKEEQVENFIKIKIQ
RKFFEKWEQYVQEENTWKEAKLNFVMKKRQNILRKCFNELRDRLNDGKIDKYTYY
AAKYKKEQVLKEKYFQKFLQFSRNHRSNRLKLERTQQTAQNNLKKLAFNHLKQLK
SEKKERQIIKDDIKMKQSLLEKKISFDRFINNIRSILCFKKKKEILNKAIEIQLK
QHSLLSMIDNFRIIKYFKIQDQRASEFYNKNLSSKFFYHLKLFLFNNRERVENTE
SYNQLRIINKHHKQWQKFVQLNKSKEQKYKDARILYFLYRMMIMILNDNDYQISQ
QRNIQFEAFKEQVLYLQKMNQILNNQQQKENYQSFGKGESEDEQIDPTHQSMMQN
SSSNNNLMSNHKKLLPNQKSKNYLFSRSTQATAMGNNVNPNQVFDTVRSFSPAPA
RQHDNKTSRNENHNQDQQFLSENDQSDNQRMQRNLSEQNFVYQTQRQSQSNILKV
YENQEMMNEQQINEEIAIQIIGHGIFFTYPSILSINYYNKTQTEKLFQSHRNLNQ
FILSKSFKNWVTFLRSRNDFRKKMLNKIYQKHFDAMKIYSTKSQCLRFCVEKMQK
KLNKKTVENVFREMSLRAQERKNSRNGFKIIREKIEKKLLQKYFKIYRREFSSSR
GYSENYEQAGIYYKKWLIVQSFQAIQNYANRQKMVRDVISTKFQTKSQNQMSRIF
FAWRIYSDKRRQRNFIYQQIRQIYEKKVYKECLFALANYRDKHSKSTKNKNIVKS
YLFNKYIVNTFQKILNYSKSHKIKSILTDKIRIAYKQKLMQNYLHKLKDYKNYRQ
KKVTLQAKNTEKVEKVFQKKHFRAWYKLGCRNQSFRYLVDLVKRLQLSRFFVIMK
YLRQRDFQKQKIIKSDHLIFLKLTIFNAFVKYYRKRKYERKSLEYIKCRQQINYA
KQSMKQWKKLHSYNKNVTYLCAKSIIAIKNEILLKYFNKLKQKWFLKSQENKFIK
ENQIKMKRKILLGLRKYTTYKINNYENMIAINEKRKKQIKQNILYIWLRKLFNKQ
RQEDVSRAIIKYRKHKVLQTWADLFNIKNNLHNPVKVSDFQGFKRLEETQEIHII
TTNRGKKRNLRQFFFNMLKLNQKILQQKVFSCLKNLINERKIENKKSDQIQFKCE
TDLLTKYLLQWQKSSQKKINKYNMIVKLRSVFQKYQKRIGFEAIQGQEQIYLELI
QKSKKAVTQRQKSIKMKSFNKLKAYYLKKRKIAKRKLELDELVQRNNTLNFFKKL
KFYAYKKQENKQKNVYIQDYLYLNLLKKVFNKIRTYQIIKQTLAQKSLKLQSYLN
KKKLRRGFKQIQQNFSESKSDMQNTIQSLKAYRMNLQLKSFAVLRKYMNIQKLKS
QKYNSAFNKYYFSLATRIFGALKTYILNKNIEKDNHLYILDQYRQRKQVEIKKGI
LMVWKYYTNQSINQVQQFRSCIEASVLKSKFVEWKIKTHLLKDKRMKYNIIKNSN
NYKLRAKLFKLWQQRAKLNLVLTNIFVYHAKIEIKKRLLKWNQSKNLLKKIVNKS
QQQVISKPRSADDIQKMRQVFCMIKEMAQNTHSIKKDQNLRQKQINDQNVFKQFT
LQFKASQLAEKLNQLRYFSSAQQFIFNLKQMYIQKKQDKALAKKSERLNSPKFQK
NQIKNSMIQQTLKEQKLKDEFQKLSKLISRKQKELLSGSLLNLKDFVNYQNNIQI
QANLHHDRQLQQKTFKLWKKFVESSKQFSSVLGQVLTKALKRCQQQKLRDAFRQI
QIRYIKIKAANIVSSCIDRSVKRQYAQKLFELYEQFKSKTQVLRYLIENHQIKMN
TQRAIQFFNILKNLKIQAERSKMKCKEYLFIRRIKQMKSVLTILQIYTQYRRNKN
DRYQKAHLFWENKSKQKYLYFWARAYQNAQQYEEYQQDQFDQQEFYEQQQKLVEN
ELMQQLALHHQQQVNQQGNIQQLTKQEQEEQLRYLQQQYEILKQQQQQMLQKQQQ
TYHQQNQQQNQRYLSNQSEQFQSDENEYYNEEPVTYSDANYINIPINYNPNSNYD
QNIGIQQKINQIQQENKYDYQDQDMADLLFDKPRQYIPQQQRQQIQSYENIQKQS
NIIQQEHLIIKEQSEEHESGNDSQLQKYLRESQSYNQENQNDSYQNDQENKSQER
ESKIESYQIQSQNESYEQIHSYQQQDKDIHQHDHELVQQNQNQSQGQDQHEEQQY
TFSQDEQKSSSNTSKNILNNNYEQQQQNLSNQQQNMIQQQQLIQQQQQQLLQQLQ
QAQQQKQINMSFENIDQNQADKSQVEDYKEDDFYNQGEFLEQSEEDSQEQTNFML
QQYLLQKQESFVQMVFNVWRKFTIDKKIKRNQEEEAIETAYQVYENNLSRRVFLE
WKEVCQERINMSKQQMRSYLYACFSSWKMFSKEKKLLKKYLSEAELDEQLAYTPQ
TTDRLNLLFNNNDPRSSQQKFQRSGSYNNLEGSNKTSSDSQKSVSLASALFTGKL
KIQDTSNLDKNAPH

51

CRP1

Tetrahymena thermophilia CRP1 (calcium regulator
protein 1) appears to be a member of the sodium/calcium
exchanger protein family. It contains one putative
sodium/calcium exchanger domain, which has an E-value
of 3.2*10^-13, indicating that it is reasonably related
to this domain sequence. It is possible that this
protein regulates Ca2+ cation concentration within the
cell, where the movement of Ca2+ in or out of the
cytoplasm is contingent upon the concentration of Na+
in the cell. M. Huen and M. Greeley

52

deleted

53

RAD54

In yeast, DNA-dependent ATPase that stimulates strand
exchange; modifies the topology of double-stranded DNA;
involved in the recombinational repair of double-strand
breaks in DNA during vegetative growth and meiosis

54

HOP2,
HOPP2,
MNDP1,
MND1

Hop2 and Mnd1 are meiosis-specific proteins that
function in a complex in budding yeast. Their general
architecture is strikingly similar, and therefore they
are potentially homologous protein families. The
Hop2-Mnd1 system seems to have undergone duplication in
the evolutionary history of Tetrahymena, because both
protein families are represented by two homologs with
distinct expression patterns in this species. Just as
for HOP2 (meiotic) and HOPP2 (ubiquitous), there is a
meiotic (MND1)and a ubiquitously expressed (MNDP1)
version, which raises the possibility that a meiotic
and a ubiquitous Mnd1p-Hop2p complex exists.

58

Named RPL8 in Klinge et al. Science 2011

59

TWI12

Gene Model error: The open reading frame for the major
protein product starts at an upstream in-frame ATG,
adding 17 amino acids to the N-terminus of the
predicted protein (Couvillion et al., Mol. Cell, 2012).

60

Gene Information: TTHERM_00865050 is a homolog of
annotated and functionally characterized Orc1 in other
experimental organisms (24% amino acid sequence
identity, 49% similarity to human Orc1). Orc1 is a
component of the heterohexameric origin recognition
complex (ORC) found to be involved in initiation of DNA
replication. TtOrc1 has canonical Walker A and B motifs
(involved in ATP binding and hydrolysis). TtORC is
unusual in that it contains an integral RNA subunit
(26T RNA) that binds to its cognate DNA target in the
ribosomal DNA (rDNA) replication origin. Identified
in: Tetrahymena ORC contains a ribosomal RNA
fragment that participates in rDNA origin
recognition Mohammad M Mohammad,1,*† Taraka R
Donti,1,* J Sebastian Yakisich,1 Aaron G Smith,2 and
Geoffrey M Kapler1,2,a PMID: 2140106 Characterization
of a novel origin recognition complex-like complex:
implications for DNA recognition, cell cycle control,
and locus-specific gene amplification. Mohammad M, York
RD, Hommel J, Kapler GM. Mol Cell Biol. 2003
Jul;23(14):5005-17. PMID:12832485 Differential
targeting of Tetrahymena ORC to ribosomal DNA and
non-rDNA replication origins. Donti TR, Datta S,
Sandoval PY, Kapler GM. PMID: 19153611 Nucleic Acid
Interactions (with the ORC complex): 26T RNA
(5’-AUGUCUAAGUGUGAUGAUAAACGAAAAAAAAUAAAAAUUAA-3’).
Type I element T-rich strand: essential cis-acting
replication determinant in ribosomal DNA origin of
replication. (Location 5’ non-transcribed spacer) (C3
rDNA type IB element T-rich strand, T51:
5’-CTCAAAAGTTGCAAAAGTTCGGAAGGTTTACTATTTTTGTTTTTTTTTT-
3’). – requires 26T RNA and ATP dsDNA – non rDNA
chromosomes Protein Interaction Partners: TtOrc2
(Co-migration on a native gel, detection by WB).
Biochemical Activities (of ORC complex): ATP
binding, likely ATP hydrolysis DNA binding - typeI
element T-rich strand DNA RNA binding – 26T
RNA Regulation & Expression: mRNA and protein: Cell
cycle regulated Maximal protein expression at G1/S
border, degraded in S phase

61

ORC1

Gene Information: TTHERM_00865050 is a homolog of
annotated and functionally characterized Orc1 in other
experimental organisms (24% amino acid sequence
identity, 49% similarity to human Orc1). Orc1 is a
component of the heterohexameric origin recognition
complex (ORC) found to be involved in initiation of DNA
replication. TtOrc1 has canonical Walker A and B motifs
(involved in ATP binding and hydrolysis). TtORC is
unusual in that it contains an integral RNA subunit
(26T RNA) that binds to its cognate DNA target in the
ribosomal DNA (rDNA) replication origin.

62

ORC1

Nucleic Acid Interactions (with the ORC complex): 26T
RNA
(5’-AUGUCUAAGUGUGAUGAUAAACGAAAAAAAAUAAAAAUUAA-3’).
Type I element T-rich strand: essential cis-acting
replication determinant in ribosomal DNA origin of
replication. (Location 5’ non-transcribed spacer) (C3
rDNA type IB element T-rich strand, T51:
5’-CTCAAAAGTTGCAAAAGTTCGGAAGGTTTACTATTTTTGTTTTTTTTTT-
3’). – requires 26T RNA and ATP dsDNA – non rDNA
chromosomes

63

ORC1

Protein Interaction Partners: TtOrc2 (Co-migration on a
native gel, detection by WB).

64

ORC1

Biochemical Activities (of ORC complex): ATP binding,
likely ATP hydrolysis DNA binding - typeI element
T-rich strand DNA RNA binding – 26T RNA

65

ORC1

Regulation & Expression: mRNA and protein: Cell cycle
regulated Maximal protein expression at G1/S border,
degraded in S phase

66

ORC2

Gene Information: TTHERM_00684560 against human ORC
subunit 2 protein e-value= 8e-16 Reverse BLAST of
NP_006181.1 against TGD: TTHERM_00684560 hypothetical
protein e-value= 8e-15.

67

ORC2

The conserved Origin Recognition Complex (ORC)
determines the sites for replication initiation in
eukaryotic chromosomes and serves as a scaffold for
pre-replicative complex (pre-RC) assembly. Although ORC
subunits are conserved in eukaryotes, the cis-acting
DNA sequence requirements for replicator function are
not.

68

ORC2

Nucleic Acid Interactions: Orc2p bound to streptavidin
sepharose in 26T RNA aptamer-tagged strains (TD152 and
MM202, respectively)

69

ORC2

Protein Interaction Partners: Tetrahymena thermophila
ORC physically associates with Orc1p in western
blotting (native gel electrophoresis and
immunoprecipitation analyses. Western blotting was
similarly used to monitor the migration of
nuclease-treated ORC complexes under native EMSA gel
conditions. The mobility of Orc1p and Orc2p increased
following MNase and RNase A treatment, but was
unaltered by DNase I (Figure 3D). Orc1p and Orc2p
co-migrated under all conditions, suggesting that they
remain associated after the RNA is destroyed.

70

ORC2

Biochemical Activities: Consistent with previous
analyses of Orc2p/Tt-p69 and histone H3 (Mohammad et
al, 2003), ∼50% of Orc2 was rendered soluble by DNase
I. TtORC also crossreacts with a rabbit polyclonal
antibodies raised against Xenopus laevis / Orc2p.

71

ORC2

Regulation & Expression: Orc2p crossreactive subunit,
Tt-p69, localizes to the macronucleus during vegetative
S phase. Cell cycle regulated Maximal protein
expression at G1/S border

72

MCM6

Gene Information: MCM6 is a gene coding for a protein
product associated with replicative origins in G1 phase
during pre-replicative complex assembly. ORC recruits
MCM6p on non-rDNA chromosomes. Mcm6p ChIP analysis was
performed with affinity-purified rabbit antibodies
directed against amino acids 34–51
(GKKIKYYREKALLLKIYE) of the T. thermophila MCM6 protein
(Tetrahymena Genome Database gene prediction:
TTHERM-00448570, e value versus human MCM6
(NP_005906.2): 1.0e-172. Human MCM6 (NP_005906.2)
versus TGD TTHERM-0048570 e value : 1.0e-178.

73

MCM6

Nucleic Acid Interactions: Non-rDNA and rDNA origin in
cells synchronized at the G1/S border.

74

MCM6

Protein Interaction Partners: Not assessed

75

MCM6

Biochemical Activities: Predicted helicase activity for
dsDNA as a component of MCM2-7 complex

76

TIF1

Gene Information: Tif1 is a non-ORC Type-I binding
factor associated with ssDNA, particularly rDNA
associated with replication initiation. Essential
cis-acting replication determinant in ribosomal DNA
origin of replication. (Location 5’ non-transcribed
spacer) Limited homology to Whirly family proteins in
plants (transcription factors that bind to single
strand DNA target sequences), but this homology is
restricted to the DNA binding domain.

77

TIF1

Nucleic Acid Interactions: Tif1 assocates with the
A-rich strand of rDNA in vivo, and can be purified to
associate with the T-rich strand in vitro.

78

TIF1

Biochemical Activities: Regulates timing of rDNA origin
activation. Involved in the S phase DNA damage
checkpoint response. Involved in unique ssDNA origin of
replication recognition. TIF1 disruption mutants are
hypersensitive to hydroxyurea and
methylmethanesulfonate, inducers of DNA damage in all
examined eukaryotes.

79

TIF1

Regulation & Expression: TIF1 interacts with A-rich
strand at the rDNA origins and the T-rich strand at the
rDNA promoter. TIF1p localization is dynamically
regulated as it moves into the micro- and macronucleus
during the respective S phases.

80

ATR1

Gene Information: The phosphatidylinositol 3-kinase
(PI3K)-related sensor kinase ATR is a key player in the
signaling of induced DNA damage and self-inflicted DNA
cuts in vegetative and meiotic cells (Richardson et
al., 2004; Bassing and Alt, 2004; Hunter, 2008). In
higher eukaryotes ATR is recruited by the MRX/MRN
complex and possibly other unknown factors to the sites
of damage and phosphorylates a host of target proteins
to arrest replication forks and prevent new origins
from firing. (Kurz and Lees-Miller,
2004). TTHERM_01008650 BLAST against human ATR1
NP_001175.2 e value : 6.0 e-5. Reverse BLAST of human
ATR1 (NP_001175.2) against TTHERM_01008650 e value :
3e-48

81

ATR1

Nucleic Acid Interactions: Involved in ssDNA binding at
rDNA origin and promoter. Sensing and repair
mechanisms unknown.

82

ATR1

Protein Interaction Partners: Not determined

83

ATR1

Biochemical Activities: Ability to arrest cell cycle is
inhibited by caffeine.

84

ATR1

Regulation & Expression: Activated / Induced by DNA
damage

85

ASI2

Gene Information: ASI2 is a gene regulating
endocycling in Tetrahymena thermophila. Though
nonessential for vegative growth, it is upregulated
after meiosis and is involved in the creation of a new
MAC. Introduced via transduction with ASI2-GFP plasmid
to establish parental cells that showed transcription
of ASI2 occurs both in MAC and parental cells at
conjugation.

86

ASI2

Nucleic Acid Interactions: ASI2p independent of ssRNA
synthesis/accumulation

87

ASI2

Regulation & Expression: The Tetrahymena gene ASI1
(anlagen stage induced 1) was isolated from a cDNA
library of genes that are up-regulated during
development of the macronuclear anlagen. As its name
implies, the abundance of ASI2 mRNA peaks at 9 h of
mating, early in macronuclear anlagen development.

88

OGL1

Tetrahymena thermophila’s OGL1 protein is homologous
to proteins from the HhH-GPD and OGG-N superfamilies,
which are associated with DNA repair. It contains two
domains; the first domain (E-value= 3.0 -17), in the
HhH-GPD family, is a Helix-hairpin-helix and Gly/Pro
rich loop, found on proteins that remove base lesions.
The second domain (E-value=6.9-13), is common to
oxoguanine gylcosylases, also known as OGG1, which
removes 8-oxoG lesions. The closest homologs are in
Scheffersomyces stipitis, a negative Crabtree yeast,
and in Taphrina deformans, a fungi/plant pathogen, with
46% identical residues. OGL1 may be an essential
protein in preventing mutations in DNA that lead to a
short lifespan, early aging, and cancer. Paragraph by:
Lillian Horin, Maite Cortes Garcia, Francis Ryu,
Forrest Fulgenzi, Keck Science Center, Pitzer College

89

TTHERM_00530720

The first 2769 bp and later 3243 bp of TTHERM_00530720
(6012 bp) were expressed for MicNup98B and Nup96,
respectively.

91

MacNup98A coding sequence is split in TTHERM_00071070
and TTHERM_00071080

92

APAT1

APAT1 contains an Asp domain (E-value 3.9e-32).
Proteins that contain this domains typically catalyze
the transfer of acetyl groups and include pepsin-like
aspartate proteases. APAT1 is likely to cut peptide
bonds, take out the aspartyl group, and substitute it
with an acetyl group. Paragraph by: Anna Cechony and
Marzia Zendali (undergraduates), Keck Science
Department, Scripps College.

93

MTA6,
MTB6

The germline MAT locus was discovered in 1953 and
remains the only known Mating type locus in T.
thermophila. The mat-1-like allele codes for mating
type I,II,III,V,VI. The MTA and MTB genes determine
mating type.These genes code for trans-membrane
proteins that may localize to the cell surface. The
proteins may play a role in self/non-self recognition,
since cell-cell contact is required to stimulate cells
for mating. The MTA6 and MTB6 genes have been shown to
be necessary for mating type recognition, but may also
play a role in cell-cell recognition during mating.

95

The Germ line MAT locus was discovered in 1953 and
remains the only known Mating type locus in T.
thermophila. The mat-1-like allele codes for mating
type 1,2,3,5,6. MTA and MTB genes determine mating
type. Mating type genes code for trans-membrane domain
proteins that can localize to the cell surface could
play a role in self/non-self recognition, since
cell-cell contact is required to stimulate cells to
mate. MTB6 locus is responsible for mating type
recognition,but may also may play a role in cell-cell
recognition for mating.

97

MSH4

Msh4 (together with Msh5) is required for normal
chiasma formation

98

MSH5

Msh5 (together with Msh4) is required for normal
chiasma formation

99

MSH5

Transcript is annotated by gene_000007168

100

PMS2

TTHERM_01109940 is a close homologs to budding yeast
MutL family member, MLH3. TTHERM_01109940p is the first
candidate in a BLAST search with Mlh3 as bait, but it
is the best hit in a reciprocal BLAST search with Pms1.
It is also the best hit with Mlh2 as bait.
TTHERM_00127000p is the best hit in a reciprocal BLAST
search with Mlh1. Altogether, it is likely that
TTHERM_00127000p is the ortholog of Mlh1, whereas
TTHERM_01109940p could be any of Pms1, Mlh2 or Mlh3,
but an unambiguous assignment is not possible

101

MLH3

Referred to by the previous annotation
(TTHERM_01044360) in the paper, pubmed ID: 25217051.

102

RAD2

Macronuclear knockout did not display a notable
vegetative growth or meiotic defect, but was defective
in postmeiotic development

103

COI12

The Tetrahymena Hsp90 co-chaperone Coi12p promotes
scnRNA loading into the Argonaute protein Twi1p in both
ATP-dependent and ATP-independent manners.

104

GIW1,
TWI1

Giw1p binds to Twi1p complexed with single-stranded,
but not double-stranded, scnRNAs and that this
interaction selectively promotes the MAC localization
of the mature Twi1p-scnRNA complex (Noto et al. 2010).

105

GIW1,
COI12,
TWI1

ATP-dependent and ATP-independent activities of Coi12p
facilitate scnRNA loading by counteracting the
Twi1p-binding protein Giw1p, which is important for
sorting scnRNAs to Twi1p (Woehrer et al. 2015).

106

CROP1

The IQ-calmodulin motif information given in Gene
Browser is based on old information. Recent studies
have shown an sf-assemblin domain associated with
microtubule structure.

107

Zygotically-expressed Twi1p and Twi11p are loaded with
Late-scnRNAs and are important for DNA elimination
(Noto et al. 2015).

108

TWI1,
TWI11

Maternally-expressed Twi1p is loaded with Early-scnRNAs
expressed from the MIC at early conjugation stages
while zygotically-expressed Twi1p and Twi11p are loaded
with Late-scnRNAs expressed from the new MAC at late
conjugation stages (Noto et al. 2015).

109

HEN1,
TWI1

Twi1p-associated scnRNAs are 2'-O-methylated at their
3' ends by the RNA methyltransferase Hen1p (Kurth &
Mochizuki 2009).

110

JUB1,
PDD1

Jub1p promotes heterochromatin body formation and
dephosphorylation of the Heterochromatin Protein 1-like
protein Pdd1p. Because Pdd1p dephosphorylation promotes
the electrostatic interaction between Pdd1p and RNA in
vitro and heterochromatin body formation in vivo, it
has been proposed that heterochromatin body is
assembled by the Pdd1p-RNA interaction.

111

JUB1,
JUB2,
JUB3,
JUB4,
HPL2,
COI3,
HPL1,
COI16

This protein co-localizes with Pdd1p in heterochromatin
body in the new macronucleus.

112

LIA3

In cells lacking LIA3 (ΔLIA3), the excision of IESs
bounded by specific G-rich polypurine tracts was
impaired and imprecise, whereas the removal of IESs
without such controlling sequences was unaffected.
Lia3p binds to oligonucleotides containing these
polypurine tracts, which form parallel G-quadruplex
structures in vitro.