Gene Paragraphs at TGD

No. Paragraph Text Gene Name
1 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. PDD1
2 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. DCL1, HHT2, PDD1, PDD3, TWI1
3 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. CDK1
4 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. CDK1
5 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. CDK1
6 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). HEH2
7 HEH2 appears to be located on the right arm of micronuclear chromosome 2 based on mapping REP6, a locus upstream of HEH2. HEH2
8 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. HHO1, MLH1
9 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. CDC2, CYP1, HHO1, NGOA1
10 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). MYO1, MYO10, MYO11, MYO12, MYO13, MYO2, MYO3, MYO4, MYO4 , MYO5, MYO9
11 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) CMB1
12 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. THD1
13 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. THD1
14 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. FSF1
15 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. SPO11
16 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. HOP3
17 Knockout prevents SPO11-dependent elongation of meiotic nuclei. Involved in the signaling of meiotic DSBs and other DNA damage. ATR1
18 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). MBD1
19 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). DNF1 , FLP1, FLP10, FLP11, FLP12, FLP13, FLP14, FLP15, FLP16, FLP17, FLP18, FLP19, FLP2, FLP4, FLP5, FLP6, FLP7, FLP8, FLP9
22 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). LIA4
23 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 ABC3
24 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 STF1
25 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 NHX1
26 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 NHX2
27 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. GTR4
28 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 ABC2
29 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 MAF4
30 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. PKC2
31 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. PMR1
33 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 TIC1
35 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. PKD1
36 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. STP1
38 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. MSC1
39 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. CCT3
40 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. CUT1
41 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. MTP1
42 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. CCT2
43 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. ICT1
44 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. STD1
45 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. ATA2
46 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. AKM1
51 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 CRP1
53 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 RAD54
54 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. HOP2
55 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. HOP3
56 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. MNDP1
57 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. MND1
59 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). TWI12
61 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. ORC1
62 ORC1
63 Protein Interaction Partners: TtOrc2 (Co-migration on a native gel, detection by WB). ORC1
64 Biochemical Activities (of ORC complex): ATP binding, likely ATP hydrolysis DNA binding - typeI element T-rich strand DNA RNA binding – 26T RNA ORC1
65 Regulation & Expression: mRNA and protein: Cell cycle regulated Maximal protein expression at G1/S border, degraded in S phase ORC1
66 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. ORC2
67 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. ORC2
68 Nucleic Acid Interactions: Orc2p bound to streptavidin sepharose in 26T RNA aptamer-tagged strains (TD152 and MM202, respectively) ORC2
69 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. ORC2
70 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. ORC2
71 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 ORC2
72 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. MCM6
73 Nucleic Acid Interactions: Non-rDNA and rDNA origin in cells synchronized at the G1/S border. MCM6
74 Protein Interaction Partners: Not assessed MCM6
75 Biochemical Activities: Predicted helicase activity for dsDNA as a component of MCM2-7 complex MCM6
76 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. TIF1
77 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. TIF1
78 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. TIF1
79 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. TIF1
80 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 ATR1
81 Nucleic Acid Interactions: Involved in ssDNA binding at rDNA origin and promoter. Sensing and repair mechanisms unknown. ATR1
82 Protein Interaction Partners: Not determined ATR1
83 Biochemical Activities: Ability to arrest cell cycle is inhibited by caffeine. ATR1
84 Regulation & Expression: Activated / Induced by DNA damage ATR1
85 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. ASI2
86 Nucleic Acid Interactions: ASI2p independent of ssRNA synthesis/accumulation ASI2
87 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. ASI2
88 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 OGL1
89 The first 2769 bp and later 3243 bp of TTHERM_00530720 (6012 bp) were expressed for MicNup98B and Nup96, respectively. (no standard gene name)
92 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. AAT1
93 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. MTA6
94 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. MTB6
97 Msh4 (together with Msh5) is required for normal chiasma formation MSH4
98 Msh5 (together with Msh4) is required for normal chiasma formation MSH5
99 The gene model is incorrect. Transcript is annotated as gene_000007168 in TFGD MSH5
100 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 PMS2
101 Referred to by the previous annotation (TTHERM_01044360) in the paper, pubmed ID: 25217051. MLH3
103 The Tetrahymena Hsp90 co-chaperone Coi12p promotes scnRNA loading into the Argonaute protein Twi1p in both ATP-dependent and ATP-independent manners. COI12
104 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). GIW1, TWI1
105 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). COI12, GIW1, TWI1
106 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. CROP1
108 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). TWI1, TWI11
109 Twi1p-associated scnRNAs are 2'-O-methylated at their 3' ends by the RNA methyltransferase Hen1p (Kurth & Mochizuki 2009). HEN1, TWI1
110 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. JUB1, PDD1
111 This protein co-localizes with Pdd1p in heterochromatin body in the new macronucleus. COI16, COI3, COI6, HPL2, JUB1, JUB2, JUB3, JUB4, JUB6
112 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. LIA3
114 Coi7p directly interacts with Coi6p and is required for the stable accumulation of Coi6p. COI6, COI7
115 Coi6p, its interaction partners Coi7p and Lia5p, and the histone demethylase Jmj1p are crucial for confining the production of small RNAs and the formation of heterochromatin to the eliminated sequences. The loss of Coi6p, Coi7p or Jmj1p causes ectopic DNA elimination. COI6, COI7, JMJ1, LIA5
116 Bime2 protein is distantly related to budding yeast Rdh54/Tid1 and the vertebrate Rad54B helicases. In the bime2 deletion mutant, meiotic crossovers are reduced to an estimated 18% of the wild-type number. BIME2
117 HA-tagged RNase H1.3 localizes to early meiotic micronuclei. RNH13 gene knockout causes aberrant numbers of nuclei in exconjugants. RNH13
119 Tetrahymena thermophilia’s TPPT1 protein is homologous with proteins in the Y phosphatase family associated with the removal of phosphate groups from tyrosine residues. It contains 1 domain (E-value= 2.9E-67), which is a Y phosphatase domain. The closest homologs are found in Paramecium tetraurelia, Ichthyopthirius multifiliis, a freshwater fish disease, and Stentor coeruleus, a large ciliate. It is possible that this protein is involved in cell signaling pathways. Paragraph by: Margot Chisholm, Keck Science Center, Pitzer College. (no standard gene name)
120 The SNR8 protein is homologous to proteins from the APC Superfamily which is associated with the use of cations as substrate to transport solutes. SNR8 contains one domain (Evalue= 4.0e-77) in the Sodium Neurotransmitter Symporter family that is responsible for the reuptake of neurotransmitters in presynaptic terminals. The closest homologs are in Pseudocohnilembus persalinus, a marine ciliate, Paramecium tetraurelia a unicellular organism that feeds on bacteria, with 51% and 42% identical residues. SNR8 may be an essential protein in terminating the presence and thus the effects of signaling molecules in Tetrahymena thermophila. Paragraph by: Benjamin Wolters, Claremont McKenna College. (no standard gene name)
121 Tetrahymena thermophila’s MRNO20 protein is homologous to proteins from the 1APM superfamily, which is associated with transmembrane receptor linked kinases and other cytoplasmic proteins, and the 1B0X superfamily. It contains three domains, the first being composed of six Morn Repeats (E-value= 1E-10 to 1E-22) at the N terminus. The next domain is SAM 1, which functions in protein kinase cascades and RNA binding (E-value= 1.3E-9), and correlates with homologs in the 1B0X family. The eighth domain is tyrosine kinase protein, which transfers a phosphate group from ATP to another protein in signal transduction kinase cascade and homologs with transmembrane receptor linked kinases, specifically in cell division (E-value= 3.3E-66). The closest homologs are I. multifiliis, a disease in freshwater fish, P. tetraurelia, a ciliate common in ponds, and P. persalinus a disease of mariculture fish. MRNO20 is an essential protein that are integral in cell division, in which mutations can lead can lead to Parkinson’s disease and gastric cancer in mammals. Paragraph by: Kate DeMarsh, Ananya Venkatesh, Scripps College MRNO20
122 Tetrahymena thermophila’s THK1 protein is homologous with protein kinases. It has three domains: Protein kinase domain (E-value = 2.7E-54), Flagellin hook IN motif (E-value = 6.7E-13), and Tyrosine kinase (E-value = 1.30E-93). The first and third domains contain the catalytic function of protein kinases, which phosphorylate proteins. The second domain does not yet have a determined function, but it is located in many flagellar hook proteins. The closest homologs are in Paramecium tetraurelia strain d4-2, a freshwater protest, Ichthyophthirius multifiliis, a freshwater spot disease, and Vitrella brassicaformis CCMP3155. It is possible this protein functions as a tyrosine kinase . Paragraph by Lynnlee Duck-Reynolds and Ann Ly (undergraduates), Keck Science Center, Scripps College. (no standard gene name)
123 The UBQ1 protein contains one domain. The domain (E-value=2.4E-11) is a zinc finger structure that binds two zinc cations and some DNA, RNA, or protein molecules. The closest homologs are in Paramecium tetraurelia strain d4-2, stylonychia lemnae, and oxytricha trifallax. UBQ1 may play an integral role in the ubiquitination pathway, which attaches ubiquitin to substrate proteins. The effect of ubiquitination may affect the substrate protein in various ways including: marking for degradation, altering location, changing protein activity, or promoting and preventing protein interactions. (no standard gene name)
124 This protein is a homolog of proteins in the polycystic cation channel transmembrane protein family. It contains one domain; the domain (E-value = 1.2 -10) is known as CL0030, which contains the cation channel region of PKD1 and PKD2 proteins. PKD1 and PKD2 functions through a common signaling pathway that is necessary for normal tubulogenesis. Tubulogenesis is the formation of tubules in epithelial or endothelial cells that transport liquid and gas throughout the body. In humans, the mutations in PKD1 and PKD 2 form thousands of cysts which inhibits the protein from efficiently carrying liquid and gas throughout the body. It is possible that in Tetrahymena this protein is an integral membrane protein. Paragraph by: Deborah Yi-an Lin, Keck Science Department, Scripps College (no standard gene name)
125 Tetrahymena thermophilia’s KIN31 protein has one domain between amino acids 31-442 with e-value 3.1e-65. The kinesin motor domain supports several cellular functions including mitosis, meiosis, and cellular transport. Kinesin proteins tend to walk toward positive ends of microtubules. The closest homologs are in Paramecium tetraurelia and Callorhinchus milii, a cartilaginous fish. Paragraph by: Jenniluyn Nguyen (undergraduate), Keck Science Department, Scripps College. (no standard gene name)
126 This protein is homologous to proteins that contain helicase and SANT domains, which are associated with transcription. It contains three domains; the first two domains (score=22.832, 18.839), in the helicase family, indicates that the protein’s function, which involves the binding of ATP, could be related to the separation of double-stranded nucleic acids. The third domain (score=10.421) belongs to the SANT domain, which indicates that the protein is involved in chromatin-remodeling or transcription regulation via protein-protein interactions. The closest homologs are in Ichthyophthirius multifiliis, with 77% identical residues and Pseudocohnilembus persalinus,with 54% identical residues. It is possible that this protein is an enzyme with helicase activity that functions to remodel chromatin or regulate transcription. Paragraph by: Madison Seto, Keck Science Department, Scripps College (no standard gene name)
127 Former TTHERM_00420400 contained TTHERM_00420400, TTHERM_000420399, and TTHERM_000420398. Woehrer et al (2015) called the former TTHERM_00420400 as COI14. The primers used for their gene expression analysis by RT-PCR are complementary to TTHERM_000420399. Therefore, TTHERM_000420399 takes over the name COI14. According to Saettone et al. (2018), the new TTHERM_00420400 is similar to Ada2-associated protein and thus now called AAP8. AAP8
128 The FACT-complex is a critical transcription regulator and an H2A/H2B chaperone. Affinity purification followed by mass spectrometry (AP-MS) of endogenously tagged T. thermophila histones H2A/H2B identified Cet1 and Pob3 subunits of the FACT complex as high-confidence interacting partners. Indirect immunofluorescence studies using endogenously tagged Cet1 indicated that it localized to both the MAC and MIC during vegetative growth. AP-MS analysis using Tetrahymena Cet1 as a bait protein revealed Pob3 and subunits of RNA polymerase as high-confidence co-purifying proteins (Ashraf et al. 2019). CET1
129 The FACT-complex is a critical transcription regulator and an H2A/H2B chaperone. Affinity purification followed by mass spectrometry (AP-MS) of endogenously tagged T. thermophila histones H2A/H2B identified Cet1 and Pob3 subunits of the FACT complex as high-confidence interacting partners. Indirect immunofluorescence studies using endogenously tagged Cet1 indicated that it localized to both the MAC and MIC during vegetative growth. AP-MS analysis using Tetrahymena Cet1 as a bait protein revealed Pob3 and subunits of RNA polymerase as high-confidence co-purifying proteins (Ashraf et al. 2019). POB3
130 HIAP1 was identified as a high-confidence interacting partner of histones H2A/H2B and Hv1 in affinity purification followed by mass spectrometry experiments. HIAP1 shares sequence similarity with nucleoplasmin 1 (CNPL1 in Tetrahymena) due to stretches of acidic residues HIAP1
131 NPM-family proteins are H2A/H2B chaperones with important roles in various cellular processes. Vertebrates have three NPM proteins (NPM 1-3) whereas invertebrates contain only a single Npm-like protein. Human NPM1 functions in many processes, including histone chaperoning, chromatin remodeling, transcription regulation, genome stability, apoptosis, and embryogenesis. Tetrahymena CNPL1 shares conserved domain architecture with NPM-family members and is an ortholog of NPM1 protein. CNPL1 co-purified with histone H2A as a high-confidence interacting partner. CNPL1 localizes to MAC during vegetative growth (Ashraf et al. 2019). CNPL1
132 Emit1 and Emit2 tether the Mediator complex to the nucleus and activate transcription. Emit2 tethers Rib1 to chromatin to position the transcription machinery. Rib1 promotes the formation of small RNA precursors to guide DNA elimination EMIT1
133 Emit1 and Emit2 tether the Mediator complex to the nucleus and activate transcription. Emit2 tethers Rib1 to chromatin to position the transcription machinery. Rib1 promotes the formation of small RNA precursors to guide DNA elimination EMIT2
134 Ftt18p localizes to the conjugation junction and the periphery of the selected haploid micronucleus during sexual reproduction. It interacts (CoIP) with Semi1p. FTT18
135 Semi1 interacts (CoIP) with Zfr3 and Ftt18 and colocalizes with Zfr3 at the periphery of the selected haploid micronucleus. SEMI1
136 Zfr3 interacts (CoIP) with Semi1 and colocalizes with Semi1 at the periphery of the selected haploid micronucleus in sexual reproduction. ZFR3
137 Cyc28 is required for the coordinated progression of meiosis (SUPR000497) CYC28
138 The gene model is incorrect. See gene_000008668 in FGD for the correct transcript sequence SPO11
139 The gene model is incorrect. See gene_000003690 in TFGD for the transcript sequence MND1
140 Based on protein sequence homology, this is more likely MCM7 (no standard gene name)
141 The MCM7 gene is incorrectly annotated - its actual ID is TTHERM_000011759. MCM7
142 Melg2 protein localizes to the micronucleus during meiotic prophase. In a melg2 deletion mutant, homologous chromosome pairing and bivalent formation are strongly reduced, and the arrangement of centromeres and telomeres within the meiotic nucleus is abnormal. MELG2
143 Melg1 protein localizes to the micronucleus during meiotic prophase. In a deletion mutant, homologous chromosome pairing and bivalent formation are slightly reduced. The gene is incorrectly annotated in TGD. The large transcript encompasses predicted genes TTHERM_00711850 and TTHERM_00711858 (see FGD, gene_000000331). MELG1
144 Melg3 protein interacts with Tass1 (co-IP) and localizes to the telomeric tip of the micronucleus during meiotic prophase. In a melg3 deletion mutant, meiotic homologous chromosome pairing and bivalent formation are moderately reduced. MELG3
145 RebL1 physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Genome-wide analyses indicated that RebL1 binds within genic and intergenic regions. RebL1 depletion inhibited cellular growth and reduced the expression levels of multiple genes during Tetrahymena vegetative growth (Nabeel-Shah et al.2021). RebL1
146 Affinity purification followed by mass spectrometry analysis indicated that Lin9 interacts with Anqa1, RebL1, Jinn1 and Jinn2 proteins (Nabeel-Shah et al. 2021). Lin9
147 MybL1 was detected as a high-confidence interaction partner of RebL1 and Anqa1 during growth and conjugation. MybL1 interaction with these proteins is possibly in the context of putative MuvB complex to form an activator MMB-complex (Nabeel-Shah et al. 2021). MybL1
148 MybL1 was detected as a high-confidence interaction partner of RebL1 and Anqa1 conjugation (Nabeel-Shah et al. 2021). MybL2
149 Anqa1 is homolog of human Lin54, subunit of MuvB complex. In Tetrahymena putative MuvB complex contains three conserved subunits including RebL1, Lin9 and Anqa1 (putative orthologs of human Rbbp4/7, Lin9 and Lin54, respectively). Additionally, two divergent subunits Jinn1 and Jinn2 are precited to be part of this putative MuvB in Tetrahymena. RebL1, Lin9 and Anqa1 reciprocally co-purified with each other during vegetative growth and conjugation. Additionally, IPRA1 and Myb-like proteins interacted with Anqa1 and RebL1. Human MuvB-complex regulates cell-cycle gene expression by forming either DREAM- or B-Myb-MuvB (MMB) complexes. Anqa1 ChIP-seq identified sequence motif that shared similarity with CHR element. Tetrahymena contains at least 14 Lin54-like genes, which were named as Anqa1-14 after the ‘ANQA’ mythological creature thought to appear once in ages (Nabeel-Shah et al. 2021). Anqa1