Gene Paragraphs at TGD Wiki

Paragraph NoParagraph TextGene Name
1The 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
2A 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.TWI1,
HHT2,
PDD1,
PDD3,
DCL1
3Cyclin-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
4Tetrahymena 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
5The 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
6HEH2 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
7HEH2 appears to be located on the right arm of micronuclear chromosome 2 based on mapping REP6, a locus upstream of HEH2.HEH2
8The 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
9HHO1 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.HHO1,
CDC2,
NgoA,
CYP1
10Proteins 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,
MYO2,
MYO3,
MYO4,
MYO5,
MYO8,
MYO9,
MYO10,
MYO11,
MYO12,
MYO13
11A 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
12THD1, 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
13Tetrahymena 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
14A 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
15Spo11p 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
16HOP2B 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.TTHERM_01190440
17Knockout prevents SPO11-dependent elongation of meiotic nuclei. Involved in the signaling of meiotic DSBs and other DNA damage.ATR1
18MBD1 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
19The 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).FLP11,
FLP5,
FLP7,
FLP4,
FLP12,
FLP9,
FLP3,
FLP1,
FLP2,
FLP10,
FLP13,
FLP6,
FLP14,
FLP15,
FLP16,
FLP8,
FLP17,
FLP18,
FLP19
2019
212
22LIA4 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
23ABC3 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 CollegeABC3
24Solute 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 CollegeSTF1
25NHX1 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 CollegesNHX1
26NHX2 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 CollegesNHX2
27GTP4 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.GTP4
28ABC2 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 CollegesABC2
29Tetrahymena 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 CollegeMAF4
30PKC2 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