ABSTRACT
The homologous Saccharomyces cerevisiae genes CES1 and CES4 act as high copy suppressors of temperature-sensitive mutations of Ceg1p, the yeast mRNA capping enzyme. Neither CES1 nor CES4 is essential for cell growth. We find that a double deletion mutant ([Delta]ces1 [Delta]ces4) grows at 25-37°C, but not at 16°C. [Delta]ces1 [Delta]ces4 cells display gross defects in cell shape and budding even at permissive temperatures. Functional analysis of CES1 deletion mutants defines a 145 amino acid C-terminal segment of the 915 amino acid Ces1 protein that is necessary and sufficient to complement the [Delta]ces1 [Delta]ces4 cold-sensitive phenotype, to restore normal morphology and to suppress the temparature-sensitive mutant ceg1-25. A 147 amino acid C-terminal segment of the 942 amino acid Ces4 protein is sufficient to carry out these same functions. Within this carboxyl domain Ces1p and Ces4p are 80% identical to one another. We report isolation of CES1 in a separate screen for high copy suppression of a temperature-sensitive mutation (A79V) of the yeast translation initiation factor Tif1p (eIF-4A). Deletion of the N-terminal 249 amino acids of Ces1p abolished tif1-A79V suppressor function. CES4 on a multicopy plasmid was unable to suppress tif1-A79V. We surmise that whereas the carboxyl domains of Ces1p and Ces4p are functionally redundant in controlling cell morphology and in suppressing ceg1-25, full-length Ces1p and Ces4p evince distinct genetic interactions that are likely mediated by their N-terminal segments.
The m7GpppN cap has been postulated to play a role in virtually every transaction of eukaryotic mRNA, including splicing, polyadenylation, transport, translation and decay. A genetic analysis of cap function has become feasible only recently, as the mRNA capping and methylating enzymes have been purified from Saccharomyces cerevisiae and the genes encoding them have been identified (1,2). Yeast mRNA guanylyltransferase (capping enzyme) is a 52 kDa protein encoded by the CEG1 gene (1). Ceg1p reacts with GTP to form a covalent enzyme-GMP intermediate. The enzyme transfers the GMP to a 5'-diphosphate-terminated RNA to form the GpppN cap structure, which is then methylated at N-7 of the cap guanosine in a reaction catalyzed by the 50 kDa S.cerevisiae Abd1 protein (2). The guanylyltransferase and methyltransferase activities of Ceg1p and Abd1p are essential for yeast cell growth, i.e. mutations of CEG1 or ABD1 that eliminate enzyme activity in vitro are invariably lethal in vivo (3-7).
We recently reported isolation of temperature-sensitive (ts) capping enzyme mutants and identification of multicopy suppressors of the ceg1-ts growth defect (8). We reasoned that capping enzyme suppressor (CES) genes might encode proteins that either interact with Ceg1p or impact on cap-dependent transactions in vivo. Four CES genes were identified, two of which, CES1 and CES4, encode extensively similar proteins (915 and 942 amino acids respectively) of unknown function (8). We found that neither gene was essential and that a double knock-out was viable.
Other investigators have encountered CES1 (alternatively named ZDS1) or CES4 (alternatively named ZDS2) during genetic screening for high copy suppression of a variety of conditional growth phenotypes (9-11; D.Burke, personal communication; C.Glover, personal communication). The genetic backgrounds suppressed by CES1 and CES4 have no clear connection with each other. Suppression encompasses genes involved in cell polarity, transcription, cell cycle control, chromosome stability and protein modification (reviewed in 9). Elucidating the physiological role of Ces1p and Ces4p and connecting the suppressor phenotypes to a common biological process presents a fascinating challenge. In the present study we exploit the observation that a double deletion of CES1 and CES4 results in an inability to grow at low temperature to identify the essential structural components of Ces1p and Ces4p. We find that the C-terminal segment of either Ces1p or Ces4p is sufficent to complement the [Delta]ces1 [Delta]ces4 cs growth phenotype. The carboxyl domain is essential for suppression of capping enzyme mutant ceg1-25. We also report identification of CES1 as a high copy suppressor of a temperature-sensitive mutation in the yeast translation initiation factor eIF-4A. This suggests that CES1 overexpression may facilitate cap-dependent RNA transactions.
The strains used in this study derive from the diploid strain YPH274 (MATa/MAT[alpha] trp1[Delta]1/trp1[Delta]1 his3[Delta]200/his3[Delta]200 ura3-52/ura3-52 ade2-101/ade2-101 lys2-801/lys2-801 leu2-[Delta]1/leu2-[Delta]1). CES1 was disrupted in YPH274 by a hisG-URA3-hisG cassette (8,12). Haploids were selected after sporulation. The Ura+ haploid strain YBS101 (MATa his3 ura3 leu2 trp1 lys2 ces1::hisG-URA3-hisG) carries a chromosomal deletion of CES1. Strains YBS102 (MATa his3 ura3 leu2 trp1 lys2) and YBS103 (MAT[alpha] his3 ura3 leu2 trp1 lys2) were derived from sister spores of YBS101. Plating of YBS101 on 5-FOA yielded the Ura- strain YBS105 (MATa his3 ura3 leu2 trp1 lys2 ces1::hisG). CES4 was disrupted in YBS105 by a hisG-URA3-hisG cassette, yielding strain YBS104 (MATa his3 ura3 leu2 trp1 lys2 ces1::hisG ces4::hisG-URA3-hisG). After selection for cells that had lost the URA3 marker by recombination between the hisG repeats we obtained the [Delta]ces1 [Delta]ces4 double deletion strain YBS106 (MATa his3 ura3 leu2 trp1 lys2 ces1::hisG ces4::hisG). CES4 was singly disrupted in YBS102 to yield the [Delta]ces4 strain YBS107 (MATa his3 ura3 leu2 trp1 lys2 ces4::hisG). The CES1 and CES4 gene disruption cassettes were described previously (8).
A NcoI restriction site was introduced at the start codon of the CES1 open reading frame by site-directed mutagenesis. A 1008 bp EcoRI-StuI fragment containing the NcoI cleavage site was exchanged for the corresponding fragment in the 2µ plasmid pCES1-Hinc2 (8). The resulting plasmid, pCES1-N, extended from 309 bp upstream of the CES1 start codon to 467 bp downstream of the stop codon. This clone was active in suppressing the temperature-sensitive growth defect of ceg1-25. N-Terminal deletion mutants of CES1 were constructed by PCR amplification with mutagenic primers that introduced a NcoI restriction site and a methionine codon in lieu of the codons for Asp250, Pro358 and Ser422. The PCR products were digested with NcoI and KpnI, then inserted into pCES1-N so as to replace a 1.38 kb NcoI-KpnI fragment of the wild-type CES1 gene with in-frame restriction fragments encoding serially deleted Ces1 polypeptides. The mutated genes were named according to the amino acid coordinates of their polypeptide products, i.e. CES1(250-915), CES1(358-915) and CES1(422-915). Additional N-terminal CES1 deletion mutants were constructed by introducing NcoI sites with methionine codons in place of the codons for Asn529, Thr569, Asn613, His654, Lys688, Thr731, Ser771, Ala796 and Thr829. The PCR products were digested with NcoI and SacII, then cloned into pCES1-N that had been cut with NcoI and SacII. This yielded mutant alleles CES1(529-915), CES1(569-915), CES1(613-915), CES1(654-915), CES1(688-915), CES1(731-915), CES1(771-915), CES1(796-915) and CES1(829-915).
C-Terminal deletion mutants of CES1 were constructed by excising gene fragments from pCES1-Hinc2 and inserting them into YEp24. CES1(1-712) contains a HincII-XbaI fragment extending from nt -645 to +2139. CES1(1-626) contains a HincII-HindIII fragment from nt -645 to +1878. CES1(1-537) contains a HincII-SacI fragment from nt -645 to +1611.
CES4 deletions were constructed in stages. First, the promoter region (-500 to +3) of CES4 was PCR amplified by using two mutagenic primers. The sense strand primer introduced a BamHI site 500 bp upstream of the translation initiation codon; the antisense primer introduced a NcoI site at the start codon and a XbaI site downstream of the NcoI site. The 2µ CES4 plasmid pDC1 (a gift of Desmond Clarke and Dan Burke) was used as the template for PCR amplification. The PCR product was digested with BamHI and XbaI and the fragment inserted into pBluescript-KS+ to yield pKS-CES4(5'). Second, an XbaI-SacII fragment extending from nt +2818 to +3718 of CES4 was inserted into pKS-CES4(5') to yield the plasmid pKS-CES4(5')(3'). Third, the CES4 coding region was PCR amplified with mutagenic primers that introduced a NcoI restriction site and a methionine codon in lieu of the codons for Glu707, Glu796 and Ser841. The PCR products were digested with NcoI and XbaI and then inserted into pKS-CES4(5')(3'). Finally, XhoI-SacI fragments containing the truncated CES4 genes were excised from the Bluescript-based plasmids and inserted into YEp24.
Yeast strain SS13-3A (MATa his3 ade2 leu2 trp1 ura3 tif1::HIS3 tif2::ADE2) is deleted at the two chromosomal loci (TIF1 and TIF2) encoding the translation factor eIF-4A (13). Viability of SS13-3A is dependent on maintenance of an extrachromosomal copy of TIF1. The strain used in this study contains plasmid pSSC120 (CEN LEU2 tif1-A79V), which bears a temperature-sensitive tif1 allele (14). This strain grows at 25 but not at 37°C. The conditional phenotype is caused by a single coding change resulting in substitution of valine for alanine at residue 79 of eIF-4A (14). SS13-3A/pSSC120 was transformed with 2µ URA3 plasmids containing CES1, CES4 and various deletion mutants of CES1 and CES4. A control transformation was performed with plasmid YCplac33-TIF1 (CEN URA3 TIF1), which contains the wild-type TIF1 gene. Ura+ transformants were selected at 25°C. Single colonies were amplified and then streaked onto synthetic medium lacking uracil (SD Ura-). The plates were incubated at 25 and 37°C.
Single deletion mutants [Delta]ces1 and [Delta]ces4 formed wild-type sized colonies at 30°C. The double deletion mutant strain [Delta]ces1 [Delta]ces4 was viable at 30°C, but the colony size was smaller (Fig. 1). Conditional phenotypes were sought by testing cell growth at other temperatures. The [Delta]ces1 and [Delta]ces4 strains grew at 37, 25 and 16°C (Fig. 1 and data not shown). The [Delta]ces1 [Delta]ces4 double mutants formed colonies at 37, 30 and 25°C, but failed to grow at 16°C (Fig. 1). Hence, the loss of both gene products confers a cold-sensitive (cs) growth phenotype.
Microscopic examination of [Delta]ces4 cells grown to mid log phase in liquid culture at permissive temperature revealed unbudded and budded cells (Fig. 2) that were indistinguishable in appearance from wild-type cells. [Delta]ces1 cells displayed a mild defect in morphogenesis in that they tended to form elongated buds (Fig. 2). In contrast, [Delta]ces1 [Delta]ces4 cells were grossly misshapen (Fig. 2). Large mother cells elaborated very long buds that were punctuated by multiple constrictions at regular intervals. The distal tip of the bud projection was sometimes malformed. A few cells had schmoo-like protuberances. Bi and Pringle (9) and Yu et al. (11) noted similar morphological defects in [Delta]zds1 [Delta]zds2 deletion strains (equivalent to [Delta]ces1 [Delta]ces4).
Introduction of the CES1 gene on a centromeric or multicopy plasmid complemented the cs phenotype of the [Delta]ces1 [Delta]ces4 strain and restored growth at 16°C (Fig. 3). Cells transformed with the vectors alone did not grow. CES4 on a multicopy plasmid also complemented the cs phenotype (Fig. 3). (CEN CES4 was not tested.) Microscopic examination of the transformants showed that the morphological defect was complemented in parallel with the growth defect (not shown). We conclude that Ces1p and Ces4p carry out overlapping functions that are conditionally essential for cell growth.
Ces1p is a hydrophilic 915 amino acid protein (8). The amino acid sequence of Ces1p is uninformative with respect to its potential function. Complementation of the cold-sensitive growth phenotype of the [Delta]ces1 [Delta]ces4 strain affords a simple test of CES1 function that we applied to the analysis of CES1 alleles containing N- and C-terminal deletions. All CES1 mutants were cloned into a 2µ vector under transcriptional control of the natural CES1 promoter. This allowed us to test in parallel the ability of the mutant alleles to function as multicopy suppressors of a temperature-sensitive mutation in the CEG1 gene encoding the mRNA capping enzyme, this being the basis for our original isolation of CES1.
Deletion of the N-terminal 249 amino acids of Ces1p had no impact on its ability to complement [Delta]ces1 [Delta]ces4 growth at 16°C (Fig. 4A). Nine additional incremental deletions showed that the N-terminal 770 amino acids could be eliminated with no effect on complementation activity. The CES1(771-915) allele also corrected the morphogenesis defect of the [Delta]ces1 [Delta]ces4 mutant (not shown). Hence, a C-terminal 145 amino acid fragment of Ces1p was fully functional by these two criteria. The CES1(796-915) allele, encoding a 120 amino acid C-terminal fragment, was partially active in complementing [Delta]ces1 [Delta]ces4 growth at 16°C, whereas CES1(829-915) was incapable of cs complementation (Fig. 4A).
The allele CES1(1-712), which lacks the C-terminal 203 amino acids, was inactive in the complementation assay, as were two more extensively truncated alleles, CES1(1-626) and CES1(1-537), from which 289 and 378 C-terminal residues were deleted respectively (Fig. 4A). We conclude from these results that: (i) the N-terminal 85% of Ces1p is dispensable for the essential function of CES1 at 16°C; (ii) the C-terminal polypeptide segment is necessary and sufficient for this function.
ceg1-25 is a temperature-sensitive mutation of the yeast mRNA capping enzyme (8). ceg1-25 cells are able to form colonies at the restrictive temperature (37°C) when they are transformed with CES1 on a multicopy plasmid (8). Truncated versions of CES1 were introduced into ceg1-25 and the transformants tested for growth at 37°C. We found that CES1(688-915) was as active as the full-length gene in suppressing ceg1-25. Alleles CES1(731-915) and CES1(771-915) were partially active, whereas CES1(796-915) and CES1(829-915) were non-functional (Fig. 4A). C-Terminal deletions of CES1 abrogated suppressor function. We conclude that the N-terminus of the Ces1p protein is dispensable for suppressor function, just as it is for complementation, and that the C-terminus is necessary and sufficient for suppression. The cut-off point for loss of suppressor activity by incremental N-terminal deletion (residue 771) was only 15 amino acid residues proximal to the transition point, beyond which complementation function was lost (residue 796) (Fig. 4A). We infer that the two phenotypic manifestations of CES1 function are tightly linked within the C-terminal protein domain.
Deleted alleles of CES4 under transcriptional control of the natural CES4 promoter were cloned into a 2µ plasmid vector and tested for complementation and suppressor activities in vivo. We found that elimination of 706 or 795 amino acids from the N-terminus of the 942 amino acid Ces4p protein had no effect on complementation, whereas deletion of 840 residues abolished complementation activity (Fig. 4B). The truncated allele CES4(796-942) corrected the [Delta]ces1 [Delta]ces4 morphogenesis defect (not shown). CES4(707-942) and CES4(796-942) were partially active as high copy suppressors of ceg1-25, i.e. the colonies formed at 37°C by the mutant alleles were smaller in size than those of wild-type CES4 transformants. Suppression was eliminated by further truncation to residue 840. These results show that a 147 amino acid C-terminal fragment of Ces4p was functional in both assays.
Ces1p and Ces4p display 50-80% identity to each other within a series of conserved sequence blocks that span the entire length of both proteins (8). Yet only the C-terminal sixth of either polypeptide is relevant to the overlapping function of these proteins in cell growth at reduced temperatures and to their ability to compensate for diminished capping enzyme function at high temperature. Alignment of the C-terminal domains of Ces1p and Ces4p highlights a 101 amino acid segment (positions 804-904 in Ces1p and 816-916 in Ces4p) within which 82 of the residues are identical and five more positions are occupied by conserved non-identical sidechains (Fig. 4C).
Cap-dependent recruitment of mRNA to the 40S ribosome is mediated by translation initiation factor eIF-4F, which binds to the methylated cap structure. Mammalian eIF-4F consists of three subunits: eIF-4E (cap binding protein), eIF-4G and eIF-4A (reviewed in 17). Mammalian eIF-4A is an RNA-dependent ATPase that, together with eIF-4B, functions to unwind RNA secondary structures during ribosomal scanning for the AUG initiation codon (16). Saccharomyces cerevisiae genes TIF1 and TIF2 encode identical eIF-4A proteins. Yeast strain SS13-3A/pSSC120 contains chromosomal deletions in the TIF1 and TIF2 genes encoding translation initiation factor eIF-4A (13). Viability is sustained by maintenance of a temperature-sensitive allele tif1-A79V on a CEN LEU2 plasmid (pSSC120). Coppolecchia et al. (13) have reported isolation of multicopy suppressors of the temperature-sensitive growth phenotype by transformation of the tif1-A79V strain with a 2µ plasmid library of yeast genomic DNA. Two distinct genes, STM1 and STM2, restored growth at the non-permissive temperature (37°C). Sequencing of the STM1 gene (also called TIF3) revealed that it encodes the yeast homolog of mammalian translation initiation factor eIF-4B (13,17).
CES1 and CES4 encode structurally similar proteins with overlapping functions in cell morphology. In the absence of Ces1p and Ces4p yeast cells form abnormally long bud appendages. The microscopic appearance of [Delta]ces1 [Delta]ces4 cells suggests that cytokinesis does not proceed to completion after emergence of the first bud from the mother cell and that new rounds of budding ensue from the same site on the mother cell, each round accompanied by incomplete cytokinesis; hence, the regularly spaced constrictions. Insofar as the loss of Ces1p and Ces4p causes overzealous budding, we infer that these proteins normally exert a negative influence on bud formation. Bi and Pringle (9) and Yu et al. (11) reported similar defects in cell shape in [Delta]zds1 [Delta]zds2 deletion strains (equivalent to [Delta]ces1 [Delta]ces4).
We have exploited the observation that [Delta]ces1 [Delta]ces4 cells have a cold-sensitive growth phenotype to identify the minimum functional domains of Ces1p and Ces4p. A 145 amino acid carboxyl domain of Ces1p or a 147 amino acid carboxyl domain of Ces4p suffice in complementing cs growth and correcting the morphological defect of [Delta]ces1 [Delta]ces4 cells. It is remarkable that the N-terminal 85% of both proteins are dispensable for these functions.
Bi and Pringle (9) identified ZDS1 (CES1) as a high copy antagonist of the ability of overexpressed CDC42 to suppress a temperature-sensitive allele of cdc24. Cdc42p is a [rho]-type GTPase essential for establishment of cell polarity during budding (18). Cdc24p functions as a guanine nucleotide exchange factor for Cdc42p (19). Bi and Pringle suggest that the negative regulatory effects of Ces1p on budding are mediated through genetic interactions between Ces1p and Cdc42p at the bud site (9). This model is supported by immunolocalization of overexpressed Ces1p protein at the bud site (9).
It is tempting to speculate that the C-terminal domains of Ces1p and Ces4p interact directly with Cdc42p and thereby affect interactions between Cdc42p and other components of CDC42-dependent signal transduction pathways. Ces1p and Ces4p could either: (i) promote the interactions of some effectors with Cdc42p, e.g. those that limit or negatively regulate Cdc42p activity; (ii) destabilize Cdc42p interaction with positive effectors of Cdc42p; (iii) do both. In preliminary experiments using the two-hybrid system we have not been able to detect a binary interaction between the carboxyl domain of Ces1p and Cdc42p (B.Schwer, unpublished results). Thus it is possible that Ces1p and Ces4p impact on budding via higher order protein-protein interactions.
A central issue regarding CES1 and CES4 is whether the high copy suppressor screens that led to identification of these genes illuminate physiological properties of the two proteins and, if so, how. Both CES1 and CES4 are allele-specific high copy suppressors of mutations in the mRNA capping enzyme (8). We have now shown that capping enzyme suppressor function is mediated by the same protein domain responsible for normal cell morphology and low temperature growth. This outcome was by no means self-evident. For example, another capping enzyme suppressor, CES2, was found to be identical to ESP1, an essential gene required for nuclear division. Deletion analysis showed that the 1573 amino acid protein Esp1p is composed of two distinct functional domains (8). The C-terminal portion of Esp1p is essential for cell growth, but dispensable for suppression of mutations in capping enzyme. The N-terminus of Esp1p does not support cell growth, but does have capping enzyme suppressor activity (8).
What remains elusive is a biochemical explanation for the ability of the short carboxyl domain of Ces1p and Ces4p to perform two seemingly unrelated functions, i.e. ensuring proper budding and suppressing a capping enzyme mutation. It is conceivable that the carboxyl domains of Ces1p and Ces4p suppress the capping enzyme mutants by virtue of their effects on GTP binding proteins that mediate cap-dependent or cap-facilitated RNA transactions in vivo. Translation initiation and RNA transport are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GNEFs) that are specific for the pertinent GTPase, just as bud emergence and bud site selection in yeast are regulated by GAPs and GNEFs specific for the GTPases Cdc42p and Bud1p respectively (20-23). We speculate that Ces1p and Ces4p, which may normally regulate Cdc42p, can also impact on other GTPase-regulated pathways when they are expressed at supra-physiological levels. The idea that capping enzyme suppression by CES1 and CES4 is mediated via effects on a GTPase pathway is bolstered by the finding that capping enzyme mutations are suppressed by BUD5, a non-essential gene involved in bud site selection, which encodes a GNEF for the Bud1p GTPase (8,23).
Our present findings emphasize the overlapping functions of the Ces1p and Ces4p carboxyl domains in complementing [Delta]ces1 [Delta]ces4 and suppressing ceg1-25. Yet, data presented here and elsewhere suggest that CES1 and CES4 are not functionally redundant in every genetic assay. The present study documents a new activity of CES1 in suppressing a mutation of eIF-4A, a translation initiation factor that functions in concert with other translation factors to effect binding of capped mRNAs to the 40S ribosome and transit of the ribosome to the initiator AUG. There is at least a conceptual link between the activities of Ces1p in compensating for mutations in cap formation and cap-dependent translation initiation. Yet, the structural requirements for the two suppressor functions appear to be distinct, insofar as tif1-A79V suppression was abolished by N-terminal CES1 deletions that had no effect on ceg1-25 suppression. CES4, which suppressed ceg1-25 at 37°C, was not able to suppress tif1-A79V at 37°C.
Bi and Pringle (9) noted that ZDS2 (CES4) is inactive in the high copy suppression assay in which ZDS1 was isolated, i.e. ZDS2 does not antagonize suppression of a cdc24-ts mutation by multicopy CDC42. Yu et al. (11) isolated ZDS2 in a screen for high copy suppression of the temperature-sensitive growth phenotype of a sin4 null mutant; ZDS1 is non-functional in this suppression assay. Overexpression of Ces1p and Ces4p may elicit distinctive effects on the basis of differing affinities of their N-terminal domains for different cellular effector molecules. Indeed, it is entirely possible, if not likely, that Ces1p and Ces4p perform functions (ancillary to budding) to which the conserved N-terminal domains do contribute. The putative targets of overexpressed Ces1p and Ces4p need not be limited to GTPases. Indeed, it is noteworthy that several groups have isolated CES1 or CES4 by screening for high copy suppression of protein kinase mutants (10,11; C.Glover, personal communication). Our collection of Ces1p and Ces4p mutants may prove useful in delineating the structural requirements for the rest of the `Zillion Different Suppressor' activities of these two proteins.
ACKNOWLEDGEMENTS
This work was supported by grants from the US National Institutes of Health (GM52470) and the Swiss National Science Foundation.
Nucleic Acids Research
Pages
Introduction
Materials And Methods
Yeast strains
N-Terminal deletion mutants of CES1
C-Terminal deletions of CES1
Deletion mutants of CES4
Suppression of a temperature-sensitive mutation of eIF-4A
Results
Deletion of CES1 and CES4 elicits a cold-sensitive growth phenotype
Gross morphological abnormalities caused by deletion of CES1 and CES4
Complementation of [Delta]ces1 [Delta]ces4 by either CES1 or CES4
Structure-function analysis of Ces1p
Effects of CES1 mutations on capping enzyme suppression
Structure-function analysis of CES4
A conserved C-terminal domain of Ces1p and Ces4p
CES1 is a high copy suppressor of a temperature-sensitive eIF-4A mutation
Discussion
References
REFERENCES
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