Molecular basis of the functional distinction between Cln1 and Cln2 cyclins

Quilis, Inma; Igual, J. Carlos

doi:10.4161/cc.21505

Cited by 11 publications

(23 citation statements)

References 62 publications

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“…Cln1 contained a PEST in a similar region, between amino acids 398 and 424 (PESTb), although it was predicted with a very low value (0.85); another PEST sequence between amino acids 234 and 275 (PESTa) was predicted in Cln1 with a value of 14.12, which was absent in Cln2. In order to determine the relevance of these PEST sequences or additional regions in cyclin degradation, the strategy used consisted in studying the degradation of chimeric cyclins obtained by the exchange of the equivalent regions between Cln1 and Cln2 . The first question to be addressed was whether the PESTb of Cln1 was functional given its low prediction value.…”

Section: Resultsmentioning

confidence: 99%

“…). The Cln2 fragment inserted in Chimera 4 contained a nuclear export signal . Hence, this result could indicate that cyclin stability might be affected by its subcellular location, so the nuclear export of the cyclin resulted in greater instability.…”

Section: Resultsmentioning

confidence: 99%

“…Another possibility lies in the fact that the N‐terminal region of Cln1 and Cln2 contains the sequences that drive their nuclear import . Cdc4 is located mainly in the nucleus so recognition by SCF Cdc4 is conditioned by the subcellular localization of the target protein.…”

Section: Discussionmentioning

confidence: 99%

“…Centromeric plasmids pCLN1 and pCLN2 expressing HA‐tagged versions of Cln1 and Cln2, respectively, were a gift from Dr. M. Aldea. Centromeric plasmids expressing HA‐tagged chimeric cyclins or CLN1 and CLN2 genes under the control of the ADH1 promoter, were described in . Centromeric plasmids pNE104 and pNE108 expressing Cln2 fused to a canonical active or inactive NLS, respectively, were a gift from Dr. B. Futcher .…”

Section: Methodsmentioning

confidence: 99%

“…In some cases, the functional distinction seems to be caused by quantitative differences at the expression level. More recently, cyclin‐specific docking motifs in target proteins that bind preferentially to Cln2 , and a nuclear export mechanism present only in Cln2 that contributes to the functional distinction between Cln1 and Cln2 , have been described. As regards Cln1,2 degradation, most of the studies have been performed with antibodies that recognize either both cyclins or Cln2 alone, and many of the results reported for Cln2 have been extended to Cln1.…”

mentioning

confidence: 99%

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A comparative study of the degradation of yeast cyclins Cln1 and Cln2

Quilis

Igual

2016

FEBS Open Bio

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The yeast cyclins Cln1 and Cln2 are very similar in both sequence and function, but some differences in their functionality and localization have been recently described. The control of Cln1 and Cln2 cellular levels is crucial for proper cell cycle initiation. In this work, we analyzed the degradation patterns of Cln1 and Cln2 in order to further investigate the possible differences between them. Both cyclins show the same half‐life but, while Cln2 degradation depends on ubiquitin ligases SCFGrr1 and SCFCdc4, Cln1 is affected only by SCFGrr1. Degradation analysis of chimeric cyclins, constructed by combining fragments from Cln1 and Cln2, identifies the N‐terminal sequence of the proteins as responsible of the cyclin degradation pattern. In particular, the N‐terminal region of Cln2 is required to mediate degradation by SCFCdc4. This region is involved in nuclear import of Cln1 and Cln2, which suggests that differences in degradation may be due to differences in localization. Moreover, a comparison of the cyclins that differ only in the presence of the Cln2 nuclear export signal indicates a greater instability of exported cyclins, thus reinforcing the idea that cyclin stability is influenced by their localization.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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A comparative study of the degradation of yeast cyclins Cln1 and Cln2

Quilis

Igual

2016

FEBS Open Bio

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Identifying novel protein phenotype annotations by hybridizing protein–protein interactions and protein sequence similarities

et al. 2016

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Studies of protein phenotypes represent a central challenge of modern genetics in the post-genome era because effective and accurate investigation of protein phenotypes is one of the most critical procedures to identify functional biological processes in microscale, which involves the analysis of multifactorial traits and has greatly contributed to the development of modern biology in the post genome era. Therefore, we have developed a novel computational method that identifies novel proteins associated with certain phenotypes in yeast based on the protein-protein interaction network. Unlike some existing network-based computational methods that identify the phenotype of a query protein based on its direct neighbors in the local network, the proposed method identifies novel candidate proteins for a certain phenotype by considering all annotated proteins with this phenotype on the global network using a shortest path (SP) algorithm. The identified proteins are further filtered using both a permutation test and their interactions and sequence similarities to annotated proteins. We compared our method with another widely used method called random walk with restart (RWR). The biological functions of proteins for each phenotype identified by our SP method and the RWR method were analyzed and compared. The results confirmed a large proportion of our novel protein phenotype annotation, and the RWR method showed a higher false positive rate than the SP method. Our method is equally effective for the prediction of proteins involving in all the eleven clustered yeast phenotypes with a quite low false positive rate. Considering the universality and generalizability of our supporting materials and computing strategies, our method can further be applied to study other organisms and the new functions we predicted can provide pertinent instructions for the further experimental verifications.

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A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle

Teufel

Tummler

Flöttmann

et al. 2019

Sci Rep

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Oscillating gene expression is crucial for correct timing and progression through cell cycle. In Saccharomyces cerevisiae , G1 cyclins Cln1–3 are essential drivers of the cell cycle and have an important role for temporal fine-tuning. We measured time-resolved transcriptome-wide gene expression for wild type and cyclin single and double knockouts over cell cycle with and without osmotic stress. Clustering of expression profiles, peak time detection of oscillating genes, integration with transcription factor network dynamics, and assignment to cell cycle phases allowed us to quantify the effect of genetic or stress perturbations on the duration of cell cycle phases. Cln1 and Cln2 showed functional differences, especially affecting later phases. Deletion of Cln3 led to a delay of START followed by normal progression through later phases. Our data and network analysis suggest mutual effects of cyclins with the transcriptional regulators SBF and MBF.

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Molecular basis of the functional distinction between Cln1 and Cln2 cyclins

Cited by 11 publications

References 62 publications

A comparative study of the degradation of yeast cyclins Cln1 and Cln2

A comparative study of the degradation of yeast cyclins Cln1 and Cln2

Identifying novel protein phenotype annotations by hybridizing protein–protein interactions and protein sequence similarities

A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle

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