Genes adopt non‐optimal codon usage to generate cell cycle‐dependent oscillations in protein levels

Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into components arising from the cell cycle and stochastic processes. The latter stochastic component represents contributions from bursty expression and errors incurred during partitioning of molecules between daughter cells. These formulae reveal an interesting trade-off: cell-cycle dependencies that amplify the noise contribution from bursty expression also attenuate the contribution from partitioning errors. We investigate the existence of optimum strategies for coupling expression to the cell cycle that minimize the stochastic component. Intriguingly, results show that a zero production rate throughout the cell cycle, with expression only occurring just before cell division, minimizes noise from bursty expression for a fixed mean protein level. By contrast, the optimal strategy in the case of partitioning errors is to make the protein just after cell division. We provide examples of regulatory proteins that are expressed only towards the end of the cell cycle, and argue that such strategies enhance robustness of cell-cycle decisions to the intrinsic stochasticity of gene expression.

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Iron Chelation, Cell Cycle-Dependent Kinases and HIV-1 Transcription.

Blood ◽

10.1182/blood.v108.11.1550.1550 ◽

2006 ◽

Vol 108 (11) ◽

pp. 1550-1550

Author(s):

Tatyana Ammosova ◽

Zufan Debebe ◽

Xiaomei Niu ◽

Des R. Richardson ◽

Marina Jerebtsova ◽

...

Keyword(s):

Cell Cycle ◽

T Cells ◽

Rna Polymerase Ii ◽

Iron Chelation ◽

Iron Chelators ◽

Intracellular Iron ◽

Cyclin T1 ◽

Protein Levels ◽

Cycle Dependent ◽

Hiv 1

Abstract Iron chelation leads to reduced cell cycle-dependent kinase 2 (CDK2) activity (reviewed in Biochim Biophys Acta2002;1603:31–46). Elongation of HIV-1 transcription is mediated by the interaction of HIV Tat with host cell cycle-dependent kinase 9 (CDK9)/cyclin T1, which phosphorylates the C-terminal domain of RNA polymerase II, and our recent studies indicate that CDK2 is also required for Tat-dependent transcription. We hypothesized that iron chelation may inhibit HIV transcription via reduced activity of cell cycle-dependent kinases. We utilized 2-hydroxy-1-naphthylaldehyde isonicotinoyl hydrazone (311; previously shown to inhibit CDK2 expression) and 4-[3,5-bis-(hydroxyphenyl) -1,2,4-triazol-1-yl]-benzoic acid (ICL670) to chelate intracellular iron. We analyzed the effect of these chelators on HIV-1 transcription using HeLa MAGI and CEM-GFP T-cells containing an integrated HIV-1 promoter and infected with adenovirus expressing HIV-1 Tat protein. Both chelators inhibited Tat-induced HIV-1 transcription, most profoundly in CEM-GFP T-cells. The chelators also inhibited one round of HIV-1 replication in CEM-T cells infected with pseudotyped HIV-1 virus. Treatment of HeLa MAGI and CEM-GFP T-cells with iron chelators decreased CDK9 protein levels and, to a lesser extent, CDK2 protein levels. Our findings provide evidence that iron chelators may inhibit HIV-1 transcription by altering expression of CDK9 and CDK2.

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Novel Control of S Phase of the Cell Cycle by Ubiquitin-conjugating Enzyme H7

Molecular Biology of the Cell ◽

10.1091/mbc.e08-01-0036 ◽

2009 ◽

Vol 20 (1) ◽

pp. 1-9 ◽

Cited By ~ 19

Author(s):

Elizabeth A. Whitcomb ◽

Edward J. Dudek ◽

Qing Liu ◽

Allen Taylor

Keyword(s):

Cell Cycle ◽

S Phase ◽

Regulatory Proteins ◽

Protein Levels ◽

Proteolytic Pathway ◽

Dynamic Cell ◽

Ubiquitin Conjugating Enzyme ◽

Phase Progression ◽

Cycle Dependent ◽

Cycle Regulation

Timely degradation of regulatory proteins by the ubiquitin proteolytic pathway (UPP) is an established paradigm of cell cycle regulation during the G2/M and G1/S transitions. Less is known about roles for the UPP during S phase. Here we present evidence that dynamic cell cycle–dependent changes in levels of UbcH7 regulate entrance into and progression through S phase. In diverse cell lines, UbcH7 protein levels are dramatically reduced in S phase but are fully restored by G2. Knockdown of UbcH7 increases the proportion of cells in S phase and doubles the time to traverse S phase, whereas UbcH7 overexpression reduces the proportion of cells in S phase. These data suggest a role for UbcH7 targets in the completion of S phase and entry into G2. Notably, UbcH7 knockdown was coincident with elevated levels of the checkpoint kinase Chk1 but not Chk2. These results argue that UbcH7 promotes S phase progression to G2 by modulating the intra-S phase checkpoint mediated by Chk1. Furthermore, UbcH7 levels appear to be regulated by a UPP. Together the data identify novel roles for the UPP, specifically UbcH7 in the regulation of S phase transit time as well as in cell proliferation.

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CDK9 Is Constitutively Expressed throughout the Cell Cycle, and Its Steady-State Expression Is Independent of SKP2

Molecular and Cellular Biology ◽

10.1128/mcb.23.15.5165-5173.2003 ◽

2003 ◽

Vol 23 (15) ◽

pp. 5165-5173 ◽

Cited By ~ 49

Author(s):

Judit Garriga ◽

Sabyasachi Bhattacharya ◽

Joaquim Calbó ◽

Renée M. Marshall ◽

May Truongcao ◽

...

Keyword(s):

Cell Cycle ◽

Ubiquitin Ligase ◽

Proteasome Inhibitors ◽

Elongation Factor ◽

Dependent Manner ◽

Protein Levels ◽

Ubiquitin Ligase Complex ◽

A Cell ◽

Cycle Dependent ◽

Interfering Rna

ABSTRACT CDK9 is a CDC2-related kinase and the catalytic subunit of the positive-transcription elongation factor b and the Tat-activating kinase. It has recently been reported that CDK9 is a short-lived protein whose levels are regulated during the cell cycle by the SCFSKP2 ubiquitin ligase complex (R. E. Kiernan et al., Mol. Cell. Biol. 21:7956-7970, 2001). The results presented here are in contrast to those observations. CDK9 protein levels remained unchanged in human cells entering and progressing through the cell cycle from G0, despite dramatic changes in SKP2 expression. CDK9 levels also remained unchanged in cells exiting from mitosis and progressing through the next cell cycle. Similarly, the levels of CDK9 protein did not change as cells exited the cell cycle and differentiated along various lineages. In keeping with these observations, the kinase activity associated with CDK9 was found to not be regulated during the cell cycle. We have also found that endogenous CDK9 is a very stable protein with a half-life (t 1/2) of 4 to 7 h, depending on the cell type. In contrast, when CDK9 is overexpressed, it is not stabilized and is rapidly degraded, with a t 1/2 of less than 1 h, depending on the level of expression. Treatment of cells with proteasome inhibitors blocked the degradation of short-lived proteins, such as p27, but did not affect the expression of endogenous CDK9. Ectopic overexpression of SKP2 led to reduction of p27 protein levels but had no effect on the expression of endogenous CDK9. Finally, downregulation of endogenous SKP2 gene expression by interfering RNA had no effect on CDK9 protein levels, whereas p27 protein levels increased dramatically. Therefore, the SCFSKP2 ubiquitin ligase does not regulate CDK9 expression in a cell cycle-dependent manner.

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Cell cycle localization dynamics of mitochondrial DNA polymerase IC in African trypanosomes

Molecular Biology of the Cell ◽

10.1091/mbc.e18-02-0127 ◽

2018 ◽

Vol 29 (21) ◽

pp. 2540-2552 ◽

Cited By ~ 5

Author(s):

Jeniffer Concepción-Acevedo ◽

Jonathan C. Miller ◽

Michael J. Boucher ◽

Michele M. Klingbeil

Keyword(s):

Cell Cycle ◽

Mitochondrial Dna ◽

Dna Polymerase ◽

Dna Polymerases ◽

Dynamic Environment ◽

African Trypanosomes ◽

Protein Levels ◽

Replication Sites ◽

Cycle Dependent ◽

Mitochondrial Dna Polymerase

Trypanosoma brucei has a unique catenated mitochondrial DNA (mtDNA) network called kinetoplast DNA (kDNA). Replication of kDNA occurs once per cell cycle in near synchrony with nuclear S phase and requires the coordination of many proteins. Among these are three essential DNA polymerases (TbPOLIB, IC, and ID). Localization dynamics of these proteins with respect to kDNA replication stages and how they coordinate their functions during replication are not well understood. We previously demonstrated that TbPOLID undergoes dynamic localization changes that are coupled to kDNA replication events. Here, we report the localization of TbPOLIC, a second essential DNA polymerase, and demonstrate the accumulation of TbPOLIC foci at active kDNA replication sites (antipodal sites) during stage II of the kDNA duplication cycle. While TbPOLIC was undetectable by immunofluorescence during other cell cycle stages, steady-state protein levels measured by Western blot remained constant. TbPOLIC foci colocalized with the fraction of TbPOLID that localized to the antipodal sites. However, the partial colocalization of the two essential DNA polymerases suggests a highly dynamic environment at the antipodal sites to coordinate the trafficking of replication proteins during kDNA synthesis. These data indicate that cell cycle–dependent localization is a major regulatory mechanism for essential mtDNA polymerases during kDNA replication.

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PTOV1 Enables the Nuclear Translocation and Mitogenic Activity of Flotillin-1, a Major Protein of Lipid Rafts

Molecular and Cellular Biology ◽

10.1128/mcb.25.5.1900-1911.2005 ◽

2005 ◽

Vol 25 (5) ◽

pp. 1900-1911 ◽

Cited By ~ 66

Author(s):

Anna Santamaría ◽

Elisabeth Castellanos ◽

Valentí Gómez ◽

Patricia Benedit ◽

Jaime Renau-Piqueras ◽

...

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Nuclear Localization ◽

Nuclear Translocation ◽

Subcellular Fractionation ◽

Major Protein ◽

Dependent Manner ◽

Protein Levels ◽

A Cell ◽

Cycle Dependent

ABSTRACT PTOV1 is a mitogenic protein that shuttles between the nucleus and the cytoplasm in a cell cycle-dependent manner. It consists of two homologous domains arranged in tandem that constitute a new class of protein modules. We show here that PTOV1 interacts with the lipid raft protein flotillin-1, with which it copurifies in detergent-insoluble floating fractions. Flotillin-1 colocalized with PTOV1 not only at the plasma membrane but, unexpectedly, also in the nucleus, as demonstrated by immunocytochemistry and subcellular fractionation of endogenous and exogenous flotillin-1. Flotillin-1 entered the nucleus concomitant with PTOV1, shortly before the initiation of the S phase. Protein levels of PTOV1 and flotillin-1 oscillated during the cell cycle, with a peak in S. Depletion of PTOV1 significantly inhibited nuclear localization of flotillin-1, whereas depletion of flotillin-1 did not affect nuclear localization of PTOV1. Depletion of either protein markedly inhibited cell proliferation under basal conditions. Overexpression of PTOV1 or flotillin-1 strongly induced proliferation, which required their localization to the nucleus, and was dependent on the reciprocal protein. These observations suggest that PTOV1 assists flotillin-1 in its translocation to the nucleus and that both proteins are required for cell proliferation.

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Cell Cycle Regulation of the Pdx1 Transcription Factor in Developing Pancreas and Insulin-Producing β Cells

10.2337/figshare.13622903.v1 ◽

2021 ◽

Author(s):

Ada Admin ◽

Xiaogdong Zhu ◽

Alexis Oguh ◽

Morgan A. Gingerich ◽

Scott A. Soleimanpour ◽

...

Keyword(s):

Cell Cycle ◽

Cell Function ◽

Current Evidence ◽

Β Cells ◽

Β Cell ◽

Proliferating Cells ◽

Dynamic Regulation ◽

Protein Levels ◽

Β Cell Function ◽

Cycle Dependent

Current evidence indicates that proliferating β cells express lower levels of some functional cell identity genes, suggesting that proliferating cells are not optimally functional. Pdx1 is important for β-cell specification, function, and proliferation and is mutated in monogenic forms of diabetes. However, its regulation during the cell cycle is unknown. Here we examined Pdx1 protein expression in immortalized β cells, maternal mouse islets during pregnancy, and mouse embryonic pancreas. We demonstrate that Pdx1 localization and protein levels are highly dynamic. In non-mitotic cells, Pdx1 is not observed in constitutive heterochromatin, nucleoli, and most areas containing repressive epigenetic marks. At prophase, Pdx1 is enriched around the chromosomes prior to Ki67 coating the chromosome surface. Pdx1 uniformly localized in the cytoplasm at prometaphase and became enriched around the chromosomes again at the end of cell division, prior to nuclear envelope formation. Cells in S phase have lower Pdx1 levels than cells at earlier cell cycle stages, and over-expression of Pdx1 in INS-1 cells prevents progression toward G2, suggesting that cell cycle-dependent regulation of Pdx1 is required for completion of mitosis. Together, we find that Pdx1 localization and protein level are tightly regulated throughout the cell cycle. This dynamic regulation has implications for the dichotomous role of Pdx1 in β-cell function and proliferation.

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Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism

10.1101/2019.12.17.880252 ◽

2019 ◽

Cited By ~ 1

Author(s):

Heidi M. Blank ◽

Ophelia Papoulas ◽

Nairita Maitra ◽

Riddhiman Garge ◽

Brian K. Kennedy ◽

...

Keyword(s):

Cell Cycle ◽

Lipid Metabolism ◽

Cell Division ◽

Ribosome Biogenesis ◽

Budding Yeast ◽

Eukaryotic Cell ◽

Yeast Cells ◽

Protein Levels ◽

Coordinate Control ◽

Cycle Dependent

ABSTRACTEstablishing the pattern of abundance of molecules of interest during cell division has been a long-standing goal of cell cycle studies. In several systems, including the budding yeast Saccharomyces cerevisiae, cell cycle-dependent changes in the transcriptome are well studied. In contrast, few studies queried the proteome during cell division, and they are often plagued by low agreement with each other and with previous transcriptomic datasets. There is also little information about dynamic changes in the levels of metabolites and lipids in the cell cycle. Here, for the first time in any system, we present experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from un-arrested, growing, and synchronously dividing yeast cells. Overall, transcript and protein levels were correlated, but specific processes that appeared to change at the RNA level (e.g., ribosome biogenesis), did not do so at the protein level, and vice versa. We also found no significant changes in codon usage or the ribosome content during the cell cycle. We describe an unexpected mitotic peak in the abundance of ergosterol and thiamine biosynthesis enzymes. Although the levels of several metabolites changed in the cell cycle, by far the most significant changes were in the lipid repertoire, with phospholipids and triglycerides peaking strongly late in the cell cycle. Our findings provide an integrated view of the abundance of biomolecules in the eukaryotic cell cycle and point to a coordinate mitotic control of lipid metabolism.

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The anaphase-promoting complex/cyclosome (APC/C): cell-cycle-dependent and -independent functions

Biochemical Society Transactions ◽

10.1042/bst0380065 ◽

2010 ◽

Vol 38 (1) ◽

pp. 65-71 ◽

Cited By ~ 78

Author(s):

Eusebio Manchado ◽

Manuel Eguren ◽

Marcos Malumbres

Keyword(s):

Cell Cycle ◽

Spindle Assembly Checkpoint ◽

26S Proteasome ◽

Anaphase Promoting Complex ◽

Neuronal Structure ◽

Beneficial Effects ◽

Protein Levels ◽

Independent Functions ◽

Cycle Dependent ◽

And Function

The APC/C (anaphase-promoting complex/cyclosome) is an E3 ubiquitin ligase that targets specific substrates for degradation by the 26S proteasome. APC/C activity depends on two cofactors, namely Cdc20 (cell division cycle 20) and Cdh1, which select the appropriate targets for ubiquitination. It is well established that APC/C is a target of the SAC (spindle assembly checkpoint) during mitosis and has critical roles in controlling the protein levels of major regulators of mitosis and DNA replication. In addition, recent studies have suggested new cell-cycle-independent functions of APC/C in non-mitotic cells and specifically in neuronal structure and function. Given the relevant functions of APC/C in cell proliferation and neuronal physiology, modulating APC/C activity may have beneficial effects in the clinic.

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Cell Cycle Regulation of the Pdx1 Transcription Factor in Developing Pancreas and Insulin-Producing β Cells

10.2337/figshare.13622903 ◽

2021 ◽

Author(s):

Ada Admin ◽

Xiaogdong Zhu ◽

Alexis Oguh ◽

Morgan A. Gingerich ◽

Scott A. Soleimanpour ◽

...

Keyword(s):

Cell Cycle ◽

Cell Function ◽

Current Evidence ◽

Β Cells ◽

Β Cell ◽

Proliferating Cells ◽

Dynamic Regulation ◽

Protein Levels ◽

Β Cell Function ◽

Cycle Dependent

Current evidence indicates that proliferating β cells express lower levels of some functional cell identity genes, suggesting that proliferating cells are not optimally functional. Pdx1 is important for β-cell specification, function, and proliferation and is mutated in monogenic forms of diabetes. However, its regulation during the cell cycle is unknown. Here we examined Pdx1 protein expression in immortalized β cells, maternal mouse islets during pregnancy, and mouse embryonic pancreas. We demonstrate that Pdx1 localization and protein levels are highly dynamic. In non-mitotic cells, Pdx1 is not observed in constitutive heterochromatin, nucleoli, and most areas containing repressive epigenetic marks. At prophase, Pdx1 is enriched around the chromosomes prior to Ki67 coating the chromosome surface. Pdx1 uniformly localized in the cytoplasm at prometaphase and became enriched around the chromosomes again at the end of cell division, prior to nuclear envelope formation. Cells in S phase have lower Pdx1 levels than cells at earlier cell cycle stages, and over-expression of Pdx1 in INS-1 cells prevents progression toward G2, suggesting that cell cycle-dependent regulation of Pdx1 is required for completion of mitosis. Together, we find that Pdx1 localization and protein level are tightly regulated throughout the cell cycle. This dynamic regulation has implications for the dichotomous role of Pdx1 in β-cell function and proliferation.

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