Structural principles in cell-cycle control: beyond the CDKs

Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

Background

Changes in the abundance of ovarian proteins play a key role in the regulation of reproduction. However, to date, no studies have investigated such changes in pubescent goats. Herein we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography–tandem mass spectrometry to analyze the expression levels of ovarian proteins in pre-pubertal (n = 3) and pubertal (n = 3) goats.

Results

Overall, 7,550 proteins were recognized; 301 (176 up- and 125 downregulated) were identified as differentially abundant proteins (DAPs). Five DAPs were randomly selected for expression level validation by Western blotting; the results of Western blotting and iTRAQ analysis were consistent. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that DAPs were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways. Besides, gene ontology functional enrichment analysis revealed that several DAPs enriched in biological processes were associated with cellular process, biological regulation, metabolic process, and response to stimulus. Protein–protein interaction network showed that proteins interacting with CDK1, HSPA1A, and UCK2 were the most abundant.

Conclusions

We identified 301 DAPs, which were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways, suggesting the involvement of these processes in the onset of puberty. Further studies are warranted to more comprehensively explore the function of the identified DAPs and aforementioned signaling pathways to gain novel, deeper insights into the mechanisms underlying the onset of puberty.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08699-y.

Cell cycle kinases predicted from conserved biophysical properties

Machine-learning techniques can classify functionally related proteins where homology-transfer as well as sequence and structure motifs fail. Here, we present a method that aimed at complementing homology-transfer in the identification of cell cycle control kinases from sequence alone. First, we identified functionally significant residues in cell cycle proteins through their high sequence conservation and biophysical properties. We then incorporated these residues and their features into support vector machines (SVM) to identify new kinases and more specifically to differentiate cell cycle kinases from other kinases and other proteins. As expected, the most informative residues tend to be highly conserved and tend to localize in the ATP binding regions of the kinases. Another observation confirmed that ATP binding regions are typically not found on the surface but in partially buried sites, and that this fact is correctly captured by accessibility predictions. Using these highly conserved, semi-buried residues and their biophysical properties, we could distinguish cell cycle S/T kinases from other kinase families at levels around 70-80% accuracy and 62-81% coverage. An application to the entire human proteome predicted at least 97 human proteins with limited previous annotations to be candidates for cell cycle kinases.

Cyclin G2 is a centrosome-associated nucleocytoplasmic shuttling protein that influences microtubule stability and induces a p53-dependent cell cycle arrest

Cyclin G2 is an atypical cyclin that associates with active protein phosphatase 2A. Cyclin G2 gene expression correlates with cell cycle inhibition; it is significantly upregulated in response to DNA damage and diverse growth inhibitory stimuli, but repressed by mitogenic signals. Ectopic expression of cyclin G2 promotes cell cycle arrest, cyclin dependent kinase 2 inhibition and the formation of aberrant nuclei [Bennin, D. A., Don, A. S., Brake, T., McKenzie, J. L., Rosenbaum, H., Ortiz, L., DePaoli-Roach, A. A., and Horne, M. C. (2002). Cyclin G2 associates with protein phosphatase 2A catalytic and regulatory B' subunits in active complexes and induces nuclear aberrations and a G(1)/S-phase cell cycle arrest. J Biol Chem 277, 27449-67]. Here we report that endogenous cyclin G2 copurifies with centrosomes and microtubules (MT) and that ectopic G2 expression alters microtubule stability. We find exogenous and endogenous cyclin G2 present at microtubule organizing centers (MTOCs) where it colocalizes with centrosomal markers in a variety of cell lines. We previously reported that cyclin G2 forms complexes with active protein phosphatase 2A (PP2A) and colocalizes with PP2A in a detergent-resistant compartment. We now show that cyclin G2 and PP2A colocalize at MTOCs in transfected cells and that the endogenous proteins copurify with isolated centrosomes. Displacement of the endogenous centrosomal scaffolding protein AKAP450 that anchors PP2A at the centrosome resulted in the depletion of centrosomal cyclin G2. We find that ectopic expression of cyclin G2 induces microtubule bundling and resistance to depolymerization, inhibition of polymer regrowth from MTOCs and a p53-dependent cell cycle arrest. Furthermore, we determined that a 100 amino acid carboxy-terminal region of cyclin G2 is sufficient to both direct GFP localization to centrosomes and induce cell cycle inhibition. Colocalization of endogenous cyclin G2 with only one of two GFP-centrin-tagged centrioles, the mature centriole present at microtubule foci, indicates that cyclin G2 resides primarily on the mother centriole. Copurification of cyclin G2 and PP2A subunits with microtubules and centrosomes, together with the effects of ectopic cyclin G2 on cell cycle progression, nuclear morphology and microtubule growth and stability, suggests that cyclin G2 may modulate the cell cycle and cellular division processes through modulation of PP2A and centrosomal associated activities.

The Ups and Downs of Modeling the Cell Cycle

We discuss the impact of mathematical modeling on our understanding of the cell cycle. Although existing, detailed models confirm that the known interactions in the cell cycle can produce oscillations and predict behaviors such as hysteresis, they contain many parameters and are poorly constrained by data which are almost all qualitative. Questions about the basic architecture of the oscillator may be more amenable to modeling approaches that ignore molecular details. These include asking how the various elaborations of the basic oscillator affect the robustness of the system and how cells monitor their size and use this information to control the cell cycle.

Cyclin-dependent kinases phosphorylate p73 at threonine 86 in a cell cycle-dependent manner and negatively regulate p73

p73 transcription factors are members of the p53 family and participate in developmental processes and DNA damage response. p73 expression was shown to be regulated during the cell cycle, suggesting that p73 might play a role in cell growth and might be a target for cyclin-dependent kinases. Consistent with this hypothesis, we discovered that p73 interacts physically with various cyclins (A, B, D, and E). Furthermore, cyclin A/CDK1/2, cyclin B/CDK1/2, and cyclin E/CDK2 complexes can phosphorylate multiple p73 isoforms in vitro at threonine 86. A specific antibody directed against phosphorylated Thr86 showed that this site is phosphorylated in vivo and that such phosphorylation is regulated in a cell cycle-dependent manner. Thr86 phosphorylation is induced during S phase and is maximal in the G2/M phase. Accordingly inhibitors of cell growth, such as p16 and serum starvation, reduce Thr86 phosphorylation. Finally, we found that cyclin-dependent kinase (CDK)-dependent Thr86 phosphorylation represses the ability of p73 to induce endogenous p21 expression. Our results demonstrate that p73 proteins are targets of CDK complexes and that phosphorylation on Thr86 by CDKs regulates p73 functions.

Cycling at the interface between neurodevelopment and neurodegeneration

The discovery of cell cycle regulators has directed cell research into uncharted territory. In dividing cells, cell cycle-associated protein kinases, which are referred to as cyclin-dependent-kinases (Cdks), regulate proliferation, differentiation, senescence and apoptosis. In contrast, all Cdks in post-mitotic neurons, with the notable exception of Cdk5, are silenced. Surprisingly, misregulation of Cdks occurs in neurons in a wide diversity of neurological disorders, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Ectopic expression of these proteins in neurons potently induces cell death with hallmarks of apoptosis. Deregulation of the unique, cell cycle-unrelated Cdk5 by its truncated co-activator, p25 and p29, contributes to neurodegeneration by altering the phosphorylation state of non-membrane-associated proteins and possibly through the induction of cell cycle proteins. On the other hand, cycling Cdks such as Cdk2, Cdk4 and Cdk6, initiate death pathways by derepressing E2F-1/Rb-dependent transcription at the neuronal G1/S checkpoint. Thus, Cdk5 and cycling Cdks may have little in common in the healthy CNS, but they likely conspire in leading neurons to their demise.

Interactions of SV40 large T antigen and other viral proteins with retinoblastoma tumour suppressor

Simian virus 40 large T antigen, human papilloma virus E7 and adenovirus E1A are all potent oncoproteins that can induce several types of tumours. One of the major functions of these oncoproteins is to interact with the retinoblastoma tumour suppressor protein, Rb, a master switch of the mammalian cell cycle, and to inactivate its function. Rb promotes cell-cycle arrest by recruiting and regulating proteins involved in the transcription of cell proliferation genes. The binding of viral oncoproteins to Rb disrupts the Rb-E2F complex, a central component in the Rb-mediated cell-cycle network. The crystal structures of Rb pocket-viral oncoprotein complexes indicate that the viral proteins recognise a highly conserved region in the Rb pocket through a common motif, LxCxE, and through other unique regions within each viral protein. Although the mechanism of Rb inactivation by viral proteins is not fully understood, information at the atomic level about the interactions between the Rb pocket and viral proteins is providing some insights into how viral proteins dissociate E2F from Rb and thus how they deregulate the cell cycle.

RBP95, a novel leucine zipper protein, binds to the retinoblastoma protein

We recently identified a novel cDNA encoding a retinoblastoma protein (pRb)-associated protein. It was named RBP95, which was composed of 838 amino acid residues with a calculated molecular size of 94,789 Da. Northern blot analysis showed a single mRNA of about 4. 5 kb ubiquitously expressed in human tissues. RH mapping results showed that RBP95 is mapped to chromosome region 16p11.2-11.1. Sequence analysis indicated that RBP95 contains a conserved pRb-binding motif LXCXE. Interaction between pRb and RBP95 was confirmed in vivo and in vitro. This interaction requires the LXCXE motif of RBP95 and the entire pocket region of pRb. Each point-mutant of the conserved amino acid residues in pRb-binding motif of RBP95 would destroy its interaction with pRb. RBP95 also contains a basic region leucine zipper and could homodimerize through its leucine zipper region. RBP95 was located in the nucleus with a special pattern when expressed as a GFP fusion in HeLa cells. All these findings suggested that RBP95, a new member of pRb-associated protein, may function as a regulation factor in the process of RNA polymerase II-mediated transcription and/or transcriptional processing.

Cyclin-dependent kinases: inhibition and substrate recognition

Four unresolved issues of cyclin-dependent kinase (CDK) regulation have been addressed by structural studies this year - the mechanism of CDK inhibition by members of the INK4 family of CDK inhibitors, consensus substrate sequence recognition by CDKs, the role of the cyclin subunit in substrate recognition and the structural mechanism underlying CDK inhibition by phosphorylation.