Genome-wide expression analysis of plant cell cycle modulated genes

Genome-wide expression analysis is rapidly becoming an essential tool for identifying and analysing genes involved in, or controlling, various biological processes ranging from development to responses to environmental cues. The control of cell division involves the temporal expression of different sets of genes, allowing the dividing cell to progress through the different phases of the cell cycle. A landmark study using DNA microarrays to follow the patterns of gene expression in synchronously dividing yeast cells has allowed the identification of several hundreds of genes that are involved in the cell cycle. Although DNA microarrays provide a convenient tool for genome-wide expression analysis, their use is limited to organisms for which the complete genome sequence or a large cDNA collection is available. For other organisms, including most plant species, DNA fragment analysis based methods, such as cDNA-AFLP, provide a more appropriate tool for genome-wide expression analysis. Furthermore, cDNA-AFLP exhibits properties that complement DNA microarrays and, hence, constitutes a useful tool for gene discovery.     

Expression of the nucleus-encoded chloroplast division genes and proteins regulated by the algal cell cycle

Chloroplasts have evolved from a cyanobacterial endosymbiont and their continuity has been maintained by chloroplast division, which is performed by the constriction of a ring-like division complex at the division site. It is believed that the synchronization of the endosymbiotic and host cell division events was a critical step in establishing a permanent endosymbiotic relationship, such as is commonly seen in existing algae. In the majority of algal species, chloroplasts divide once per specific period of the host cell division cycle. In order to understand both the regulation of the timing of chloroplast division in algal cells and how the system evolved, we examined the expression of chloroplast division genes and proteins in the cell cycle of algae containing chloroplasts of cyanobacterial primary endosymbiotic origin (glaucophyte, red, green, and streptophyte algae). The results show that the nucleus-encoded chloroplast division genes and proteins of both cyanobacterial and eukaryotic host origin are expressed specifically during the S phase, except for FtsZ in one graucophyte alga. In this glaucophyte alga, FtsZ is persistently expressed throughout the cell cycle, whereas the expression of the nucleus-encoded MinD and MinE as well as FtsZ ring formation are regulated by the phases of the cell cycle. In contrast to the nucleus-encoded division genes, it has been shown that the expression of chloroplast-encoded division genes is not regulated by the host cell cycle. The endosymbiotic gene transfer of minE and minD from the chloroplast to the nuclear genome occurred independently on multiple occasions in distinct lineages, whereas the expression of nucleus-encoded MIND and MINE is regulated by the cell cycle in all lineages examined in this study. These results suggest that the timing of chloroplast division in algal cell cycle is restricted by the cell cycle-regulated expression of some but not all of the chloroplast division genes. In addition, it is suggested that the regulation of each division-related gene was established shortly after the endosymbiotic gene transfer, and this event occurred multiple times independently in distinct genes and in distinct lineages.     

Regulation of the G1 phase of the mammalian cell cycle

In any multi-cellular organism,the balance between cell division and cell death maintains a constant cell number.Both cell division cycle and cell death are highly regulated events.Whether the cell will proceed through the cycle or not,depends upon whether the conditions required at the checkpoints during the cycle and fulfilled.In higher eucaryotic cells,such as mammalian cells,signals that arrest the cycle usually act at a G1 checkpoint.Cells that pass this restriction point are committed to complete the cycle.Regulation of the G1 phase of the cell cycle is extremely complex and involves many different families of proteins such as retinoblastoma family,cyclin dependent kinases,cyclins,and cyclin kinase inhibitors.     

Genome-wide screening for gene function using RNAi in mammalian cells

Mammalian genome sequencing has identified numerous genes requiring functional annotation. The discovery that dsRNA can direct gene-specific silencing in both model organisms and mammalian cells through RNA interference (RNAi) has provided a platform for dissecting the function of independent genes. The generation of large-scale RNAi libraries targeting all predicted genes within mouse, rat and human cells, combined with the large number of cell-based assays, provides a unique opportunity to perform high-throughput genetics in these complex cell systems. Many different formats exist for the generation of genome-wide RNAi libraries for use in mammalian cells. Furthermore, the use of these libraries in either genetic screens or genetic selections allows for the identification of known and novel genes involved in complex cellular phenotypes and biological processes, some of which underpin human disease. In this review, we examine genome-wide RNAi libraries used in model organisms and mammalian cells and provide examples of how these information rich reagents can be used for determining gene function, discovering novel therapeutic targets and dissecting signalling pathways, cellular processes and complex phenotypes.     

Identification of promoter elements responsible for transcriptional inhibition of polo-like kinase 1 and topoisomerase IIalpha genes by p21(WAF1/CIP1/SDI1)

Induction of p21 (WAF1/CIP1/SDI1), a physiological mediator of cell cycle arrest, inhibits multiple genes involved in cell division. We have investigated the determinants of p21- mediated inhibition of two of these genes, polo-like kinase 1 (PLK1) and topoisomerase IIalpha (TOPO IIalpha) p21 expression from an inducible promoter in human HT1080 cells rapidly decreases cellular levels of PLK1 and TOPO IIalpha promoters in transient and stable transfection assays. Promoter mutagenesis studies show that inhibition of the PLK1 promoter by p21 is mediated in part by tandem sequences CDE (cell cycle-dependent element) and CHR (cell cycle genes homology region). p21 response of the TOPO IIalpha promoter inhibition and the effects of promoter mutations differ under the conditions of growth arrest produced by p21 induction or by mimosine, a cell cycle inhibitor that increases p21 RNA but not protein expression in HT1080 cells. These results indicate that inhibition of cell division-associated genes by p21 is mediated by different but overlapping mechanisms, which are not a general con-sequence of cell cycle arrest.     

Initiation of Chromosomal DNA Replication in Mammalian Cell-Free Systems

Chromosomal DNA replication is a fundamental part of the cell division cycle of eukaryotes, and its disruption often leads to genome instability and cancer. A focus for regulation is the initiation of the first replication forks, marking the transition from G1 to S phase. Direct biochemical investigation of the establishment and further progression of chromosomal DNA replication in human somatic cell nuclei has become possible through a cell-free system that obeys cell cycle control. Since its development less than a decade ago, several modifications and adaptations of the original system have been reported, which have led to temporal resolution of replication complex assembly and to the identification of novel DNA replication factors. Here, I will review the different systems, highlight fundamental differences and unifying concepts, and discuss their potential for understanding chromosomal DNA replication in somatic mammalian cells.     

Further Characterization of Expression of Auxin-Induced Genes in Tobacco (Nicotiana tabacum) Cell-Suspension Cultures

We have described the modulation of four auxin-regulated genes during the growth cycle of suspension-cultured tobacco (Nicotiana tabacum [L.] var White Burley) cells. The genes were transiently expressed 2 to 8 h after transfer of stationary phase cells to fresh medium, during the transition from the quiescent phase of cells leaving the mitotic cycle to the synthesis phase of the cell cycle. After this transient induction, the cells showed a decreased sensitivity to auxin. Although the expression pattern suggests that induction of these genes might be important for cell division, over-production of antisense mRNA for one of these genes (pCNT103) did not influence cell division in transgenic tobacco cells. Furthermore, stimuli such as salicylic acid were capable of inducing gene expression but were unable to restore cell division. Although these data do not conclusively exclude a role for these genes in cell division, their significance in this process is discussed in view of their homology with other auxin-induced genes and in view of the specificity of hormone-induced early responses.     

Inference of cell cycle-dependent proteolysis by laser scanning cytometry

Mechanisms that couple protein turnover to cell cycle progression are critical for coordinating the events of cell duplication and division. Despite the importance of cell cycle-regulated proteolysis, however, technologies to measure this phenomenon are limited, and typically involve monitoring cells that are released back into the cell cycle after synchronization. We describe here the use of laser scanning cytometry (LSC), a technical merger between fluorescence microscopy and flow cytometry, to determine cell cycle-dependent changes in protein stability in unperturbed, asynchronous, cultures of mammalian cells. In this method, the ability of the LSC to accurately measure whole cell fluorescence is employed, together with RNA fluorescence in situ hybridization and immunofluorescence, to relate abundance of a particular RNA and protein in a cell to its point at the cell cycle. Parallel monitoring of RNA and protein levels is used, together with protein synthesis inhibitors, to reveal cell cycle-specific changes in protein turnover. We demonstrate the viability of this method by analyzing the proteolysis of two prominent human oncoproteins, Myc and Cyclin E, and argue that this LSC-based approach offers several practical advantages over traditional cell synchronization methods.     

Profiling of the Mammalian Mitotic Spindle Proteome Reveals an ER Protein,OSTD-1, as Being Necessary for Cell Division and ER Morphology

Cell division is important for many cellular processes including cell growth, reproduction, wound healing and stem cell renewal. Failures in cell division can often lead to tumors and birth defects. To identify factors necessary for this process, we implemented a comparative profiling strategy of the published mitotic spindle proteome from our laboratory. Of the candidate mammalian proteins, we determined that 77% had orthologs in Caenorhabditis elegans and 18% were associated with human disease. Of the C. elegans candidates (n=146), we determined that 34 genes functioned in embryonic development and 56% of these were predicted to be membrane trafficking proteins. A secondary, visual screen to detect distinct defects in cell division revealed 21 genes that were necessary for cytokinesis. One of these candidates, OSTD-1, an ER resident protein, was further characterized due to the aberrant cleavage furrow placement and failures in division. We determined that OSTD-1 plays a role in maintaining the dynamic morphology of the ER during the cell cycle. In addition, 65% of all ostd-1 RNAi-treated embryos failed to correctly position cleavage furrows, suggesting that proper ER morphology plays a necessary function during animal cell division.     

Cell Cycle,Differentiation and Regeneration: Where to Begin?

Hair cells, the sensory cells of inner ear, perform essential functions in hearing and balance. However, mammalian hair cells, like most of the CNS neurons, lack the capacity to regenerate. This is in sharp contrast to lower vertebrates in which hair cell regeneration occurs spontaneously through cell division of supporting cells, which leads to hearing restoration. It is believed that the lack of regeneration in mammals is, to a large degree, due to the block of cell cycle re-entry imposed by negative cell growth genes in the inner ear. Recent studies have identified retinoblastoma gene, a well-known tumor suppressor, as the key gene involved in cell cycle exit of inner ear sensory cells. In the inner ear of pRb conditional knockout mice, hair cells undergo continuous cell division, and at the same time differentiate and become functional. Cell division continues in early postnatal cochlea and adult vestibule. Remarkably, the vestibular hair cells without pRb survive, and function at both the cellular and system levels. The time course and effects of pRb inhibition shows that there is a separation between the roles of pRb in cell cycle exit, and subsequent maturation and apoptosis. Those studies reveal distinctly different roles of pRb in the cochlear and vestibular sensory epithelia. The review discusses additional areas to be studied for regeneration of mature hair cells, and highlights the importance of transient and reversible block of pRb function as one of the routes to be explored for regeneration.     

RNA Synthesis during Synchronous Cell Division in Cultured Explants of Jerusalem Artichoke Tuber

Explants of Jerusalem artichoke tuber tissue were cultured innutrient medium with the hormone, 2,4-dichlorophenoxyaceticacid. After a lag period, 90 per cent of the cells divided synchronously.During the first two cell cycles, the rate of ribosomal RNAsynthesis increased sharply in two steps; before the onset ofDNA synthesis for the first division, and early in interphasebefore the second division. Rates of RNA and protein accumulation,and phosphate uptake also increased sharply at these times.From experiments with explants in which DNA synthesis and celldivision had been inhibited, it was concluded that the stepwisepattern of ribosomal RNA synthesis was not caused by the replicationof ribosomal RNA genes, as can happen in mammalian cells. Instead,the periodicity of metabolism was found to be independent ofthe DNA synthesis-cell division cycle. A cause of the stepwisenature of ribosomal RNA synthesis is suggested. It is considered that despite the high synchrony of division,the system is not completely suited for the study of eventsassociated with the cell cycle in higher plants. However, thesynchrony of much of early metabolism suits it to the studyof induction of cell division in previously non-dividing cells,and the consequent process of de-differentiation.