Antisense-mediated regulation of Annexin VII gene expression during the transition from growth to differentiation in Dictyostelium discoideum

Ion Signaling in Cell Motility and Development in Dictyostelium discoideum

Cell-to-cell communication is fundamental to the organization and functionality of multicellular organisms. Intercellular signals orchestrate a variety of cellular responses, including gene expression and protein function changes, and contribute to the integrated functions of individual tissues. Dictyostelium discoideum is a model organism for cell-to-cell interactions mediated by chemical signals and multicellular formation mechanisms. Upon starvation, D. discoideum cells exhibit coordinated cell aggregation via cyclic adenosine 3',5'-monophosphate (cAMP) gradients and chemotaxis, which facilitates the unicellular-to-multicellular transition. During this process, the calcium signaling synchronizes with the cAMP signaling. The resulting multicellular body exhibits organized collective migration and ultimately forms a fruiting body. Various signaling molecules, such as ion signals, regulate the spatiotemporal differentiation patterns within multicellular bodies. Understanding cell-to-cell and ion signaling in Dictyostelium provides insight into general multicellular formation and differentiation processes. Exploring cell-to-cell and ion signaling enhances our understanding of the fundamental biological processes related to cell communication, coordination, and differentiation, with wide-ranging implications for developmental biology, evolutionary biology, biomedical research, and synthetic biology. In this review, I discuss the role of ion signaling in cell motility and development in D. discoideum.

Cell-cycle checkpoint for transition from cell division to differentiation

In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell's transition from growth to differentiation is of general importance for the development of organisms, and terminally differentiated cells such as nerve cells never divide. Meanwhile, the growth rate speeds up when cells turn malignant. The cellular slime mold Dictyostelium discoideum grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A critical checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been precisely specified in the cell cycle of D. discoideum Ax-2 cells. Accordingly, integration of GDT point-specific events with starvation-induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross-talks. As was expected from the presence of the GDT point, the cell's positioning in cell masses and subsequent cell-type choices occur depending on the cell's phase in the cell cycle at the onset of starvation. Since novel and multiple functions of mitochondria in various respects of development including the initiation of differentiation have been directly realized in Dictyostelium cells, they are also reviewed in this article.

Noncoding RNA in development

Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.

The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway

Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum. This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, RrpC. In contrast, the expression of DIRS-1 small RNAs was not altered in any of the analyzed strains. This suggests the presence of multiple RNAi pathways in D. discoideum. In addition, we isolated several small RNAs with antisense complementarity to mRNAs. Three of these mRNAs are developmentally regulated. Interestingly, all three corresponding genes express longer antisense RNAs from which the small RNAs may originate. In at least one case, the longer antisense RNA is complementary to the spliced but not the unspliced pre-mRNA, indicating synthesis by an RNA-dependent RNA polymerase.

Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum

The traditional view of RNA being merely an intermediate in the transfer of genetic information, as mRNA, spliceosomal RNA, tRNA, and rRNA, has become outdated. The recent discovery of numerous regulatory RNAs with a plethora of functions in biological processes has truly revolutionized our understanding of gene regulation. Tiny RNAs such as microRNAs and small interfering RNAs play vital roles at different levels of gene control. Small nucleolar RNAs are much more abundant than previously recognized, and new functions beyond processing and modification of rRNA have recently emerged. Longer non-coding RNAs (ncRNAs) can also have important regulatory roles in the cell, e.g., antisense RNAs that control their target mRNAs. The majority of these important findings arose from analyses in various model organisms. In this review, we focus on ncRNAs in the social amoeba Dictyostelium discoideum. This important genetically tractable model organism has recently received renewed attention in terms of discovery, regulation and functional studies of ncRNAs. Old and recent findings are discussed and put in context of what we today know about ncRNAs in other organisms.

CgDN24: A gene involved in hyphal development in the fungal phytopathogen Colletotrichum gloeosporioides

A cDNA corresponding to a transcript induced in culture by N starvation, was identified in Colletotrichum gloeosporioides by a differential hybridisation strategy. The cDNA comprised 905 bp and predicted a 215 aa protein; the gene encoding the cDNA was termed CgDN24. No function for CgDN24 could be predicted by database homology searches using the cDNA sequence and no homologues were found in the sequenced fungal genomes. Transcripts of CgDN24 were detected in infected leaves of Stylosanthes guianensis at stages of infection that corresponded with symptom development. The CgDN24 gene was disrupted by homologous recombination and this led to reduced radial growth rates and the production of hyphae with a hyperbranching phenotype. Normal sporulation was observed, and following conidial inoculation of S. guianensis, normal disease development was obtained. These results demonstrate that CgDN24 is necessary for normal hyphal development in axenic culture but dispensable for phytopathogenicity.

Regulation of growth and differentiation in Dictyostelium

In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell's transition from growth to differentiation is of general importance not only for the development of organisms but also for the initiation of malignant transformation, in which this process is reversed. The cellular slime mold Dictyostelium, a wonderful model organism, grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A strict checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been specified in the cell cycle of D. discoideum Ax-2 cells. Accordingly, integration of GDT point-specific events with starvation-induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross-talks. As was expected from the presence of GDT points, the cell's positioning in cell masses and subsequent cell-type choices occur depending on the cell's phase in the cell cycle at the onset of starvation. Since novel and somewhat unexpected multiple functions of mitochondria in cell movement, differentiation, and pattern formation have been well realized in Dictyostelium cells, they are reviewed in this article.

Unique behavior and function of the mitochondrial ribosomal protein S4 (RPS4) in early Dictyostelium development

Certain proteins encoded by mitochondrial DNA (mt-DNA), including mt-ribosomal protein S4 (rps4), appear to play important roles in the initiation of cell differentiation. Partial disruption of rps4 in Dictyostelium discoideum Ax-2 cells by means of homologous recombination greatly impairs the progression of differentiation, while the the rps4(OE) cells in which the rps4 mRNA was overexpressed in the extra-mitochondrial cytoplasm exhibit enhanced differentiation (Inazu et al., 1999). We have prepared a specific anti-RPS4 antibody and generated transformants (rps4(AS) cells) by antisense-mediated gene inactivation of rps4. Surprisingly, in the rps4(AS) cells the progress of differentiation was found to be markedly inhibited, suggesting that the antisense rps4 RNA synthesized in the extra-mitochondrial cytoplasm might be as effective as the partial disruption of rps4 gene. Immunostaining of the rps4(OE) cells with the anti-RPS4 antibody demonstrated that the RPS4 protein synthesized in the extra-mitochondrial cytoplasm is capable of moving to the nucleus, as predicted by PSORTII. Taken together with the results obtained using immunostained Ax-2 cells, we propose a possible pathway of RPS4 translocation coupled with differentiation.

Haploinsufficiency of Anx7 tumor suppressor gene and consequent genomic instability promotes tumorigenesis in the Anx7(+/-) mouse

Annexin 7 (ANX7) acts as a tumor suppressor gene in prostate cancer, where loss of heterozygosity and reduction of ANX7 protein expression is associated with aggressive metastatic tumors. To investigate the mechanism by which this gene controls tumor development, we have developed an Anx7(+/-) knockout mouse. As hypothesized, the Anx7(+/-) mouse has a cancer-prone phenotype. The emerging tumors express low levels of Anx7 protein. Nonetheless, the wild-type Anx7 allele is detectable in laser-capture microdissection-derived tumor tissue cells. Genome array analysis of hepatocellular carcinoma tissue indicates that the Anx7(+/-) genotype is accompanied by profound reductions of expression of several other tumor suppressor genes, DNA repair genes, and apoptosis-related genes. In situ analysis by tissue imprinting from chromosomes in the primary tumor and spectral karyotyping analysis of derived cell lines identify chromosomal instability and clonal chromosomal aberrations. Furthermore, whereas 23% of the mutant mice develop spontaneous neoplasms, all mice exhibit growth anomalies, including gender-specific gigantism and organomegaly. We conclude that haploinsufficiency of Anx7 expression appears to drive disease progression to cancer because of genomic instability through a discrete signaling pathway involving other tumor suppressor genes, DNA-repair genes, and apoptosis-related genes.

Prognostic significance of annexin VII expression in glioblastomas multiforme in humans

Object. Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor in adults. It is nearly uniformly fatal, with a median survival time of approximately 1 year, despite modern treatment modalities. Nevertheless, a range of survival times exists around this median. Efforts to understand why some patients live longer or shorter than the average may provide insight into the biology of these neoplasms. The annexin VII (ANX7) gene is located on the human chromosome 10q21, a site long hypothesized to harbor tumor suppressor genes associated with prostate and other cancers. To test whether ANX7 expression might be a predictor for GBMs, we examined ANX7 expression, p53 accumulation, and the MIB-1 labeling index in a retrospective series of 99 GBMs.

Methods. In all 99 cases, the patient's age, Karnofsky Performance Scale (KPS) score before surgery, extent of surgery, tumor location, and immunohistochemical features were analyzed using univariate and multivariate analyses to identify whether any significance exists among ANX7 expression, p53 accumulation, the MIB-1 labeling index, and survival time. Kaplan—Meier analyses demonstrated that a higher KPS score before surgery (< 0.0001), total tumor excision (p = 0.0072), young patient age (p = 0.03), and ANX7 expression (p = 0.0006) correlated with longer survival. Multivariate Cox regression analyses demonstrated that ANX7 expression was the strongest predictor of outcome (p < 0.0001), independent of all other variables. In addition, ANX7 expression correlated with higher MIB-1 immunostaining, but did not correlate with p53 accumulation. Moreover, a significant positive correlation was observed between p53 and MIB-1 staining.

Conclusions. These findings indicate that a higher KPS score before surgery, total tumor excision, young patient age, and ANX7 expression correlate with longer survival in patients with GBMs. Multivariate Cox regression analyses demonstrated that ANX7 expression was the strongest predictor of outcome (p < 0.0001) and was independent of all other variables.

ANX7, a candidate tumor suppressor gene for prostate cancer

The ANX7 gene is located on human chromosome 10q21, a site long hypothesized to harbor a tumor suppressor gene(s) (TSG) associated with prostate and other cancers. To test whether ANX7 might be a candidate TSG, we examined the ANX7-dependent suppression of human tumor cell growth, stage-specific ANX7 expression in 301 prostate specimens on a prostate tissue microarray, and loss of heterozygosity (LOH) of microsatellite markers at or near the ANX7 locus. Here we report that human tumor cell proliferation and colony formation are markedly reduced when the wild-type ANX7 gene is transfected into two prostate tumor cell lines, LNCaP and DU145. Consistently, analysis of ANX7 protein expression in human prostate tumor microarrays reveals a significantly higher rate of loss of ANX7 expression in metastatic and local recurrences of hormone refractory prostate cancer as compared with primary tumors (P = 0.0001). Using four microsatellite markers at or near the ANX7 locus, and laser capture microdissected tumor cells, 35% of the 20 primary prostate tumors show LOH. The microsatellite marker closest to the ANX7 locus showed the highest rate of LOH, including one homozygous deletion. We conclude that the ANX7 gene exhibits many biological and genetic properties expected of a TSG and may play a role in prostate cancer progression.

Cell cycle-dependent regulation of early developmental genes

Cell cycle phase at the onset of development in Dictyostelium influences cell fate. Cells in the G2 phase, which tend to become spores, show a more rapid induction of expression of the cell surface receptor involved in the chemotaxis. We show that differential induction of developmental expression is restricted to some transcripts, including those encoding proteins required for chemotaxis, and thus is not due to general transcriptional repression during mitosis. We also show that cells showing rapid induction of one such gene are preferentially located at the centre of early aggregates. These results are consistent with cells derived from G2 phase being at the centre of early aggregates because selective differences in gene regulation render them more efficient at aggregation.

Transient expression of a mitochondrial gene cluster including rps4 is essential for the phase-shift of Dictyostelium cells from growth to differentiation

Using synchronized Dictyostelium discoideum Ax-2 cells and the differential display method, a mitochondrial gene cluster (referred to as differentiation-associated gene 3; dia3) was isolated as one of the genes expressed specifically during the transition of Ax-2 cells from growth to differentiation. The dia3 gene encodes for a mitochondrial protein cluster (NADH dehydrogenase (NAD) subunit 11, 5, ribosomal protein S4 (RPS4), RPS2, and NAD4L). Northern blot analysis using nonsynchronized Ax-2 cells has shown that the dia3 RNA of about 8 kb is scarcely expressed during the vegetative growth phase, and the maximal expression was attained at 2 h after starvation. To analyze the gene function of dia3, we tried inactivation of rps4 by means of homologous recombination and obtained several transformed clones showing mitochondrial DNA heteroplasmy. The transformed cells grew normally in nutrient medium, but their development after starvation was greatly impaired, thus resulting in the failure of many cells to differentiate. In this connection, the cAMP receptor 1 (car1) expression, which is one of the earliest markers of differentiation, was found to be markedly reduced in the rps4-inactivated cells.

Overexpression of CAF1 encoding a novel Ca2+-binding protein stimulates the transition of Dictyostelium cells from growth to differentiation

Among the expressed genes associated with the switch-over of Dictyostelium cells from cell proliferation to differentiation, the Calfumirin-1 (CAF1) gene has been shown to be preferentially expressed at the initial step of differentiation, encoding a novel Ca2+-binding protein (Abe & Maeda 1995). To analyze precisely the function of CAF1, transformants overexpressing the CAF1 mRNA at the vegetative growth phase and also CAF1-null mutants were prepared, and their developmental features were compared with those of parental wild-type cells. As a result, the CAF1-overexpression was found to promote cell differentiation, possibly through prompt induction of the cAMP receptor 1 (CAR1) gene expression. In addition, the CAF1-overexpressing cells were able to differentiate even under low external Ca2+ ([Ca2+]e) conditions around 10(-6) mol/L at which non-transformed wild-type cells never differentiated. Unexpectedly, however, the CAF1-null mutant produced by homologous recombination exhibited apparently normal development to form fruiting bodies on non-nutrient agar. These results seem to indicate that CAF1-overexpression has a stimulatory effect on differentiation, but that the CAF1 protein is not necessarily required for the phase-shift of cells from growth to differentiation.

Underexpression of a novel gene, dia2, impairs the transition of Dictyostelium cells from growth to differentiation

In Dictyostelium discoideum Ax-2 cells, a specific point (PS-point) in the cell cycle from which they initiate differentiation in response to starvation has been specified. Using synchronized Ax-2 cells and the differential display method, a novel gene (differentiation-associated gene 2; dia2) was isolated as one of the genes expressed specifically during the shift of Ax-2 cells from growth to differentiation. The dia2 gene codes a lysine- and leucine-rich protein with a predicted molecular mass of 16.9 kDa. Northern blot analysis has shown that the dia2 mRNA, of 0.7 kb, accumulates in differentiating cells starved just before the PS-point, while there is no detectable expression in vegetatively growing cells. Antisense-mediated gene inactivation of dia2 greatly inhibited the progress of differentiation, presumably through the reduced expression of cAMP receptor 1 (car1). Thus, the DIA2 expression was suggested to have an essential role in the initiation of differentiation, closely relating to the cAMP signaling system.

Combinatorial selection of a small RNA that induces amplification of IncFII plasmids in Escherichia coli

Cellular RNAs play fundamental roles as genetic messages, structural components and, in some cases, as catalytic agents. The ability to create vast combinatorial libraries of random RNA sequences has previously been exploited in vitro to identify RNA aptamers with desirable binding specificities, and to isolate RNAs with novel catalytic properties. Despite the advantages of in vitro selections from RNA libraries, there is no way to predict if the identified RNAs can function in living cells. We are therefore exploring random RNA expression libraries in Escherichia coli to search for small RNAs with novel functions. Here we describe selections that identified a small RNA (approximately 260 nucleotides) capable of altering the copy-number control circuitry of IncFII plasmids. The novel RNA appears to function by annealing to a region of the mRNA encoding the plasmid replicator protein. The resulting RNA-RNA hybrid permits translation of the replicator protein, but blocks base-pairing with a natural negative regulatory RNA. Implications of this in vivo selection strategy are discussed.

The signals for starvation response are transduced through elevated [Ca2+]i in Dictyostelium cells

The mechanism by which cells recognize starvation to allow subsequent cellular development was analyzed using Dictyostelium discoideum, with special emphasis on Ca2+ as a crucial signal transducer in intra- and intercellular communications. As was expected, the cytosolic Ca2+ concentration ([Ca2+]i) in aequorin-expressing cells (RHI76 derived from D. discoideum Ax-3) was temporarily increased, when 3-5 microM thapsigargin (Tg), a specific inhibitor of the Ca(2+)-ATPase, was added into the cells incubated in semistarvation medium (SS-medium: 1 vol of growth medium plus 7 vol either of 20 mM Na2/K-phosphate buffer (pH 6.2) or of Bonner's salt solution (BSS)). Essentially the same result was obtained by the application of 5 microM nigericin (Ng), an acid ionophore to cells under the semistarved condition. Here it is of interest to note that in the SS-medium Tg and Ng are capable of enhancing cell differentiation as exemplified well by the earlier acquisition of chemotactic response to cAMP, possibly inducing the starvation response through the [Ca2+]i increase. From Western blot analysis of phosphotyrosine (pTyr)-containing proteins using anti-pTyr antibody, it was found that the pTyr-phosphorylation levels of 97-, 80-, and 45-kDa proteins increase specifically in response to starvation. Interestingly, Tg and Ng induced such a change of the 80-kDa protein in the cells incubated in the SS-medium. Taken together these results strongly suggest that the temporal increase of [Ca2+]i may be a matter of importance for signal transduction coupled with starvation response.

Preferential expression of the cDNA encoding the proteasome subunit during the growth/differentiation transition of Dictyostelium cells

A proteasome subunit-1 gene (DAPS-1) was isolated as one preferentially expressed during the transition from growth to differentiation in Dictyostelium discoideum cells, using the differential display method. The DAPS-1 cDNA sequence with a length of 882 bp encodes a protein (Mr. 23.4 kDa) consisting of 213 amino acids. The deduced amino acid sequence of DAPS-1 showed 61% and 58% identity to the proteasome subunit Y of Xenopus laevis and Homo sapiens, respectively and 48% and 47% identity to the proteasome subunit LMP2 of Homo sapiens and Orizas latipes, respectively. Northern analysis revealed that a 1.0 kb of DAPS-1 mRNA is predominantly expressed during the early stage of differentiation induced by starvation. This seems to indicate that the DAPS-1 protein may be involved in proteolysis coupled with active exchange of the cellular protein composition during the phase-shift of Dictyostelium cells from the proliferative to differentiated state.