Angelika A. Noegel

The genome of the social amoeba Dictyostelium discoideum

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal–fungal lineage after the plant–animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

Filamins as integrators of cell mechanics and signalling

Filamins are large actin-binding proteins that stabilize delicate three-dimensional actin webs and link them to cellular membranes. They integrate cellular architectural and signalling functions and are essential for fetal development and cell locomotion. Here, we describe the history, structure and function of this group of proteins.

Dictyostelium amoebae that lack G-actin-sequestering profilins show defects in F-actin content, cytokinesis, and development

To study in vivo functions of the ubiquitous actin-binding protein profilin, we generated by antisense and gene disruption techniques Dictyostelium mutants that lack one or both of the profilin isoforms. Whereas the single mutants showed an essentially unchanged phenotype, the behavior of the double mutant was drastically altered. Motility was significantly reduced, single cells were up to 10 times larger than wild-type cells and showed a broad rim of filamentous actin below the plasma membrane, the filamentous actin concentration was increased by about 60%-70%, and development was blocked prior to fruiting body formation. Furthermore, double mutants could not be grown in shaking culture under normal conditions, reflecting an impaired cytokinesis. The aberrant phenotype could be rescued by reintroducing a functional profilin I or profilin II gene. The data in this study suggest that profilin functions in Dictyostelium amoebae primarily as an actin-sequestering protein.

Sequence and analysis of chromosome 2 of Dictyostelium discoideum

The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene density, about 1 gene per 2.6 kilobases (kb), is surpassed only by Saccharomyces cerevisiae (one per 2 kb) and is similar to that of Schizosaccharomyces pombe (one per 2.5 kb). If we assume that the other chromosomes have a similar gene density, we can expect around 11,000 genes in the D. discoideum genome. A significant number of the genes show higher similarities to genes of vertebrates than to those of other fully sequenced eukaryotes. This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom, placing it close to the base of metazoan evolution.

Calcium‐sensitive non‐muscle α‐actinin contains EF‐hand structures and highly conserved regions

The F‐actin crosslinking molecule α‐actinin from the slime mould Dictyostelium discoideum carries two characteristics EF‐hand structures at the C‐terminus. The calcium‐binding loops contain all necessary liganding oxygens and most likely form the structural basis for the calcium sensitivity of strictly calcium‐regulated non‐muscle α‐actinins. Furthermore, the sequence exhibits at the N‐terminal site of the molecule a high degree of homology to chicken fibroblast α‐actinin. This stretch of amino acids appears to have remained essentially constant during evolution and might represent the actin‐binding site. The findings have led us to propose a model for the inhibitory action of Ca2+ on non‐muscle α‐actinins.

A mechanical unfolding intermediate in an actin-crosslinking protein

Many F-actin crosslinking proteins consist of two actin-binding domains separated by a rod domain that can vary considerably in length and structure. In this study, we used single-molecule force spectroscopy to investigate the mechanics of the immunoglobulin (Ig) rod domains of filamin from Dictyostelium discoideum (ddFLN). We find that one of the six Ig domains unfolds at lower forces than do those of all other domains and exhibits a stable unfolding intermediate on its mechanical unfolding pathway. Amino acid inserts into various loops of this domain lead to contour length changes in the single-molecule unfolding pattern. These changes allowed us to map the stable core of ∼60 amino acids that constitutes the unfolding intermediate. Fast refolding in combination with low unfolding forces suggest a potential in vivo role for this domain as a mechanically extensible element within the ddFLN rod.

The hybrid histidine kinase DokA is part of the osmotic response system of Dictyostelium.

We have used PCR to identify a Dictyostelium homolog of the bacterial two‐component system. The gene dokA codes for a member of the hybrid histidine kinase family which is defined by the presence of conserved amino acid sequence motifs corresponding to an N‐terminal receptor domain, a central kinase and a C‐terminal response regulator moiety. Potential function of the regulator domain was demonstrated by phosphorylation in vitro. dokA mutants are deficient in the osmoregulatory pathway, resulting in premature cell death under high osmotic stress. Under less stringent osmotic conditions, cells grow at a normal rate, but development at the multicellular stage is altered. dokA is a member of a family of histidine kinase‐like genes that play regulatory roles in eukaryotic cell function.

Redundancy in the microfilament system: Abnormal development of dictyostelium cells lacking two F-actin cross-linking proteins

We generated by gene disruption Dictyostelium cells that lacked both the F-actin cross-linking proteins, alpha-actinin and gelation factor. Several major cell functions, such as growth, chemotaxis, phagocytosis, and pinocytosis, were apparently unaltered. However, in all double mutants, development was greatly impaired. After formation of aggregates, cells were very rarely able to form fruiting bodies. This ability was rescued when mutant and wild-type strains were mixed in a ratio of 70 to 30. The developmental program in the mutant was not arrested, since the expression pattern of early and late genes remained unchanged. Development of the mutant was rendered normal when a functional alpha-actinin gene was introduced and expressed, showing the morphogenetic defect to be due to the absence of the two F-actin cross-linking proteins. These findings suggest the existence of a functional network allowing mutual complementation of certain actin-binding proteins.

Homologous recombination in the Dictyostelium alpha-actinin gene leads to an altered mRNA and lack of the protein.

Mutation of the alpha‐actinin gene in Dictyostelium has been achieved by transforming cells with the Dictyostelium transformation vector pDNeoII containing a 1.2 kb fragment of the alpha‐actinin gene. Transformants deficient in alpha‐actinin, an actin‐binding protein, produced an altered mRNA that lacked the 3′ portion of the coding region. The defect in alpha‐actinin production was not due to integration of the vector within the gene, but was apparently caused by errors produced during homologous recombination between the introduced alpha‐actinin sequence and its complementary sequence in the coding region of the endogenous gene.

Complete sequence and transcript regulation of a cell adhesion protein from aggregating Dictyostelium cells.

Three cDNA clones coding for the contact site A (csA) protein, a cell adhesion molecule of Dictyostelium discoideum, were isolated by screening a cDNA library with monoclonal antibodies. Two of these clones contained the complete coding region for the csA protein of 1542 bp including a sequence of 57 bp coding for the leader. The N terminus of the mature protein, as it was published previously, was identified in the amino acid sequence derived from both full‐length cDNA clones. Southern blot analysis suggests the presence of only one csA gene in the haploid genome. Accumulation of the csA‐specific message of 1.9 kb begins during development on nitrocellulose filters at 9 h of starvation, and reaches a maximum at 12 h, the time of cell aggregation. Expression of the csA glycoprotein follows closely accumulation of the transcripts. In the multicellular slug stage following cell aggregation, the amount of csA transcripts rapidly declines to low levels.