A luciferase expression system for Physarum that facilitates analysis of regulatory elements

cDNA cloning, expression and homology modeling of a luciferase from the firefly Lampyroidea maculata

The cDNA of a firefly luciferase from lantern mRNA of Lampyroidea maculata has been cloned, sequenced and functionally expressed. The cDNA has an open reading frame of 1647 bp and codes for a 548-residue-long polypeptide. Noteworthy, sequence comparison as well as homology modeling showed the highest degree of similarity with H. unmunsana and L. mingrelica luciferases, suggesting a close phylogenetic relationship despite the geographical distance separation. The deduced amino acid sequence of the luciferase gene of firefly L. maculata showed 93% identity to H. unmunsana. Superposition of the three-dimensional model of L. maculata luciferase (generated by homology modeling) and three dimensional structure of Photinus pyralis luciferase revealed that the spatial arrangements of Luciferin and ATP-binding residues are very similar. Putative signature of AMPbinding domain among the various firefly species and Lampyroidea maculata was compared and a striking similarity was found. Different motifs and sites have been identified in Lampyroidea maculata by sequence analysis. Expression and purification of luciferase from Lampyroidea maculata was carried out using Ni-NTA Sepharose. Bioluminescence emission spectrum was similar to Photinus pyralis luciferase.

Detecting functional interactions in a gene and signaling network by time-resolved somatic complementation analysis

Somatic complementation by fusion of two mutant cells and mixing of their cytoplasms occurs when the genetic defect of one fusion partner is cured by the functional gene product provided by the other. We have found that complementation of mutational defects in the network mediating stimulus-induced commitment and sporulation of Physarum polycephalum may reflect time-dependent changes in the signaling state of its molecular building blocks. Network perturbation by fusion of mutant plasmodial cells in different states of activation, and the time-resolved analysis of somatic complementation effects can be used to systematically probe network structure and dynamics. Time-resolved somatic complementation quantitatively detects regulatory interactions between the functional modules of a network, independent of their biochemical composition or subcellular localization, and without being limited to direct physical interactions.

Genomic structure of the luciferase gene and phylogenetic analysis in the Hotaria-group fireflies

The luminescent fireflies have species specific flash patterns, being recognized as sexual communication. The luciferase gene is the sole enzyme responsible for bioluminescence. We describe here the complete nucleotide sequence and the exon-intron structure of the luciferase gene of the Hotaria-group fireflies, H. unmunsana, H. papariensis and H. tsushimana. The luciferase gene of the Hotaria-group firefly including the known H. parvula spans 1950 bp and consisted of six introns and seven exons coding for 548 amino acid residues, suggesting highly conserved structure among the Hotaria-group fireflies. Although only one luciferase gene was cloned from H. papariensis, each of the two sequences of the gene was found in H. unmunsana (U1 and Uc) and H. tsushimana (T1 and T2). The amino acid sequence divergence among H. unmunsana, H. papariensis, and H. tsushimana only ranged from zero to three amino acid residues, but H. parvula differed by 10-11 amino acid residues from the other Hotaria-group fireflies, suggesting a divergent relationship of this species. Phylogenetic analysis using the deduced amino acid sequences of the luciferase gene resulted in a monophyletic group in the Hotaria excluding H. parvula, suggesting a close relationship among H. unmunsana, H. papariensis and H. tsushimana. Additionally, we also analyzed the mitochondrial cytochrome oxidase I (COI) gene of the Hotaria-group fireflies. The deduced amino acid sequence of the COI gene of H. unmunsana was identical to that of H. papariensis and H. tsushimana, but different by three positions from H. parvula. In terms of nucleotide sequences of the COI gene, intraspecific sequence divergence was sometimes larger than interspecies level, and phylogenetic analysis placed the three species into monophyletic groups unresolved among them, but excluded H. parvula. In conclusion, our results suggest that H. unmunsana, H. papariensis and H. tsushimana are very closely related or might be an identical species, at least based on the luciferase and COI genes.

Molecular cloning and expression of a cDNA encoding the luciferase from the firefly, Hotaria unmunsana

We have cloned and characterized a cDNA encoding the luciferase from the firefly, Hotaria unmunsana. The cDNA encoding the luciferase of H. unmunsana was isolated by RT-PCR with a gene-specific primer set. The cDNA encoding the luciferase of H. unmunsana is 1644 base pairs long with an open reading frame of 548 amino acid residues. The deduced amino acid sequence of the luciferase gene of H. unmunsana showed 98.0 and 96.8% identity to H. parvula and Luciola mingrelica, respectively. Phylogenetic analysis further confirmed that the deduced amino acid sequences of the H. unmunsana luciferase gene belonged to the same subfamily, Luciolinae. Southern blot analysis of genomic DNA suggested the presence of the H. unmunsana luciferase gene as a single copy and Northern blot analysis confirmed light organ-specific expression at the transcriptional level. The cDNA encoding the luciferase of H. unmunsana was expressed as a 61-kDa band in the baculovirus-infected insect cells and the extracts of the recombinant baculovirus-infected cells emitted luminescence in the luciferase activity assay.

The one-kilobase DNA fragment upstream of the ardC actin gene of Physarum polycephalum is both a replicator and a promoter

The 1-kb DNA fragment upstream of the ardC actin gene of Physarum polycephalum promotes the transcription of a reporter gene either in a transient-plasmid assay or as an integrated copy in an ectopic position, defining this region as the transcriptional promoter of the ardC gene (PardC). Since we mapped an origin of replication activated at the onset of S phase within this same fragment, we examined the pattern of replication of a cassette containing the PardC promoter and the hygromycin phosphotransferase gene, hph, integrated into two different chromosomal sites. In both cases, we show by two-dimensional agarose gel electrophoresis that an efficient, early activated origin coincides with the ectopic PardC fragment. One of the integration sites was a normally late-replicating region. The presence of the ectopic origin converted this late-replicating domain into an early-replicating domain in which replication forks propagate with kinetics indistinguishable from those of the native PardC replicon. This is the first demonstration that initiation sites for DNA replication in Physarum correspond to cis-acting replicator sequences. This work also confirms the close proximity of a replication origin and a promoter, with both functions being located within the 1-kb proximal region of the ardC actin gene. A more precise location of the replication origin with respect to the transcriptional promoter must await the development of a functional autonomously replicating sequence assay in Physarum.

G1-phase arrest is not a prerequisite for encystment in Physarum

Amoebae of the Myxomycete Physarum polycephalum form resistant, walled cysts when the food bacteria in a culture have been consumed. No G1 phase has been detected in the vegetative amoebal cell cycle, most of which comprises the G2 phase. Mature cysts are also in G2, but it has been reported that a G1 phase of roughly 24 h, followed by an S phase, is obligatory prior to encystment. We used flow cytometry to determine the distribution of DNA contents in amoebal cultures at intervals during vegetative growth and encystment. In all cultures, the cells were predominantly in G2 phase, and the percentage of cells with G1 DNA content remained very low. We conclude that an extended G1 phase of 24 h did not occur in our cultures and cannot be a prerequisite for encystment.

Contact with a solid substratum induces cysts in axenic cultures ofPhysarum polycephalum amoebae: mannitol-induced detergent-resistant cells are not true cysts

Previous workers reported thatPhysarum polycephalum amoebae cultured in liquid axenic medium were induced to form cysts by the addition of mannitol. Their criterion for encystment was the formation of detergent (Triton)-resistant cells (TRC). In this study the frequencies of TRC in suspensions of amoebae from various treatments were compared with counts of cell types identified by transmission electron microscopy. Amoebae treated with mannitol in axenic liquid culture formed 50% TRC after 17 h but no walled cysts were found. It was concluded that TRC induced by mannitol were dense, rounded cells without walls. In contrast, TRC formed after growth to stationary phase on bacterial lawns were walled cells. When resuspended in growth medium, most mannitol-induced TRC reverted to active amoebae within a few minutes, whereas TRC formed on bacteria remained Triton resistant for many hours. It was concluded that delayed reversion of TRC was a more reliable indication of wall formation than Triton resistance alone. Transfer of amoebae from liquid culture to the surface of diluted axenic agar medium resulted in the formation of walled cysts identical in appearance with those formed on bacterial lawns. The results indicated that efficient encystment requires a solid substratum as well as nutrient deprivation.