John Cullum

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

MOTIVATION The genome of the social amoeba Dictyostelium discoideum contains an unusually large number of polyketide synthase (PKS) genes. An analysis of the genes is a first step towards understanding the biological roles of their products and exploiting novel products. RESULTS A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2-5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT-PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.

Analysis of Large Deletions and Characterization of the Deletion Endpoints Associated with an Amplifiable DNA Region in Streptomyces Lividans

The phenomenon, that Streptomyces species can lose spontaneously certain phenotypes at frequenzies between 10–3 and 10–1 has been recognized since at least 1913 (Beijerinck 1913). This genetic instability is very common in many Streptomyces species and can affect a variety of genes; however, only specific genes are affected in any one strain (reviewed by Cullum et al., 1986; Hutter and Eckhardt, 1988). Frequently antibiotic producing strains, including some of commercial importance, are subject to genetic instability: they lose the ability to produce antibiotics (e.g. tetracyclines), i.e. they “degenerate”. As plasmid-curing agents such as acriflavine and ethidium bromide or UV-irradiation increased the frequency of mutation drastically, several authors suggested that the loss of a plasmid caused the loss of antibiotic production and they concluded that genes (or regulatory genes) for antibiotic production are coded on plasmids.

Analysis of Amplifications and Deletions in Streptomyces Species

Genetic instability is very common in Streptomyces species, and was one of the first reported properties (Beijerinck, 1913). Usually genetic instability has been detected as influencing easily scored phenotypes such as pigment production (Gregory and Huang, 1964), sporulation, auxotrophy (Redshaw et al., 1979) and antibiotic resistance (Freeman et al., 1977). In some cases genetic instability affects antibiotic production and can be a serious problem in industrial fermentations.

KEGG orthology-based annotation of the predicted proteome of Acropora digitifera

BackgroundContemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics.DescriptionSequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics.ConclusionsWe advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.