A deep coverage Dictyostelium discoideum genomic DNA library replicates stably in Escherichia coli

A GoldenBraid cloning system for synthetic biology in social amoebae

GoldenBraid is a rapid, modular, and robust cloning system used to assemble and combine genetic elements. Dictyostelium amoebae represent an intriguing synthetic biological chassis with tractable applications in development, chemotaxis, bacteria–host interactions, and allorecognition. We present GoldenBraid as a synthetic biological framework for Dictyostelium, including a library of 250 DNA parts and assemblies and a proof-of-concept strain that illustrates cAMP-chemotaxis with four fluorescent reporters coded by one plasmid.

dictyBase and the Dicty Stock Center (version 2.0) - a progress report

After serving the Dictyostelium community for many years, the first version of dictyBase (Chisholm et al., 2006; Fey et al., 2006) was in need of a decisive update. The original dictyBase software was not adaptable to more current demands such as handling the import of large-scale data from recently sequenced genomes, keeping up with changes in the Gene Ontology (GO), or handling the automatic annotation of over 20,000 new strains. Therefore, we have embarked on a complete overhaul of dictyBase. The new infrastructure will allow the introduction of new data, such as more expressive GO annotations and Dictyostelium disease orthologs. A modern user interface aims to streamline usage of the database including orders from the Dicty Stock Center (DSC). New displays will allow novel views including the combination of data in two new tools. With the underlying software infrastructure now in place, dictyBase software engineers and curators are currently adding the user interfaces, new tools and content pages for the evolving version 2.0 of dictyBase. This review highlights the emerging status of the new dictyBase, updated pages and annotations that will soon be available in the new environment, an overview of our annotation procedures, and plans to involve the community in curation efforts.

The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development

Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.

Reliable handling of highly A/T-rich genomic DNA for efficient generation of knockin strains of Dictyostelium discoideum

Background

Social amoeba, Dictyostelium discoideum, is a well-established model organism for studying cellular physiology and developmental pattern formation. Its haploid genome facilitates functional analysis of genes by a single round of mutagenesis including targeted disruption. Although the efficient generation of knockout strains based on an intrinsically high homologous recombination rate has been demonstrated, successful reports for knockin strains have been limited. As social amoeba has an exceptionally high adenine and thymine (A/T)-content, conventional plasmid-based vector construction has been constrained due to deleterious deletion in E. coli.

Results

We describe here a simple and efficient strategy to construct GFP-knockin cassettes by using a linear DNA cloning vector derived from N15 bacteriophage. This allows reliable handling of DNA fragments whose A/T-content may be as high as 85 %, and which cannot be cloned into a circular plasmid. By optimizing the length of recombination arms, we successfully generate GFP-knockin strains for five genes involved in cAMP signalling, including a triple-colour knockin strain.

Conclusions

This robust strategy would be useful in handling DNA fragments with biased A/T-contents such as the genome of lower organisms and the promoter/terminator regions of higher organisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0267-8) contains supplementary material, which is available to authorized users.