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- MINIREVIEW] On the study of microbial transcriptomes using second- and third-generation sequencing technologies
- Sang Chul Choi
- J. Microbiol. 2016;54(8):527-536. Published online August 2, 2016
- DOI: https://doi.org/10.1007/s12275-016-6233-2
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- 11 Crossref
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Abstract
- Second-generation sequencing technologies transformed the study of microbial transcriptomes. They helped reveal the transcription start sites and antisense transcripts of microbial species, improving the microbial genome annotation. Quantification of genome-wide gene expression levels allowed for functional studies of microbial research. Ever-evolving sequencing technologies are reshaping approaches to studying microbial transcriptomes. Recently, Oxford Nanopore Technologies delivered a sequencing platform called MinION, a third-generation sequencing technology, to the research community. We expect it to be the next sequencing technology that enables breakthroughs in life science fields. The studies of microbial transcriptomes will be no exception. In this paper, we review microbial transcriptomics studies using second- generation sequencing technology. We also discuss the prospect of microbial transcriptomics studies with thirdgeneration sequencing.
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Research Support, Non-U.S. Gov't
- Differential Expression of citA Gene Encoding the Mitochondrial Citrate Synthase of Aspergillus nidulans in Response to Developmental Status and Carbon Sources
- In Sook Min , Ji Young Bang , Soon Won Seo , Cheong Ho Lee , Pil Jae Maeng
- J. Microbiol. 2010;48(2):188-198. Published online May 1, 2010
- DOI: https://doi.org/10.1007/s12275-010-0096-8
- 41 View
- 0 Download
- 6 Scopus
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Abstract
- As an extension of our previous studies on the mitochondrial citrate synthase of Aspergillus nidulans and cloning of its coding gene (citA), we analyzed differential expression of citA in response to the progress of development and change of carbon source. The cDNA consisted of 1,700 nucleotides and was predicted to encode a 474-amino acid protein. By comparing the cDNA sequence with the corresponding genomic sequence, we confirmed that citA gene contains 7 introns and that its transcription starts at position -26 (26-nucleotide upstream from the initiation codon). Four putative CreA binding motifs and three putative stress-response elements (STREs) were found within the 1.45-kb citA promoter region. The mode of citA expression was examined by both Northern blot and confocal microscopy using green fluorescent protein (sGFP) as a vital reporter. During vegetative growth and asexual development, the expression of citA was ubiqiutous throughout the whole fungal body including mycelia and conidiophores. During sexual development, the expression of citA was quite strong in cleistothecial shells, but significantly weak in the content of cleistothecia including ascospores. Acetate showed a strong inductive effect on citA expression, which is subjected to carbon catabolite repression (CCR) caused by glucose. The recombinant fusion protein CitA40::sGFP (sGFP containing the 40-amino acid N-terminal segment of CitA) was localized into mitochondria, which supports that a mitochondrial targeting signal is included within the 40-amino acid N-terminal segment of CitA.
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