'Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. ... More
Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.
AuthorsMao C, Evans C, Jensen RV, Sobral BW
JournalBMC Microbiol
PubMed ID18454850
Sinorhizobium meliloti is an agriculturally important model symbiont. There is an ongoing need to update and improve its genome annotation. In this study, we used a high-throughput pyrosequencing approach to sequence the transcriptome of S. meliloti, and search for new bacterial genes missed in the previous genome annotation. This is ... More
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.
AuthorsHe S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P
JournalNat Methods
PubMed ID20852648
The predominance of rRNAs in the transcriptome is a major technical challenge in sequence-based analysis of cDNAs from microbial isolates and communities. Several approaches have been applied to deplete rRNAs from (meta)transcriptomes, but no systematic investigation of potential biases introduced by any of these approaches has been reported. Here we ... More
Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production.
AuthorsWierckx NJ, Ballerstedt H, de Bont JA, de Winde JH, Ruijssenaars HJ, Wery J
JournalJ Bacteriol
PubMed ID17993537
The unknown genetic basis for improved phenol production by a recombinant Pseudomonas putida S12 derivative bearing the tpl (tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation ... More
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
AuthorsHe H, Cai L, Skogerbø G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G, Chen R
JournalNucleic Acids Res
PubMed ID16738136
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns ... More