Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum

Sooyoung Franck, William L. Franck, Sean R. Birke, Woo Suk Chang, Dipen P. Sangurdekar, Eddie Cytryn, Trupti Joshi, Michael Sadowsky, Gary Stacey, Dong Xu, David W. Emerich

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes expressed during symbiotic nitrogen fixation. The majority of annotated genes represented in the reiterated transcript pool with increased expression had already been identified by prior experimentation demonstrating the validity of the reiterated transcript approach. The majority of all reiterated transcripts with increased expression in bacteroids were hypothetical genes suggesting many symbiotic processes have yet to be identified. Genes for carbon metabolism, amino acid metabolism, energy metabolism and transport genes were represented by only a few reiterated transcripts suggesting these annotated processes do not participate in symbiosis, are masked by experimental conditions, or are fulfilled by hypothetical/unknown genes. Bioinformatic analysis revealed a statistically significant bias of the AG content of the reiterated transcripts with increased expression. A DNA motif identified in the reiterated transcripts with decreased expression was found preceding malate dehydrogenase (bll0456) and demonstrated to perform a role in expression of the gene.

Original languageEnglish (US)
Pages (from-to)123-135
Number of pages13
Issue number3
StatePublished - Jul 2014

Bibliographical note

Funding Information:
This research was supported by grant 2004-35604-14708 from USDA/CSREES/NRI. We thank S. Crosby and M. Heinz at the Genome Sequencing Center at Washington University School of Medicine for slide printing and conducting the initial microarray hybridizations.

Publisher Copyright:
© 2014, Springer Science+Business Media Dordrecht.


  • Bacteroids
  • Microarray
  • Symbiosis
  • Transcriptomics


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