Nucleic Acids Research, gky142, https://doi.org/10.1093/nar/gky142
Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3–Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3–Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.
Environ Microbiol Rep. 2016 Nov 28. [Epub ahead of print]
Faoro H1,2, Rene Menegazzo R1, Battistoni F3, Gyaneshwar P4, do Amaral FP5, Taulé C3, Rausch S4, Gonçalves Galvão P6, de Los Santos C3, Mitra S4, Heijo G3, Sheu SY7, Chen WM7, Mareque C3, Zibetti Tadra-Sfeir M1, Ivo Baldani J6, Maluk M8, Paula Guimarães A6, Stacey G5, de Souza EM1, Pedrosa FO1, Magalhães Cruz L1, James EK8.
The genome of Azoarcus olearius DQS-4T , a N2 -fixing Betaproteobacterium isolated from oil-contaminated soil in Taiwan, was sequenced and compared with other Azoarcus strains. The genome sequence showed high synteny with Azoarcus sp. BH72, a model endophytic diazotroph, but low synteny with five non-plant-associated strains (Azoarcus CIB, Azoarcus EBN1, Azoarcus KH32C, A. toluclasticus MF63T and Azoarcus PA01). Average Nucleotide Identity (ANI) revealed that DQS-4T shares 98.98% identity with Azoarcus BH72, which should now be included in the species A. olearius. The genome of DQS-4T contained several genes related to plant colonization and plant growth promotion, such as nitrogen fixation, plant adhesion and root surface colonization. In accordance with the presence of these genes, DQS-4T colonized rice (Oryza sativa) and Setaria viridis, where it was observed within the intercellular spaces and aerenchyma mainly of the roots. Although they promote the growth of grasses, the mechanism(s) of plant growth promotion by A. olearius strains is unknown, as the genomes of DQS-4T and BH72 do not contain genes for indole acetic acid (IAA) synthesis nor phosphate solubilization. In spite of its original source, both the genome and behaviour of DQS-4T suggest that it has the capacity to be an endophytic, nitrogen-fixing plant growth-promoting bacterium.
PMID:27893193 DOI: 10.1111/1758-2229.12502
Plant and Soil, 2016
In this work, an ammonium-excreting strain (HM053) of A. brasilense was further characterized genetically and biochemically, and its abilities to colonize and promote wheat growth were determined. Methods Immunoblot, reverse transcription-qPCR, and DNA sequencing were used for HM053 characterization. To analyze wheat-A. brasilense interaction nifH::gusA fusions in the wild-type FP2 (FP2-7) and HM053 (HM053-36) backgrounds were employed.
Plant and Soil, 2017
The adaptation of plants to land ecosystems involves complex rhizosphere interactions between organic matter and microbial communities. Border cells (BC) constitute the first living boundary in plant-soil ecosystems and play an important role in environmental sensing and signaling in response to different biotic and abiotic conditions. In this study, we evaluate the effect of humic acid on the release of BCs and its impact on the colonization of Herbaspirillum seropedicae at maize root tips.