Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability

Abstract

Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero_2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero_1277, and an inner membrane ferrous iron permease, coded by Hsero_2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero_1277 and Hsero_3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero_2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero_2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.

Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant–Endophyte Interactions

“…Then, in turn, the hosts provided tissue sites suitable for endophytic growth (Utturkar et al, 2016;Schmid et al, 2017). This phenomenon indicates that a co-cultured endophyte displays more upregulated genes capable of promoting growth fitness of both organisms than non-co-cultured endophytes (Ambrose and Belanger, 2012;Yi et al, 2017;Zhou et al, 2017;Trovero et al, 2018).…”

Transcriptomic Response of the Diazotrophic Bacteria Gluconacetobacter diazotrophicus Strain PAL5 to Iron Limitation and Characterization of the fur Regulatory Network

“…As expected, in our in vitro assays in which G. diazotrophicus grew under iron-limiting conditions, catecholate siderophore-mediated acquisition systems ( fiu ) and TonB-dependent receptors (e.g., cirA ) appeared to be the most successful strategies for overcoming iron limitations. Similar expression profiles of fiu and cirA were observed in Herbaspirillum seropedicae under iron-limiting conditions [ 23 ]. It is important to highlight the induction of the exbB gene that is part of the tonB-exbB-exbD operon; the TonB–ExbB–ExbD protein complex participates in the active transport of iron–siderophore complexes, nickel complex, carbohydrates and vitamin B12 across the outer membrane [ 24 ].…”

“…However, a larger number of ABC-type sugar transporters were upregulated after the addition of iron. A sugar ABC transporter periplasmic protein was upregulated in H. seropedicae under iron starvation conditions [ 23 ]. This balance could be an artifact of the bacteria saving energy, since their metabolism is very active and the initial iron deficiency, an enzymatic cofactor for many central carbon metabolic reactions, affects the energetic balance, resulting in low activity of carbon metabolism.…”

Linking rhizosphere bacterial diversity and soil fertility in tobacco plants under different soil types and cropping pattern in Tanzania: A pilot study

“…Since tobacco is a dense nutrients feeder crop, more uptakes of P, K and S result in decreasing levels of these nutrients in the soil ( Table 1 ). On the other hand, bacteria species under Proteobacteria have also been reported to fix N in the soils and hence increasing soil total N after tobacco ( Table 1 ; Balsanelli et al., 2015 ; Trovero et al., 2018 ; Zúñiga-Feest et al., 2018 ). Chloroflexi, another dominant phylum identified in tobacco growing areas, reported to catalase Mn and also involved in the nitrification process in soils ( Sorokin et al., 2012 ; Baginski and Sommerhalter, 2017 ).…”