Indole enhances the survival of Pantoea ananatis YJ76 in face of starvation conditions

Indole inhibited the expression of csrA gene in Escherichia coli

Indole is a very important signal molecule which plays multiple regulatory roles in many physiological and biochemical processes of bacteria, but up to now, the reasons for its wide range of functions have not been revealed. In this study, we found that indole inhibits the motility, promotes glycogen accumulation and enhances starvation resistance of Escherichia coli. However, the regulatory effects of indole became insignificant while the global csrA gene was mutated. To reveal the regulatory relationship between indole and csrA, we studied the effects of indole on the transcription level of csrA, flhDC, glgCAP and cstA, and also the sensing of the promoters of the genes on indole. It was found that indole inhibited the transcription of csrA, and only the promoter of the csrA gene can sense indole. Namely, indole indirectly regulated the translation level of FlhDC, GlgCAP and CstA. These data indicates that indole regulation is related with the regulation of CsrA, which may throw light on the regulation mechanism research of indole.

A new l-serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

Indole is traditionally known as a metabolite of l-tryptophan and now as an important signaling molecule in bacteria, however, the understanding of its upstream synthesis regulation is very limited. Pantoea ananatis YJ76, a predominant diazotrophic endophyte isolated from rice (Oryza sativa), can produce indole to regulate various physiological and biochemical behaviors. We constructed a mutant library of YJ76 using the mTn5 transposon insertion mutation method, from which an indole-deficient mutant was screened out. Via high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR), the transposon was determined to be inserted in a gene (RefSeq: WP014605468.1) of unknown function that is highly conserved at the intraspecific level. Bioinformatics analysis implied that the protein (Protein ID: WP089517194.1) encoded by the mutant gene is most likely to be a new orphan substrate-binding protein (SBP) for amino acid ABC transporters. Amino acid supplement cultivation experiments and surface plasmon resonance revealed that the protein could bind to l-serine (KD  = 6.149 × 10-5  M). Therefore, the SBP was named as SerBP. This is the first case that a SBP responds to l-serine ABC transports. As a precursor of indole synthesis, the transmembrane transported l-serine was directly correlated with indole signal production and the mutation of serBP gene weakened the resistance of YJ76 to antibiotics, alkali, heavy metals, and starvation. This study provided a new paradigm for exploring the upstream regulatory pathway for indole synthesis of bacteria.

Microbial Production Potential of Pantoea ananatis: From Amino Acids to Secondary Metabolites

Pantoea ananatis, a gram-negative bacterium belonging to the Erwiniaceae family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also provides us with various beneficial characteristics, such as the growth promotion of their host plants and increased crop yield. Some isolated non-pathogenic strains are promising for the microbial production of useful substances. P. ananatis AJ13355 was isolated as an acidophilic bacterium and was used as an excellent host to produce L-glutamic acid under acidic conditions. The genome sequence of P. ananatis AJ13355 was determined, and specific genome-engineering technologies were developed. As a result, P. ananatis was successfully used to construct a bacterial strain that produces cysteine, a sulfur-containing amino acid that has been difficult to produce through fermentation because of complex regulation. Furthermore, by heterologous expression including plant-derived genes, construction of a strain that produces isoprenoids such as isoprene and linalool as secondary metabolites was achieved. P. ananatis is shown to be a useful host for the production of secondary metabolites, as well as amino acids, and is expected to be used as a platform for microbial production of bioactive substances, aromatic substances, and other high-value-added substances of plant origin in the future.

The role of Lys2-Cl- -Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli

As a homo-oligomeric protein, the disassembly of Escherichia coli RbsD decamer produces a urea-unfolded oligomeric intermediate structure, as the dissociation speed of the protein is lower than that of the unfolding process. There are five Lys2-Cl^- -Lys2 salt linkages to connect these subunits. To explore the role of the salt linkages in these oligomeric intermediates, the Lys2Ala mutated in the N-terminal of E. coli RbsD protein subunit was designed. It was found that the RbsD mutation protein (RbsD:K2A) loses its minor larger oligomers, which exist in RbsD, and displays other several oligomeric states (less than decamers), meanwhile the state of the oligomers depends on the protein concentration. It was also found that compared with RbsD, the crosslinking capability of the subunits of RbsD:K2A is weaker, while the crosslinking rate of dimers is higher, RbsD:K2A needs to substantially adjust its conformation to meet the space requirements when combined with d-ribose. On the basis of these results, we suggest that Lys2-Cl^- -Lys2 salt linkages in E. coli RbsD protein play an important role in stabilizing the intermediate products of oligomers and maintaining interaction between the intermediate products of oligomers, which may shed light on the study of these oligomeric proteins.

Pantoea agglomerans YS19 poly(A) polymerase I gene possesses the indole-sensing sequence in the promoter region

Pantoea agglomerans YS19 is a predominant diazotrophic endophyte with multiple growth-promoting effects on its host plant that was isolated from rice. Indole is confirmed to induce many changes of physiological and biochemical characteristics in bacteria. Although YS19 cannot produce indole, it can sense indole in the environment and be regulated by indole. Here, using gfp as a reporter gene, we constructed a series of recombinant plasmids containing the promoter region of the poly(A) polymerase I gene (pcnB) fused with gfp, and compared the green fluorescence intensity at different concentrations of exogenous indole by a flow cytometer. In this research, we confirmed that exogenous indole significantly inhibited the expression of pcnB by its promoter; the regulation sequence sensitive to indole in the promoter region of the pcnB gene (In-pcnB) was between -129 and -88 bp. In-pcnB is widely distributed and strictly conserved in the same genus. These results suggest novel roles of In-pcnB in P. agglomerans YS19, showing its special relation to the indole regulatory pathway.

Extracellular DNA enhances the formation and stability of symplasmata in Pantoea agglomerans YS19

Extracellular DNA (eDNA) is an important polymeric substance that plays essential roles in cell aggregation and nutrient provision for the sessile bacteria. eDNA in bacterial biofilms was extensively studied. Here we found that eDNA also exists in symplasmata, a bacterial cell aggregate, which is different to a biofilm, in the rice enophyte Pantoea agglomerans YS19. We found that exogenous eDNA enhanced the formation and stability of symplasmata significantly, and that, exogenous eDNA also improved the stress resistance and colonization ability of the bacterium on host rice. These results strongly indicate novel roles of the eDNA in Pantoea agglomerans YS19, showing its special relation to the stress-resistance and endophyte-host association of the strain.