LuxR-Type Regulator AclR1 of Azorhizobium caulinodans Regulates Cyclic di-GMP and Numerous Phenotypes in Free-Living and Symbiotic States

LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes

Although there is some evidence to suggest that LuxR-solo proteins participate in inter-species or even inter-kingdom communication, most of the LuxR-solo protein functions are unknown. We have characterized the LuxR402 regulator of Novosphingobium sp. HR1a, a bacterial strain with the ability to establish high numbers in the plant rhizosphere and able to degrade a wide range of polycyclic aromatic hydrocarbons. LuxR402 controls the aggregation state of the bacterial culture; cultures of a mutant strain lacking this regulator flocculate in less than 3 h without agitation. We have demonstrated that the bacterial surface of the mutant is highly hydrophobic and that the mutant cells assimilate sugars slower than the wild-type. The flocculation mechanism has been demonstrated to be involved in the survival of the strain under unfavorable conditions; the luxR402 gene is repressed and produces flocculation in the presence of salicylate, a substrate that, although being assimilated by Novosphingobium, is toxic to cells at high concentrations. The flocculation of cultures in industrial setups has mainly been achieved through the addition of chemicals; these studies open up the possibility of controlling the flocculation by regulating the level of expression of the luxR402 gene.

Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571

Protein acetylation can quickly modify the physiology of bacteria to respond to changes in environmental or nutritional conditions, but little information on these modifications is available in rhizobia. In this study, we report the lysine acetylome of Azorhizobium caulinodans strain ORS571, a model rhizobium isolated from stem nodules of the tropical legume Sesbania rostrata that is capable of fixing nitrogen in the free-living state and during symbiosis. Antibody enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were used to characterize the acetylome. There are 2,302 acetylation sites from 982 proteins, accounting for 20.8% of the total proteins. Analysis of the acetylated motifs showed the preferences for the amino acid residues around acetylated lysines. The response regulator CheY1, previously characterized to be involved in chemotaxis in strain ORS571, was identified as an acetylated protein, and a mutation of the acetylated site of CheY1 significantly impaired the strain's motility. In addition, a Zn+-dependent deacetylase (AZC_0414) was characterized, and the construction of a deletion mutant strain showed that it played a role in chemotaxis. Our study provides the first global analysis of lysine acetylation in ORS571, suggesting that acetylation plays a role in various physiological processes. In addition, we demonstrate its involvement in the chemotaxis process. The acetylome of ORS571 provides insights to investigate the regulation mechanism of rhizobial physiology. IMPORTANCE Acetylation is an important modification that regulates protein function and has been found to regulate physiological processes in various bacteria. The physiology of rhizobium A. caulinodans ORS571 is regulated by multiple mechanisms both when free living and in symbiosis with the host; however, the regulatory role of acetylation is not yet known. Here, we took an acetylome-wide approach to identify acetylated proteins in A. caulinodans ORS571 and performed clustering analyses. Acetylation of chemotaxis proteins was preliminarily investigated, and the upstream acetylation-regulating enzyme involved in chemotaxis was characterized. These findings provide new insights to explore the physiological mechanisms of rhizobia.

A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571

Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICE^Ac) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICE^Ac, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICE^Ac and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICE^Ac by 18.5%. We propose the feasibility of constructing a minimal ICE^Ac element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.

TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plantaricin EF biosynthesis and enhanced plantaricin EF production. Its production was 17.30 mg/L in 163 (Lp_2642), which was 1.29-fold higher than that of the original strain. The regulation mechanism demonstrated that Lp_2642 can bind to three sites of plnA promoter, which enhances its transcription and expression, thereby increasing plantaricin EF production. Amino acids Asn-100, Asn-64, and Thr-69 may play a key role in the binding of Lp_2642. These results provide a novel strategy for mass production of plantaricin EF, which facilitates its large-scale production and application in the agriculture and food industries as a preservative.

The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant

Bacterial signal transduction pathways are important for a variety of adaptive responses to environment, such as two-component systems (TCSs). In this paper, we reported the characterization of a transcriptional regulator in Azorhizobium caulinodans ORS571, ActR, with an N-terminal receiver domain and one C-terminal OmpR/PhoB-type DNA binding domain. Sequence analysis showed that ActR shared a high similarity with FtcR regulator of Brucella melitensis 16M known to be involved in flagellar regulation. The structural gene of this regulator was largely distributed in Alphaproteobacteria, in particular in Rhizobiales and Rhodobacterales, and was located within clusters of genes related to motility functions. Furthermore, we studied the biological function of ActR in A. caulinodans grown at the free-living state or in association with Sesbania rostrata by constructing actR gene deletion mutant. In the free-living state, the bacterial flagellum and motility ability were entirely deleted, the expression of flagellar genes was downregulated; and the exopolysaccharide production, biofilm formation, and cell flocculation decreased significantly compared with those of the wild-type strain. In the symbiotic state, ΔactR mutant strain showed weakly competitive colonization and nodulation on the host plant. These results illustrated that FtcR-like regulator in A. caulinodans is involved in flagellar biosynthesis and provide bacteria with an effective competitive nodulation for symbiosis. These findings improved our knowledge of FtcR-like transcriptional regulator in A. caulinodans.

Rediscovering bacterial exopolysaccharides of terrestrial and marine origins: novel insights on their distribution, biosynthesis, biotechnological production, and future perspectives

Bacteria exist in colonies as aggregates or associated with surfaces forming biofilms rather than planktonic cells. Living in such a unique manner is always mediated via a matrix of extracellular polymeric substances, which are composed mainly of polysaccharides or specifically exopolysaccharides (EPS). Biofilm formation and hence EPS production are affected by biotic and abiotic factors inducing/inhibiting several involved genes and other molecules. In addition, various aspects of bacterial EPS regarding: physiological functions, molecular weight, and chemical composition were demonstrated. Recent investigations have revealed a wide spectrum of EPS chemical and physicochemical properties showing promising applications in different industrial sectors. For instance, lactic acid bacteria (LAB)- and marine-derived EPS exhibit: immunomodulatory, antioxidant, antitumor, bioremediation of heavy metals, as well as thickening and viscosity modifiers in the food industry. However, bacterial EPS have not yet been commercially implemented, in contrast to plant-derived analogues. The current review aims to rediscover the EPS structural and biosynthetic features derived from marine and terrestrial bacteria, and applications as well.

Maltose effective improving production and regulatory biosynthesis of plantaricin EF in Lactobacillus plantarum 163

Plantaricin EF, a kind of natural antibacterial substance, has shown inhibitory effect on most pathogen and spoilage microorganisms, which possessed great potential in food preservation. However, the lower production of plantaricin EF has limited its large-scale production and application. In this study, the effect of maltose on plantaricin EF production and its regulation mechanism in Lactobacillus plantarum 163 were investigated. Maltose significantly improved the biomass and plantaricin EF production, which increased by 3.35 and 3.99 times comparing to the control without maltose, respectively. The maximum production of plantaricin E and F in fed-batch fermentation were 10.55 mg/L and 22.94 mg/L, respectively. Besides, qPCR results showed that maltose remarkably improved transcription of plnA, plnB, plnD, plnE, plnF, plnG1 and plnH, and heighten transcription of lamR, lamK, hpk6 and rrp6. These results provided an effective method to enhance plantaricin EF production and revealed a possible regulatory mechanism from transcriptome results that hpk6, rrp6, lamK and lamR were relative to plantaricin EF production. Genes, hpk6 and rrp6, promote transcription of plnG1, whereas lamK and lamR enhance transcription of plnA, plnB and plnD, which increased plantaricin EF production. KEYPOINTS: • Maltose was proved to be effective in promoting the biosynthesis of plantaricin EF. • Maltose promoted the transcription of biosynthesis and secretion genes of plantaricin EF. • Up-regulation of genes lamR, lamK, hpk6 and rrp6 heightened the plantaricin EF production.

FixJ family regulator AcfR of Azorhizobium caulinodans is involved in symbiosis with the host plant

Background

A wide variety of bacterial adaptative responses to environmental conditions are mediated by signal transduction pathways. Two-component signal transduction systems are one of the predominant means used by bacteria to sense the signals of the host plant and adjust their interaction behaviour. A total of seven open reading frames have been identified as putative two-component response regulators in the gram-negative nitrogen-fixing bacteria Azorhizobium caulinodans ORS571. However, the biological functions of these response regulators in the symbiotic interactions between A. caulinodans ORS571 and the host plant Sesbania rostrata have not been elucidated to date.

Results

In this study, we identified and investigated a two-component response regulator, AcfR, with a phosphorylatable N-terminal REC (receiver) domain and a C-terminal HTH (helix-turn-helix) LuxR DNA-binding domain in A. caulinodans ORS571. Phylogenetic analysis showed that AcfR possessed close evolutionary relationships with NarL/FixJ family regulators. In addition, six histidine kinases containing HATPase_c and HisKA domains were predicted to interact with AcfR. Furthermore, the biological function of AcfR in free-living and symbiotic conditions was elucidated by comparing the wild-type strain and the ΔacfR mutant strain. In the free-living state, the cell motility behaviour and exopolysaccharide production of the ΔacfR mutant were significantly reduced compared to those of the wild-type strain. In the symbiotic state, the ΔacfR mutant showed a competitive nodule defect on the stems and roots of the host plant, suggesting that AcfR can provide A. caulinodans with an effective competitive ability for symbiotic nodulation.

Conclusions

Our results showed that AcfR, as a response regulator, regulates numerous phenotypes of A. caulinodans under the free-living conditions and in symbiosis with the host plant. The results of this study help to elucidate the involvement of a REC + HTH_LuxR two-component response regulator in the Rhizobium-host plant interaction.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02138-w.

Effects of Calcium and Signal Sensing Systems on Azorhizobium caulinodans Biofilm Formation and Host Colonization

Biofilm formation is important for establishing plants-microbe associations. The role of calcium on biofilm formation has been studied in many bacteria except rhizobia. In this study, we investigated the role of calcium for biofilm formation in Azorhizobium caulindans, which forms nodules in the stem and root of its host plant Sesbania rostrata. We found that calcium is essential for A. caulindans biofilm formation, in addition to the presence of extracellular matrix components, eDNA and proteins. Also, calcium-mediated biofilm formation was tested with chemotaxis, motility, cyclic di-GMP synthesis, and quorum sensing mutants. Finally, calcium was found to promote S. rostrata root colonization of A. caulinodans. In total, these results show that calcium is essential for A. caulindans biofilm formation, and it affects the interaction between A. caulinodans and host plant.