Control of hydroxyproline catabolism inSinorhizobium meliloti

Soybean nodulation shapes the rhizosphere microbiome to increase rapeseed yield

INTRODUCTION

Crop rotation, a crucial agricultural practice that enhances soil health and crop productivity, is widely used in agriculture worldwide. Soybeans play a crucial role in crop rotation owing to their nitrogen-fixing ability, which is facilitated by symbiotic bacteria in their root systems. The soybean-rapeseed rotation is an effective agricultural practice in the Yangtze River Basin of China. However, the mechanism underlying the effectiveness of this system remains unknown.

OBJECTIVES

The aim of this study was to decipher the mechanisms by which previous soybean cultivation enhances the growth of subsequent rapeseed.

METHODS

Soybeans with three distinct nodulation genotypes were rotated with rapeseed, and the impact of previous soybean cultivation on subsequent rapeseed growth was evaluated by examining the soybean root secretome and soil rhizosphere microbiome.

RESULTS

Soybean-rapeseed rotation significantly enhanced subsequent rapeseed growth and yield, especially when supernodulating soybean plants were used, which released the most nitrogen into the soil rhizosphere. The differences in soybean nodulation capability led to variations in root exudation, which in turn influenced the bacterial communities in the rhizosphere. Notably, the supernodulating soybean plants promoted Sphingomonadaceae family of bacteria growth by secreting oleic acid and cis-4-hydroxy-D-proline, and further attracted them through cis-4-hydroxy-D-proline. Furthermore, the exogenous application of Sphingomonadaceae bacteria, either alone or in combination with rhizobia, significantly enhanced the growth of rapeseed.

CONCLUSION

Our data definitively demonstrated the crucial role of previous soybean cultivation in enhancing the yield of rapeseed, with the assistance of Sphingomonadaceae bacteria and rhizobia. This study elucidates the role of soybean nodulation in rhizosphere bacterial dynamics, highlighting its importance in sustainable agricultural practices.

A broadly distributed predicted helicase/nuclease confers phage resistance via abortive infection

There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.

From Glycals to Nitrogen Heterocycles and Carbocycles via "Cleavage-Intramolecular Recombination Strategy"

Glycals (carbohydrate enol-ethers) have enjoyed profound applications in organic synthesis for more than a century. They not only serve as versatile glycosyl donors or as substrates for Ferrier rearrangement, but also find extensive synthetic applications especially as a "chiral pool" for accomplishing the synthesis of a variety of natural and biologically important compounds. As cyclic enol ethers, they demonstrate high reactivity and are among the most and variously transformable monosaccharide derivatives. The uniqueness of the reactivity of glycals is that they can be synthetically tuned to get a library of derivatives through stereo- and regioselective introduction of a variety of functional groups at C1, C2, C3 as well as C4 carbons of the sugar. We have developed a practical approach for stereoselective mono- and diamination of glycals and over the years utilized these scaffolds for the synthesis of a variety of biologically important nitrogen heterocycles and carbocycles through a "Diversity Oriented Approach". Our synthetic strategy in this direction mainly relied on the cleavage of ring O-C bond of the sugar followed by an "intramolecular recombination" reaction. Utilizing this strategy, we have accomplished the synthesis of several biologically important natural products, their analogues and related unnatural derivatives. Examples of such compounds reported from our group include polyhydroxypyrrolidines, DMDP, anisomycin, steviamine, pochonicine, conduramines, bulgecinine, aminocyclitols, azepanes, 4-hydroxy-D-proline, azanucleosides and their analogues. A personal account highlighting these syntheses is presented here.

Minimal gene set from Sinorhizobium (Ensifer) meliloti pSymA required for efficient symbiosis with Medicago

Reduction of N₂ gas to ammonia in legume root nodules is a key component of sustainable agricultural systems. Root nodules are the result of a symbiosis between leguminous plants and bacteria called rhizobia. Both symbiotic partners play active roles in establishing successful symbiosis and nitrogen fixation: while root nodule development is mostly controlled by the plant, the rhizobia induce nodule formation, invade, and perform N₂ fixation once inside the plant cells. Many bacterial genes involved in the rhizobia-legume symbiosis are known, and there is much interest in engineering the symbiosis to include major nonlegume crops such as corn, wheat, and rice. We sought to identify and combine a minimal bacterial gene complement necessary and sufficient for symbiosis. We analyzed a model rhizobium, Sinorhizobium (Ensifer) meliloti, using a background strain in which the 1.35-Mb symbiotic megaplasmid pSymA was removed. Three regions representing 162 kb of pSymA were sufficient to recover a complete N₂-fixing symbiosis with alfalfa, and a targeted assembly of this gene complement achieved high levels of symbiotic N₂ fixation. The resulting gene set contained just 58 of 1,290 pSymA protein-coding genes. To generate a platform for future synthetic manipulation, the minimal symbiotic genes were reorganized into three discrete nod, nif, and fix modules. These constructs will facilitate directed studies toward expanding the symbiosis to other plant partners. They also enable forward-type approaches to identifying genetic components that may not be essential for symbiosis, but which modulate the rhizobium's competitiveness for nodulation and the effectiveness of particular rhizobia-plant symbioses.

A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2)

Bacteria from the genus Streptomyces have been long exploited as the most prolific producers of antibiotics, other secondary metabolites and enzymes. They are important members of soil microbial communities that can adapt to changing conditions thank to the fine regulation of gene expression in response to environmental signals. Streptomyces coelicolor A3(2) is a model organism for molecular studies with the most deeply recognized interactions within the complex metabolic and regulatory network. However, details about molecular signals recognized by specialized regulatory proteins as well as their direct targets are often missing. We describe here a zinc-binding protein HypR (SCO6294) which belongs to FadR subfamily of GntR-like regulators. The DNA sequence 5'-TACAATGTCAC-3' recognized by the HypR protein in its own promoter region was identified by DNase I footprinting. Binding of six DNA fragments containing similar sequences located in other promoter regions were confirmed by the electrophoretic mobility shift assay (EMSA). The sequences of 7 in vitro-determined binding sites were assembled to generate a logo of the HypR binding motif, 5'-CTNTGC(A/C)ATGTCAC-3'. Comparison of luciferase reporter genes expression under the control of cloned promoter regions in S. coelicolor A3(2) wild type and deletion mutant strains revealed, that the HypR protein acts as a repressor of its target genes. Genes belonging to the regulon of HypR code for enzymes putatively involved in collagen degradation and utilization of L-hydroxyproline (L-Hyp) as concluded from predicted structure and conserved domains. Their transcription is induced in the wild type strain by the addition of L-Hyp to the culture medium. Moreover, knockout of one of the genes from the predicted L-Hyp utilization operon abolished the ability of the strain to grow on L-Hyp as a sole source of carbon. To our knowledge, this work is the first indication of the existence of the pathway of L-hydroxyproline catabolism in Streptomycetes.

Itaconic acid inhibits growth of a pathogenic marine Vibrio strain: A metabolomics approach

The antimicrobial role of itaconic acid (ITA) has been recently discovered in mammalian cells. In our previous studies, we discovered that marine molluscs biosynthesise substantial quantities of ITA when exposed to marine pathogens, but its antimicrobial function to Vibrio bacteria is currently unknown. Thus, in this study, we used an untargeted gas chromatography-mass spectrometry (GC-MS) platform to identify metabolic changes of Vibrio sp. DO1 (V. corallyliticus/neptunius-like isolate) caused by ITA exposure. Vibrio sp. DO1 was cultured in Luria-Bertani broth supplemented with 3 mM sodium acetate and with different concentrations of ITA (0, 3 and 6 mM) for 24 h. The results showed that ITA completely inhibited Vibrio sp. growth at 6 mM and partially inhibited the bacterial growth at 3 mM. A principal component analysis (PCA) revealed a clear separation between metabolite profiles of Vibrio sp. DO1 in the 3 mM ITA treatment and the control, which were different in 25 metabolites. Among the altered metabolites, the accumulation of glyoxylic acid and other metabolites in glyoxylate cycle (cis-aconitic acid, isocitric acid and fumaric acid) together with the increase of isocitrate lyase (ICL) activity in the 3 mM ITA treatment compared to the control suggest that ITA inhibited Vibrio sp. growth via disruption of central carbon metabolism.

Characterization of cis-4-hydroxy-D-proline dehydrogenase from Sinorhizobium meliloti

The hypO gene from Sinorhizobium meliloti, located within the trans-4-hydroxy-L-proline metabolic gene cluster, was first successfully expressed in the host Pseudomonas putida. Purified HypO protein functioned as a FAD-containing cis-4-hydroxy-D-proline dehydrogenase with a homomeric structure. In contrast to other known enzymes, significant activity for D-proline was found, confirming a previously proposed potential involvement in D-proline metabolism.

Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus

Halobacillus halophilus, a moderately halophilic bacterium, accumulates a variety of compatible solutes including glycine betaine, glutamate, glutamine, proline, and ectoine to cope with osmotic stress. Non-targeted analysis of intracellular organic compounds using 1H-NMR showed that a large amount of trans-4-hydroxy-L-proline (Hyp), which has not been reported as a compatible solute in H. halophilus, was accumulated in response to high NaCl salinity, suggesting that Hyp may be an important compatible solute in H. halophilus. Candidate genes encoding proline 4-hydroxylase (PH-4), which hydroxylates L-proline to generate Hyp, were retrieved from the genome of H. halophilus through domain searches based on the sequences of known PH-4 proteins. A gene, HBHAL_RS11735, which was annotated as a multidrug DMT transporter permease in GenBank, was identified as the PH-4 gene through protein expression analysis in Escherichia coli. The PH-4 gene constituted a transcriptional unit with a promoter and a rho-independent terminator, and it was distantly located from the proline biosynthetic gene cluster (pro operon). Transcriptional analysis showed that PH-4 gene expression was NaCl concentration-dependent, and was specifically induced by chloride anion, similar to the pro operon. Accumulation of intracellular Hyp was also observed in other bacteria, suggesting that Hyp may be a widespread compatible solute in halophilic and halotolerant bacteria.

Characterization of a Novel cis-3-Hydroxy-l-Proline Dehydratase and a trans-3-Hydroxy-l-Proline Dehydratase from Bacteria

Hydroxyprolines, such as trans-4-hydroxy-l-proline (T4LHyp), trans-3-hydroxy-l-proline (T3LHyp), and cis-3-hydroxy-l-proline (C3LHyp), are present in some proteins including collagen, plant cell wall, and several peptide antibiotics. In bacteria, genes involved in the degradation of hydroxyproline are often clustered on the genome (l-Hyp gene cluster). We recently reported that an aconitase X (AcnX)-like hypI gene from an l-Hyp gene cluster functions as a monomeric C3LHyp dehydratase (AcnX_{Type I}). However, the physiological role of C3LHyp dehydratase remained unclear. We here demonstrate that Azospirillum brasilense NBRC 102289, an aerobic nitrogen-fixing bacterium, robustly grows using not only T4LHyp and T3LHyp but also C3LHyp as the sole carbon source. The small and large subunits of the hypI gene (hypI_S and hypI_L, respectively) from A. brasilense NBRC 102289 are located separately from the l-Hyp gene cluster and encode a C3LHyp dehydratase with a novel heterodimeric structure (AcnX_{Type IIa}). A strain disrupted in the hypI_S gene did not grow on C3LHyp, suggesting its involvement in C3LHyp metabolism. Furthermore, C3LHyp induced transcription of not only the hypI genes but also the hypK gene encoding Δ¹-pyrroline-2-carboxylate reductase, which is involved in T3LHyp, d-proline, and d-lysine metabolism. On the other hand, the l-Hyp gene cluster of some other bacteria contained not only the AcnX_{Type IIa} gene but also two putative proline racemase-like genes (hypA1 and hypA2). Despite having the same active sites (a pair of Cys/Cys) as hydroxyproline 2-epimerase, which is involved in the metabolism of T4LHyp, the dominant reaction by HypA2 was clearly the dehydration of T3LHyp, a novel type of T3LHyp dehydratase that differed from the known enzyme (Cys/Thr).IMPORTANCE More than 50 years after the discovery of trans-4-hydroxy-l-proline (generally called l-hydroxyproline) degradation in aerobic bacteria, its genetic and molecular information has only recently been elucidated. l-Hydroxyproline metabolic genes are often clustered on bacterial genomes. These loci frequently contain a hypothetical gene(s), whose novel enzyme functions are related to the metabolism of trans-3-hydroxyl-proline and/or cis-3-hydroxyl-proline, a relatively rare l-hydroxyproline in nature. Several l-hydroxyproline metabolic enzymes show no sequential similarities, suggesting their emergence by convergent evolution. Furthermore, transcriptional regulation by trans-4-hydroxy-l-proline, trans-3-hydroxy-l-proline, and/or cis-3-hydroxy-l-proline significantly differs between bacteria. The results of the present study show that several l-hydroxyprolines are available for bacteria as carbon and energy sources and may contribute to the discovery of potential metabolic pathways of another hydroxyproline(s).

Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase

In the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase X is not functionally annotated. The corresponding gene (LhpI) was often located within the bacterial gene cluster involved in L-hydroxyproline metabolism. Screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-L-proline to Δ¹-pyrroline-2-carboxylate. Furthermore, electron paramagnetic resonance and site-directed mutagenic analyses suggests the presence of a mononuclear Fe(III) center, which may be coordinated with one glutamate and two cysteine residues. These properties were significantly different from those of other aconitase members, which catalyze the isomerization of α- to β-hydroxy acids, and have a [4Fe-4S] cluster-binding site composed of three cysteine residues. Bacteria with the LhpI gene could degrade cis-3-hydroxy-L-proline as the sole carbon source, and LhpI transcription was up-regulated not only by cis-3-hydroxy-L-proline, but also by several isomeric 3- and 4-hydroxyprolines.

Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti

BACKGROUND

Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. Despite the wide distribution of these enzymes, their biological roles are unclear in part because the reaction catalyzed by these enzymes can be by-passed by other pathways. The N2-fixing alfalfa symbiont Sinorhizobium meliloti contains both a NAD(P)-malic enzyme (DME) and a separate NADP-malic enzyme (TME) and to help understand the role of these enzymes, we investigated growth, metabolomic, and transcriptional consequences resulting from loss of these enzymes in free-living cells.

RESULTS

Loss of DME, TME, or both enzymes had no effect on growth with the glycolytic substrate, glucose. In contrast, the dme mutants, but not tme, grew slowly on the gluconeogenic substrate succinate and this slow growth was further reduced upon the addition of glucose. The dme mutant strains incubated with succinate accumulated trehalose and hexose sugar phosphates, secreted malate, and relative to wild-type, these cells had moderately increased transcription of genes involved in gluconeogenesis and pathways that divert metabolites away from the TCA cycle. While tme mutant cells grew at the same rate as wild-type on succinate, they accumulated the compatible solute putrescine.

CONCLUSIONS

NAD(P)-malic enzyme (DME) of S. meliloti is required for efficient metabolism of succinate via the TCA cycle. In dme mutants utilizing succinate, malate accumulates and is excreted and these cells appear to increase metabolite flow via gluconeogenesis with a resulting increase in the levels of hexose-6-phosphates and trehalose. For cells utilizing succinate, TME activity alone appeared to be insufficient to produce the levels of pyruvate required for efficient TCA cycle metabolism. Putrescine was found to accumulate in tme cells growing with succinate, and whether this is related to altered levels of NADPH requires further investigation.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Comparative genomics approaches are broadly used for analysis of transcriptional regulation in bacterial genomes. In this work, we identified binding sites and reconstructed regulons for 33 orthologous groups of transcription factors (TFs) in 196 reference genomes from 21 taxonomic groups of Proteobacteria. Overall, we predict over 10 600 TF binding sites and identified more than 15 600 target genes for 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs from Escherichia coli and/or Shewanella that are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages of Proteobacteria. By comparing gene contents of the reconstructed regulons, we identified the core, taxonomy-specific and genome-specific TF regulon members and classified them by their metabolic functions. Detailed analysis of ArgR, TyrR, TrpR, HutC, HypR and other amino-acid-specific regulons demonstrated remarkable differences in regulatory strategies used by various lineages of Proteobacteria. The obtained genomic collection of in silico reconstructed TF regulons contains a large number of new regulatory interactions that await future experimental validation. The collection provides a framework for future evolutionary studies of transcriptional regulatory networks in Bacteria. It can be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed regulons.

Molecular characterization of LhpR in control of hydroxyproline catabolism and transport in Pseudomonas aeruginosa PAO1

Utilization of hydroxy-l-proline (l-Hyp) in Pseudomonas aeruginosa requires conversion of l-Hyp to d-Hyp followed by the d-Hyp dehydrogenase pathway; however, the molecular mechanism in control of l-Hyp catabolism and transport was not clear. DNA microarray analysis revealed twelve genes in two adjacent loci that were induced by exogenous l-Hyp and d-Hyp. The first locus includes lhpABFE encoding a Hyp epimerase (LhpA) and d-Hyp dehydrogenase (LhpBEF), while the second locus codes for a putative ABC transporter (LhpPMNO), a protein of unknown function (LhpH), Hyp/Pro racemase (LhpK) and two enzymes in l-Hyp catabolism (LhpC and LhpG). Proximal to these two loci, lhpR encodes a transcriptional regulator of the AraC family. The importance of these genes on l-Hyp catabolism was supported by growth phenotype analysis on knockout mutants. Induction of the lhpA and lhpP promoters by exogenous l-Hyp and d-Hyp was demonstrated by the measurement of β-galactosidase activities from promoter-lacZ fusions in PAO1, and no induction could be detected in the ΔlhpR mutant. Induction of the lhpA promoter by d-Hyp was completely abolished in the lhpA lhpK double mutant devoid of two epimerases, while the induction effect of l-Hyp remained unchanged. The purified His-tagged LhpR binds specifically to the lhp promoter regions, and formation of nucleoprotein complexes is affected by the presence of l-Hyp but not d-Hyp. Putative LhpR binding sites were deduced from serial deletions and comparative genomic sequence analysis. In summary, expression of lhp genes for Hyp catabolism and uptake requires the transcriptional activator LhpR and l-Hyp as the signalling compound.

L-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti

Sinorhizobium meliloti forms N2-fixing root nodules on alfalfa, and as a free-living bacterium, it can grow on a very broad range of substrates, including l-proline and several related compounds, such as proline betaine, trans-4-hydroxy-l-proline (trans-4-l-Hyp), and cis-4-hydroxy-d-proline (cis-4-d-Hyp). Fourteen hyp genes are induced upon growth of S. meliloti on trans-4-l-Hyp, and of those, hypMNPQ encodes an ABC-type trans-4-l-Hyp transporter and hypRE encodes an epimerase that converts trans-4-l-Hyp to cis-4-d-Hyp in the bacterial cytoplasm. Here, we present evidence that the HypO, HypD, and HypH proteins catalyze the remaining steps in which cis-4-d-Hyp is converted to α-ketoglutarate. The HypO protein functions as a d-amino acid dehydrogenase, converting cis-4-d-Hyp to Δ(1)-pyrroline-4-hydroxy-2-carboxylate, which is deaminated by HypD to α-ketoglutarate semialdehyde and then converted to α-ketoglutarate by HypH. The crystal structure of HypD revealed it to be a member of the N-acetylneuraminate lyase subfamily of the (α/β)8 protein family and is consistent with the known enzymatic mechanism for other members of the group. It was also shown that S. meliloti can catabolize d-proline as both a carbon and a nitrogen source, that d-proline can complement l-proline auxotrophy, and that the catabolism of d-proline is dependent on the hyp cluster. Transport of d-proline involves the HypMNPQ transporter, following which d-proline is converted to Δ(1)-pyrroline-2-carboxylate (P2C) largely via HypO. The P2C is converted to l-proline through the NADPH-dependent reduction of P2C by the previously uncharacterized HypS protein. Thus, overall, we have now completed detailed genetic and/or biochemical characterization of 9 of the 14 hyp genes.

IMPORTANCE

Hydroxyproline is abundant in proteins in animal and plant tissues and serves as a carbon and a nitrogen source for bacteria in diverse environments, including the rhizosphere, compost, and the mammalian gut. While the main biochemical features of bacterial hydroxyproline catabolism were elucidated in the 1960s, the genetic and molecular details have only recently been determined. Elucidating the genetics of hydroxyproline catabolism will aid in the annotation of these genes in other genomes and metagenomic libraries. This will facilitate an improved understanding of the importance of this pathway and may assist in determining the prevalence of hydroxyproline in a particular environment.

Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution

Proline racemase (ProR) is a member of the pyridoxal 5’-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR.　A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.

Examination of prokaryotic multipartite genome evolution through experimental genome reduction

Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N₂-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this multipartite genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism's niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. pSymB).

Rhizobia are free-living bacteria of agricultural and environmental importance that form root-nodules on leguminous plants and provide these plants with fixed nitrogen. Many of the rhizobia have a multipartite genome, as do several plant and animal pathogens. All isolates of the alfalfa symbiont, Sinorhizobium meliloti, carry three large replicons, the chromosome (∼3.7 Mb), pSymA megaplasmid (∼1.4 Mb), and pSymB chromid (∼1.7 Mb). To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid. As the resulting strain was viable, we could perform a detailed phenotypic analysis and these data provided significant insight into the biology and metabolism of S. meliloti. The data lend direct experimental evidence in understanding the evolution and role of the multipartite genome. Specifically the large secondary replicons increase the organism's niche range, and this advantage offsets the metabolic burden of these replicons on the cell. Additionally, the single-chromosome strain offers a useful platform to facilitate future forward genetic approaches to understanding and manipulating the symbiosis and plant-microbe interactions.

Plant-derived compatible solutes proline betaine and betonicine confer enhanced osmotic and temperature stress tolerance to Bacillus subtilis

L-Proline is a widely used compatible solute and is employed by Bacillus subtilis, through both synthesis and uptake, as an osmostress protectant. Here, we assessed the stress-protective potential of the plant-derived L-proline derivatives N-methyl-L-proline, L-proline betaine (stachydrine), trans-4-L-hydroxproline and trans-4-hydroxy-L-proline betaine (betonicine) for cells challenged by high salinity or extremes in growth temperature. l-Proline betaine and betonicine conferred salt stress protection, but trans-4-L-hydroxyproline and N-methyl-L-proline was unable to do so. Except for L-proline, none of these compounds served as a nutrient for B. subtilis. L-Proline betaine was a considerably better osmostress protectant than betonicine, and its import strongly reduced the l-proline pool produced by B. subtilis under osmotic stress conditions, whereas a supply of betonicine affected the L-proline pool only modestly. Both compounds downregulated the transcription of the osmotically inducible opuA operon, albeit to different extents. Mutant studies revealed that L-proline betaine was taken up via the ATP-binding cassette transporters OpuA and OpuC, and the betaine-choline-carnitine-transporter-type carrier OpuD; betonicine was imported only through OpuA and OpuC. L-Proline betaine and betonicine also served as temperature stress protectants. A striking difference between these chemically closely related compounds was observed: L-proline betaine was an excellent cold stress protectant, but did not provide heat stress protection, whereas the reverse was true for betonicine. Both compounds were primarily imported in temperature-challenged cells via the high-capacity OpuA transporter. We developed an in silico model for the OpuAC-betonicine complex based on the crystal structure of the OpuAC solute receptor complexed with L-proline betaine.

Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacterium Sinorhizobium meliloti

A large proportion of genes within a genome encode proteins that play a role in metabolism. The Alphaproteobacteria are a ubiquitous group of bacteria that play a major role in a number of environments. For well over 50 years, carbon metabolism in Rhizobium has been studied at biochemical and genetic levels. Here, we review the pre- and post-genomics literature of the metabolism of the alphaproteobacterium Sinorhizobium meliloti. This review provides an overview of carbon metabolism that is useful to readers interested in this organism and to those working on other organisms that do not follow other model system paradigms.

Bacterial synthesis of D-amino acids

Recent work has shed light on the abundance and diversity of D-amino acids in bacterial extracellular/periplasmic molecules, bacterial cell culture, and bacteria-rich environments. Within the extracellular/periplasmic space, D-amino acids are necessary components of peptidoglycan, and disruption of their synthesis leads to cell death. As such, enzymes responsible for D-amino acid synthesis are promising targets for antibacterial compounds. Further, bacteria are shown to incorporate a diverse collection of D-amino acids into their peptidoglycan, and differences in D-amino acid incorporation may occur in response to differences in growth conditions. Certain D-amino acids can accumulate to millimolar levels in cell culture, and their synthesis is proposed to foretell movement from exponential growth phase into stationary phase. While enzymes responsible for synthesis of D-amino acids necessary for peptidoglycan (D-alanine and D-glutamate) have been characterized from a number of different bacteria, the D-amino acid synthesis enzymes characterized to date cannot account for the diversity of D-amino acids identified in bacteria or bacteria-rich environments. Free D-amino acids are synthesized by racemization or epimerization at the α-carbon of the corresponding L-amino acid by amino acid racemase or amino acid epimerase enzymes. Additionally, D-amino acids can be synthesized by stereospecific amination of α-ketoacids. Below, we review the roles of D-amino acids in bacterial physiology and biotechnology, and we describe the known mechanisms by which they are synthesized by bacteria.

Key roles of microsymbiont amino acid metabolism in rhizobia-legume interactions

Rhizobia are bacteria in the α-proteobacterial genera Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium and Bradyrhizobium that reduce (fix) atmospheric nitrogen in symbiotic association with a compatible host plant. In free-living and/or symbiotically associated rhizobia, amino acids may, in addition to their incorporation into proteins, serve as carbon, nitrogen or sulfur sources, signals of cellular nitrogen status and precursors of important metabolites. Depending on the rhizobia-host plant combination, microsymbiont amino acid metabolism (biosynthesis, transport and/or degradation) is often crucial to the establishment and maintenance of an effective nitrogen-fixing symbiosis and is intimately interconnected with the metabolism of the plant. This review summarizes past findings and current research directions in rhizobial amino acid metabolism and evaluates the genetic, biochemical and genome expression studies from which these are derived. Specific sections deal with the regulation of rhizobial amino acid metabolism, amino acid transport, and finally the symbiotic roles of individual amino acids in different plant-rhizobia combinations.

Identification and characterization of trans-3-hydroxy-l-proline dehydratase and Δ(1)-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-l-proline metabolism of bacteria

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The bacterial metabolic pathway of trans-3-hydroxy-l-proline (T3LHyp) has been identified.

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Azospirillum brasilense can grow on T3LHyp as a sole carbon source.

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The T3LHyp pathway comprises T3LHyp dehydratase and Δ¹-pyrroline-2-carboxylate reductase.

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This pathway is similar to one found in mammals.

trans-4-Hydroxy-l-proline (T4LHyp) and trans-3-hydroxy-l-proline (T3LHyp) occur mainly in collagen. A few bacteria can convert T4LHyp to α-ketoglutarate, and we previously revealed a hypothetical pathway consisting of four enzymes at the molecular level (J Biol Chem (2007) 282, 6685–6695; J Biol Chem (2012) 287, 32674–32688). Here, we first found that Azospirillum brasilense has the ability to grow not only on T4LHyp but also T3LHyp as a sole carbon source. In A. brasilense cells, T3LHyp dehydratase and NAD(P)H-dependent Δ¹-pyrroline-2-carboxylate (Pyr2C) reductase activities were induced by T3LHyp (and d-proline and d-lysine) but not T4LHyp, and no effect of T3LHyp was observed on the expression of T4LHyp metabolizing enzymes: a hypothetical pathway of T3LHyp → Pyr2C → l-proline was proposed. Bacterial T3LHyp dehydratase, encoded to LhpH gene, was homologous with the mammalian enzyme. On the other hand, Pyr2C reductase encoded to LhpI gene was a novel member of ornithine cyclodeaminase/μ-crystallin superfamily, differing from known bacterial protein. Furthermore, the LhpI enzymes of A. brasilense and another bacterium showed several different properties, including substrate and coenzyme specificities. T3LHyp was converted to proline by the purified LhpH and LhpI proteins. Furthermore, disruption of LhpI gene from A. brasilense led to loss of growth on T3LHyp, d-proline and d-lysine, indicating that this gene has dual metabolic functions as a reductase for Pyr2C and Δ¹-piperidine-2-carboxylate in these pathways, and that the T3LHyp pathway is not linked to T4LHyp and l-proline metabolism.

Discovery of new enzymes and metabolic pathways by using structure and genome context

Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by 'predicting' the intermediates in the glycolytic pathway in Escherichia coli. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) and cis-4-hydroxy-D-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.

Amino acids in the rhizosphere: from plants to microbes

Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.