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Abbreviated scheme for the utilization of ornithine in the biosynthesis of polyamines, ornithine lipids, and the siderophore vicibactin. A portion of the arginine biosynthetic pathway from the intermediate N -acetylornithine (NAO) is shown (see also Figure 3). Abbreviations: Polyamine biosynthesis (Section ‘‘Polyamine biosynthesis and utilization’’): Adc, arginine decarboxylase; Hss, homospermidine synthase; Odc, ornithine decarboxylase; SpeB, agmatinase. Ornithine lipid biosynthesis (Section ‘‘Ornithine lipid biosynthesis and function’’): OlsA, lyso-ornithine lipid acyltransferase; OlsB, ornithine acyltransferase; OlsC and OlsE, ornithine lipid hydroxylases. S1, S2, P1 and P2 refer to structurally different species of ornithine lipids. The pathway shown is that of R. tropici CIAT899 (Vences-Guzm  ́n et al., 2011) but ornithine lipids are also made by S. meliloti by a similar pathway (Gao et al., 2004). Vicibactin biosynthesis (Section ‘‘Vicibactin biosynthesis and function’’): VbsA, condensation of D-3-hydroxybutyrate with ornithine; VbsC, acetylase; VbsL, epi- merase; VbsO, ornithine hydroxylase; VbsS, non-ribosomal peptide synthase. This pathway is specific for R. leguminosarum bv. viciae (Carter et al., 2002). Other abbreviations: L -Arg, L -arginine; L -Orn, L -ornithine. 

Abbreviated scheme for the utilization of ornithine in the biosynthesis of polyamines, ornithine lipids, and the siderophore vicibactin. A portion of the arginine biosynthetic pathway from the intermediate N -acetylornithine (NAO) is shown (see also Figure 3). Abbreviations: Polyamine biosynthesis (Section ‘‘Polyamine biosynthesis and utilization’’): Adc, arginine decarboxylase; Hss, homospermidine synthase; Odc, ornithine decarboxylase; SpeB, agmatinase. Ornithine lipid biosynthesis (Section ‘‘Ornithine lipid biosynthesis and function’’): OlsA, lyso-ornithine lipid acyltransferase; OlsB, ornithine acyltransferase; OlsC and OlsE, ornithine lipid hydroxylases. S1, S2, P1 and P2 refer to structurally different species of ornithine lipids. The pathway shown is that of R. tropici CIAT899 (Vences-Guzm ́n et al., 2011) but ornithine lipids are also made by S. meliloti by a similar pathway (Gao et al., 2004). Vicibactin biosynthesis (Section ‘‘Vicibactin biosynthesis and function’’): VbsA, condensation of D-3-hydroxybutyrate with ornithine; VbsC, acetylase; VbsL, epi- merase; VbsO, ornithine hydroxylase; VbsS, non-ribosomal peptide synthase. This pathway is specific for R. leguminosarum bv. viciae (Carter et al., 2002). Other abbreviations: L -Arg, L -arginine; L -Orn, L -ornithine. 

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Abstract 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 protei...

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... are synthesized by the decarboxylation of basic amino acids by amino acid decarb- oxylases that are usually specific for one or sometimes two amino acid substrates ( Lee et al., 2007). The decarboxylation products of ornithine, arginine and lysine are putrescine, agmatine and cadaverine, respectively ( Figure 6). A given rhizobial genome will often encode several amino acid decarboxylases, usually annotated as ornithine/arginine/ lysine decarboxylases. ...
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... putatively encoding enzymes that produce other polyamines from the products of amino acid decarboxylation are also encoded in rhizobial genomes. These include agmatinase (SpeB), which hydrolyzes agmatine to putrescine and urea ( Figure 6). In S. meliloti 1021, for example, speB is contiguous with but independently transcribed from the arginine biosynthetic gene argC (Díaz et al., 2011), and speB2 (smc01967) occurs immediately downstream of a putative spermidine/putrescine ABC transport system encoded by genes smc01963!smc01966, which are homologs of potC, B, A, and D, respectively. ...
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... S. meliloti 1021 olsA (encoding lyso-ornithine lipid acyltransferase; EC 2.3.1.; Figure 6) mutant lacked ornithine lipids, but had no growth defect in phosphate-limited media and formed symbiotically effective nodules on alfalfa ( López-Lara et al., 2005;Weissenmayer et al., 2002). In Rhizobium tropici CIAT899, however, mutants deficient in hydroxylated-OL synthesis were more sensitive to acid and temperature stress, and on bean were less competitive and formed poorly developed nodules that fixed significantly less nitrogen than the wild type. ...
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... would be further metabolized by the TCA cycle. Abbreviations are as listed in Figure 6. ...
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... Barnett et al., 2004;Djordjevic, 2004 Figure 6) are induced under low iron conditions. However, inactivation of various genes in the vicibactin pathway did not result in a defective symbiosis with pea or vetch inoculated with the mutants under either iron-rich or iron-deficient conditions. ...

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... However, the substrates consumed by microorganisms in the fenugreek soil plots are amino acids, amines, and amides. These findings can be attributed to the fact that the consumption of amines and amides contributes to the need for nitrogen sources by rhizobium [70]. Additionally, ref [22] showed that the presence of a cover crop, mainly grass species, had some influence on soil ecology and led to soils utilizing more carbon sources than soils without cover crops. ...
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... However, the substrates consumed by microorganisms in the fenugreek soil plots are amino acids, amines, and amides. These findings can be attributed to the fact that the consumption of amines and amides contributes to the need for nitrogen sources by rhizobium [70]. Additionally, ref [22] showed that the presence of a cover crop, mainly grass species, had some influence on soil ecology and led to soils utilizing more carbon sources than soils without cover crops. ...
... By conducting a comparative analysis of metabolite changes in AS and EB roots, it was observed that various amino acids associated with flowering and root development exhibited differential alterations ( Figure 3). Amino acids have multiple functions, including their role as constituents of proteins, as carbon, nitrogen, or sulfur sources, as indicators of cellular nitrogen status, and as precursors of significant metabolites [39]. Leucine and arginine have been implicated in the process of root development [40,41]. ...
... The phenylalanine content exhibited a significant increase from May to June and maintained a higher level. The rapid increase in glutamic and alanine content levels was observed from EB-Aug to EB-Sep, potentially facilitating plants' flowering and fruiting processes [39]. The observation suggests that the lignification process in the root coincided with premature underground bolting. ...
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... Methionine synthesis, which is provided by the host plant to the nodules, has been reported to be essential for efficient nodulation by various rhizobia (Barra et al. 2006). Tyrosine and phenylalanine are aromatic amino acid produced by the shikimate pathway which require phosphoenolpyruvate as substrate (Dunn 2014). Tyrosine is essential for the nodule formation and can be used by the bacteroid as source of carbon and nitrogen (Saha et al. 2016). ...
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... Amino acids and biogenic amines frequently occur or are secreted by the roots and nodules of legumes (i.e., phenylethylamine and putrescine) since they are of great biological importance and considered chemo-attractants for Rhizobiales (Compton and Scharf, 2021;Fujihara, 2008;Fujihara et al., 2002;Moe, 2013). Rhizobiales demand a high quantity of amino acids for protein metabolism, carbon, nitrogen and sulfur sources, signaling status of cellular nitrogen, multiple metabolite precursors and amines (such as β-phenethylamine and putrescine necessary for growth, motility, resistance to stress, biofilm formation, among others) (Becerra-Rivera and Dunn, 2019; Compton and Scharf, 2021;Dunn, 2017;Dunn, 2015;Hidalgo-Castellanos et al., 2021;Wang et al., 2020). Therefore, the reduction of A rel of Rhizobiales as a consequence of high concentrations nZnO 2 could impact the typical functions of the alfalfa rhizosphere soil communities, similar to that observed when these taxa decrease in natural conditions (Chouhan et Soil enzymatic activity is directly related to the intrinsic characteristics of soil (i.e., type, pH, exposure time, humidity, presence of metals, among others) and the BC that inhabit it, which makes it difficult to compare experiment results among different studies even when similar concentrations of NPs have been used (García-Gómez et al., 2018;Jośko et al., 2019;Kumar et al., 2019;Kwak et al., 2017;Qian et al., 2016;Shen et al., 2015;Tondey et al., 2021;You et al., 2018). ...
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... Amino acids, as well as their incorporation into proteins, serve as precursors of various metabolites, sources of nitrogen, carbon and sulfur, and signals of cellular nitrogen status in both free-living rhizobia and symbiotic bacteroids (Dunn 2015). In free-living rhizobia, many amino acids are required for the growth (Becker et al. 2004). ...
... When rhizobia differentiated into bacteroids, biosynthesis of most amino acids is down-regulated, and they are obtained largely from the host during SNF (Day et al. 2001). In addition, the process of symbiotic nitrogen fixing is accompanied by a severe reduction in ammonia assimilation into amino acids, allowing the export of ammonia to the host (Dunn 2015). Interestingly, specific amino acids needed for microaerobic metabolism and nitrogen fixation are synthesized in large quantities by de novo or by protein/amino acid turnover in nitrogen-fixing bacteroids (Vercruysse et al. 2011). ...
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Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
... After absorbing by root systems, they can be used as precursors for new amino acids and proteins required by plants, and participate in the synthesis of organic compounds such as sugars and lipids through the tricarboxylic acid cycle. 41,42 However, there were notable differences in the type and content of free amino acids in AAFs prepared from different raw materials. [15][16][17] Different amino acids have different physiological effects on plants, and this leads to the functional diversity of AAFs. ...
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... These pathways are mostly legume-diazotroph interaction-specific and needed for the legume seedlings to get activated during the initiation of the symbiotic association. Glutathione metabolism-related pathway is related to ROS-scavenging during diazotrophic interaction and nodulation (Mandon et al., 2021); amino acid metabolism (biosynthesis, transport, and/or degradation) and are often crucial for the establishment and maintenance of an effective nitrogen-fixing symbiosis process, which is intimately interconnected with the metabolism of the plant (Dunn, 2014); nitrogen signaling and metabolism (Carvalho et al., 2014); and symbiosome-related pathways (phagosome). It is reported that the root cells accommodate the rhizobia by the suppression and defunctionalization of their vacuole and also by retargeting some tonoplast proteins to symbiosome (Gavrin et al., 2014). ...
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Understanding the beneficial plant–microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, “Plant pathogen interaction” and “MAPK signaling,” were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant–diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant–diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant–diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.
... The BJS_08261 protein was identified as an oxidoreductase enzyme, a succinate-semialdehyde dehydrogenase (GabD protein, EC 1.2.1.24) involved in the GABA (γ-aminobutyric acid) metabolism [81]. When R. leguminosarum bv. ...
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Background Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod -gene inducer. Results A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium , others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. Conclusions All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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