Amino acids in the rhizosphere: From plants to microbes

Moe, Luke A.

doi:10.3732/ajb.1300033

Cited by 297 publications

(174 citation statements)

References 174 publications

(263 reference statements)

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“…roots, leaves, shoots, flowers, and seeds, including zones of interaction between roots and the surrounding soil, the rhizosphere; Rout and Southworth, 2013). The rhizosphere is the region of the soil being continuously influenced by plant roots through the rhizodeposition of exudates, mucilages, and sloughed cells (Uren, 2001;Bais et al, 2006;Moe, 2013). Thus, plant roots can influence the surrounding soil and inhabiting organisms.…”

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confidence: 99%

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

2014

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There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.

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Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

2014

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“…Proline import into strain JH642 occurred with a K m of 6.8 Ϯ 0.7 M and a V max of 118 Ϯ 4 nmol (min mg protein) Ϫ1 (Fig. 4A), demonstrating that a B. subtilis wild-type strain can readily acquire proline from scarce environmental resources, such as root exudates and plant-mediated deposits in the rhizosphere (2,25). When proline import was measured at a final substrate concentration of 40 M, a substrate concentration at which no proline uptake activity was previously detectable in a putP opuE double mutant strain (SMB12) grown in SMM with glucose as the carbon source and ammonium as the nitrogen source (10), L-[…”

Section: Ganocation (Apc) Superfamily Of Transporters (Tc Accession Nmentioning

confidence: 99%

“…Utilization of proline as a nutrient requires its capture from environmental sources, such as root exudates and organic deposits in the rhizosphere (2,25), and relies on the PutB-and PutC-mediated catabolism to glutamate (10), a central intermediate in the interconnected carbon and nitrogen utilization systems of B. subtilis (26,27). The PutP transporter mediates the uptake of proline for its use as a nutrient, and the induction of the expression of the catabolic putBCP operon by an external supply of the substrate proline reflects this role (10,28,29).…”

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The γ-Aminobutyrate Permease GabP Serves as the Third Proline Transporter of Bacillus subtilis

et al. 2014

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bPutP and OpuE serve as proline transporters when this imino acid is used by Bacillus subtilis as a nutrient or as an osmostress protectant, respectively. The simultaneous inactivation of the PutP and OpuE systems still allows the utilization of proline as a nutrient. This growth phenotype pointed to the presence of a third proline transport system in B. subtilis. We took advantage of the sensitivity of a putP opuE double mutant to the toxic proline analog 3,4-dehydro-DL-proline (DHP) to identify this additional proline uptake system. DHP-resistant mutants were selected and found to be defective in the use of proline as a nutrient. Whole-genome resequencing of one of these strains provided the lead that the inactivation of the ␥-aminobutyrate (GABA) transporter GabP was responsible for these phenotypes. DNA sequencing of the gabP gene in 14 additionally analyzed DHPresistant strains confirmed this finding. Consistently, each of the DHP-resistant mutants was defective not only in the use of proline as a nutrient but also in the use of GABA as a nitrogen source. The same phenotype resulted from the targeted deletion of the gabP gene in a putP opuE mutant strain. Hence, the GabP carrier not only serves as an uptake system for GABA but also functions as the third proline transporter of B. subtilis. Uptake studies with radiolabeled GABA and proline confirmed this conclusion and provided information on the kinetic parameters of the GabP carrier for both of these substrates.

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“…Hydroxyprolines represent rich sources of nitrogen and carbon for microorganisms in soil and other environments containing decomposing biological material (9,10). Microorganisms that utilize hydroxyproline for growth have been isolated from soil, and a pathway for the catabolism of trans-4-L-Hyp by Pseudomonas was elucidated by Adams and coworkers in the 1960s (see reference 11 and …”

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l-Hydroxyproline andd-Proline Catabolism in Sinorhizobium meliloti

et al. 2016

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Sinorhizobium meliloti IMPORTANCEHydroxyproline 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.4-Hydroxyproline and 3-hydroxyproline in animal and plant proteins are formed through the posttranslational modification of proline residues by the enzyme proline hydroxylase. In some bacteria, hydroxyproline is synthesized from free L-proline, where it is employed in the synthesis of secondary metabolites (1, 2). 4-Hydroxyproline has two chiral carbon atoms, and of its four isomeric forms, trans-4-hydroxy-L-proline (trans-4-L-Hyp) and cis-4-hydroxy-D-proline (cis-4-D-Hyp) appear to be the two most common isomers. trans-4-

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Amino acids in the rhizosphere: From plants to microbes

Cited by 297 publications

References 174 publications

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

The γ-Aminobutyrate Permease GabP Serves as the Third Proline Transporter of Bacillus subtilis

l-Hydroxyproline andd-Proline Catabolism in Sinorhizobium meliloti

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