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      Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes

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          Abstract

          Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C 4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.

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          Most cited references206

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          Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

          Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a substantial update of this in silico toolbox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include (i) network gap filling, (ii) (13)C analysis, (iii) metabolic engineering, (iv) omics-guided analysis and (v) visualization. As with the first version, the COBRA Toolbox reads and writes systems biology markup language-formatted models. In version 2.0, we improved performance, usability and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the toolbox and validate results. This toolbox lowers the barrier of entry to use powerful COBRA methods.
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            A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae.

            Plants have evolved a number of adaptive responses to cope with growth in conditions of limited phosphate (Pi) supply involving biochemical, metabolic, and developmental changes. We prepared an EMS-mutagenized M(2) population of an Arabidopsis thaliana transgenic line harboring a reporter gene specifically responsive to Pi starvation (AtIPS1::GUS), and screened for mutants altered in Pi starvation regulation. One of the mutants, phr1 (phosphate starvation response 1), displayed reduced response of AtIPS1::GUS to Pi starvation, and also had a broad range of Pi starvation responses impaired, including the responsiveness of various other Pi starvation-induced genes and metabolic responses, such as the increase in anthocyanin accumulation. PHR1 was positionally cloned and shown be related to the PHOSPHORUS STARVATION RESPONSE 1 (PSR1) gene from Chlamydomonas reinhardtii. A GFP::PHR1 protein fusion was localized in the nucleus independently of Pi status, as is the case for PSR1. PHR1 is expressed in Pi sufficient conditions and, in contrast to PSR1, is only weakly responsive to Pi starvation. PHR1, PSR1, and other members of the protein family share a MYB domain and a predicted coiled-coil (CC) domain, defining a subtype within the MYB superfamily, the MYB-CC family. Therefore, PHR1 was found to bind as a dimer to an imperfect palindromic sequence. PHR1-binding sequences are present in the promoter of Pi starvation-responsive structural genes, indicating that this protein acts downstream in the Pi starvation signaling pathway.
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              Applications of genome-scale metabolic reconstructions

              The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                18 December 2018
                2018
                : 9
                : 1860
                Affiliations
                [1] 1Centre for Soybean Research, State Key Laboratory of Agrobiotechnology , Shatin, Hong Kong
                [2] 2School of Life Sciences, The Chinese University of Hong Kong , Shatin, Hong Kong
                Author notes

                Edited by: Benjamin Gourion, UMR2594 Plant Interactions Laboratory Microorganisms (LIPM), France

                Reviewed by: George Colin DiCenzo, Università degli Studi di Firenze, Italy; Michael Frederick Dunn, National Autonomous University of Mexico, Mexico

                *Correspondence: Hon-Ming Lam, honming@ 123456cuhk.edu.hk

                This article was submitted to Plant Microbe Interactions, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2018.01860
                6305480
                30619423
                f665887a-d1c3-4f98-88a0-07744e86eb3e
                Copyright © 2018 Liu, Contador, Fan and Lam.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 21 September 2018
                : 30 November 2018
                Page count
                Figures: 2, Tables: 3, Equations: 1, References: 221, Pages: 18, Words: 0
                Categories
                Plant Science
                Review

                Plant science & Botany
                rhizobia,bacteroids,nitrogen fixation,legumes,root nodule,phosphate homeostasis,metabolism,symbiosis

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