scholarly journals Genome-Scale Metabolic Modelling of Lifestyle Changes in Rhizobium leguminosarum

mSystems ◽  
2022 ◽  
Author(s):  
Carolin C. M. Schulte ◽  
Vinoy K. Ramachandran ◽  
Antonis Papachristodoulou ◽  
Philip S. Poole
Keyword(s):  
Sustainable Agriculture ◽  
Soil Bacteria ◽  
Rhizobium Leguminosarum ◽  
Lifestyle Changes ◽  
Plant Roots ◽  
Cereal Crops ◽  
Nodule Formation ◽  
Metabolic Modelling ◽  
Detailed Understanding ◽  
Genome Scale

Rhizobia are soil bacteria that induce nodule formation on plant roots and differentiate into nitrogen-fixing bacteroids. A detailed understanding of this complex symbiosis is essential for advancing ongoing efforts to engineer novel symbioses with cereal crops for sustainable agriculture.

scholarly journals Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum

2021 ◽  
Author(s):  
Carolin C.M. Schulte ◽  
Vinoy Ramachandran ◽  
Antonis Papachristodoulou ◽  
Philip Poole
Keyword(s):  
Rhizobium Leguminosarum ◽  
Expression Patterns ◽  
Agricultural Practices ◽  
Metabolic Model ◽  
Lifestyle Changes ◽  
Plant Host ◽  
A Genome ◽  
Infection Threads ◽  
Mutualistic Relationship ◽  
Genome Scale

Biological nitrogen fixation in rhizobium-legume symbioses is of major importance for sustainable agricultural practices. To establish a mutualistic relationship with their plant host, rhizobia transition from free-living bacteria in soil to growth down infection threads inside plant roots and finally differentiate into nitrogen-fixing bacteroids. We reconstructed a genome-scale metabolic model for Rhizobium leguminosarum and integrated the model with transcriptome, proteome, metabolome and gene essentiality data to investigate nutrient uptake and metabolic fluxes characteristic of these different lifestyles. Synthesis of leucine, polyphosphate and AICAR is predicted to be important in the rhizosphere, while myo-inositol catabolism is active in undifferentiated nodule bacteria in agreement with experimental evidence. The model indicates that bacteroids utilize xylose and glycolate in addition to dicarboxylates, which could explain previously described gene expression patterns. Histidine is predicted to be actively synthesized in bacteroids, consistent with transcriptome and proteome data for several rhizobial species. These results provide the basis for targeted experimental investigation of metabolic processes specific to the different stages of the rhizobium-legume symbioses.

scholarly journals Metabolic control of nitrogen fixation in rhizobium-legume symbioses

2021 ◽  
Vol 7 (31) ◽  
pp. eabh2433
Author(s):  
Carolin C. M. Schulte ◽  
Khushboo Borah ◽  
Rachel M. Wheatley ◽  
Jason J. Terpolilli ◽  
Gerhard Saalbach ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Tricarboxylic Acid Cycle ◽  
Oxygen Demand ◽  
Metabolic Model ◽  
Redox Balance ◽  
Ammonia Assimilation ◽  
Nodule Formation ◽  
Flux Analysis ◽  
Carbon And Nitrogen ◽  
Genome Scale

Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.

scholarly journals Consistency, Inconsistency and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome Scale Metabolic Modelling

2018 ◽  
Author(s):  
Nhung Pham ◽  
Ruben Van Heck ◽  
Jesse van Dam ◽  
Peter Schaap ◽  
Edoardo Saccenti ◽  
...  
Keyword(s):  
Systems Medicine ◽  
Biochemical Reactions ◽  
Metabolic Modelling ◽  
Research Areas ◽  
Limit Model ◽  
Metabolic Models ◽  
Genome Scale ◽  
Manual Verification

Genome scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in eleven biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping.

scholarly journals Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Inmaculada García-Romero ◽  
Juan Nogales ◽  
Eduardo Díaz ◽  
Eduardo Santero ◽  
Belén Floriano
Keyword(s):  
Metabolic Modelling ◽  
Genome Scale

scholarly journals Nod Factor-Induced Expression of Leghemoglobin to Study the Mechanism of NH4NO3 Inhibition on Root Hair Deformation

1997 ◽  
Vol 10 (2) ◽  
pp. 215-220 ◽  
Author(s):  
Renze Heidstra ◽  
Gerd Nilsen ◽  
Francisco Martinez-Abarca ◽  
Ab van Kammen ◽  
Ton Bisseling
Keyword(s):  
Gene Expression ◽  
Root Hair ◽  
Rhizobium Leguminosarum ◽  
Cortical Cell ◽  
Brefeldin A ◽  
Marker Genes ◽  
Nodule Formation ◽  
Cdna Clones ◽  
Nod Factor ◽  
Root Hair Deformation

Nod factors secreted by Rhizobium leguminosarum bv. viciae induce root hair deformation, the formation of nodule primordia, and the expression of early nodulin genes in Vicia sativa (vetch). Root hair deformation is induced within 3 h in a small, susceptible zone (±2 mm) of the root. NH4NO3, known to be a potent blocker of nodule formation, inhibits root hair deformation, initial cortical cell divisions, and infection thread formation. To test whether NH4NO3 affects the formation of a component of the Nod factor perception-transduction system, we studied Nod factor-induced gene expression. The differential display technique was used to search for marker genes, which are induced within 1 to 3 h after Nod factor application. Surprisingly, one of the isolated cDNA clones was identified as a leghemoglobin gene (VsLb1), which is induced in vetch roots within 1 h after Nod factor application. By using the drug brefeldin A, it was then shown that VsLb1 activation does not require root hair deformation. The pVsLb1 clone was used as a marker to show that in vetch plants grown in the presence of NH4NO3 Nod factor perception and transduction leading to gene expression are unaffected.

Influence of Siduron and its Degradation Products on Soil Microflora

Weed Science ◽  
1968 ◽  
Vol 16 (4) ◽  
pp. 417-420 ◽  
Author(s):  
M. L. Fields ◽  
D. D. Hemphill
Keyword(s):  
Degradation Product ◽  
Soil Bacteria ◽  
Rhizobium Leguminosarum ◽  
Degradation Products ◽  
Streptomyces Griseus ◽  
Soil Microflora ◽  
Aspergillus Versicolor ◽  
Rhizopus Nigricans ◽  
Thiobacillus Thioparus ◽  
Soil Ciliates

The herbicide l-(2-methylcyclohexyl)-3-phenylurea (siduron) suppressed the growth of soil bacteria,Azotobacter sp.andChlorella vulgariswhereas siduron had no effect on actinomycetes, filamentous fungi, soil ciliates and other algae. Siduron had no effect upon the growth ofThiobacillus thioparus, Euglena gracilis, andStreptomyces griseus.The degradation product, 2-methylcyclohexylamine (hereinafter referred to as 2-MCHA) suppressed the growth ofAztobacter chroococcumand soil ciliates. Aniline, another degradation product of siduron, depressed the growth ofAspergillus versicolorandA. fischeri;however,A. ochraceus, A. candidus, A. clavatus, A. nidulans, A. flavus, Botrytis cinerea, andRhizopus nigricanswere not affected. None of these fungi was influenced in growth by 2-MCHA.Streptomyces griseusgrew significantly less in the presence of aniline. The growth ofChlamydomonas pyrenoidosa, C. radiata, Anabaena catenula, andRhizobium leguminosarumwere not influenced by 10 ppm aniline or 10 ppm 2-MCHA.

scholarly journals High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

2019 ◽  
Vol 22 (1) ◽  
pp. 255-269 ◽  
Author(s):  
Juan Nogales ◽  
Joshua Mueller ◽  
Steinn Gudmundsson ◽  
Francisco J. Canalejo ◽  
Estrella Duque ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
High Quality ◽  
Metabolic Modelling ◽  
Genome Scale ◽  
High Quality Genome

Erratum to: Two novel chromosomal loci influence cultivar-specific nodulation failure in the interaction between strain ANU794 and subterranean clover cv. Woogenellup

2002 ◽  
Vol 29 (7) ◽  
pp. 907
Author(s):  
Louise F. Roddam ◽  
Wendy R. Lewis-Henderson ◽  
Michael A. Djordjevic
Keyword(s):  
Rhizobium Leguminosarum ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Gene Interaction ◽  
Nodule Formation ◽  
Synthesis Inhibitor ◽  
Reading Frame ◽  
Ribosomal Protein L9 ◽  
Microbe Interactions ◽  
Cultivar Specificity

The nodulation failure resulting from the interaction between Rhizobium leguminosarum biovar trifolii strain ANU794 and the Trifolium subterraneum cv. Woogenellup was examined by transposon mutagenesis to resolve whether multiple determinants were involved in cultivar-specificity. Three new transposon-induced mutants of ANU794 (W72, W78 and W710) with significantly enhanced nodulation ability on cv. Woogenellup were identified. The W72 and W78 mutations are chromosomally-located, whereas the W710 mutation isplasmid-located. The ethylene synthesis inhibitor, aminoethoxyvinylglycine, fails to enhance the nodulation ability of ANU794, ANU7943 (csn1::Tn5) and W78 on cv. Woogenellup, but enhances the nodulation ability of W72,W710 and ANU7941 (nodM::Tn5). DNA sequencing of the W78 locus reveals strong homology to an unknown Mycobacterium open reading frame, and to several bacterial non-haem chloroperoxidases. The previously identified csn1 locus showed homology to the 50S ribosomal protein, L9, with the Tn5 insertion being located in the 5′-untranslated region. The results suggest that cultivar-specificity is mediated by at least two independent mechanisms or determinants, and not by a simple gene-for-gene interaction. The role of ethylene in cultivar specificity is discussed. Cultivar-specific interactions may prove useful in identifying pathways involved in efficient nodule formation and plant-microbe interactions.

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