Biosynthesis of lysine in plants: the putative role of meso-diaminopimelate dehydrogenase

Chatterjee, S. K.; Singh, Bijay; Gilvarg, Charles

doi:10.1007/bf00039539

Cited by 18 publications

(16 citation statements)

References 29 publications

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“…The prerequisite to apply such IVET system is that the mutation cannot be complemented by metabolites from the plant or associated microorganisms. The probability that a dapB mutation would be complemented by DAP of plant origin is very low, due to the strict regulation mechanisms in the biosynthetic pathway of lysine (6,18). Therefore, the dapB-based IVET system should also be suitable for isolating genes important for infection of rice roots and survival within the plant.…”

Section: Discussionmentioning

confidence: 99%

“…For histochemical analysis, rice roots were washed in PBS and transferred to 0.1 M phosphate buffer (pH 7), containing 0.5 mg of X-Gluc/ml, 0.5 mM K 3 Fe(CN) 6 and 0.5 mM K 4 Fe(CN) 6 as oxidation catalysts, and 10 mM EDTA to mitigate the partial inhibition of the enzyme by the oxidation catalysts. Roots were stained overnight at 37°C in this buffer, rinsed with PBS, and analyzed microscopically with Nikon Optiphot-2.…”

Section: Isolation Of Genes Induced In Vivomentioning

confidence: 99%

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Development and Application of a dapB -Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15

Rediers

Bonnecarrère

Rainey

et al. 2003

Appl Environ Microbiol

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Pseudomonas stutzeri A15 is a nitrogen-fixing bacterium isolated from paddy rice. Strain A15 is able to colonize and infect rice roots. This strain may provide rice plants with fixed nitrogen and hence promote plant growth. In this article, we describe the use of dapB-based in vivo expression technology to identify P. stutzeri A15 genes that are specifically induced during colonization and infection (cii). We focused on the identification of P. stutzeri A15 genes that are switched on during rice root colonization and are switched off during free-living growth on synthetic medium. Several transcriptional fusions induced in the rice rhizosphere were isolated. Some of the corresponding genes are involved in the stress response, chemotaxis, metabolism, and global regulation, while others encode putative proteins with unknown functions or without significant homology to known proteins.Rice (Oryza sativa L.) is the staple food of over 40% of the world's population. Considering the increase in the world's population and the limited possibility to expand the acreage under cultivation, increasing the yield of rice production is of great concern. Yields in systems with a low input of N fertilizer can be increased considerably by a higher level of fertilization. However, the environmental concerns raised against the extensive use of fertilizers necessitate the search for alternatives. One of the explored alternatives is biofertilization through the interaction between nitrogen-fixing plant-growth-promoting rhizobacteria and rice.The diazotrophic strain A15 was isolated during surveys for nitrogen-fixing bacteria in the rhizosphere of paddy rice grown in China with suboptimal N fertilization (78). Yield increases of 3 to 7% have been reported for field-grown rice inoculated with strain A15 (77). Initially, this strain was phenotypically characterized as Alcaligenes faecalis, but the taxonomic position of strain A15 was reinvestigated, and it was reclassified as Pseudomonas stutzeri (69). It has been shown that the strain A15 nitrogen fixation genes (nif) are expressed in the rice rhizosphere (68). Since strain A15 is able to infect rice roots and survive within rice plants (24,67,79), it may provide rice plants with fixed nitrogen and hence promote plant growth. However, direct evidence for bacterial N transfer to the plants is still lacking.At present, the mechanisms that enable strain A15 to colonize and infect rice roots and survive within rice plants are not known. The lack of a readily scored plant phenotype has hampered the identification and characterization of the P. stutzeri A15 genes that are required for interaction with the host plant. Because conditions during bacterium-host interactions are difficult to mimic in vitro, new techniques have been devised to study in vivo gene expression; these include differential fluorescence induction, signature-tagged mutagenesis, RNA arbitrarily primed PCR, and in vivo expression technology (IVET) (reviewed in references 8, 22, and 51). In this study, an IVET strategy was dev...

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Section: Discussionmentioning

confidence: 99%

Section: Isolation Of Genes Induced In Vivomentioning

confidence: 99%

Development and Application of a dapB -Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15

Rediers

Bonnecarrère

Rainey

et al. 2003

Appl Environ Microbiol

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“…Studies of crude cell extracts had shown that plants do not catalyse reactions specific to the succinylase, acetylase or dehydrogenase branches of the pathway. This was subsequently confirmed with the observation that annotated plant genomes, including that from Arabidopsis thaliana, lack some or all genes associated with the three classical branches (Chatterjee et al, 1994;Hudson et al, 2005). The identification and characterisation of LL-DAP-AT from A. thaliana demonstrated for the first time the means by which plant species catalyse the conversion of THDP to meso-DAP via the aminotransferase sub-pathway .…”

Section: Aminotransferase Pathway 61 Function Of Diaminopimelate Amimentioning

confidence: 57%

Enzymology of Bacterial Lysine Biosynthesis

Dogovski¹,

Atkinson²,

Dommaraju³

et al. 2012

Biochemistry

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“…The pathway using succinylated intermediates is widely distributed among prokaryotic species, whereas the one using acetylated intermediates shows a narrower phylogenetic distribution (32). A highly abbreviated DAP pathway exists in which a single enzyme, DAP dehydrogenase (Ddh, EC 1.4.1.16), produces m-DAP from THDPA, NADPH, and NH 4 ϩ (20,37). A metabolic redundancy occurs in Corynebacterium glutamicum which has both the Ddh and the succinylated pathways for lysine production (26).…”

mentioning

confidence: 99%

“…The LL-DAP aminotransferase has been reported from plants, cyanobacteria, and Chlamydia (14,19), where it appears to be the sole route for m-DAP-lysine biosynthesis. This assumption is based on the absence of orthologs for the acyl and Ddh path-way enzymes in the genome sequences of these species and the absence of acyl pathway enzyme activities demonstrated from several different plant species (4,13,19). The plant and cyanobacterial enzymes show exquisite substrate specificity in that they are able to distinguish LL-DAP from its isomer m-DAP.…”

mentioning

confidence: 99%

Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of ll -Diaminopimelate Aminotransferase

2008

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A variant of the diaminopimelate (DAP)-lysine biosynthesis pathway uses an LL-DAP aminotransferase (DapL, EC 2.6.1.83) to catalyze the direct conversion of L-2,3,4,5-tetrahydrodipicolinate to LL-DAP. Comparative genomic analysis and experimental verification of DapL candidates revealed the existence of two diverged forms of DapL (DapL1 and DapL2). DapL orthologs were identified in eubacteria and archaea. In some species the corresponding dapL gene was found to lie in genomic contiguity with other dap genes, suggestive of a polycistronic structure. The DapL candidate enzymes were found to cluster into two classes sharing approximately 30% amino acid identity. The function of selected enzymes from each class was studied. Both classes were able to functionally complement Escherichia coli dapD and dapE mutants and to catalyze LL-DAP transamination, providing functional evidence for a role in DAP/lysine biosynthesis. In all cases the occurrence of dapL in a species correlated with the absence of genes for dapD and dapE representing the acyl DAP pathway variants, and only in a few cases was dapL coincident with ddh encoding meso-DAP dehydrogenase. The results indicate that the DapL pathway is restricted to specific lineages of eubacteria including the Cyanobacteria, Desulfuromonadales, Firmicutes, Bacteroidetes, Chlamydiae, Spirochaeta, and Chloroflexi and two archaeal groups, the Methanobacteriaceae and Archaeoglobaceae.meso-Diaminopimelate (m-DAP) is the immediate precursor of lysine in prokaryotes and plants (3,25), and in many eubacteria, m-DAP is also required for the synthesis of murein (34). In addition to the m-DAP pathway, another, completely different method has evolved for the biosynthesis of lysine (33) involving the intermediate compound ␣-amino adipic acid. The ␣-amino adipic acid pathway is found in most fungi (32), and a modification of it is found in selected eubacterial and archaeal species (21).Four different variants of the m-DAP-lysine pathway have been discerned, and they are depicted in Fig. 1. All share the initial and terminal steps but differ in the reactions at the center of the pathway. The common reactions include the first, in which aspartate ␤-semialdehyde is condensed with pyruvate to produce dihydrodipicolinate; the second, in which dihydrodipicolinate is reduced to L-2,3,4,5-tetrahydrodipicolinate (THDPA); and the final reaction, in which m-DAP is decarboxylated to form lysine. The enzymes catalyzing these reactions, dihydrodipicolinate synthase (DapA, EC 4.2

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Biosynthesis of lysine in plants: the putative role of meso-diaminopimelate dehydrogenase

Cited by 18 publications

References 29 publications

Development and Application of a dapB -Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15

Development and Application of a dapB -Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15

Enzymology of Bacterial Lysine Biosynthesis

Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of ll -Diaminopimelate Aminotransferase

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