Biosynthesis and metabolism of arginine in bacteria

Cunin, Raymond; Glansdorff, Nicolas; Pierard, André; Stalon, Victor

doi:10.1128/mr.50.3.314-352.1986

Cited by 496 publications

(81 citation statements)

References 372 publications

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“…cryptic chlorination installs a leaving group for subsequent cyclopropanation 32 . Cryptic acylation is found in the biosyntheses of arginine 33 , butirosin 34 , 35 , and the polyoxin N-terminal amino acid, carbamoylpolyoxamic acid 36 (CPOAA, 18 ), and is thought to function as a protecting group. Transient phosphorylation has been reported to act as a leaving group for dehydration in the biosynthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) 37 .…”

Section: Discussionmentioning

confidence: 99%

Cryptic phosphorylation in nucleoside natural product biosynthesis

et al. 2020

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Kinases are annotated in many nucleoside biosynthetic gene clusters (BGCs) but generally are considered responsible only for self-resistance. Here, we report an unexpected 2’-phosphorylation of nucleoside biosynthetic intermediates in the nikkomycin and polyoxin pathways. This phosphorylation is a unique cryptic modification as it is introduced in the third of seven steps during aminohexuronic acid (AHA) nucleoside biosynthesis, retained throughout the pathway’s duration, and is removed in the last step of the pathway. Bioinformatic analysis of reported nucleoside BGCs suggests the presence of cryptic phosphorylation in other pathways and the importance of functional characterization of kinases in nucleoside biosynthetic pathways in general. This study also functionally characterized all of the enzymes responsible for AHA biosynthesis and revealed that AHA is constructed via a unique oxidative C-C bond cleavage reaction. The results suggest a divergent biosynthetic mechanism for three classes of antifungal nucleoside natural products.

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Section: Discussionmentioning

confidence: 99%

Cryptic phosphorylation in nucleoside natural product biosynthesis

et al. 2020

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“…Specifically, an ornithine carbamoyltransferase (OTCase, Q4K7R3, p = 0.000) was upregulated 3‐fold (with both n ‐BPBA and Acros commercial NAs) compared with controls. There are two classes of OTCase, anabolic and catabolic that function in arginine metabolism (Cunin et al, 1986 ). All anabolic OTCases, except those found in Pseudomonas spp.…”

Section: Resultsmentioning

confidence: 99%

“…All anabolic OTCases, except those found in Pseudomonas spp. catalyze both directions of the reaction (Cunin et al, 1986 ). In some prokaryotes including Pseudomonads, OTCase can degrade arginine by the reverse mechanism in the arginine dihydrolase pathway (Cunin et al, 1986 ).…”

Section: Resultsmentioning

confidence: 99%

Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf‐5

et al. 2021

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Naphthenic acids (NAs) are carboxylic acids with the formula (C n H 2n + Z O 2 ) and are among the most toxic, persistent constituents of oil sands process‐affected waters (OSPW), produced during oil sands extraction. Currently, the proteins and mechanisms involved in NA biodegradation are unknown. Using LC‐MS/MS shotgun proteomics, we identified proteins overexpressed during the growth of Pseudomonas fluorescens Pf‐5 on a model NA (4′‐ n ‐butylphenyl)‐4‐butanoic acid ( n ‐BPBA) and commercial NA mixture (Acros). By day 11, >95% of n ‐BPBA was degraded. With Acros, a 17% reduction in intensity occurred with 10–18 carbon compounds of the Z family −2 to −14 (major NA species in this mixture). A total of 554 proteins ( n ‐BPBA) and 631 proteins (Acros) were overexpressed during growth on NAs, including several transporters (e.g., ABC transporters), suggesting a cellular protective response from NA toxicity. Several proteins associated with fatty acid, lipid, and amino acid metabolism were also overexpressed, including acyl‐CoA dehydrogenase and acyl‐CoA thioesterase II, which catalyze part of the fatty acid beta‐oxidation pathway. Indeed, multiple enzymes involved in the fatty acid oxidation pathway were upregulated. Given the presumed structural similarity between alkyl‐carboxylic acid side chains and fatty acids, we postulate that P . fluorescens Pf‐5 was using existing fatty acid catabolic pathways (among others) during NA degradation.

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“…Both systems catalyze the conversion of arginine into ornithine leading to the production of ammonia as part of the acid tolerance mechanism. Furthermore, the arginine deiminase system also provides ATP via the enzymatic step of ornithine carbamoyltransferase arcB (Cunin et al, 1986). Interestingly, two additional copies of ornithine carbamoyltransferase were also essential (argF1, encoded by SMc02137, and arcB2, encoded by SM_b20472), emphasizing the importance of genetic redundancy in arginine deiminasedependent ATP synthesis during symbiosis.…”

Section: Transposon Sequencing Reveals Symbiosis Genes Involved In the Uptake And Catabolism Of Argininementioning

confidence: 99%

Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation

Flores-Tinoco

Tschan

Fuhrer

et al. 2020

Molecular Systems Biology

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Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plantprovided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N 2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.

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Biosynthesis and metabolism of arginine in bacteria

Cited by 496 publications

References 372 publications

Cryptic phosphorylation in nucleoside natural product biosynthesis

Cryptic phosphorylation in nucleoside natural product biosynthesis

Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf‐5

Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation

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