A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound

Fujita, Masaya; Mori, Kosuke; Hara, Hirofumi; Hishiyama, Shojiro; Kamimura, Naofumi; Masai, Eiji

doi:10.1038/s42003-019-0676-z

Cited by 43 publications

(60 citation statements)

References 53 publications

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“…A previous phylogenetic analysis has indicated that SLG_34550 just downstream of tonB2 is classified into a clade comprising of known iron uptake TBDRs 15 . This gene, designated as fiuA , was deleted to obtain a fiuA mutant (Δ fiuA ), and the capacity of the mutant to grow on VA, PCA, and SEMP was measured (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Based on similarity with known iron uptake TBDRs, we found four putative iron uptake TBDRs (SLG_04340, SLG_04380, SLG_10860, and SLG_17010) in addition to fiuA (Table S2). These TBDR genes were classified into two phylogenetic clades, containing siderophore and haem uptake TBDRs 15 . A Fur box-like sequence was found just upstream of each gene except SLG_04340 (Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…16% 14 . Since the Sphingomonad strains have a large number of TBDR genes (from 39 to 153), they may play important roles not only in iron acquisition but also in other functions 15,49 . Five of the ten strains investigated showed the presence of TBDR-like genes, which showed 49-54% amino acid sequence identity with fiuA .…”

Section: Resultsmentioning

confidence: 99%

“…Samples were incubated at 30 °C with shaking (60 rpm) until OD 600 of the culture reached 0.5. Then, the cells were further incubated with or without 100 μM DIP and 100 μM FeCl 2 for 2 h. β-galactosidase activity of the cells was measured using 2-nitrophenyl-β-D-galactopyranoside as described previously 15 and expressed as Miller units.…”

Section: Methodsmentioning

confidence: 99%

“…Ferrous iron is also contained in the active centre and an iron-sulphur cluster of the oxygenase (LigXa) and the ferredoxin (LigXc) components of the multicomponent DDVA O -demethylase, respectively 42 . Analysis of the outer membrane transporters of lignin-derived aromatic compounds in SYK-6 has indicated that ddvT , one of the 74 TBDR genes, encodes the DDVA outer membrane transporter, and tonB1 is involved in this transport among the six tonB 15 . On the other hand, disruption of tonB2 was seen to affect the growth of SYK-6 and decrease the activity of ferrous iron-requiring DDVA O -demethylase, thereby suggesting that tonB2 plays a role in the iron acquisition process.…”

Section: Introductionmentioning

confidence: 99%

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Iron acquisition system ofSphingobiumsp. strain SYK-6, a degrader of lignin-derived aromatic compounds

Fujita

Sakumoto

Tanatani

et al. 2020

Preprint

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23Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial 24 degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae 25 comprises various degraders of recalcitrant aromatic compounds; however, little is known 26 about their iron acquisition system. Here, we investigated the iron acquisition system in a 27 model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain 28 SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent 29 receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs 30 encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and 31 tonB2 (SLG_34550), one of the six tonB comprising the Ton complex which enables 32 TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB 33 (SLG_36840) played an important role in iron uptake across the inner membrane. The 34 promoter activities of most of the iron uptake genes were induced under iron-limited 35 conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake 36 regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved 37 in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation 38 of the iron acquisition system promises better understanding of the bacterial degradation 39 mechanisms of aromatic compounds.40 41 42Iron is an essential nutrient utilised as a cofactor for enzymes that control various life 43 phenomena such as respiration, dissimilation, and stress response 1 . Iron exists mainly in 44 ferrous and ferric forms. Ferrous iron is soluble and highly bioavailable; however, the 45 predominant form of iron in the environment is an insoluble ferric form 2 . Ferric iron in soil 46 and water is solubilised by forming complexes with organic ligands such as siderophores, 47 humic acid, lipids, proteins, and polysaccharides 3,4 . Many bacteria secrete specific 48 high-affinity siderophores which form complexes with ferric iron and then uptake these 49 ferric-siderophore complexes to enhance iron acquisition over competitors [5][6][7] . Besides, 50 pathogenic bacteria can acquire haem and transferrin specifically from their host cells 8,9 . 51 Gram-negative bacteria need to transport iron through both the outer and inner 52 membranes. TonB-dependent receptors (TBDRs) mediate transport of ferric complexes (e.g. 53 siderophore, haem, and transferrin) across the outer membrane 1,10,11 . TBDRs utilize energy 54 derived from the proton motive force transmitted by TonB-ExbB-ExbD complex (Ton 55 complex) localised in the inner membrane (Ton system) 12 . Beside siderophores, the Ton 56 system is involved in the uptake of vitamin B12, saccharide, aromatic compounds, and metals 57 such as nickel, copper, and lanthanoid [13][14][15][16][17][18] . The uptake of the ferric complex across the inner 58 membrane is mainly achieved by ATP-binding cassette (ABC) transporters 11...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Iron acquisition system ofSphingobiumsp. strain SYK-6, a degrader of lignin-derived aromatic compounds

Fujita

Sakumoto

Tanatani

et al. 2020

Preprint

Self Cite

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Developing Rhodococcus opacus and Sphingobium sp. coculture systems for valorization of lignin‐derived dimers

Cai

et al. 2022

Biotech & Bioengineering

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Bioconversion is being regarded as a promising way for lignin valorization because it enables funneling diverse lignin components into single compounds, overcoming the heterogeneity of lignin. Although numerous lignin‐derived aromatic monomers have been funneled to target compounds in previous studies, the bioconversion of low‐molecular‐weight lignin (LMW‐lignin) fragments, for example, lignin‐derived dimers, has been rarely systematically studied, impeding further conversion of lignin. In this study, coculture systems were designed and developed to funnel multiple lignin‐derived dimers to cis, cis‐muconate and gallate by combining lignin‐derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium Rhodococcus opacus. With the developed coculture systems, β‐O‐4 type dimer guaiacylglycerol‐β‐guaiacyl ether, 4‐O‐5 type dimer 4,4′‐dihydroxydiphenyl ether, β‐5 type dimer balanophonin, β‐β type dimer pinoresinol, β‐1 type dimer 1,2‐bis(4‐hydroxy‐3‐methoxyphehyl)‐1,3‐propanediol and 5‐5 type dimer 5,5′‐dehydrodivanillate were converted to cis, cis‐muconate. Additionally, the developed coculture systems also showed potential in conversion of lignin‐derived dimers to gallate. The application of alkali lignin for cis, cis‐muconate production further demonstrated the effectiveness of the designed coculture systems. Overall, the developed coculture systems are beneficial to lignin biological valorization, and also provide references for the valorization of other bio‐resources.

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The Name Is Barrel, β-Barrel

Hayashi,

Buchanan,

Botos

2024

Methods in Molecular Biology

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A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound

Cited by 43 publications

References 53 publications

Iron acquisition system ofSphingobiumsp. strain SYK-6, a degrader of lignin-derived aromatic compounds

Iron acquisition system ofSphingobiumsp. strain SYK-6, a degrader of lignin-derived aromatic compounds

Developing Rhodococcus opacus and Sphingobium sp. coculture systems for valorization of lignin‐derived dimers

The Name Is Barrel, β-Barrel

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