Isolation and characterization of<i>Rhizobium</i>sp. strain YS-1r that degrades lignin in plant biomass

Jackson, Colin; Couger, Matthew Brian; Prabhakaran, Madhu; Ramachandriya, Karthikeyan D.; Canaan, Patricia; Fathepure, Babu Z.

doi:10.1111/jam.13401

Cited by 31 publications

(23 citation statements)

References 63 publications

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“…When forest ecosystems are fertilized with N, trees likely reduce the C subsidies they send to rhizosphere microbes, which can alter the structure and function of not only fungal communities but also bacterial communities as well. These potential shifts in bacterial community composition are consequential given recent evidence that bacteria can synthesize enzymes to degrade simple and complex C (i.e., polyphenols, lignin) in soil organic matter (SOM; Datta et al., ; De Gonzalo, Colpa, Habib, & Fraaije, ; Jackson, Couger, Prabhakaran, Ramachandriya, & Canaan, ) and that shifts in bacterial function can reduce enzyme activities under N fertilization (Freedman, Upchurch, Zak, & Cline, ). As such, enzyme activity declines in response to N fertilization may result from parallel shifts in plant, bacterial, and fungal function; whereby reductions in plant C allocation to rhizosphere microbes indirectly alter fungal and bacterial community composition, decrease the energy available to synthesize enzymes, and ultimately reduce the fungal and bacterial community's ability to degrade SOM.…”

Section: Introductionmentioning

confidence: 99%

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Carrara

Walter

Hawkins

et al. 2018

Global Change Biology

148

105

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Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant-microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root-microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long-term (>25 years), whole-watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.

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Section: Introductionmentioning

confidence: 99%

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Carrara

Walter

Hawkins

et al. 2018

Global Change Biology

148

105

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“…strain YS-1r maybe be involved in this process. 145 Bacterial P450s involved in biosynthetic pathways that include shikimate metabolites have been found associated with non-ribosomal peptide synthetases (NRPS; vide infra) and in alkaloid biosynthesis (vide supra). These enzymes catalyse the hydroxylation of aromatic amino acids such as tyrosine and tryptophan.…”

Section: Shikimate Biosynthesis Pathwaysmentioning

confidence: 99%

Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism

et al. 2018

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The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways. 1.Introduction to P450s 2.Chemistry of P450 enzymes 3.Bacterial biosynthesis pathways involving P450s 3.1Terpene metabolism 3.1. Battersby (1925Battersby ( -2018 to the molecular understanding of biosynthesis over the course of their careers.

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“…Deconstructing lignin is of great interest due to its application in transforming lignocellulose to biofuels and commodity chemicals (1). The discovery that bacteria are able to at least partially deconstruct lignin has accelerated the study of enzymes and pathways potentially involved in lignin depolymerization and the catabolism of the resulting products (2,3). Among bacterial strains able to grow on ligninderived aromatic compounds, Sphingobium sp.…”

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confidence: 99%

“…Among bacterial strains able to grow on ligninderived aromatic compounds, Sphingobium sp. strain SYK-6 (hereafter referred to as SYK-6) has emerged as one of the best characterized, with pathways having been identified for the catabolism of ␤-aryl ethers, pinoresinol, diaryl propane, phenylcoumarane, and 2,2Ј-dihydroxy-3,3Ј-dimethoxy-5,5Ј-dicarboxybiphenyl (DDVA) 3 (4,5). DDVA is thought to be derived from the biphenyl unit present in lignin.…”

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confidence: 99%

The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily

Kuatsjah¹,

Chan

Kobylarz

et al. 2017

Journal of Biological Chemistry

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Strain SYK-6 of the bacterium sp. catabolizes lignin-derived biphenyl via a-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the -cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the and / values as 9.3 ± 0.6 s and 2.5 ± 0.2 × 10 m s, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.

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Isolation and characterization ofRhizobiumsp. strain YS-1r that degrades lignin in plant biomass

Abstract: The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.

Cited by 31 publications

References 63 publications

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism

The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily

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